REVIEW | doi:10.20944/preprints202008.0366.v1
Subject: Medicine & Pharmacology, Pediatrics Keywords: vaccine; age; pneumonia; influenza virus; seasonal influenza; influenza imprinting; infant; infant immunity; immune response
Online: 17 August 2020 (12:04:58 CEST)
Influenza virus infection causes severe respiratory illness in people worldwide, disproportionately affecting infants. The immature respiratory tract coupled with the developing immune system is thought to synergistically play a role in the increased disease severity in younger age groups. Although vaccines remain the best solution for protecting this vulnerable population, no vaccines are available for those under 6 months, and for infants aged 6 months to 2 years, the vaccine elicits a dampened immune response. Dampened immune responses may be due to unique features of the infant immune system and a lack of pre-existing immunity. Unlike older children and adults, the infant immune system is Th2 skewed and has less antigen presenting cells and soluble immune factors. Paradoxically, we know that a person’s first infection with the influenza virus during infancy or childhood leads to the establishment of life-long immunity toward that particular virus strain. This is called influenza imprinting. To provide better protection against influenza virus infection and disease in infants, more research must be conducted to understand the imprinting event. We contend that by understanding influenza imprinting in the context of the infant immune system and the infant’s immature respiratory tract, we will be able to design more effective influenza vaccines for both infants and adults. Working through the lens of imprinting, using infant influenza animal models such as mice and ferrets, which have proven useful for infant immunity studies, we will gain a better understanding of imprinting and its implications regarding vaccine design. This review examines literature regarding infant immune development, current vaccine strategies, respiratory development, and the importance of researching the imprinting event in infant animal models to develop more effective and protective vaccines for young children.
ARTICLE | doi:10.20944/preprints201812.0317.v1
Subject: Life Sciences, Virology Keywords: universal influenza vaccine; chimeric hemagglutinin; nucleoprotein; live attenuated influenza vaccine; sequential immunization; ferret model
Online: 27 December 2018 (10:14:21 CET)
The development of universal influenza vaccines, i.e. vaccines that can provide broad protection against seasonal and potentially pandemic influenza viruses, has been a priority for more than 20 years. Several approaches have been proposed that redirect the adaptive immune responses from immunodominant hypervariable regions to low-immunogenic but highly conserved regions of viral proteins. Here we induced broadly reactive anti-hemagglutinin (HA) stalk antibody by sequential immunizations with live attenuated influenza vaccines (LAIVs) expressing chimeric HA (cHA). These vaccines contained the HA stalk domain from H1N1pdm09 virus but antigenically unrelated globular head domains from avian influenza viruses H5N1, H8N4 and H9N2. In addition, the source of the viral nucleoprotein (NP) of the LAIV strains was changed from A/Leningrad/17 master donor virus (MDV) to wild-type (WT) H1N1pdm09 virus, in order to induce CD8 T-cell immune responses more relevant to current infections. To avoid any difference in protective effect of the various anti-neuraminidase (NA) antibodies, all LAIVs were engineered to contain the NA gene of Len/17 MDV. Naïve ferrets were immunized with three doses of (i) classical LAIVs containing non-chimeric HA and NP from MDV (LAIVs (NP-MDV)); (ii) cHA-based LAIVs containing NP from MDV (cHA LAIVs (NP-MDV)); and (iii) cHA-based LAIVs containing NP from H1N1pdm09 virus (cHA LAIVs (NP-WT)). A high-dose challenge with H1N1pdm09 virus induced significant pathology in the control, non-immunized ferrets, including high virus titers in respiratory tissues, clinical signs of disease and histopathological changes in nasal turbinates and lung tissues. All three vaccination regimens protected animals from clinical manifestations of disease: immunized ferrets did not lose weight or show clinical symptoms, and their fever was significantly lower than in the control group. Further analysis of virological and pathological data revealed the following hierarchy in the cross-protective efficacy of the vaccines: cHA LAIVs (NP-WT) > cHA LAIVs (NP-MDV) > LAIVs (NP-MDV). This ferret study showed that prototype universal LAIVs that combine the two approaches of inducing anti-HA stalk antibody and more relevant CD8 T-cell immune responses are highly promising candidates for further clinical development.
ARTICLE | doi:10.20944/preprints202110.0036.v1
Online: 4 October 2021 (09:44:35 CEST)
There are scarce data regarding flu vaccination among people with HIV infection (PWHIV). The goal of this explorative study is to assess hesitancy toward influenza vaccination in a group of PWHIV during the pandemic. A questionnaire was administered to 219 patients vaccinated at our clinic during the 2020-2021 campaign. It evaluated subjects’ adherence over the last 3 seasonal vaccination campaigns, vaccine confidence, complacency and convenience, and the effect of the pandemic on the choice to vaccinate. The population was divided into two groups: fully adherent (all 3 campaigns, 117 patients) and non-fully adherent (1 or 2 campaigns, 102 patients). Adherence increased in non-fully adherent group in 2020-2021, but the pandemic did not affect the choice. Misbelieves emerged: influenza vaccine was considered protective SARS-CoV-2 (22.8% of total population); almost half of all patients thought influenza vaccine could improve their CD4+ cell level (57.3% in fully adherent, 40.2% in non-fully adherent, p<0.05). A quarter of the non-fully adherent group would not have vaccinated in a location other than our clinic (24.5% vs 11.9% in fully adherent group, p<0.05). Conclusively, offering a secure and private space for vaccination seems to encourage vaccination; healthcare professionals should improve counselling to increase adherence and correct misbeliefs.
ARTICLE | doi:10.20944/preprints202106.0304.v1
Online: 11 June 2021 (08:41:04 CEST)
Influenza B virus (IBV) is a major respiratory pathogen of humans, particularly in the elderly and children and vaccines are the most effective way to control it. In previous work, incorporation of two mutations (E580G, S660A) along with the addition of a HA epitope tag in the PB1 segment of B/Brisbane/60/2008 (B/Bris) resulted in an attenuated strain that was safe and effective as a live attenuated vaccine. A third attempted mutation (K391E) in PB1 was not always stable. Interestingly, viruses that maintained the K391E mutation were associated with the mutation E48K. To explore the contribution of the E48K mutation for stability of the K391E mutation, a vaccine candidate was generated by inserting both mutations along with attenuating mutations E580G and S660A in PB1 of B/Bris (B/Bris PB1att 4M). Serial passage of the B/Bris PB1att 4M vaccine candidate in eggs and MDCK indicated high stability. In silico structural analysis revealed a potential interaction between amino acids at positions 48 and 391. In mice, B/Bris PB1att 4M was safe and provided complete protection against homologous challenge. These results confirm the compensatory effect of mutation E48K to stabilize the K391E mutation, resulting in a safer, yet still protective, IBV LAIV vaccine.
Subject: Medicine & Pharmacology, Allergology Keywords: COVID-19; vaccine; vaccine hesitancy; Healthcare Workers; Flu vaccine; Influenza; SARS-CoV-2
Online: 12 April 2021 (12:33:15 CEST)
Despite the research conducted worldwide, there is no treatment specific for SARS-CoV-2 infection with efficacy proven by randomized controlled trials. A chance for a breakthrough is vaccinating the majority of the global population. The public opinion surveys on vaccine hesitancy prompted our team to investigate the Polish medical community's attitude towards the SARS-CoV-2 and influenza vaccinations. In-person and online surveys of Healthcare Workers (HCWs): doctors, nurses, medical students, and other allied health professionals (n=419) took place between 14.09.2020 and 5.11.2020. In our study, 68.7% of respondents would like to be vaccinated with the COVID-19 vaccine. The safety and efficacy of vaccination against COVID-19 would persuade 86.3% of hesitant and those who would refuse to be vaccinated. 3.1% of all respondents claimed that no argument would convince them to get vaccinated. 61.6% of respondents declared a willingness to receive an influenza vaccination, of which 83.3% were also inclined to receive the planned COVID-19 vaccination. Although a significant part of respondents - 62.5% (262/419) indicated, they trusted the influenza vaccine more than the COVID-19 vaccine in direct comparison, more respondents intended to get the COVID-19 vaccination than the influenza vaccine in the 2020/2021 season.
ARTICLE | doi:10.20944/preprints202210.0119.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: influenza; vaccine; adult; vaccine effectiveness; elderly; older adults
Online: 10 October 2022 (10:14:42 CEST)
Older adults (age ≥65) are at high risk of influenza morbidity and mortality. This study evaluated the impact of a hypothetical two-dose influenza vaccine regimen per season to reduce symptomatic flu cases by providing preseason (first dose) and mid-season (second dose) protection to offset waning vaccine effectiveness (VE). The Framework for Reconstructing Epidemiological Dynamics (FRED), an agent-based modeling platform, was used to compare typical one-dose vaccination to a two-dose vaccination strategy. Primary models incorporated waning VE of 10% per month and varied influenza season timing (December through March) to estimate cases and hospitalizations in older adults. Additional scenarios modeled reductions in uptake and VE of the second dose, and overall waning. In seasons with later peaks, two vaccine doses had the largest potential to reduce cases (14.4% with February peak, 18.7% with March peak) and hospitalizations (13.1% with February peak, 16.8% with March peak). Reductions in cases and hospitalizations still resulted but decreased when 30% of individuals failed to receive a second dose, second dose VE was reduced, or overall waning was reduced to 7% per month. Agent-based modeling indicates that two influenza vaccine doses could decrease cases and hospitalizations in older individuals. The highest impact occurred in the more frequently observed late-peak seasons. The beneficial impact of the two-dose regimen persisted despite model scenarios of reduced uptake of the second dose, decreased VE of the second dose, or overall VE waning.
ARTICLE | doi:10.20944/preprints202106.0180.v1
Subject: Life Sciences, Biochemistry Keywords: LAIV, Influenza, HA, IGIP, IgA, IgG, vaccine, natural adjuvant
Online: 7 June 2021 (13:03:43 CEST)
Live attenuated influenza virus (LAIV) vaccines elicit a combination of systemic and mucosal immunity by mimicking a natural infection. To further enhance protective mucosal responses, we incorporated the gene encoding the IgA-inducing protein (IGIP) into the LAIV genomes of the cold-adapted A/Leningrad/134/17/57 (H2N2) strain (caLen) and the experimental attenuated backbone A/turkey/Ohio/313053/04 (H3N2) (OH/04att). Incorporation of IGIP into the caLen background led to a virus that grew poorly in prototypical substrates. In contrast, IGIP in the OH/04att background (IGIP-H1att) virus grew to titers comparable to the isogenic backbone H1att (H1N1) without IGIP. IGIP-H1att- and H1caLen-vaccinated mice were protected against lethal challenge with a homologous virus. The IGIP-H1att vaccine generated robust serum HAI responses in naïve mice against the homologous virus, equal or better than those obtained with the H1caLen vaccine. Analyses of IgG and IgA responses using a protein microarray revealed qualitative differences in humoral and mucosal responses between vaccine groups. Overall, serum and bronchoalveolar lavage samples from the IGIP-H1att group showed trends towards increased stimulation of IgG and IgA responses compared to H1caLen samples. In summary, introduction of genes encoding immunomodulatory functions into a candidate LAIV that can serve as natural adjuvants to improve overall vaccine safety and efficacy.
ARTICLE | doi:10.20944/preprints202104.0072.v1
Subject: Life Sciences, Biochemistry Keywords: T cells; protein immunodominance; cytokine polarization; influenza viruses; vaccine
Online: 2 April 2021 (14:28:32 CEST)
The role of T cell immunity has been acknowledged in recent vaccine development and evaluation. We tested the humoral and cellular immune responses to Flucelvax®, a quadrivalent inactivated seasonal influenza vaccine containing two influenza A (H1N1 Singapore/GP1908/2015 IVR-180 and H3N2 North Carolina/04/2016) and two influenza B (Iowa/06/2017 and Singapore/INFTT-16-0610/2016) virus strains, using peripheral blood mononuclear cells stimulated by pools of peptides overlapping all the individual influenza viral protein components. Baseline reactivity was detected against all four strains both at the level of CD4 and CD8 responses and targeting different proteins. CD4 T cell reactivity was mostly directed to HA/NA proteins in influenza B strains, and NP/M1/M2/NS1/NEP proteins in the case of the Influenza A strains. CD8 responses to both influenza A and B viruses preferentially targeted the more conserved core viral proteins. Following vaccination, both CD4 and CD8 responses against the various influenza antigens were increased in day 15 to day 91 post vaccination period and maintained a Th1 polarized profile. Importantly, no vaccine interference was detected, with the increased responses balanced across all 4 included viral strains for both CD4 and CD8 T cells, and targeting HA and multiple additional viral antigens.
Subject: Medicine & Pharmacology, Allergology Keywords: influenza; intensive care unit; vaccine effectiveness; length of stay
Online: 24 May 2021 (15:02:34 CEST)
Seasonal influenza is a common cause of hospital admission, especially in older people and those with comorbidities. The objective of this study was to determine influenza vaccine effectiveness (VE) in preventing intensive care admissions and shortening the length of stay (LOS) in hospitalized laboratory-confirmed influenza cases (HLCI) in Catalonia (Spain).A retrospective cohort study was carried out during the 2017-2018 season in HLCI aged ≥ 18 years from 14 public hospitals. Differences in means and proportions were assessed using a t-test or a chi-square test as necessary and the differences were quantified using standardized effect measures; Cohen’s d for quantitative and Cohen’s w for categorical variables. Adjusted influenza vaccine effectiveness in preventing severity was estimated by multivariate logistic regression where the adjusted VE = (1-adjusted odds ratio) ·100%; adjustment was also made using the propensity score.We analyzed 1414 HLCI aged ≥ 18 years; 465 (33%) were vaccinated, of whom 437 (94%) were aged ≥ 60 years, 269 (57.8%) were male and 295 (63.4%) were positive for influenza type B. ICU admission was required in 214 (15.1%) cases. There were 141/1118 (12.6%) ICU admissions in patients aged ≥ 60 years and 73/296 (24.7%) in those aged < 60 years (p<0.001). The mean LOS and ICU LOS did not differ significantly between vaccinated and unvaccinated patients. There were 52/465 (11.2%) in vaccinated cases) ICU admissions in vaccinated cases vs. 162/949 (17.1%) in unvaccinated cases. Patients admitted to the ICU had a longer hospital LOS (mean: 22.4 [SD 20.3] days) than those who were not (mean: 11.1 [SD14.4] days); p<0.001. Overall, vaccination was associated with a lower risk of ICU admission. Taking virus types A and B together, the estimated adjusted VE in preventing ICU admission was 31% (95% CI 1-52; p=0.04). When stratified by viral type, the aVE was 40% for type A (95% CI -11-68; p = 0.09) and 25% for type B (95% CI -18-52; p = 0.21). Annual influenza vaccination may prevent ICU admission in cases of HLCI. A non-significantly shorter mean hospital stay was observed in vaccinated cases. Our results support the need to increase vaccination uptake and public perception of the benefits of influenza vaccination in groups at a higher risk of hospitalization and severe outcomes.
REVIEW | doi:10.20944/preprints202208.0008.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: influenza; antivirals; anti-influenza; influenza drugs; the flu
Online: 1 August 2022 (05:41:34 CEST)
Antigenic drift in influenza strains allows viruses to avoid being fully suppressed by seasonal vaccines. As a result, public interest has led to increased scrutiny and reevaluation of anti-influenza antiviral drugs as possible solutions. Unfortunately, many anti-influenza drugs developed around the globe suffer from a lack of sufficient clinical trials, as well as a lack of toxicity data. This is especially true of Arbidol, a popularly used drug for the prevention and treatment of influenza strains in China and Russia. Neuraminidase inhibitors, which were developed in the United States, also fall victim to inconclusive clinical trials and adverse effects. Adamantanes, while proven to be effective in treating influenza A, are encountering rapid, widespread cross-resistance. Baloxavir marboxil, a newer anti-influenza medication, shows promise in treating acute uncomplicated influenza, and may avoid the development of resistance when coadministered with other antiviral drugs. This review explores the antivirals available for influenzas treatment at this time.
REVIEW | doi:10.20944/preprints202110.0210.v1
Subject: Life Sciences, Immunology Keywords: influenza vaccine; influenza; vaccine; epidemiology; vaccine effectiveness; perceived barriers
Online: 14 October 2021 (10:07:05 CEST)
The reason for this dissertation is to establish the effects of vaccination on the elderly (>65 years old) in Hong Kong in reducing flu infection. Influenza vaccine uptake in the elderly (˃65 years old) in Hong Kong significantly increased in 2003 after the SARS epidemic. The exact impacts of influenza vaccine among the elderly in Hong Kong are a subject of contention. The effectiveness of the influenza vaccine comes from observed studies which may be prejudiced since it is difficult to identify and justify the evidence. A review of various literatures has shown that influenza causes serious illness and death particularly highly vulnerable groups such as adults aged 65 years and above. Therefore, more efforts should be initiated to reduce mortality caused by influenza among the elderly. According to the WHO (2005), vaccination is among the most effective approach for preventing death associated with influenza to vulnerable groups such as the elderly.
ARTICLE | doi:10.20944/preprints202211.0545.v1
Subject: Biology, Animal Sciences & Zoology Keywords: H5N1; HPAI; avian influenza; highly pathogenic avian influenza; outbreak; poultry
Online: 29 November 2022 (09:11:22 CET)
In 2021/2022, the re-emergence of highly pathogenic avian influenza (HPAI) occurred in Europe. The outbreak was seeded from two sources, resident and reintroduced viruses, which is unprecedented in the recorded history of avian influenza. The dominating subtype was H5N1, representing a reversion to the original A/goose/Guangdong/1/1996-like subtype combination. In this study, we present a whole genome sequence and a phylogenetic analysis of 57 H5N1 HPAI and two low pathogenic avian influenza (LPAI) H5N1 strains collected in the Czech Republic during 2021/2022. Phylogenetic analysis revealed close relationships between H5N1 genomes from poultry and wild birds and secondary transmission in commercial geese. The genotyping showed considerable genetic heterogeneity among Czech H5N1 viruses with six different HPAI genotypes, three of which were apparently unique. In addition, second-order reassortment relationships were observed with the direct involvement of co-circulating H5N1 LPAI strains. The genetic distance between Czech H5N1 HPAI and the closest LPAI segments available in the database illustrates the profound gaps in our knowledge of circulating LPAI strains. The changing dynamics of HPAI in the wild may increase the likelihood of future HPAI outbreaks and present new challenges in poultry management, biosecurity, and surveillance.
ARTICLE | doi:10.20944/preprints202206.0058.v1
Subject: Biology, Other Keywords: H5N8; HPAI; avian influenza; Highly Pathogenic avian influenza; outbreak; poultry
Online: 6 June 2022 (03:59:27 CEST)
In 2020-2021, the second massive dissemination of a highly-pathogenic avian influenza (HPAI) of H5Nx subtype occurred in Europe. During this period, the virus caused numerous outbreaks in poultry, including in the Czech Republic. In the present study, we provide an insight into the genetic variability of the Czech/2021 (CZE/2021) H5N8 viruses to determine the relationships between strains from wild and domestic poultry and to infer transmission routes between the affected flocks of commercial poultry. For this purpose, whole genome sequencing and phylogenetic analysis of 70 H5N8 HPAI genomes representing 79.7% of the cases were performed. All CZE/2021 H5N8 viruses belonged to the 22.214.171.124b H5 lineage and circulated without reassortment, retaining the A/chicken/Iraq/1/2020 H5N8-like genotype constellation. Phylogenetic analysis suggested frequent local transmission of H5N8 HPAI from wild birds to minor poultry and extensive farm-to-farm spread among commercial poultry farms. In addition, the analysis suggested one cross-border transmission event. Indirect transmission via contaminated materials was considered the most likely source of infection. Improved biosecurity and increased collaboration between the field veterinarians and the laboratory are essential to limit the local spread of the virus and to reveal and interrupt critical routes of infection.
ARTICLE | doi:10.20944/preprints202202.0153.v2
Subject: Life Sciences, Other Keywords: winter mortality; trends; season; estimated influenza mortality; pandemic influenza; aging
Online: 25 February 2022 (14:24:30 CET)
Trends in excess winter mortality (EWM) were investigated from the winter of 1900/01 to 2019/20. During the 1918-1919 Spanish flu epidemic a maximum EWM of 100% was observed in both Denmark and the USA. During the Spanish flu epidemic in the USA 70% of excess winter deaths were coded to influenza. EWM steadily declined from the Spanish flu peak to a minimum around the 1970’s to 1980’s. There is evidence that this decline was accompanied by a shift in deaths away from the winter, and that the EWM calculation shifted from a maximum around April to June in the early 1900’s to around March since 1967. EWM has a good correlation with the number of estimated influenza deaths, but in this context influenza pandemics after the Spanish flu only had an EWM equivalent to that for seasonal influenza. Using data from 1980 onward the effect of influenza vaccination on EWM was examined using a large international data set. No effect of increasing influenza vaccination could be discerned; however, there are multiple competing forces influencing EWM which will obscure any underlying trend, e.g., increasing age at death, multimorbidity, dementia, polypharmacy, diabetes, and obesity – all of which either interfere with vaccine effectiveness or are risk factors for influenza death. After adjusting the trend in EWM in the USA influenza vaccination can be seen to be masking higher winter deaths among a high morbidity US population. Winter deaths are clearly the outcome of a complex system of competing long-term trends.
ARTICLE | doi:10.20944/preprints202105.0050.v1
Online: 5 May 2021 (12:32:39 CEST)
Influenza A viruses (IAVs) evolve via point mutations and reassortment of viral gene segments. The patterns of reassortment in different host species differ considerably. We investigated the genetic diversity of IAVs in wild ducks and compared it with the viral diversity in gulls. The complete genomes of 38 IAVs of H1N1, H1N2, H3N1, H3N2, H3N6, H3N8, H4N6, H5N3, H6N2, H11N6 and H11N9 subtypes isolated from wild mallard duck and gull habitants of a pond in Moscow city, Russia were sequenced. The sequences were closely related to those of avian IAVs isolated in Sweden and the Netherlands. The analysis of phylogenetic trees showed that stable viral genotypes do not persist from year to year in ducks owing to frequent gene reassortment. For comparison, similar analyses were carried out using sequences of IAVs isolated in the same period from ducks and gulls in the Netherlands. Our results revealed a significant difference in diversity and rates of reassorment of IAVs in ducks and gulls.
ARTICLE | doi:10.20944/preprints202103.0297.v1
Online: 11 March 2021 (08:36:21 CET)
Airborne transmission of seasonal and pandemic influenza viruses is responsible for their epidemiological success and public health burden in humans. Efficient airborne transmission of H1N1 influenza virus relies on receptor specificity and pH of fusion of the surface glycoprotein hemagglutinin (HA). In this study, we examine the role of HA pH of fusion on transmissibility of a cell culture-adapted H3N2 virus. Mutations in the HA head at positions 78 and 212 of A/Perth/16/2009 (H3N2), which were selected after cell culture adaptation, decrease the acid stability of the virus from a pH of 5.5 (WT) to 5.8 (mutant). In addition, we observed that this mutant H3N2 virus replicated to higher titers in cell culture but had reduced airborne transmission in the ferret model. These data demonstrate that, like H1N1 HA, the pH of fusion for H3N2 HA is a determinant of efficient airborne transmission. Surprisingly, we demonstrate that the NA segment noncoding regions can impact the pH of fusion of reassortant viruses. Taken together, our data confirm that HA acid stability is an important characteristic of epidemiologically successful human influenza viruses and is influenced by HA/NA balance.
ARTICLE | doi:10.20944/preprints201901.0136.v2
Online: 18 January 2019 (12:42:19 CET)
With the increasing pace of global warming, it is important to understand the role of meteorological factors in influenza virus (IV) epidemics. In this study, we investigated the impact of temperature, UV index, humidity, wind speed, atmospheric pressure, and precipitation on IV activity in Norway, Sweden, Finland, Estonia, Latvia and Lithuania during 2010-2018. Both correlation and machine learning analyses revealed that low temperature and low UV indexes were the most predictive meteorological factors for IV epidemics in the Northern European countries. Our in vitro experiments confirmed that low temperature and UV radiation preserved IV infectivity. Associations between these meteorological factors and IV activity could improve surveillance and promote development of accurate predictive models for future influenza outbreaks in Northern Europe.
ARTICLE | doi:10.20944/preprints202012.0327.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Vaccine platform; papaya mosaic virus (PapMV); rod shape nanoparticle; influenza M2e; influenza nucleocapsid, sortase (SrtA).
Online: 14 December 2020 (12:24:44 CET)
Background: The papaya mosaic virus (PapMV) vaccine platform is a rod-shape nanoparticle made of the recombinant PapMV coat protein (CP) self-assembled around a non-coding ssRNA template. The PapMV nanoparticle induces innate immunity through stimulation of the toll-like receptors (TLR) 7 and 8. The display of the vaccine antigen at the surface of the nanoparticle, associated with the co-stimulation signal via TLR7/8, ensures a strong stimulation of the immune response, which is ideal for the development of candidate vaccines. In this study, we assess the impact of where the peptide antigen is fused, either at the surface or at the extremities of the nanoparticles, on the immune response directed to that antigen. Methods: Two different peptides from influenza A virus were used as model antigens. The conserved M2e peptide was chosen as the B-cell epitope, and a peptide derived from the nucleocapsid was chosen as the CTL epitope. These peptides were coupled at two different positions on the PapMV CP, the N- (PapMV-N) or the C-terminus (PapMV-C) using the transpeptidase activity of Sortase A (SrtA). The immune responses, both humoral and CD8+ T cell-mediated, directed to the peptide antigens in the two different fusion contexts were analyzed and compared. The impact of coupling density at the surface of the nanoparticle was also investigated. Conclusions: The results demonstrate that coupling of the peptide antigens at the N-terminus (PapMV-N) of the PapMV CP led to an enhanced immune response to the coupled peptide antigens as compared to coupling to the C-terminus. The difference between the two vaccine platforms is linked to the enhanced capacity of the PapMV-N vaccine platform to stimulate the TLR7/8. We also demonstrated that the strength of the immune response increases with the density of coupling at the surface of the nanoparticles.
REVIEW | doi:10.20944/preprints201909.0306.v1
Subject: Life Sciences, Immunology Keywords: influenza virus; humoral response; hemagglutinin (HA) of influenza virus; broad neutralizing antibody(bnAb); heterosubtypic immunity of influenza; original antigenic sin "OAS"; "universal" influenza vaccine; protein microarray assay; mPLEX-Flu assay; multiple dimensional assays (MDA))
Online: 27 September 2019 (08:34:56 CEST)
The human antibody response to influenza virus infection or vaccination is as complicated as it is essential for protection against flu. The constant antigenic changes of the virus to escape human herd immunity hinder the yearly selection of vaccine strains since it is hard to predict which virus strains will circulate for the coming flu season. A "universal" influenza vaccine that could induce broad cross-influenza subtype protection would help to alleviate this burden. However, the human antibody response is intricate and often obscure, with factors like antigenic seniority or original antigenic sin "OAS", and back-boosting ensuring that each person mounts a unique immune response to infection or vaccination with any new influenza virus strain. Notably, the effects of existing antibodies on cross-protective immunity after repeated vaccinations are unclear. More research is needed to characterize the mechanisms at play, but traditional assays such as hemagglutinin inhibition (HAI) and microneutralization (MN) are excessively limited in scope and too resource-intensive to effectively meet this challenge. In the past ten years, new multiple dimensional assays (MDAs) have been developed to help overcome these problems by simultaneously measuring antibodies against a large panel of influenza hemagglutinin (HA) proteins with a minimal amount of sample in a high throughput way. MDAs will likely be a powerful tool for accelerating the study of the humoral immune response to influenza vaccination and the development of a universal influenza vaccine.
REVIEW | doi:10.20944/preprints202107.0694.v1
Subject: Life Sciences, Biochemistry Keywords: H9N2; influenza; aerosol; interspecies; zoonotic; pandemic
Online: 30 July 2021 (10:13:42 CEST)
Influenza A viruses (IAV) are widespread viruses affecting avian and mammalian species worldwide. Outbreaks of IAV in poultry are usually associated with substantial morbidity and mortality, significantly affecting the poultry industry and food security. IAVs from avian species can be transmitted to mammals including humans and, thus, they are of inherent pandemic concern. Most of the efforts to understand the pathogenicity and transmission of avian origin IAVs have been focused on H5 and H7 subtypes due to their highly pathogenic phenotype in poultry. However, IAV of the H9 subtype that circulate endemically in poultry flocks in some regions of the world have also been associated with cases of zoonotic infections. As a result, the World Health Organization includes avian origin H9N2 IAV among the top in the list of IAVs of pandemic concern. In this review, we discuss the interspecies transmission of H9N2 between avian and mammalian species and the molecular factors that are thought relevant for this spillover. Additionally, we discuss factors that have been associated with the ability of these viruses to transmit through the respiratory route in mammalian species.
ARTICLE | doi:10.20944/preprints202010.0100.v1
Online: 5 October 2020 (17:24:27 CEST)
After the influenza H1N1 pandemic of 2009, the seasonal A/Brisbane/59/2007 strain was replaced by the A/California/07/2009 strain for the influenza virus vaccine composition. After several seasons with no indications on the occurrence of antigenic drift, A/Michigan/45/2015 was chosen as the H1N1 vaccine strain for season 2017/2018. Since the immune response to influenza is shaped by the history of exposure to antigenically similar strains, the potential cross-protection between seasonal human influenza vaccine strains and the emerging pandemic strains was investigated. Human serum samples were tested by haemagglutination inhibition and single radial haemolysis assays against A/Brisbane/59/2007, A/California/07/2009, and A/Michigan/45/2015 strains. Strong cross-reactions between A/California/07/2009 and A/Michigan/45/2015 strains were observed in 2009/2010, most likely induced by the start of the 2009 pandemic, and the subsequent post-pandemic seasons from 2010/2011 onwards when A/California/07/2009 becomes the predominant strain. In 2014/2015 season, population immunity against A/California/07/2009 and A/Michigan/45/2015 strains increased again, associated with strong cross-reactions. While haemagglutination inhibition assay has a higher sensitivity for detection of new seasonal drift, the single radial haemolysis assay is an excellent tool to determine the presence of pre-existing immunity, allowing a potential prediction on the booster potential of influenza vaccines against newly emerging drifted strains.
REVIEW | doi:10.20944/preprints201905.0273.v1
Subject: Biology, Animal Sciences & Zoology Keywords: influenza virus; vaccines; passive immunization; immunotherapeutics
Online: 22 May 2019 (11:31:15 CEST)
Influenza is a disease that poses a significant health burden worldwide. Vaccination is the best way to prevent influenza virus infections. However, conventional vaccines are only effective for a short period of time due to the propensity of influenza viruses to undergo antigenic drift and antigenic shift. The efficacy of these vaccines is uncertain from year-to-year due to potential mismatching between the circulating viruses and vaccine strains, mutations arising due to egg adaptation, and potential contamination of the vaccine virus stock. Subsequently, the inability to store these vaccines long-term and vaccine shortages are challenges that need to be overcome. Conventional vaccines are also less effective for certain populations, including the young, old, and immunocompromised. This warrants for diverse efficacious vaccine developmental approaches, involving both active and passive immunization. As opposed to active immunization platforms (requiring the use of whole or portions of pathogens as vaccines), the rapidly developing passive immunization involves administration of either pathogen-specific or broadly acting antibodies against a kind or class of pathogens as a prophylactic treatment to corresponding acute infection. Several antibodies with broadly acting capacities have been discovered that may serve as means to suppress influenza viral infection and allow the process of natural immunity to engage opsonized pathogens whilst boosting immune system by antibody-dependent mechanisms that bridge the innate and adaptive arms. By that, passive immunotherapeutics approach assumes a robust tool that could aid control of influenza viruses. In this review, we comment on some improvements in influenza management and promising vaccine development platforms, with emphasis on the capacity of passive immunotherapeutics especially when coupled with the use of antivirals in the management of influenza infection.
ARTICLE | doi:10.20944/preprints202002.0022.v1
Subject: Life Sciences, Virology Keywords: influenza B virus; mammalian adaptation; amino acid substitutions; pathogenicity; influenza model; animal model; virulence; antiviral drugs
Online: 3 February 2020 (06:24:05 CET)
Over the years influenza B virus (IBV) contribute annual disease and can lead to serious respiratory disease among humans. More attention should be paid to the mammalian adaptive processes of B viruses and development of vaccines against current influenza. Because of preclinical trials of anti-influenza drugs are conducted mainly on mice, we developed adequate animal model using antigenically-relevant IBV strain for testing anti-influenza drugs and protective efficacy of flu vaccines. We serially passaged Victoria lineage (clade 1A) IBV 17 times in BALB/c mice. The adaptive amino acid substitutions were found in HA (T214I) and NA (D432N). By the electron microscopic examination, we showed spherical and elliptical shapes of IBV. Light microscopy showed that mouse-adapted B virus caused influenza pneumonia on day 6 post inoculation. We evaluated the illness pathogenicity, viral load and histopathological features of mouse-adapted IBV and estimated anti-influenza drugs and vaccine efficiency in vitro and in vivo. Assessment of investigational anti-influenza drug oseltamivir ethoxisuccinate and flu vaccine Ultrix® revealed effectivity against our mouse-adapted influenza B virus.
ARTICLE | doi:10.20944/preprints201907.0246.v1
Subject: Medicine & Pharmacology, Pathology & Pathobiology Keywords: influenza virus; imprinting; haemagglutinin; antibody titre; quadrivalent vaccine; influenza A; H1N1; split-virion; isotype; virus neutralization
Online: 23 July 2019 (04:03:13 CEST)
Influenza virus imprinting is now understood to significantly the influence immune responses and clinical outcome of influenza virus infections that occur later in life. Due to the yearly cycling of influenza viruses, humans are imprinted with the circulating virus of their birth year to subsequently build a complex influenza virus immune history but very little is known about how the imprinting strain influences vaccine responses. To investigate the imprinted host immune responses to split-virion vaccination, we imprinted ferrets with a sublethal dose of the historical seasonal H1N1 strain A/USSR/90/1977. After a +60 day recovery period was given to build immune memory, ferrets were immunized and the challenge at Day 123. Samples were collected throughout the time course and immunological assays were performed to investigate recall mechanisms. The preimmune-vaccinated ferrets did not experience significant disease during challenge while naïve-vaccinated ferrets had severe disease. Hemagglutination inhibition assays showed preimmune ferrets had a more robust antibody response post vaccination, increased virus neutralization activity. Virus specific immunoglobulins were of predominantly the IgG isotype suggesting B cell maturity and plasticity at vaccination. These results are important and should be considered for vaccine design.
ARTICLE | doi:10.20944/preprints202106.0410.v1
Subject: Biology, Anatomy & Morphology Keywords: highly pathogenic avian influenza viruses, pathogenicity factors.
Online: 15 June 2021 (14:29:26 CEST)
The H7 subtype of avian influenza viruses (AIV) stands out among other AIV. The H7 viruses cir-culate in ducks, poultry, equine and have repeatedly caused outbreaks of disease in humans. In or-der to study the pathogenicity factors of H7N1 viruses, several variants were obtained, starting with laboratory strain, with a history of 12 passages through chicken embryos. This strain, A/chicken/Rostock/R0p/1934(H7N1) (R0p) had only 3 substitution in HA relatively A/Chicken/Rostock/45/34(H7N1), substitution Arg140Gly among them. 10 variants of this strain was obtained and studied to ascertain its biological property, genome stability and factors of patho-genicity. Strain R0p had decreased virulence for chicken, comparing with described in literature virulence of A/FPV Rostock/34 and A/chicken/Rostock/34 viruses. After 10 passages through the chicken lungs variant was obtained much more pathogenic than the starting R0p. The study of in-termediate passages through the chicken lungs showed that the jump in pathogenicity had occurred sharply between the fifth and sixth passage. By cloning these variants, a pair of strains (R5p and R6p) were obtained, and the complete genomes of these strains were sequenced. Single amino acid substitution was revealed, namely reversion Gly140Arg in HA1. This amino acid is located at the head part of the hemagglutinin, adjacent to the receptor-binding site. In addition to the increased pathogenicity for chicken and mice, R6p differs from R5p in the pattern of foci in cell culture and an increased affinity for a negatively charged receptor analogue, while maintaining a pattern of recep-tor binding specificity and the pH optimum of the HA conformational change.
Subject: Biology, Anatomy & Morphology Keywords: highly pathogenic avian influenza viruses, pathogenicity factors.
Online: 10 May 2021 (14:22:23 CEST)
The H7 subtype of avian influenza viruses (AIV) stands out among other AIV. H7 viruses circulate in ducks, poultry, equine and have repeatedly caused outbreaks of disease in humans. In order to study the pathogenicity factors of H7N1 viruses, several laboratory variants of the A/FPV/Rostock/34 (H7N1) strain were obtained by passages in the chicken lungs. After 10 such passages, a variant was obtained that differed from the parent virus by amino acid substitutions Val109Phe in PB2, Gln621Lys in PB1, Thr32Ala and Leu586Phe in PA Gly140Arg in HA1 and Ala101Thr in HA2 (numbering by H3), Ser82Arg in M2, Arg118Lys and Met124Arg in NS1. No differences were found in proteins NA, NP, M1 and NS2. The resulting variant was hundreds of times more pathogenic for chickens than the original laboratory variant of the virus. The study of intermediate passages showed that the jump in pathogenicity occurs sharply between the fifth and sixth passage through the chicken lungs. By cloning these variants, a pair of strains (R5p and R6p) were obtained, and the complete genomes of these strains were sequenced. Single amino acid substitution was revealed, namely Gly140Arg in HA1. It is important to emphasize that this substitution is a reversion, since Arg is located in position 140 HA1 of original the A/FPV/Rostock/34 (H7N1) virus (GenBank). This amino acid is located at the head part of the hemagglutinin, adjacent to the receptor-binding site. In addition to the increased pathogenicity, R6p differs from R5p by an increased affinity for a negatively charged receptor analogue, an increased affinity for MDCK cells, while maintaining a receptor specificity profile.
ARTICLE | doi:10.20944/preprints201905.0356.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: Influenza A virus, immunology, immunotherapy, receptor; tumors
Online: 29 May 2019 (16:16:49 CEST)
Dewetting transition - a concept borrowed from fluid mechanics - is a physiological process which takes place inside the hydrophobic pores of ion channels. This transient phenomenon causes a metastable state which forbids water molecules to cross the microscopic receptors’ cavities. This leads to a decrease of conductance, a closure of the hole and, subsequently, severe impairment of cellular performance. We suggest that artificially-provoked dewetting transition in ion channels’ hydrophobic pores could stand for a molecular candidate to erase detrimental organisms, such as viruses, bacteria and cancer cells. We describe a novel type of high-affinity monoclonal antibody, which: a) targets specific trans-membrane receptor structures of harmful or redundant cells; b) is equipped with lipophilic and/or hydrophobic fragments that prevent physiological water flows inside ion channels. Therefore, we achieve an artificial dewetting transition inside receptors’ cavities which causes transmembrane ionic flows discontinuity, channel blockage and subsequent damage of morbid cells. As an example, we describe dewetting monoclonal antibodies targeting the M2 channel of the Influenza A virus: they might prevent water to enter the pores, thus leading to virion impairment.
ARTICLE | doi:10.20944/preprints202301.0480.v1
Subject: Life Sciences, Virology Keywords: avian influenza; highly pathogenic avian influenza; next generation sequencing; whole genome sequencing; nanopore technology; methods comparison; clinical validation
Online: 26 January 2023 (15:19:53 CET)
As exemplified by the global response to the SARS-CoV-2 pandemic, whole genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigated a next generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluated this platform for routine use in a diagnostic laboratory. In this study we evaluated different primer sets for the whole genome amplification of influenza A virus and evaluated five different library preparation approaches for sequencing on the nanopore platform using the MinION flow-cell. A limited amplification procedure and a rapid procedure were found to be best among the approaches taken.
REVIEW | doi:10.20944/preprints202109.0506.v1
Subject: Life Sciences, Virology Keywords: H5N8; Influenza; Virus; Antiviral; Mutation; Reassortment; Therapeutics; Vaccines
Online: 30 September 2021 (08:08:36 CEST)
2014 marked the first emergence of avian influenza A(H5N8) in Jeonbuk Province, South Korea, which then quickly spread worldwide. In the midst of the 2020-21 H5N8 outbreak, it spread to domestic poultry and wild waterfowl shorebirds, leading to the first human infection in Astrakhan Oblast, Russia. Despite being clinically asymptomatic and without direct human-to-human transmission, the World Health Organisation stressed the need for continued risk assessment given the nature of Influenza to reassort and generate novel strains. Given its promiscuity and spread to humans, the urgency to understand the mechanisms of possible species jumping to avert disastrous pandemics is increasing. Addressing the epidemiology of H5N8 and its mechanisms of species jumping and its implications, mutational and reassortment libraries can potentially be built, allowing them to be tested on various models complemented with deep-sequencing and automation. With the knowledge on mutational patterns, cellular pathways, drug resistance mechanisms and effects of host proteins can allow better preparedness against H5N8 and other influenza A viruses.
ARTICLE | doi:10.20944/preprints202106.0039.v1
Subject: Life Sciences, Virology Keywords: LAIV, Influenza, HA, IgA, IgG, vaccine, genome rearrangement
Online: 1 June 2021 (15:02:27 CEST)
Influenza B virus (IBV) is considered a major respiratory pathogen responsible for seasonal respiratory disease in humans, particularly severe in children and the elderly. Seasonal influenza vaccination is considered the most efficient strategy to prevent and control IBV infections. Live attenuated influenza virus vaccines (LAIVs) are thought to induce both humoral and cellular immune responses by mimicking a natural infection, but their effectiveness have recently come into question. Thus, the opportunity exists to find alternative approaches to improve overall influenza vaccine effectiveness. Two alternative IBV backbones were developed with re-arranged genomes, re-arranged M (FluB-RAM) and a re-arranged NS (FluB-RANS). Both re-arranged viruses showed temperature sensitivity in vitro compared to the WT type B/Bris strain, were genetically stable over multiple passages in embryonated chicken eggs and were attenuated in vivo in mice. In a prime-boost regime in naïve mice, both re-arranged viruses induced antibodies against HA with hemagglutination inhibition titers considered of protective value. In addition, antibodies against NA and NP were readily detected with potential protective value. Upon lethal IBV challenge, mice previously vaccinated with either FluB-RAM or FluB-RANS were completely protected against clinical disease and mortality. In conclusion, genome re-arrangement renders efficacious LAIV candidates to protect mice against IBV.
ARTICLE | doi:10.20944/preprints202103.0025.v1
Subject: Life Sciences, Biochemistry Keywords: Influenza; epidemiology; spatiotemporal; seasonality; global; transmission; infectious disease
Online: 1 March 2021 (14:05:52 CET)
Influenza epidemics in temperate regions display dynamics that are characterized by pronounced seasonal peaks during the winter. The general lack of influenza cases during the off-season may result from the virus physically disappearing at the end of the season, in which case it must be imported annually. Alternatively, it may result from persistent asymptomatic carriers or unnoticed local transmission chains that develop into local epidemics as conditions become conducive. Here I attempt to understand these differing explanations by analyzing the global distribution of the four major subtypes that comprise influenza over a period of 18 years based on FluNet data, the surveillance network and database compiled by the WHO, and the NCBI influenza data resource, a repository of relevant genetic information. Examining the annual proportion of each subtype, I find considerable variations in subtype annual proportions between the regions. Moreover, I find that seasonal influenza subtypes can remain confined to specific temperate regions, without showing measurable global presence. These results indicate that although largely undetected during the off-season, influenza is likely to persist locally, and imply a ‘local-global’ model where annual influenza epidemics are a mixture of local strains undergoing reactivation together with an influx of global variants.
COMMUNICATION | doi:10.20944/preprints202012.0677.v1
Subject: Life Sciences, Biochemistry Keywords: highly pathogenic avian influenza virus; H5N8; falcated duck
Online: 28 December 2020 (10:32:26 CET)
We isolated two highly pathogenic avian influenza viruses (HPAIVs) of subtype H5N8 clade 126.96.36.199b from falcated duck (Anas falcata) feces and environmental water collected at an overwintering site in Japan. Our isolates were almost genetically identical to each other and showed high genetic similarity with H5N8 HPAIVs recently isolated in South Korea, a distant part of Japan, and European countries. These results suggest the potential role of falcated ducks in the dissemination of HPAIVs.
ARTICLE | doi:10.20944/preprints202003.0291.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: co-infection; coronavirus disease 2019; COVID-19; influenza
Online: 19 March 2020 (02:00:47 CET)
Background: On late December 2019, a viral pneumonia known as coronavirus disease 2019 (COVID-19), was originated from China and spread very rapidly in the world. Therefore, COVID-19 became a global concern and health problem. Methods: We presented four patients in this study. They were selected from patients who presented with pneumonia symptoms and were suspicious for COVID-19 and referred to the intended centers for COVID-19 diagnosis and management of Shiraz University of Medical Sciences in the south of Iran. Two nasopharyngeal and oropharyngeal throat swab samples were collected from each patient and tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by real-time reverse-transcriptase–polymerase-chain-reaction (RT-PCR), and also samples were sent for influenza viruses and all the respiratory panel. Results: In the present report, four patients were diagnosed in the starting days of COVID-19 disease in our center in south of Iran with co-infection of SARS-CoV-2 and influenza virus. Conclusions: This co-infection of COVID-19 and influenza highlights the importance of considering SARS-CoV-2 PCR assay regardless of other positive findings for other pathogens in the primary test during the epidemic.
REVIEW | doi:10.20944/preprints201906.0085.v1
Subject: Life Sciences, Virology Keywords: H9N2; avian influenza viruses; zoonotic; pandemic potential; poultry
Online: 11 June 2019 (07:44:44 CEST)
H9N2 avian influenza viruses have become globally widespread in poultry over the last two decades and represent a genuine threat both to the global poultry industry but also humans through their high rates of zoonotic infection and pandemic potential. H9N2 viruses are generally hyperendemic in effected countries and have been found in poultry in many new regions in recent years. In this review we examine the current global spread of H9N2 avian influenza viruses as well as their host range, tropism, transmission routes and the risk posed by these viruses to human health.
ARTICLE | doi:10.20944/preprints202209.0430.v2
Subject: Medicine & Pharmacology, Obstetrics & Gynaecology Keywords: COVID-19 vaccines; menstruation; pregnancy outcomes; Influenza vaccines; VAERS; stillbirth; miscarriage
Online: 30 December 2022 (09:39:28 CET)
Objectives Assess rates of adverse events (AE) after COVID-19 vaccines experienced by women of reproductive age, focusing on pregnancy and menstruation, using data collected by the US Centers for Disease Control and Prevention (CDC) Vaccine Adverse Events Reporting System (VAERS) database. Design Population-based retrospective cohort study. Setting US and global entries in US Centers for Disease Control and Prevention (CDC) Vaccine Adverse Events Reporting System (VAERS). Participants CDC VAERS entries from January 1, 1998 to June 30, 2022. Interventions None. Main Outcome Measures A proportional reporting ratio analysis is performed using data in the VAERS system comparing adverse events (AE) reported post-COVID-19 vaccines with that of post-Influenza vaccines. Results COVID-19 vaccines, when compared to the Influenza vaccines, are associated with a significant increase in AE with all proportional reporting ratios of > 2.0: menstrual abnormalities, miscarriage, fetal chromosomal abnormalities, fetal malformation, fetal cystic hygroma, fetal cardiac disorders, fetal arrhythmias, fetal cardiac arrest, fetal vascular malperfusion, fetal growth abnormalities, fetal abnormal surveillance, fetal placental thrombosis, low amniotic fluid, preeclampsia, premature delivery, preterm premature rupture of membrane, fetal death/stillbirth, and premature baby death (all p values were much smaller than 0.05). When normalized by time-available, doses-given, or persons-received, all COVID-19 vaccine AE far exceed the safety signal on all recognized thresholds. Conclusions Pregnancy complications and menstrual abnormalities are significantly more frequent following COVID-19 vaccinations than Influenza vaccinations. A worldwide moratorium on the use of COVID-19 vaccines in pregnancy is advised until randomized prospective trials document safety in pregnancy and long-term follow-up in offspring.
ARTICLE | doi:10.20944/preprints202206.0123.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: Influenza vaccines; Vaccine hesitancy; Healthcare workers (HCWs); South Africa
Online: 8 June 2022 (10:03:21 CEST)
Vaccination attitudes among healthcare workers (HCWs) is a vital factor for measuring their level of vaccination uptake and intention to recommend vaccinations to their patients. To our knowledge, no study has been conducted in South Africa to assess hesitancy to influenza vaccines among HCWs. We used questionnaire adapted from Betsch and colleagues to conduct an online and face-to-face cross-sectional study among HCWs at the start of COVID-19 vaccine roll-out prior to the flu season. Main outcome was influenza vaccine hesitancy. We used multivariate logistic regression to assess predictors of influenza vaccine hesitancy. Of 401 participants, 64.5% were women, 49.2% nurses, and 12.5% physicians. A total of 54.9% were willing to accept vaccination, 20.4% were undecided, and 24.7% intended to refuse. Older participants above 17-25 years and physicians were likely to receive the vaccine. Key predictors of vaccine acceptance were confidence in the effectiveness, consideration of benefits and risks, and willingness to be vaccinated to protect others. Influenza vaccine hesitancy was highest in those who did not trust that influenza vaccines are safe. For future flu seasons, tailored education programs targeting younger HCWs and more information about the composition of flu vaccines would be vital to improve vaccine uptake.
ARTICLE | doi:10.20944/preprints202106.0735.v1
Subject: Chemistry, Analytical Chemistry Keywords: Influenza A virus; lactoferrin; tetrapeptides; biophysics; antiviral agents; hemagglutinin
Online: 30 June 2021 (11:59:07 CEST)
Influenza is a highly contagious, acute respiratory illness, which represents one of the main health issues worldwide. Even though some antivirals are available, the alarming increase of virus strains resistant to them highlights the need to find new drugs. Previously, Superti et al. have deeper investigated the mechanism of the anti-Influenza virus effect of bovine Lactoferrin (bLf) and the role of its tryptic fragments (the N and C-lobes) in the antiviral activity. Recently, through a truncation library, we identified the tetrapeptides, SKHS (1) and SLDC (2), derived from bLf C-lobe fragment 418-429, which were able to bind hemagglutinin (HA) and inhibit cell infection in a concentration range of femto- to picomolar. Starting from these results, in this work, we initiated a systematic SAR study on the peptides mentioned above, through an Alanine scanning approach. We carried out binding affinity measurements by microscale thermophoresis (MST) and Surface Plasmon Resonance (SPR), and hemagglutination inhibition (HI) and virus neutralization (NT) assays on synthesized peptides. Computational studies were performed to identify possible lig-and-HA interactions. Results obtained led to the identification of an interesting peptide endowed with broad anti-Influenza activity and able to inhibit viral infection to a greater extent of reference peptide.
Online: 16 October 2020 (11:49:13 CEST)
Coronavirus disease 2019 (COVID-19) is caused by infection with the 2019 novel coronavirus 2 (2019-nCoV, now referred to as SARS-CoV-2). COVID-19 has become a global pandemic since its outbreak at the end of Dec 2019. COVID-19 could lead to severe acute respiratory disease, especially to those who have reduced immunity. Binding of the viral Spike protein (S) to its receptor ACE2 (Angiotensin Converting Enzyme 2) on the surface of target cells has been proven to be key for virus entry and infection. Although ACE2 expression in the respiratory system is necessary for pneumonia infection by SARS-CoV-2, the regulation of ACE2 gene expression remains poorly investigated, especially for patients that are in pre-pathological conditions. Here, by analyzing The Gene Expression Omnibus (GEO) database, we investigated the expression regulation of ACE2 in various kinds of primary epithelial cells from the respiratory system after varies of respiratory viruses infection such as influenza A virus (IFV), respiratory syncytial virus (RSV) and human rhinovirus (hRV). Our analyses reveal that infection of multiple kinds of respiratory viruses or influenza vaccines greatly increased ACE2 expression, suggesting that respiratory viruses infection could represent a high risk factor for developing COVID-19. We also found that the regulatory effect of influenza A virus on ACE2 expression is associated with activation of the interferon beta-induced pathway and viral RNA-activated host response. Together, our data provide a theoretical framework for clinical classification for SARS-CoV-2 infection susceptibility and could be used for future prevention and therapy treatment for COVID-19.
ARTICLE | doi:10.20944/preprints202004.0078.v1
Subject: Behavioral Sciences, Social Psychology Keywords: COVID-19; R0; WHO; social distancing; H1N1; H2N2; influenza
Online: 7 April 2020 (02:48:13 CEST)
The current outbreak of the novel coronavirus also known as COVID-19 was declared as a public health emergency by the WHO where over a million people have been affected by the disease with over 50000 deaths till date. Social distancing is a method to minimize crowd interactions and prevent the spread of disease within groups of people. This is a common practice which has been carried out over generations to minimize the spread of virus by limiting its reproduction rate (R0) among communities. The article focuses on how social distancing has been used to deal previous pandemics globally and the issues that needs to be addressed to tackle the COVID-19 threat.
ARTICLE | doi:10.20944/preprints202003.0160.v1
Subject: Life Sciences, Virology Keywords: influenza-like illness; 2019-nCoV; person-to-person transmission
Online: 10 March 2020 (05:18:19 CET)
The ongoing pandemic of the 2019 novel coronavirus disease (COVID-19) raises a global health crisis, which has resulted in 75,778 confirmed cases with 2130 deaths in China and beyond. Atypical symptom renders it challenging to earlier recognize the 2019-nCoV carrier with the potential ability of equivalent transmission. Therefore, it is needed to gain full spectrum of COVID-19. Here we report clustered COVID-19 cases of person-to-person transmission. The symptoms of typical pneumonia are shared by the two familial members, namely son (Patient 1) and father (Patient 2). Unexpectedly, an influenza-like illness (ILI) is also caused in Patient 3 having close contact with Patient 1 at personal dinner party. Combined with clinical and epidemiological study, chest computed tomography (CT) and molecular diagnosis demonstrate that all the three cases tested positive for COVID-19 with distinct symptoms by human-to-human transmission. To the best of knowledge, it closes in part (if not all), a missing gap of clinical repertoires of COVID-19 outbreaks and underlines the possibility that neglection of cryptic/asymptomatic/mild cold-like syndromes gives biased screen in the earlier stage of COVID-19 cases.
ARTICLE | doi:10.20944/preprints201805.0466.v2
Subject: Life Sciences, Immunology Keywords: influenza; serum; IgG; humoral antibody; original antigenic sin; hemagglutinin
Online: 6 July 2018 (07:53:32 CEST)
The first exposure to influenza is thought to impact subsequent immune responses later in life. The consequences of this can be seen during influenza epidemics and pandemics with differences in morbidity and mortality for different birth cohorts. There is a need for better understanding of how vaccine responses are affected by early exposures to influenza viruses. In this analysis of hemagglutination inhibition (HI) antibody responses in two cohorts of military personnel we noticed differences related to age, sex, prior vaccination, deployment and birth year. These data suggest that HI antibody production, in response to influenza vaccination, is affected by these factors. The magnitude of this antibody response is associated with, among other factors, the influenza strain that circulated following birth.
REVIEW | doi:10.20944/preprints201705.0209.v2
Subject: Life Sciences, Immunology Keywords: influenza virus; apoptosis; antiviral agent; innate immunity; host response
Online: 14 August 2017 (04:41:22 CEST)
Human influenza A viruses (IAVs) cause global pandemics and epidemics, which remain serious threats to public health because of the shortage of effective means of control. To combat the surge of viral outbreaks, new treatments are urgently needed. Developing new virus control modalities requires better understanding of virus-host interactions. Here we describe how IAV infection triggers cellular apoptosis, and how this process can be exploited towards development of new therapeutics, which might be more effective than the currently available anti-influenza drugs.
REVIEW | doi:10.20944/preprints202111.0132.v2
Subject: Medicine & Pharmacology, Other Keywords: adults; influenza; cell-cultured vaccine; egg-based vaccine; influenza vaccine; relative vaccine effectiveness; real word evidence; mutation; human / prevention & control*; comparative study
Online: 20 December 2021 (11:00:26 CET)
Avian mutations in vaccine strains obtained from embryonated eggs could impair vaccine effec-tiveness. We performed a systematic review and meta-analysis of the adjusted relative vaccine effectiveness (arVE) of seed cell-cultured influenza vaccines (ccIV) compared to egg-based influ-enza vaccines (eIV) in preventing laboratory-confirmed influenza related outcomes (IRO) or IRO by clinical codes, in subjects 18 and over. We completed the literature search in January 2021; ap-plied exclusion criteria, evaluated risk of bias of the evidence, and performed heterogeneity, pub-lication bias, qualitative, quantitative and sensitivity analyses. All estimates were computed us-ing a random approach. International Prospective Register of Systematic Reviews, CRD42021228290. We identified 12 publications that reported 26 adjusted arVE results. Five publications reported 13 laboratory confirmed arVE and seven reported 13 code-ascertained arVE. Nine publications with 22 results were at low risk of bias. Heterogeneity was explained by season and risk of bias. We found a significant 11% (8 to 14%) adjusted arVE favoring ccIV in preventing any IRO in the 2017-2018 influenza season. The arVE was 3% (-01 to 7%) in the 2018-2019 influenza season. We found moderate evidence of a significant advantage of the ccIV in preventing IRO, compared to eIV, in a well-matched A(H3N2) predominant season.
ARTICLE | doi:10.20944/preprints202012.0817.v2
Subject: Life Sciences, Microbiology Keywords: COVID-19; OC43; coronavirus; pandemic; influenza; historical revisionism; corpus linguistics
Online: 21 December 2022 (09:56:55 CET)
COVID-19 is the first known coronavirus pandemic. Nevertheless, the seasonal circulation of the four milder coronaviruses of humans – OC43, NL63, 229E and HKU1 – raises the possibility that these viruses are the descendants of more ancient coronavirus pandemics. This proposal arises by analogy to the observed descent of seasonal influenza subtypes H2N2 (now extinct), H3N2 and H1H1 from the pandemic strains of 1957, 1968 and 2009, respectively. Recent historical revisionist speculation has focussed on the influenza pandemic of 1889-1892, based on molecular phylogenetic reconstructions that show the emergence of human coronavirus OC43 around that time, probably by zoonosis from cattle. If the “Russian influenza”, as The Times named it in early 1890, was not influenza but caused by a coronavirus, the origins of the other three milder human coronaviruses may also have left a residue of clinical evidence in the 19th century medical literature and popular press. In this paper, we search digitised 19th century British newspapers for evidence of previously unsuspected coronavirus pandemics. We conclude that there is little or no corpus linguistic signal in the UK national press for large-scale outbreaks of unidentified respiratory disease for the period 1785 to 1890.
REVIEW | doi:10.20944/preprints202208.0486.v1
Subject: Biology, Other Keywords: Influenza A virus; SARS-COV-2; matrix metalloproteinases; infectious diseases
Online: 29 August 2022 (10:43:53 CEST)
Matrix metalloproteinases are involved in extracellular matrix remodeling through the degradation of extracellular matrix components and are involved in the inflammatory response by regulating the activities of TNF-alpha and IL-1beta, which are pro-inflammatory cytokines, in addition to extracellular matrix components. Since the regulation of inflammatory response and changes in the extracellular matrix by MMPs are related to the development of various diseases including lung and cardiovascular diseases, many studies have been conducted on the role of MMPs in pathogenesis. In addition, various studies have demonstrated that MMPs are involved in the pathogenesis of infectious diseases by regulating the expression and activity of MMPs by infection with pathogens. In this review, we discuss the role of MMPs in infectious diseases and the role of MMPs in inflammatory responses and present their potential as therapeutic targets in infectious diseases.
COMMUNICATION | doi:10.20944/preprints202009.0702.v1
Subject: Life Sciences, Biochemistry Keywords: SARS-CoV-2; influenza vaccine; systematic review; infection; severity; risk
Online: 29 September 2020 (09:14:03 CEST)
We reviewed the association between seasonal influenza vaccination and the risk of SARS-CoV-2 infection or complicated illness or poor outcome (e.g. severe disease, need for hospitalization or ventilatory support, or death) among COVID-19 patients. None of the studies that were reviewed (n=12) found a significant increase in the risk of infection or in the illness severity or lethality, while some reported significantly inverse associations. Our findings support measures aimed at raising influenza vaccination coverage in the coming months.
ARTICLE | doi:10.20944/preprints201710.0137.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: influenza; pulse waves; incubation period; rapid diagnostic tests; coincidence analysis
Online: 20 October 2017 (09:54:02 CEST)
Viral infections have long been the biggest threat to human survival, and from a medical perspective, the development of noninvasive high-throughput screening methods that target the incubation period to either treat diseases or limit viral spread would be strikingly effective. Using this technology to target viral incubation periods would also be inexpensive to perform. The current study proposes to transform pulse signals into a rapid diagnostic test using “coincidence analysis” in the hope of preventing or reducing the symptoms of viral infections. The heart plays a critical role in calculating and supplying the needs of all tissues of the body. Pulse waves are pressurized signals in response to heart’s calculations and include all phases of the cardiac cycle, which maintains life and provides energy needed to perform tasks. Any small movement gives a corresponding signal to pulse waves. The current study investigated conclusive data on self-limiting infections, such as common cold. We used pulse wave, coincidence analysis technology to capture signals from individuals with common cold during the incubation period and investigated if particular characteristic signals could be applied to influenza during the incubation period. Preliminary work demonstrated that pulse waves could generate signals using this technology that would be worthwhile for future research. A small amount of analytical data from common cold existed previously. The data structure is based on the idea that a single pulse wave at differing physiological conditions would have slight modifications that would be amplified and presented by various geometrical shapes after extensive data are accumulated. These geometric shapes can then be sliced vertically or horizontally to extract data during different illness stages. The significance of these findings are impressive; from a personal or a public hygiene perspective, this analytical technology provides many benefits, such as rapid and precise decision-making that can be directly visualized or can be analyzed using software programs. Also, this technology also uses futuristic wearable technology that brings practical problem solving to physiology.
ARTICLE | doi:10.20944/preprints201701.0033.v1
Subject: Life Sciences, Virology Keywords: H7N9 avian influenza; pseudovirus; neutralization assay; relative luminescence units (RLU)
Online: 6 January 2017 (10:21:52 CET)
In March 2013, a novel avian influenza A H7N9 virus was emerged in China, which cause rapidly progressive pneumonia and with a high fatality rate. Serologic studies to evaluate neutralizing antibodies of infected patients and birds are invaluable tools for immunogenicity research of H7N9 and epidemiological investigation. Conventional neutralization assays are laborious and time-consuming which also hampered by biosafety requirement. In this study, We construct and produce pseudovirus bearing the full-length hemagglutinin (HA) of H7N9 virus in the Env-defective, luciferase-expressing HIV-1 backbone. The production of lentiviral pseudovirus was analysed by HA gene specific real-time reverse-transcription PCR, transmission electron microscopy (TEM), and Western Blot assay to prove the nucleic acid replication, the morphology of virus, and the expression of HA protein in pseudovirus. After that pseudovirus based inhibition assay was established to detect neutralizing antibodies of a panel of serum samples. Our results demonstrated that H7N9 pseudovirus which had single-cycle infection was generated. By comparing the neutralization antibody titers, pseudovirus based neutralization test could be recognized as an alternative of conventional microneutralization (MN). Hence, we conclude that it is possible to use pseudovirus inhibition assay to screen sera samples, as well as evaluate vaccine-induced neutralizing antibodies against H7N9 virus.
ARTICLE | doi:10.20944/preprints201701.0010.v1
Subject: Medicine & Pharmacology, Clinical Neurology Keywords: Haemophilus influenza; Neisseria meningitidis; meningitis; vaccine efficacy evaluation; immunization schedule.
Online: 2 January 2017 (18:14:59 CET)
Meningitis is a severe disease associated with death in children under five with highest rates of infections under age of one. Vaccines for Neisseria meningitides and Haemophilus influenza are used to prevent the main causative agents of meningitis. Administration of H. influenzae type b (Hib) vaccine is recommended at 2, 4 and 6 months with a booster dose at 18 months. N. meningitidis has two commercially available vaccines, the pure polysaccharide is recommended at 24 months meanwhile the protein-conjugated vaccines at 12 months. We sought in this study to examine if coadministering the vaccines for the two main meningitis causing bacteria might be synergistic as a preliminary step towards the possibility of shuffling immunization schedule. So, we coadministered Hib vaccine with commercially available vaccines either quadrate (ACWY) polysaccharide meningococcal (Men) or conjugated meningococcal (Nim) vaccines in Balb/C mice (n = 6/group) and compared to each vaccine administered separately and controls. Thirty-five days post immunization, we measured specific antibodies titers. Hib vaccine increased Men antibody titers significantly for serotypes Y and W. When Hib vaccine was coadministrated with Nim, antibody titer for Y, W and A significantly increased. For serotype C, there was no significant difference in antibody titers among immunized groups. As for effect of meningococcal vaccines on Hib, Men significantly increased Hib antibody titers while Nim had no effect. Collectively, our data suggested that coadministration of Hib and Men or Nim vaccines was safe and had synergistic effect on immune responses elicited to both vaccines. Further studies are needed before immunization schedule modifications. Such immunization schedule recommendation should provide better protection against this life-threatening disease in young children.
ARTICLE | doi:10.20944/preprints202002.0391.v1
Subject: Life Sciences, Molecular Biology Keywords: Highly Pathogenic Avian Influenza Virus, Low Pathogenic Avian Influenza Virus, Evolution, Virulence Determinants, non-H5/H7, Cleavage Site, Chicken-to-Chicken Transmission, Virulence, Protease
Online: 26 February 2020 (11:13:35 CET)
Highly pathogenic (HP) avian influenza viruses (AIVs) are naturally restricted to H5 and H7 subtypes with a polybasic cleavage site (CS) in the hemagglutinin (HA) and any AIV with an intravenous pathogenicity index (IVPI) ≥1.2. Only few non-H5/H7 viruses fulfill the criteria of HPAIVs; nevertheless, it remains unknown why these viruses did not spread in domestic birds. In 2012, a unique H4N2 virus with a polybasic CS 322PEKRRTR/G329 was isolated from quails in California which, however, was avirulent in chickens. This is the only known non-H5/H7 virus with four basic amino acids in the HACS. Here, we investigated the virulence of this virus in chickens after expansion of the polybasic CS by substitution of T327R (322PEKRRRR/G329) or T327K (322PEKRRKR/G329) with or without reassortment with HPAIVs H5N1 and H7N7. The impact of single mutations or reassortment on virus fitness in vitro and in vivo was studied. Efficient cell culture replication of T327R/K carrying H4N2 viruses increased by trypsin, particularly in MDCK cells, and reassortment with HPAIV H5N1. Likewise, replication, virus excretion and bird-to-bird transmission of H4N2 was remarkably compromised by the CS mutations, but restored after reassortment with HPAIV H5N1, although not with HPAIV H7N7. Viruses carrying the H4-HA with or without R327 or K327 mutations and the other gene segments from HPAIV H5N1 exhibited high virulence and efficient transmission in chickens. Together, increasing the number of basic amino acids in the H4N2 HACS was detrimental for viral fitness particularly in vivo but compensated by reassortment with HPAIV H5N1. This may explain the absence of non-H5/H7 HPAIVs in poultry.
REVIEW | doi:10.20944/preprints202211.0336.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: COVID-19 Booster; Influenza and COVID-19; Vaccination Strategy; Combining Vaccination
Online: 17 November 2022 (10:31:53 CET)
Background: The uptake of COVID-19 booster vaccines has been significantly low. Therefore, it is questionable whether combining the COVID-19 booster vaccines with Influenza vaccines can increase the population's interest in taking such vaccines and manage the health pandemic effectively. Methodology: In this systematic review and meta-analysis, a synthesis of the findings and summary of a total of 30 research articles based on the topic, ‘combining influenza and COVID-19 booster vaccination strategy’ was undertaken. The research articles were identified from three databases, namely, PubMed, Cochran Library, and Google Scholar using specific keywords and inclusion criteria. However, research articles that were not peer-reviewed and not published in English were excluded from the systematic review and meta-analysis. The average risk ratio of the included articles was 0.78% based on a 95% CI. On the other hand, the heterogeneity between such studies was I2 = 35%, while the statistical significance of their findings occurred at p < 0.05. The average p-value of the included research studies was p = 0.62, implying that the null hypothesis was not rejected in almost all the studies. Results: A synthesis of the chosen research articles revealed that when influenza and COVID-19 booster vaccines are combined, there is potential for an increase in the uptake of the latter, mainly because many populations have already been accustomed to taking influenza vaccines on an annual basis. Conclusions: In this way, through such findings, medical health experts can make informed decisions to increase the population's willingness to receive the COVID-19 booster vaccines.
ARTICLE | doi:10.20944/preprints202211.0116.v1
Subject: Medicine & Pharmacology, Pediatrics Keywords: 2-year-old children; respiratory diseases; influenza; OH-PAHs; metabolites; urine
Online: 7 November 2022 (10:12:30 CET)
Aim: Exposure to polycyclic aromatic hydrocarbons (PAHs) has been in the past associated with adverse effects on human health among which belong also respiratory diseases. Our study is focused on the evaluation of PAH exposure by measuring the concentrations of their monohydroxylated metabolites (OH-PAHs) in urine and comparing their concentrations with the incidence of respiratory diseases in 2-year-old children from two locations of the Czech Republic – a control locality Ceske Budejovice and a previously highly contaminated mining district Most. Methods: The total number of 248 participants were sampled for urine samples that were analysed for the presence of 11 OH-PAHs using liquid-liquid extraction with ethyl acetate and clean-up employing dispersive solid phase extraction with a sorbent Z-Sep. Separation, identification and quantification of the target compounds was achieved by ultra-high performance liquid chromatography coupled to tandem mass spectrometry. The incidence of respiratory diseases was evaluated according to the questionnaires provided by the paediatricians. Results and discussion: The concentrations of measured OH-PAHs were higher in the urine samples collected from 2-year-old children living in Most compared to 2-year-old children from Ceske Budejovice. The same trend was observed also when the urine samples were analysed when these children were studied as newborns in our previous study. From all of the monitored respiratory diseases, only influenza due to unidentified influenza virus showed a difference between tested locations where the 2-year-old children living in Most were more frequently diagnosed with this disease. Conclusion: Even though the air pollution and lifestyle in both cities is very similar, we have observed higher incidence of respiratory diseases as well as higher concentration of OH-PAHs in urine of the 2-year-old children from Most. Therefore, we hypothesize that the population living in this previously highly contaminated location (in 1970s and 1980s) can carry some long-term health burden.
ARTICLE | doi:10.20944/preprints202107.0246.v1
Subject: Life Sciences, Biochemistry Keywords: influenza virus; virus-host interaction; commonly prescribed drugs; drug adverse reaction
Online: 12 July 2021 (11:37:07 CEST)
Background: Every year, millions of people are hospitalized, and thousands die from influenza A virus (FLUAV) infection. Most cases of hospitalizations and death occur among elderly. Many of these elderly patients are reliant on medical treatment of underlying chronic diseases, such as arthritis, diabetes, and hypertension. We hypothesized that the commonly prescribed medicines for treatment of underlying chronic diseases can affect host responses to FLUAV infection, and thus contribute to morbidity and mortality associated with influenza. Therefore, the aim of this study was to examine whether commonly prescribed medicines could affect host responses to virus infection in vitro. Methods: We first identified 45 active compounds of medicines commonly prescribed in Central Norway. Then we constructed a drug-target interaction network and identified potential implication of these interactions for FLUAV-host cell interplay. Finally, we tested the effect of 45 drugs on viability, transcription and metabolism of mock- and A/WSN/33(H1N1)-infected human retinal pigment epithelial (RPE) cells. Results: In silico drug-target interaction analysis revealed that many drugs, such as acetylsalicylic acid, atorvastatin, candesartan, and hydroxocobalam, could target and modulate FLUAV-host cell interaction. In vitro experiments showed that these and other compounds at non-cytotoxic concentrations differently affected transcription and metabolism of mock- and FLUAV-infected cells. Conclusion: Many commonly prescribed drugs modulate FLUAV-host cell interactions in vitro and therefore could affect their interplay in vivo, thus, contributing to morbidity and mortality of patients with influenza virus infections.
ARTICLE | doi:10.20944/preprints202007.0475.v2
Subject: Life Sciences, Virology Keywords: Mathematical model; SARS; COVID-19; Superspreaders; Viral outbreaks; H7N9; Influenza; zoonotic
Online: 4 August 2020 (04:53:24 CEST)
Despite great advances in understanding the dynamics of viral epidemics, the emergence of rapidly spreading, highly pathogenic viruses remains a realistic and catastrophic possibility, which current health systems may not be able to fully contain. An intriguing feature in many recent zoonotic viral outbreaks is the presence of superspreaders, which are infected individuals that cause dramatically more new cases than the average. Here I study the effect of superspreaders on the early dynamics of emerging viruses that have not gained the capacity for efficient human-to-human transmission, i.e viruses with R0 < 1. I show that superspreaders have a higher chance of rapid extinction, but under crowded conditions can lead to outbreaks, causing far more cases than regular viruses. I suggest that outbreaks of highly pathogenic superspreaders are more likely when they coincide in time and space with an unrelated outbreak leading to increased hospital admission rates. These superspreader outbreaks may be difficult to detect, especially in the context of a different epidemic in progress, and can significantly affect mortality patterns observed in affected areas.
REVIEW | doi:10.20944/preprints202008.0065.v1
Subject: Life Sciences, Microbiology Keywords: SARS-CoV-2; SARS-CoV; influenza; pneumonia; respiratory tract infectious diseases
Online: 3 August 2020 (08:44:56 CEST)
The short study implicates few basic similarities of COVID-19 such as diseases origination, symptoms, diagnosis with other relatable viral diseases viz SARS-CoV, common Flu, pneumonia etc. In the present situation, other viral diseases are frequently chaotic and misled with COVID-19 disease because of few clinical features similarities in signs and symptoms and also due to lack of specific diagnostic test. To avoid unnecessary suspects, quarantines of false positive results and to prevent the spread of COVID-19 diseases, the scientific technical research field are highly encourage to implement an efficient, rapid and sophisticated superior test for early stages of infection detection. It will be significantly convenient for physician, laboratory technicians and most importantly the common population facing a psychological disturbance.
ARTICLE | doi:10.20944/preprints202003.0203.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Chlamydia psittaci; H9N2 avian influenza virus; Coinfection; HD11 cells; immune function
Online: 12 March 2020 (09:01:04 CET)
We investigated the effect of C. psittaci and H9N2 coinfection on HD11 cells in vitro, expecting to find the potential pathogenesis of airsacculitis caused by co-infection of C. psittaci and H9N2. HD11 cells were infected with C. psittaci and/or H9N2 in a different order, and effects of the co-infection on iNOS expression and activity, NO synthesis, cell phagocytosis, and cytokines levels in HD11 cells were determined. Results showed that C. psittaci and H9N2 can significantly aggravate the mortality of HD11 cells compared to the effects of infection with one pathogen alone. In addition, infection with C. psittaci can increase the replication of H9N2 in HD11 cells, whereas decrease the iNOS level and enzyme activity as well as NO concentration of HD11 cells by H9N2 infection. We also found that C. psittaci infection alone can significantly decrease the phagocytosis of HD11 cells, compared to H9N2 infection alone. Furthermore, infection with C. psittaci can increase the mRNA expressions of type Th2 cytokines IL-6 and IL-10 of HD11 cells by H9N2 infection. All the above data indicated that primary C. psittaci infection is able to aggravate H9N2 invasion by down-regulating functions of HD11 cells
REVIEW | doi:10.20944/preprints201810.0232.v1
Subject: Biology, Other Keywords: Influenza virus; within-host viral dynamics; spatial spread; within-host evolution
Online: 11 October 2018 (07:36:15 CEST)
The spread of viral pathogens both between and within hosts is inherently a spatial process. While the spatial aspects of viral spread at the epidemiological level have been increasingly well characterized, the spatial aspects of viral spread within infected hosts are still understudied. Recent experimental studies, however, have started to shed more light on the mechanisms and spatial dynamics of viral spread within hosts. Here, we review these experimental studies as well as the limited number of computational modeling efforts that have begun to integrate spatial considerations for understanding within-host viral spread. We limit our review to influenza virus to highlight key mechanisms affecting spatial aspects of viral spread for pathogens of the respiratory tract. There is considerable empirical evidence for highly spatial within-host spread of influenza virus, yet few computational modeling studies that shed light on possible factors that structure the dynamics of this spatial spread. In existing modeling studies, there is also a striking absence of theoretical expectations of how spatial dynamics may impact the dynamics of viral populations. To mitigate this, we turn to the extensive ecological and evolutionary literature to provide informed theoretical expectations for what viral and host factors may impact the spatial patterns of within-host viral dynamics and for how spatial spread will affect the genetic composition of within-host viral populations. We end by discussing current knowledge gaps related to the spatial component of within-host influenza virus spread and the potential for within-host spatial considerations to inform the development of disease control strategies.
ARTICLE | doi:10.20944/preprints202211.0005.v1
Subject: Life Sciences, Other Keywords: Epidemics; Twitter; Natural Language Processing; Topic Modelling; Sentiment Analysis; ARI; Cholera; Ebola; HIV/AIDS; Influenza; Malaria; Spanish influenza; Swine flu; Tuberculosis; Typhus; Yellow fever; and Zika
Online: 1 November 2022 (01:17:14 CET)
At the end of 2019, while the world was being hit by the COVID-19 virus and, consequently, was living a global health crisis, many other pandemics were putting humankind in danger. The role of social media is of paramount importance in these kinds of contexts since they help health systems to cope with emergencies by contributing to conducting some activities such as the identification of public concerns, the detection of infections’ symptoms, and the traceability of the virus diffusion. In this paper, we have analyzed comments on events related to cholera, ebola, HIV/AIDS, influenza, malaria, Spanish influenza, swine flu, tuberculosis, typhus, yellow fever, and zika, collecting 369,472 tweets from the 3rd of March to the 15th of September, 2022. Our analysis has started with the collection of comments composed of unstructured texts on which we have applied natural language processing solutions. Afterward, we have employed topic modelling and sentiment analysis techniques to obtain a collection of people’s concerns and attitudes toward these pandemics. According to our findings, people's discussions were mostly about malaria, influenza, and tuberculosis and the focus was on the diseases themselves. As regards emotions, the most popular were fear, trust, and disgust where trust is mainly regarding HIV/AIDS tweets.
ARTICLE | doi:10.20944/preprints202010.0215.v1
Subject: Life Sciences, Biochemistry Keywords: epigenetic; histone; posttranslational modifications; T cells; influenza; FTICR; top-down; mass spectrometry
Online: 12 October 2020 (09:46:20 CEST)
T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) of histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis with high-field Fourier transform ion cyclotron resonance MS (FTICR-MS) can detect species missed by bottom-up approaches. We used high-resolution reversed-phase liquid chromatography (RPLC) FTICR-MS, alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. First online RPLC separation sorted histone families then weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative PTM identifications were assigned by matching peptide masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for Histone-intact protein PTM mapping (HiPTMap) and to quantify PTMs on core histones purified from CD8+ T cells directly isolated ex vivo post-influenza infection. Activation significantly reduced PTMs in vivo following influenza infection, histone maps changed as T cells migrated to infections, and T cells responding to secondary heterologous infections had significantly more PTMs enhancing transcriptional activation. Thus, HiPTMap identifies and quantifies PTMs on CD8+ T cell histones and determines their combinations in T cell states.
REVIEW | doi:10.20944/preprints202004.0234.v1
Subject: Life Sciences, Biochemistry Keywords: coronavirus; COVID-19; comorbidity; race and ethnicity; health disparities; income; inequality; influenza
Online: 15 April 2020 (09:25:47 CEST)
Recent clinical SARS-CoV-2 studies link diabetes, cardiovascular disease, and hypertension to increased disease severity. In the US, racial and ethnic minorities and low socioeconomic status (SES) individuals are more likely to have increased rates of these comorbidities, lower baseline health, limited access to care, increased perceived discrimination, and limited resources, all of which increase their vulnerability to severe disease and poor health outcomes from SARS-CoV-2. Previous studies demonstrated the disproportionate impact of pandemic and seasonal influenza on these populations, due to these risk factors. This paper reviews increased health risks and documented health disparities of racial and ethnic minorities and low SES individuals in the US. Pandemic response must prioritize these marginalized communities to minimize the negative, disproportionate impacts of SARS-CoV-2 on them and manage spread throughout the entire population. This paper concludes with recommendations applicable to healthcare facilities and public officials at various government levels.
ARTICLE | doi:10.20944/preprints201803.0149.v1
Subject: Life Sciences, Virology Keywords: influenza; H1N1; mouse adaptation; deep sequencing; polymerase; PA; PB1; defective viral genomes
Online: 19 March 2018 (08:59:26 CET)
Mice are not natural hosts for influenza A viruses (IAVs), but they are useful models for studying antiviral immune responses and pathogenesis. Serial passage of IAV in mice invariably causes the emergence of adaptive mutations and increased virulence. Typically, mouse-adaptation studies are conducted in inbred laboratory strains BALB/c and C57BL/6, which have defects in the antiviral Mx1 gene that results in increased susceptibility to infection and disease severity. Here, we report the adaptation of IAV reference strain A/California/07/2009(H1N1) (a.k.a. CA/07) in outbred Swiss Webster mice. Serial passage led to increased virulence and lung titers, and dissemination of the virus to brains. We adapted a deep-sequencing protocol to identify and enumerate adaptive mutations across all genome segments. Among mutations that emerged during mouse-adaptation, we focused on amino acid substitutions in polymerase subunits: polymerase basic-1 (PB1) T156A and F740L, and polymerase acidic (PA) E349G. These mutations were evaluated singly and in combination in minigenome replicon assays, which revealed that PA E349G increased polymerase activity. By selectively engineering these three adaptive PB1 and PA mutations into the parental CA/07 strain, we demonstrated that adaptive mutations in polymerase subunits decreased the production of defective viral genome segments with internal deletions, and dramatically increased the release of infectious virions from mouse cells. Together, these findings increase our understanding of the contribution of polymerase subunits to successful host adaptation.
ARTICLE | doi:10.20944/preprints201801.0177.v1
Subject: Life Sciences, Virology Keywords: Ebola; influenza virus; HIV; envelope protein; membrane fusion inhibitor; HR2; pentacyclic triterpenoids
Online: 19 January 2018 (04:02:15 CET)
Recent years have witnessed a breakthrough in identification of a trimer-of-hairpins motif within viral envelopes that triggers a broad range of virus-host fusion. Identifying a domain capable of controlling virus-host fusion remains a challenge due to sequence diversity, heavy glycan shielding and multiple conformations. Here, we report that HR2, a prevalent heptad repeat sequence comprising an alpha-helical coil anchored in viral membranes, is an accessible site to triterpenes, a class of widely distributed natural products. Triterpenes and their derivatives inhibit the entry of Ebola, HIV, and influenza A viruses with distinct structure-activity relationships. Specifically, triterpenoid probes, upon activation by ultraviolet light, capture the viral envelope via crosslinking the HR2 coil. Profiling the Ebola HR2 sequence using amino acid substitution, surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR) spectroscopy disclosed six constitutive residues that are accessible to triterpenoids, leading to wrapping of the hydrophobic helix by triterpenoids and blocking of the HR1-HR2 interaction, which is critical in the trimer-of-hairpins formation. This finding was also observed in the envelopes of HIV and influenza A viruses and might potentially extend to a broader variety of viruses. Our findings might translate into a shared mechanism that host utilize natural product triterpenoids to antagonize membrane fusion of respective viruses, complementing the current repertoire of antiviral agents.
REVIEW | doi:10.20944/preprints201608.0054.v1
Subject: Biology, Other Keywords: influenza virus; antiviral agent; proteomics; phosphoproteomics; metabolomics; transcriptomics; genomics; virtual ligand screening
Online: 5 August 2016 (12:41:07 CEST)
Human influenza A viruses (IAVs) cause global pandemics and epidemics. These viruses evolve rapidly, making current treatment options ineffective. To identify novel modulators of IAV-host interactions, we re-analyzed our recent transcriptomics, metabolomics, proteomics, phosphoproteomics, and genomics/virtual ligand screening data. We identified 713 potential modulators targeting 200 cellular and two viral proteins. Anti-influenza activity for 48 of them has been reported previously, whereas the antiviral efficacy of the remaining 665 is unknown. Studying anti-influenza efficacy, immuno-modulating properties and potential resistance of these compounds or their combinations may lead to the discovery of novel modulators of IAV-host interactions, which might be more effective than the currently available anti-influenza therapeutics.
ARTICLE | doi:10.20944/preprints202206.0086.v1
Subject: Mathematics & Computer Science, Computational Mathematics Keywords: non-parametric modeling; flu; influenza; COVID-19; SARS-CoV-2; Empirical Dynamic Modeling; forecasting
Online: 6 June 2022 (10:24:45 CEST)
The evolution of some epidemics, as influenza, shows common patterns both in different regions and from year to year. On the contrary, epidemics like the novel COVID-19 show quite heterogeneous dynamics and are extremely susceptible to the measures taken to mitigate their spread. In this paper we propose empirical dynamic modeling to predict the evolution of influenza in Spain’s regions. It is a non-parametric method that looks into the past for coincidences with the present to make the forecasts. Here we extend the method to predict the evolution of other epidemics at any other starting territory and we test also this procedure with Spanish COVID-19 data. We finally build influenza and COVID-19 networks to check possible coincidences in the geographical distribution of both diseases. With this, we grasp the uniqueness of the geographical dynamics of COVID-19.
REVIEW | doi:10.20944/preprints202103.0034.v1
Subject: Life Sciences, Biochemistry Keywords: respiratory illness; pathogenicity; virulence; natural selection; colds; influenza; rhinovirus; weather; climate; Tropics; summer; winter
Online: 1 March 2021 (17:14:19 CET)
This review seeks to explain four features of viral respiratory illnesses that have perplexed generations of virologists: (1) the seasonal timing of respiratory illness; (2) the common viruses causing respiratory illness worldwide, including year-round disease in the Tropics; (3) the rapid response of outbreaks to weather, specifically temperature; (4) the rapid arrival and termination of epidemics caused by influenza and other viruses. The inadequacy of the popular explanations of seasonality is discussed, and a simple hypothesis is proposed, called Temperature Dependent Viral Tropism (TDVT), that is compatible with the above features of respiratory illness. TDVT notes that viruses can transmit themselves more effectively if they moderate their pathogenicity (thereby maintaining host mobility) and suggests that endemic respiratory viruses accomplish this by developing thermal sensitivity within a range that supports organ-specific viral tropism within the human body, whereby they replicate most rapidly at temperatures below body temperature. This allows them to confine themselves to the upper respiratory tract and to avoid infecting the lungs, heart, gut etc. Biochemical and tissue-culture studies show that “wild” respiratory viruses show such natural thermal sensitivity. The typical early autumn surge of colds and the existence of respiratory illness in the Tropics year-round at intermediate levels are explained by the tendency for strains to adapt their thermal sensitivity to their local climate and season. The TDVT hypothesis has important practical implications for preventing and treating respiratory illness including Covid-19. TVDT is testable with many options for experiments to increase our understanding of viral seasonality and pathogenicity.
HYPOTHESIS | doi:10.20944/preprints202101.0389.v1
Subject: Medicine & Pharmacology, Allergology Keywords: respiratory illness; pathogenicity; virulence; natural selection; colds; influenza; rhinovirus; weather; climate; Tropics; summer; winter
Online: 19 January 2021 (16:42:56 CET)
This review seeks to explain four features of viral respiratory illnesses that have perplexed many generations of microbiologists: (1) the seasonal occurrence of viral respiratory illness; (2) the occurrence of respiratory illness year-round in the Tropics; (3) the rapid response of illness to temperature drops in temperate regions; (4) the explosive arrival and rapid termination of epidemics caused by influenza and other respiratory viruses. I discuss the inadequacy of the popular explanations of seasonality, and propose a simple hypothesis, called Temperature Dependent Viral Tropism (TD-VT), that is compatible with the above and other features of respiratory illness. TD-VT notes that viruses can often transmit themselves more effectively if they moderate their pathogenicity (thereby maintaining the mobility of their hosts) and suggests that most endemic respiratory viruses accomplish this by developing thermal sensitivity, in the sense that they normally replicate rapidly only at temperatures below normal body temperature. This allows them to confine themselves to the upper respiratory tract and to avoid infecting the lungs, heart, gut etc. I review biochemical and tissue-culture studies that found that “wild” respiratory viruses often show natural thermal sensitivity within a range that supports organ-specific tropism within the human body, and I discuss the evident tendency for viral strains to adapt their thermal sensitivity to their local climate and season. I also explore the possible misinterpretation of early experiments where volunteers were inoculated nasally with viral samples and then chilled. Next, I discuss the practical implications of the TD-VT hypothesis for preventing and treating respiratory illness. Finally, I note that the hypothesis is very testable and make suggestions for the most important experiments to increase our understanding of the seasonality and pathogenicity of viral respiratory illness.
ARTICLE | doi:10.20944/preprints202005.0505.v2
Subject: Life Sciences, Virology Keywords: COVID-19; Viral Co-infection; SARS-CoV-2; Influenza A virus; Human Immunodeficiency virus
Online: 18 June 2020 (04:57:14 CEST)
In December 2019, pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection emerged in Wuhan City, Hubei Province, China. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused epidemic disease: coronavirus disease 2019 (COVID-19) and declared COVID-19 to be the sixth international public health emergency. Cellular co-infection is a critical determinant of both viral fitness and infection outcome and plays a crucial role in shaping the host immune response to infections. In this study, sixty-eight public next-generation sequencing libraries from SARS-CoV-2 infected patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Using an alignment-free method based on K-mer mapping and extension, SARS-CoV-2 was identified in all except three patients. Influenza A H7N9 (3/68), Human immunodeficiency virus 1 (1/68), rhabdovirus isolate (3/68), Human metapneumovirus (1/68), coronaviruses NL63 (1/68), Parvovirus (1/68), Simian virus 40 (1/68), and hepatitis virus (1/68) genome sequences were detected in SARS-CoV-2 infected patients.
ARTICLE | doi:10.20944/preprints202003.0246.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: coronavirus; COVID-19; disease severity; transmission route; infection route; lung damages; cold flu influenza
Online: 15 March 2020 (14:39:19 CET)
In the war against the COVID-19 pandemic, the world is experiencing severe resource constraints. Although transmission routes are well understood, we suspect that they cause different disease consequences. We evaluate them in different forms to understand how they affect infection rates and disease severity. In determining how they affect disease outcome, we evaluated target tissue vulnerability, functional role, defense mechanisms, viral concentration, infection vicinity to target vital tissue, and host factors. We found that direct lung infection is the most lethal transmission route followed by bronchi infection. Transmissions by physical contacts, foods, and blood by low viral concentration (as expected in normal human activities) pose lower or much lower risks unless the infection is followed by subsequent lung exposures. After adding transmission route, treatment timings, and improper treatments into the list of known risk factors, we found that death rate and disability rate for young or healthy persons are nearly zero. We show that population based medical model improperly shifts nominal death rate from few vulnerable people to the population resulting in unnecessary population panic, and such panic is responsible for shutting down human activities and the world economy. Finally, we examined limitations in population-based mitigating measures and proposed for governmental and private adoption community guidelines, which are mainly to enable vulnerable people avoid exposures, prevent non-vulnerable people from serving as viral transmitters, get rid of high-risk exposure modes in working environment, improve safety for people in buses, ships and planes, and reduce death and disability rates for infected people.
REVIEW | doi:10.20944/preprints201807.0004.v1
Subject: Life Sciences, Virology Keywords: influenza; neutralising antibodies; vestigial esterase; antibody dependent cell-mediated cytotoxicity; pH-induced conformational changes
Online: 2 July 2018 (08:33:45 CEST)
Initial attempts to develop monoclonal antibodies as therapeutics to resolve influenza infections focused mainly on searching for antibodies with the potential to neutralise the virus in vitro with classical haemagglutination inhibition and micro-neutralisation assays. This led to the identification of many antibodies that bind to the head domain of haemagglutinin (HA) which generally have potent neutralisation capabilities that block viral entry or viral membrane fusion. However, this class of antibodies has a narrow breadth of protection in that they are usually strain specific. This led to the emphasis on stalk targeting antibodies which are able to bind a broad range of viral targets that span across different influenza subtypes. Recently, a third class of antibodies targeting the vestigial esterase (VE) domain have been characterised. In this review, we describe the key features of neutralising VE targeting antibodies and compare them with head and stalk class antibodies.
ARTICLE | doi:10.20944/preprints202210.0223.v1
Subject: Life Sciences, Virology Keywords: Drug discovery; Systems biology; SARS-CoV-2; Dengue; Influenza A; RSV; cell viability analysis; antivirals
Online: 17 October 2022 (03:42:37 CEST)
The SARS-CoV-2 pandemic has reemphasized the urgent need to develop broad-spectrum antiviral therapies. Wedeveloped a computational pipeline that uses scRNA-Seq data to reconstruct the metabolic state of cells and tissuesduring viral infection. Using this pipeline, we investigated the cellular capacity to produce SARS-CoV-2 virions invarious tissues and disease conditions. Subsequently, we expanded our analysis to influenza A and dengue virus andidentified several metabolic targets and their inhibitors for broad-spectrum antiviral treatment. Phenformin, an inhibitorof NADH:ubiquinone oxidoreductase, suppressed SARS-CoV-2 and dengue virus replication. Using Atpenin A5 toblock the succinate dehydrogenase inhibited SARS-CoV-2, dengue virus, influenza A virus and respiratory syncytialvirus with superior therapeutic indices. Thus, our work establishes host metabolism as druggable for broad antiviraltherapy. Moreover, our pipeline, the identified targets, and inhibitors are invaluable tools for pandemic preparedness.
Subject: Medicine & Pharmacology, Veterinary Medicine Keywords: One Health; zoonotic disease; zoonotic disease control; anthrax; brucellosis; rabies; rift valley fever; zoonotic influenza
Online: 24 September 2021 (14:19:16 CEST)
Effectively preventing and controlling zoonotic diseases requires a One Health approach that involves collaboration across sectors responsible for human health, animal health (both domestic and wildlife), and the environment, as well as other partners. Here we describe the Generalizable One Health Framework (GOHF), a five-step framework that provides structure for using a One Health approach in zoonotic disease programs being implemented at the local, sub-national, national, regional, or international level. Part of the framework is a toolkit that compiles existing resources and presents them following a stepwise schematic, allowing users to identify relevant resources as they are required. Coupled with recommendations for implementing a One Health approach for zoonotic disease prevention and control in technical domains including laboratory, surveillance, preparedness and response, this framework can mobilize One Health and thereby enhance and guide capacity building to combat zoonotic disease threats at the human-animal-environment interface.
ARTICLE | doi:10.20944/preprints201608.0230.v1
Subject: Mathematics & Computer Science, Applied Mathematics Keywords: basic reproduction number; disease free equilibrium; endemic equilibrium; local asymptotic stability; global asymptotic stability; influenza
Online: 30 August 2016 (08:54:15 CEST)
This article investigates a proposed new mathematical model that considers the infected individuals using various rate coefficients such as transmission, progression, recovery and vaccination. The fact that the dynamic analysis is completely determined by the basic reproduction number is established. More specifically, local and global stabilities of the disease-free equilibrium and the endemic equilibrium are proved under certain parameter conditions when the basic reproduction number is below or above unity. A realistic computer simulation is performed for better understanding of the variations in trends of different compartments after the outbreak of the disease.
BRIEF REPORT | doi:10.20944/preprints202204.0287.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: COVID-19; Influenza; Morbidity; Mortality; Flu; Pneumonia; Virus Infections; Preventive Medicine; Hospitalization; Internal Medicine; Respiratory illness.
Online: 29 April 2022 (04:22:05 CEST)
Abstract: Background: Our goal was to evaluate whether wearing personal protective equipment (PPE) such as an N95, or a surgical mask during the (COVID-19) pandemic had really reduced the cases of influenza in the state of Wisconsin. Methods: Respiratory Virus Surveillance Reports from the Wisconsin Department of Health Services (DHS) and the Centers for Disease Control and Prevention (CDC) were used to compare the rates of Influenza during the seasons of 2018-2019 and 2020-2021. Results: The number of cases, hospitalizations, and mortality rates with Influenza had significantly decreased in the 2020-2021 season compared to the Influenza season of 2018-2019. Discussion: Reducing the burden of influenza illnesses, hospitalizations, and deaths on the health care system is imperative. Wearing masks should be addressed for the most vulnerable.
ARTICLE | doi:10.20944/preprints202111.0184.v2
Subject: Life Sciences, Virology Keywords: baloxavir marboxil; H5N1 highly pathogenic avian influenza virus; viral replication; inhibition; lung inflammation; combination therapy; oseltamivir
Online: 12 January 2022 (13:18:58 CET)
Human infections caused by the H5 highly pathogenic avian influenza virus (HPAIV) sporadically threaten public health. The susceptibility of HPAIVs to baloxavir acid (BXA), a new class of inhibitors for the influenza virus cap-dependent endonuclease, has been confirmed in vitro, but it has not yet been fully characterized. Here, the efficacy of BXA against HPAIVs, including recent H5N8 variants, was assessed in vitro. The antiviral efficacy of baloxavir marboxil (BXM) in H5N1 virus-infected mice was also investigated. BXA exhibited similar in vitro activities against H5N1, H5N6, and H5N8 variants tested in comparison with seasonal and other zoonotic strains. Compared with oseltamivir phosphate (OSP), BXM monotherapy in mice infected with the H5N1 HPAIV clinical isolate, the A/Hong Kong/483/1997 strain, also caused a significant reduction in viral titers in the lungs, brains, and kidneys, thereby preventing acute lung inflammation and reducing mortality. Furthermore, compared with BXM or OSP monotherapy, combination treatments with BXM and OSP using a 48-hour delayed treatment model showed a more potent effect on viral replication in the organs, accompanied by improved survival. In conclusion, BXM has a potent antiviral efficacy against H5 HPAIV infections.
BRIEF REPORT | doi:10.20944/preprints202101.0266.v1
Subject: Medicine & Pharmacology, Allergology Keywords: COVID-19; SARS; HCoV-229E; MERS; influenza; virus; epithelium; asthma; allergy; inflammation; sexual dimorphism; gene expression
Online: 14 January 2021 (12:37:08 CET)
Epithelial characteristics underlying the differential susceptibility of chronic asthma to SARS-CoV-2 (COVID-19) and other viral infections are currently unclear. By revisiting transcriptomic data from patients with Th2 low versus Th2 high asthma, as well as mild, moderate and severe asthmatics, we characterized the changes in expression of human coronavirus and influenza viral entry genes relative to sex, airway location and disease endotype. We found sexual dimorphism in expression of COVID-19 genes ACE2, TMPRSS2, TMPRSS4, and SLC6A19. ACE2 receptor downregulation occurred specifically in females in Th2 high asthma, while proteases broadly assisting coronavirus and influenza viral entry, TMPRSS2 and TMPRSS4, were highly upregulated in both sexes. Overall, changes in COVID-19 gene expression were specific to Th2 high molecular endotype of asthma, and different by asthma severity and airway location. The downregulation of ACE2 (COVID-19, SARS) and ANPEP (HCoV-229E) viral receptors correlated with loss of club and ciliated cells in Th2 high asthma, while the increase in DPP4 (MERS-CoV), ST3GAL4, and ST6GAL1 (influenza) associated with an increase in goblet and basal activated cells. Overall, this study elucidates sex, airway location, disease endotype and changes in epithelial heterogeneity as factors underlying asthmatic susceptibility, or lack thereof, to COVID-19.
ARTICLE | doi:10.20944/preprints202012.0709.v1
Subject: Medicine & Pharmacology, Allergology Keywords: SARS-CoV-2; covid 19; pregnancy; passive immunization; maternal immunization; influenza vaccines; diphtheria tetanus pertussis vaccine
Online: 28 December 2020 (16:54:31 CET)
The COVID-19 pandemic has raised questions about the possible cross immunity resulting from common vaccination programs and SARS-CoV-2 infection. Therefore, the Spanish Obstetric Emergency group performed a multicenter prospective study on the vaccination status of Influenza and Tdap (diphtheria, tetanus and pertussis vaccine boost administered in adulthood) in consecutive cases of SARS-CoV-2 infection in a pregnancy cohort, in order to assess its possible association with the clinical presentation and severity of symptoms of SARS-CoV-2 infection, as well as to determine the factors that may affect vaccination adherence. 1,150 SARS-CoV-2 positive pregnant women from 78 Spanish hospitals were analyzed: 183 had not received either vaccine, 23 had been vaccinated for Influenza only, 529 for Tdap only and 415 received both vaccines. No association was observed between the vaccination status and the clinical presentation of SARS-CoV-2 infection and/or the severity of symptoms. However, a lower adherence to the administration of both vaccines was observed in the Latin-American subgroup. Based on the results above, we reinforce the importance of maternal vaccination programs in the actual pandemic. Health education campaigns should be specially targeted to groups less likely to participate in these programs, as well as for a future SARS-CoV-2 vaccination campaign.
Subject: Social Sciences, Business And Administrative Sciences Keywords: coronavirus; COVID-19; public health intervention; revive economy; disease severity; transmission route; influenza; ventilation; work environment
Online: 16 April 2020 (12:34:43 CEST)
The COVID-19 pandemic has great adverse impacts on personal life, the U.S. economy, and the world economy. Freezing all human activities is not a sustainable measure. Thus we want to develop a public intervention framework that allows people to resume personal and economic activities. In this article, we examined transmission routes, disease severity, personal vulnerability, available treatments, and person-person interactions to establish a general public intervention framework. We divide people into risk groups, non-risk group and group that may serve as viral transmitters, explore interactions between individual persons within each group and between different groups, and propose interaction behavior modifications to mitigate viral exposures. For the non-risk groups, we identified preventive measures that can help them avoid the most serious exposures and infections that pose higher death risks. The invention measures for the vulnerable groups include prior-exposure measures, heightened protective measures, interaction behavior changes, post-exposure remedial measures, and multiple factors treatments to reduce death and disability risks. The multiple interventions and two-ways defensive behavior modifications are expected to result in reduced rate of detectable infections and lowered disease severity for the vulnerable groups. In this framework, most human activities and economic activities can continue as normal. With time passing, the population acquires population immunity against the COVID-19 virus. Implementation of this intervention framework requires considerable resources and governmental effects while the multiple factors treatment protocol requires the support of health care professionals.
ARTICLE | doi:10.20944/preprints202208.0024.v1
Subject: Life Sciences, Virology Keywords: highly pathogenic avian influenza viruses; H5N8; H5N5; Clade 188.8.131.52; phylogenetic network analyses; next-generation sequencing; MinION; epidemiology
Online: 1 August 2022 (14:57:42 CEST)
During autumn/winter in 2016 – 2017 and 2020 – 2021, highly pathogenic avian influenza viruses (HPAIV) caused severe outbreaks in Germany and Europe. Multiple clade 184.108.40.206b H5 HPAI subtypes were responsible for increased mortality in wild birds and high mortality and massive losses in the poultry sector. To clarify putative entry sources and delineate interconnections between outbreaks in poultry holdings and wild birds, we applied whole-genome sequencing and phylodynamic analyses combined with the results of epidemiological outbreak investigations. Varying outbreak dynamics of the distinct reassortants allowed for the identification of individual, putatively wild bird-mediated entries into backyard holdings, several clusters comprising poultry holdings, local virus circulation for several weeks, direct farm-to-farm transmission and potential reassortment within a turkey holding with subsequent spill-over of the novel reassorted virus into the wild bird population. Whole-genome sequencing allowed for allowed for a unique high-resolution molecular epidemiology analysis of HPAIV H5Nx outbreaks, recommended to be used as a standard tool. The presented detailed account of the genetic, temporal and geographical characteristics of the recent German HPAI H5Nx situation emphasizes the role of poultry holdings as an important source of novel genetic variants and reassortants.
ARTICLE | doi:10.20944/preprints202202.0170.v1
Subject: Life Sciences, Virology Keywords: influenza virus; RNA-polymerase; RNA-polymerase II; protein-protein interaction; PPI; cap snatching; transcription; binary complementation assay
Online: 14 February 2022 (09:51:21 CET)
Influenza virus transcription is catalyzed by the viral RNA-polymerase (FluPol) through a cap-snatching activity. The snatching of the cap of cellular mRNA by FluPol is preceded by its binding to the flexible C-terminal domain (CTD) of the RPB1 subunit of RNA-polymerase II (Pol II). To better understand how FluPol brings the 3’-end of the genomic RNAs in close proximity to the host-derived primer, we hypothesized that FluPol may recognize additional Pol II subunits/domains to ensure cap-snatching. Using binary complementation assays between the Pol II and FluPol subunits and their structural domains, we revealed an interaction between the N-third domain of PB2 and RPB4. This interaction was confirmed by a co-immunoprecipitation assay and found to occur with the homologous domains of influenza B and C FluPols. Residues [1-72] of RPB4 were found critical in this interaction. Numerous punctual mutants generated at conserved positions between influenza A, B and C FluPols in the N-third domain of PB2 exhibited strong transcriptional activity defect. These results suggest that FluPol interacts with several domains/subunits of Pol II, the CTD to bind Pol II initiating host transcription and a second on RPB4 to locate FluPol at the proximity of the 5’-end of nascent host mRNA.
REVIEW | doi:10.20944/preprints202004.0054.v1
Subject: Engineering, Industrial & Manufacturing Engineering Keywords: pandemic; influenza pandemic; open source; open hardware; COVID-19; COVID-19 pandemic; medical hardware; open source medicine
Online: 6 April 2020 (12:38:59 CEST)
Distributed digital manufacturing offers a solution to medical supply and technology shortages during pandemics. To prepare for the next pandemic, this study reviews the state-of-the-art for open hardware designs needed in a COVID-19-like pandemic. It evaluates the readiness of the top twenty technologies requested by the Government of India. The results show that the majority of the actual medical products have had some open source development, however, only 15% of the supporting technologies that make the open source device possible are freely available. The results show there is still considerable work needed to provide open source paths for the development of all the medical hardware needed during pandemics. Five core areas of future work are discussed that include: i) technical development of a wide-range of open source solutions for all medical supplies and devices, ii) policies that protect the productivity of laboratories, makerspaces and fabrication facilities during a pandemic, as well as iii) streamlining the regulatory process, iv) developing Good-Samaritan laws to protect makers and designers of open medical hardware, as well as to compel those with knowledge that will save lives to share it, and v) requiring all citizen-funded research to be released with free and open source licenses.
Subject: Medicine & Pharmacology, Pathology & Pathobiology Keywords: coronavirus COVID-19; SARS; MERS; viral reproduction; immune response; lung infection influenza; deep breathing; diet; emotional stress; lifestyle
Online: 23 March 2020 (06:34:44 CET)
We conducted many model simulations to understand the causes of the damages of coronavirus (COVID-19) to lung tissue and constructed a diagram showing apparent viral reproduction, immune response and damage accumulation curves. We found that lung damages include virus-caused damage, tissue damage caused by immune responses and tissue damage caused by accumulated wastes. The virus-caused damage is proportional to the phase lag between the viral reproduction curve and the delayed adaptive immune response curve, while waste-induced damage is attributed to imbalance in removing viral, cellular and metabolic by-products. We found that treatment strategies should slow down viral reproduction and speed up immune response, and improve blood micro-circulation in the lungs. Consistent with the strategies, measures are taken to void direct lung infection, strengthen innate responses, promote immune responses, dilute viral concentration in lung tissue, maintain waste removal balance, protect heart and kidneys, control other infections, avoid allergic reactions and other inflammation, etc. We show that medical, dietary, emotional, lifestyle, environmental, mechanical factors, etc. may be simultaneously used to mitigate lung damages and prove that multiple factor health optimization method is magnitudes more powerful than a single factor treatment. Such a method does not depend on molecular specificity and can be used in parallel to antiviral drugs.
Subject: Life Sciences, Immunology Keywords: immune system; viral infection; influenza; COVID-19; micronutrients; vitamins; omega-3 fatty acids; minerals; vitamin C; vitamin D
Online: 12 March 2020 (04:30:45 CET)
Public health practices including handwashing and vaccinations help reduce the spread and impact of infections. Nevertheless, the global burden of infection is high, and additional measures are necessary. Acute respiratory tract infections, for example, are responsible for approximately 2.65 million deaths per year. The role nutrition plays in supporting the immune system is well-established. A wealth of mechanistic and clinical data show that vitamins, including vitamins A, B6, B12, C, D, E, and folate; trace elements, including zinc, iron, selenium, magnesium, and copper; and the omega-3 fatty acids eicosapentaenoic acid and docosahexaenoic acid play important and complementary roles in supporting the immune system. Inadequate intake and status of these nutrients are widespread, leading to a decrease in resistance to infections and as a consequence an increase in disease burden. Against this background the following conclusions are made: 1) Supplementation with the above micronutrients and omega-3 fatty acids is a safe, effective, and low-cost strategy to help support optimal immune function; 2) Supplementation above the RDA, but within recommended upper safety limits, for specific nutrients such as vitamins C and D is warranted; and 3) Public health officials are encouraged to include nutritional strategies in their recommendations to improve public health.
Subject: Medicine & Pharmacology, Allergology Keywords: coronavirus; COVID-19; Hepatitis C Virus (HCV); Human Immunodeficiency Virus (HIV); Influenza viruses ribonucleic acid (RNA); SARS-CoV-2
Online: 19 February 2021 (14:34:38 CET)
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the etiological agent of the current pandemic worldwide. The pathological condition induced by this pathogen is known as COVID-19 disease. SARS-CoV-2 associated pandemic has been defined as a “public health emergency of international concern” by the International Health Regulation Emergency Committee of the World Health Organization. To date, considerable efforts are in progress to develop more advanced strategies against SARS-CoV-2. Despite the numerous scientific studies published, our knowledge regarding this pathogen is still incomplete, as this virus has been identified only recently. Therefore, scientific investigation of the SARS-CoV-2 has been possible only for a short period of time and effective management of the serious forms of this disease is still lacking. Considerable efforts are in progress worldwide with the purpose to develop more advanced strategies against this pathogen. In this review, we have analyzed the structural and the biological SARS-CoV-2 characteristics and those of other well-known RNA viruses, with the aim to identify possible similarities and analogies between all these pathogens, may be a very useful approach. These infectious agents have been widely studied since several years ago and, a large series of scientific reports are available in the literature regarding this topic. Therefore, focusing on the Human Immunodeficiency Virus (HIV), Hepatitis C Virus (HCV) and Influenza viruses (IVs), we have collected their historical data, clinical manifestations, pathogenetic mechanisms and related infections. Taking advantage of the results of our research, we have assembled this narrative review, with the aim to get useful insights and lessons from HIV, HCV and IVs characteristics and, consequently, to transfer the obtained knowledge to the study of SARS-CoV-2 biology. There are well known differences between all these pathogens. In particular, they present a distinct mode of transmission, as SARS-CoV-2 and Influenza viruses are airborne pathogens, whereas HIV and HCV are bloodborne infectious agents. However, these viruses exhibit some potential common clinical manifestations and pathogenetic mechanisms and their understanding may contribute to establishing preventive measures and new therapies against SARS-CoV-2. Accordingly, we have analysed and discussed the following points: 1) the biology, the pathogenesis and the clinical manifestations of SARS-CoV-2, HIV, HCV and IVs in mankind; 2) the onset and spreading of pandemics caused by respiratory viruses according to a perspective historical point of view; 3) the possible development of a persistent SARS-CoV-2 reservoir worldwide; 4) the possibility of SARS-CoV-2 reinfection/reactivation; 5) the possible involvement and impact of climatic factors in increasing the risk of SARS-CoV-2 spreading.
ARTICLE | doi:10.20944/preprints202102.0021.v1
Subject: Life Sciences, Biochemistry Keywords: excess winter mortality; influenza; latitude; gender; age; respiratory conditions; spatiotemporal effects; female; male; pandemics; seasons; ethnic groups; respiration disorders; coinfection
Online: 1 February 2021 (12:16:39 CET)
(1) Background: To investigate the dynamic issues behind international variation in EWM. (2) A rolling EWM calculation is used to reveal seasonal changes in the EWM calculation and is especially relevant nearer to the equator. (3) Results: In addition to latitude country specific factors determine EWM. Females generally show higher EWM mainly due to respiratory conditions. The EWM for respiratory conditions in England and Wales ranges from 44% to 83% which is about double the all-cause mortality equivalent. Age has a profound effect on EWM with a peak in puberty and then increasing EWM at old age. The gap between male and female EWM seems to act as a diagnostic tool reflecting the infectious/metrological mix in each winter. Additional difference due to ethnicity are also observed. An EWM equivalent calculation for sickness absence demonstrates how additional health-related variables can be linked to EWM. (4) Conclusions: EWM does not reach a peak at the same time each year, especially so in the tropics. Countries midway between the equator and the poles show highest EWM. Differences between the genders are highly significant and seem to vary according to the mix of variables active each winter. Pandemic influenza does not elevate EWM, although seasonal influenza plays a part each winter.
Subject: Life Sciences, Biochemistry Keywords: super-resolution microscopy; advanced light microscopy; quantitative microscopy; live-cell microscopy; SMLM; STORM; SIM; STED; expansion microscopy; influenza virus; viral replication
Online: 6 January 2021 (10:40:59 CET)
With an estimated 3 to 5 million human cases annually and the potential to infect domestic and wild animal populations, influenza viruses are one of the greatest health and economic burdens to our society  and pose an ongoing threat of large-scale pandemics. Despite our knowledge of many important aspects of influenza virus biology, there is still much to learn about how influenza viruses replicate in infected cells, for instance how they use entry receptors or exploit host cell trafficking pathways. These gaps in our knowledge are due, in part, to the difficulty of directly observing viruses in living cells. In recent years, advances in light microscopy, including super-resolution microscopy and single-molecule imaging, have enabled many viral replication steps to be visualised dynamically in living cells. In particular, the ability to track single virions and their components, in real time, now allows specific pathways to be interrogated providing new insights to various aspects of the virus-host cell interaction. In this review, we discuss how state-of-the-art imaging technologies, notably quantitative live-cell and super-resolution microscopy, are shedding new nanoscale and molecular insights into influenza virus replication and revealing new opportunities for developing antiviral strategies.
Subject: Medicine & Pharmacology, Pathology & Pathobiology Keywords: coronavirus; COVID-19; viral reproduction; immune response; low temperature injury; lung damages; cold flu influenza; deep breathing exercises; diet; emotion stress; lifestyle
Online: 4 March 2020 (05:30:58 CET)
To understand great disparities in disease outcomes between CIVID-19 patients, we explore infection and host responses in kinetics. From existing data, we deduced a model that the lungs are damaged by rapidly rising flow resistance as a result of retaining white blood cells in lung tissues. The retention of white blood cells is initially triggered by viral infection but aggravated by injuries caused by low temperature. Lungs are initially damaged by fluid leakage, rapidly followed by extruding blood into alveolar spaces. The step of blood extruding is predicted to take place in a very short time. Our simulations show that as little as 0.1% retention of white blood cells in the lungs can lead to their failure in 5 to 10 days. The small degrees of imbalance implies that this imbalance could be corrected by a large number of factors that are known to reduce flow resistance. The model implies that the top priority is maintaining blood micro-circulation and preserving organ functions in the entire disease course, especially after the virus has spread the whole lungs. From exploring a large number of hypothetical infection modes, we propose preventive, mitigating and treatment strategies for ultimately ending the pandemic. The first strategy is avoiding exposures that could result in widespread damages to lungs and taking post exposure mitigating measures that would reduce disease severity. The second strategy is reducing death rate and disability rate from the current levels to one tenth for infected patients by using multiple factors health optimization method. The double reduction strategies are expected to generate a series of chain reactions that favor mitigating or ending the pandemic. Some reactions include a big reduction of the amount of viral discharges from infected patients into the air, the avoidance of panic, chronic stress and emotional distress, and cross-infections which are expected in quarantines. The double reductions would have a final effect of ending the pandemic.
REVIEW | doi:10.20944/preprints202003.0235.v2
Subject: Medicine & Pharmacology, Nutrition Keywords: acute respiratory distress syndrome (ARDS); ascorbic acid; cathelicidin; coronavirus; COVID-19; cytokine storm; influenza; observational; pneumonia, prevention; respiratory tract infection; solar radiation; treatment; UVB; vitamin C; vitamin D
Online: 30 March 2020 (05:48:43 CEST)
The world is in the grips of the COVID-19 pandemic. Public health measures that can reduce the risk of infection and death in addition to quarantines are desperately needed. This article reviews the roles of vitamin D in reducing risk of respiratory tract infections, knowledge about the epidemiology of influenza and COVID-19, and how vitamin D supplementation might be a useful measure to reduce risk. Through several mechanisms, vitamin D can reduce risk of infections. Those mechanisms include inducing cathelicidins and defensins that can lower viral replication rates and reducing concentrations of pro-inflammatory cytokines that produce the inflammation that injures the lining of the lungs, leading to pneumonia, as well as increase concentrations of anti-inflammatory cytokines. Several observational studies and clinical trials reported that vitamin D supplementation reduced risk of influenza, whereas others did not. Evidence supporting the role of vitamin D in reducing risk of COVID-19 includes that the outbreak occurred in winter, a time when 25-hydroxyvitamin D [25(OH)D] concentrations are lowest; that the number of cases in the Southern Hemisphere near the end of summer are low; that vitamin D deficiency has been found to contribute to acute respiratory distress syndrome, and that case-fatality rates increase with age and with chronic disease comorbidity, both of which are associated with lower 25(OH)D concentration. To reduce risk of infection, it is recommended that people at risk of influenza and/or COVID-19 consider taking 10,000 IU/d of vitamin D3 for a few weeks to rapidly raise 25(OH)D concentrations, followed by 5000 IU/d. The goal should be to raise 25(OH)D concentrations above 40–60 ng/ml (100–150 nmol/l). For treatment of people who become infected with COVID-19, higher vitamin D3 doses might be useful. Randomized controlled trials and large population studies should be conducted to evaluate these recommendations.
ARTICLE | doi:10.20944/preprints202006.0318.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: ventilator; pandemic; ventilation; influenza pandemic; coronavirus; coronavirus pandemic; pandemic ventilator; single-limb; open source; open hardware; COVID-19; medical hardware; RepRap; 3-D printing; open source medical hardware; embedded systems; real-time operating system
Online: 26 June 2020 (17:25:16 CEST)
This study describes the development of an automated bag valve mask (BVM) compression system, which, during acute shortages and supply chain disruptions can serve as a temporary emergency ventilator. The resuscitation system is based on the Arduino controller with a real-time operating system installed on a largely RepRap 3-D printable parametric component-based structure. The cost of the system is under $170, which makes it affordable for replication by makers around the world. The device provides a controlled breathing mode with tidal volumes from 100 to 800 milliliters, breathing rates from 5 to 40 breaths/minute, and inspiratory-to-expiratory ratio from 1:1 to 1:4. The system is designed for reliability and scalability of measurement circuits through the use of the serial peripheral interface and has the ability to connect additional hardware due to the object-oriented algorithmic approach. Experimental results demonstrate repeatability and accuracy exceeding human capabilities in BVM-based manual ventilation. Future work is necessary to further develop and test the system to make it acceptable for deployment outside of emergencies in clinical environments, however, the nature of the design is such that desired features are relatively easy to add with the test using protocols and parametric design files provided.
REVIEW | doi:10.3390/sci2030068
Subject: Keywords: COVID-19; pooling clinical trials; hyperinfection; steroids; treatment; targeted healthcare; population health management; cancer treatment; clinical research; clinical trials; developing vaccines; ranking and rating hospital quality; school closures; interventions for delirium; assessments of COVID-19 death inequities; regulatory safeguards; preventing child abuse and maltreatment; prevalence of health care worker burnout; nursing home ratings; challenging oncology practice; addressing racial; ethnic; social and economic divides; violence against sexual minority adolescents; primary tumors; metastasis; stages of cancer; reforming cancer clinical trials; supporting carers; protection and prevention; benign and malignant tumors; reforming cancer clinical trials; protection of healthcare personnel; comparing excess deaths in NYC; 1918 influenza pandemic; the possibility of full recovery from COVID-19; mental health impact of COVID-19 on young adults; ranking and rating nursing home quali
Online: 21 August 2020 (00:00:00 CEST)
The SARS-CoV-2 virus that causes the COVID-19 disease has wreaked havoc on the world community in terms of every imaginable parameter. The research output on COVID-19 has been nothing short of phenomenal, especially in the medical and biomedical sciences, where the search for a potential vaccine is being conducted in earnest. Much of the advanced research has been distributed in the leading medical journals, including the Journal of the American Medical Association (JAMA), where the latest research is distributed on a daily basis. The purpose of this paper is to provide some perspectives on 44 interesting and highly topical research papers that have been published in JAMA, at the time of writing, within the past two weeks. The diverse topics include public health, general medicine, internal medicine, oncology, paediatrics, geriatrics, and biostatistics.