ARTICLE | doi:10.20944/preprints202306.0498.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: infectivity; neutral solution; acidic solution; alkaline solution; deprotonation
Online: 7 June 2023 (07:05:54 CEST)
The preservative qualities of individual ionic compounds on the infectivity of T4 virions were elucidated. T4 virions were immersed in quasi-pure ionic solutions prior to the adsorption process, and the pfu values of these were measured following the conventional method. In neutral ionic solutions, the minimum and the optimum concentrations for preservative qualities were corresponded with the results obtained from the multi-ionic media/buffers. In acid and alkali solutions, phages show tolerances at a pH range of 5-11 in multi-ionic media/buffers. T4 virions show no tolerance in quasi-pure acid, neutral and weak alkaline conditions. The preservative quality of T4 virions was jumped up in over 10-1 mM OH- solution, equivalent to pH value over 10, which is corresponding to the pKa of the deprotonation of the DNA bases G and T. Infectivity was lost below 10-1 mM OH- and higher than 10 mM OH-. These results implicate the maintaining of infectivity of a virion may need the flexibility of the intra-capsid DNA by deprotonation.
ARTICLE | doi:10.20944/preprints202003.0325.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; infectivity; temperature; humidity
Online: 23 March 2020 (01:30:06 CET)
The pandemic threat SARS-CoV-2 is now beyond control though the country of origin of this virus had already been limited for the new infection. Number of infected people and countries have been increasing day by day. Considering the previous pandemic flues, it is hypothesizing that COVID-19 will be reduced with warming the global environmental temperature. Therefore, the current study was aimed to analyze the effect of temperature and relative humidity (RH) on spreading of SARS-CoV-2 infection. The COVID-19 confirmed cases of 31 different states in China and 70 cities of 11 countries were obtained from several online databases. The real time temperature and humidity of the respective regions were taken from an online weather forecasting data source. Correlation analyses showed that SARS-CoV-2 infectivity and spreading negatively correlated with temperature of most of the states of China or cities of the world or in a country. The effect of humidity on COVID-19 was found to be positively correlated inside the China and difference of humidity was not found among countries and/or various regions of the world. Moreover, a minimum number of COVID-19 cases have been confirmed in the temperate regions compared to regions/countries compared to regions/countries with relatively low temperature. In conclusion, the SARS-CoV-2 infection has been found in a wide range of temperatures. It might be hypothesized that comparatively elevated air temperature could play a detrimental effect for SARS-CoV-2 spread.
ARTICLE | doi:10.20944/preprints202301.0404.v1
Subject: Biology And Life Sciences, Virology Keywords: Omicron variant; Infectivity; Pathogenicity; Biothermodynamics; COVID-19; Viral evolution
Online: 23 January 2023 (08:53:40 CET)
The SARS-CoV-2 Hydra with many heads (variants) has been causing the COVID-19 pandemic for 3 years. The appearance of every new head (SARS-CoV-2 variant) causes a new pandemic wave. The last in the series is the XBB.1.5 “Kraken” variant. In the general public (social media) and in the scientific community (scientific journals), during the last several weeks since the variant has appeared, the question was raised of whether the infectivity of the new variant will be greater. This article attempts to provide the answer. Analysis of thermodynamic driving forces of binding and biosynthesis leads to the conclusion that infectivity of the XBB.1.5 variant could be increased to a certain extent. The pathogenicity of the XBB.1.5 variant seems to be unchanged compared to the other Omicron variants.
ARTICLE | doi:10.20944/preprints202301.0327.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; variant of concern; infectivity; pathogenicity; evolution; Gibbs energy
Online: 18 January 2023 (08:40:33 CET)
SARS-CoV-2 resembles the ancient mythical creature Hydra. Just like with the Hydra, when one head is cut, it is followed by appearance of two more heads, suppression of one SARS-CoV-2 variant causes appearance of newer variants. Unlike Hydra that grows identical heads, newer SARS-CoV-2 variants are usually more infective, which can be observed as time evolution of the virus at hand, which occurs through acquisition of mutations during time. The appearance of new variants is followed by appearance of new COVID-19 pandemic waves. With the appearance of new pandemic waves and determining of sequences, in the scientific community and general public the question is always raised of whether the new variant will be more virulent and more pathogenic. The two variants characterized in this paper, BA.5.2 and BF.7, have caused a pandemic wave during the late 2022. This paper gives full chemical and thermodynamic characterization of the BA.5.2 and BF.7 variants of SARS-CoV-2. Having in mind that Gibbs energy of binding and biosynthesis represent the driving forces for the viral life cycle, based on the calculated thermodynamic properties we can conclude that the newer variants are more infective than earlier ones, but that their pathogenicity has not changed.
ARTICLE | doi:10.20944/preprints202303.0007.v1
Subject: Biology And Life Sciences, Virology Keywords: Human herpesvirus 5; glycoprotein B; UL55; cell-cell fusion; entry; infectivity
Online: 1 March 2023 (03:05:22 CET)
Viruses can induce the fusion of infected and neighboring cells, leading to the formation of syncytia. Cell-cell fusion is mediated by viral fusion proteins on the plasma membrane of infected cells that interact with cellular receptors on neighboring cells. Viruses use this mechanism to spread rapidly to adjacent cells or escape host immunity. For some viruses, syncytium formation is a hallmark of infection and a known pathogenicity factor. For others, the role of syncytium formation in viral dissemination and pathogenicity remains poorly understood. Human cytomegalovirus (HCMV) is an important cause of morbidity and mortality in transplant patients and the leading cause of congenital infections. Clinical HCMV isolates have broad cell tropism but differ in their ability to induce cell-cell fusions, and little is known about the molecular determinants. We developed a system to analyze HCMV glycoprotein B (gB) variants in a defined genetic background. HCMV strains TB40/E and TR were used as vectors to compare the fusogenicity of six gB variants from congenitally infected fetuses with those from three laboratory strains. Five of them conferred the ability to induce fusion of MRC-5 human embryonic lung fibroblasts to one or both backbone strains, as determined by a split GFP-luciferase reporter system. The same gB variants were not sufficient to induce syncytia in infected ARPE-19 epithelial cells, suggesting that additional factors are involved. The system described here allows a systematic comparison of the fusogenicity of viral envelope glycoproteins and may help to clarify whether fusion-promoting variants are associated with increased pathogenicity.
ARTICLE | doi:10.20944/preprints202212.0024.v1
Subject: Computer Science And Mathematics, Probability And Statistics Keywords: Positive Poisson distribution, Under dispersion, Bayesian analysis, prediction, index of infectivity.
Online: 1 December 2022 (10:25:33 CET)
Background. COVID-19 efforts were often ineffective in controlling the spread of the pandemic. Identifying ineffective controls during a pandemic is thus vital. Method. Utilizing publicly available data on COVID deaths in the counties of US states, we create an index to capture and interpret ineffectiveness in the efforts to reduce the spread of the pandemic in US counties. This index is based on the Intervened Poisson Distribution (IPD) introduced originally by Shanmugam. Motivation for the research idea occurred while we noticed the data dispersion of the COVID deaths is smaller than the average only in some counties. Under-dispersed data is common in statistical modeling. A novel approach we adapted in this article includes the estimation of an intervention parameter estimated through iterative non-linear optimization. Results. Twenty-five counties in California, Idaho, Minnesota, Mississippi, Montana, Nebraska, North Carolina, North Dakota, Texas, and Utah were found to be ineffective in controlling for fatalities based on the expected probability distribution. A review of the policies enacted in these areas would provide insight into ineffective prevention efforts, and some of these issues are documented in current literature. Conclusion. The IPD index an innovate way to document efficacy of interventions during pandemics. The IPD may identify ineffective efforts prior to statistical models intended to evaluate efficacy of efforts.
ARTICLE | doi:10.20944/preprints202211.0470.v1
Subject: Biology And Life Sciences, Virology Keywords: Kaposi’s sarcoma-associated herpesvirus; MEK; thymidine kinases; lytic replication; infectivity; ORF21; herpesvirus
Online: 25 November 2022 (06:13:52 CET)
Kaposi’s sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus-8, is the causative agent of Kaposi’s sarcoma, Castleman’s disease, and primary effusion lymphoma. Although the functions of the viral thymidine kinases (vTK) of herpes simplex virus-1/2 and varicella zoster virus are well understood, that of KSHV ORF21 (an ortholog of vTK) is largely unknown. Here, we investigated the role of ORF21 in lytic replication and infection by generating two ORF21-mutated KSHV BAC clones: ORF21-kinase activity deficient-KSHV (21KD) and stop codon-induced ORF21-deleted-KSHV (21del). The results showed that both ORF21-mutations did not affect viral genome replication, lytic genes transcription, or the production of viral genome-encapsidated particles. ORF21 molecule-dependent function, other than the kinase function of ORF21, was involved in the infectivity of progeny virus. ORF21 was expressed at 36 h after induction of lytic replication, and endogenously expressed ORF21 was localized in the whole cytoplasm and decreased on the cell surface area. Moreover, the effects of ORF21 expression on signaling pathways and proliferation were analyzed. The results showed that ORF21 upregulated the MEK phosphorylation and anchorage-independent cell growth. These findings indicate that ORF21 plays key roles in both infection and oncogenesis of KSHV through the manipulation of cellular function.
REVIEW | doi:10.20944/preprints202009.0395.v1
Subject: Biology And Life Sciences, Virology Keywords: Spike protein, V483A, substitution mutation, virus-host cell interaction, high transmission, infectivity.
Online: 17 September 2020 (10:43:02 CEST)
Exploring the biological significance of mutations in SARS-CoV-2 coronavirus, causing the COVID–19 pandemic, has recently become an area of paramount interest for many researchers, who are pouring their tremendous efforts, in cracking the COVID–19 pandemic code. One of many such mutations that have occurred in the viral genome is V483A mutation, which is a part of the receptor-binding motif (RBM), present in the S1 domain of the spike protein. V483A mutant virus is becoming popular in North America with 36 cases so far, due to its frequent occurrences in recent days. In this review, we have assembled all information, currently available on V483A mutation, and have made a critical analysis based on the perspectives of many researchers all around the world. Comparison is made between the wild type and the V483A mutants to analyze certain factors like the type of interaction between the virus and host cell interface, binding affinity, stability, partition energy, hydrophobicity, occurrence rate, and transmissibility. Insilico dynamic analysis shows minimal alteration in the receptor-binding domain (RBD) of V483A mutant protein in free-state and no significant change of mutant tertiary structure of RBM upon binding to the ACE2 receptor. Comprehensive details about infectivity and evasion of the immune system by the virus are discussed. This information can in turn be of monumental importance in the field of vaccine and drug development because the mutants are becoming resistant to the vaccines and monoclonal antibodies.
ARTICLE | doi:10.20944/preprints202209.0318.v1
Subject: Biology And Life Sciences, Virology Keywords: BA.2.75 variant; Gibbs energy of binding; binding rate; infectivity; SARS-CoV-2
Online: 21 September 2022 (09:44:34 CEST)
Omicron BA.2.75 may become the next globally dominant strain of COVID-19 in 2022. BA.2.75 sub-variant has acquired more mutations (9) in spike protein and other genes of SARS-CoV-2 than any other variant. Thus, its chemical composition and thermodynamic properties have changed comparing to earlier variants. In this paper Gibbs energy of binding and antigen-receptor binding rate is reported for the BA.2.75 variant. Gibbs energy of binding (driving force of binding) of Omicron BA.2.75 variant is more negative than that of the competing variants BA.2 and BA.5.
ARTICLE | doi:10.20944/preprints202306.2008.v1
Subject: Environmental And Earth Sciences, Soil Science Keywords: Microbial inoculant; inoculum infectivity; inoculum effectivity; arbuscular mycorrhizal fungi, dark septate fungi; inoculum adapted to salinity
Online: 29 June 2023 (03:22:55 CEST)
Soil salinity is a limiting factor in crop productivity. Inoculating crops with microorganisms adapted to salt stress is an alternative to increasing plant salinity tolerance. Few studies have simultaneously propagated arbuscular mycorrhizal fungi (AMF) and dark septate fungi (DSF) using different sources of native inoculum from halophyte plants, and evaluated their effectiveness. This study selected, in alfalfa plants as trap culture, the infectivity of 38 microbial consortia native from rhizospheric soil (19) or roots (19) coming from six halophyte plants, as well as their effectiveness in mitigating salinity stress. Inoculation with soil resulted in 26%-56% colonization by AMF and 12%-32% by DSF. Root inoculation produced 10%-56% and 8%-24% of colonization, respectively. There was no difference in the number of spores of AMF produced with both inoculum types. The effective consortia were selected based on low Na but high P and K shoot concentrations which is relevant for plant nutrition but more for salt stress mitigation. The microbial consortia selection is presented in a more novel and applicable context, which would allow for the production of native microbial inoculants adapted to salinity to diminish the harmful effects of salinity stress in glycophyte plants in the context of sustainable agriculture.
REVIEW | doi:10.20944/preprints202308.0520.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; spike protein; mutations; viral infectivity; pathogenesis; vaccine efficacy; immune evasion; antibody neutralization; T-cell response; therapeutic targeting
Online: 7 August 2023 (10:12:28 CEST)
The SARS-CoV-2 virus, which is responsible for the COVID-19 pandemic which emerged and spread, has sparked intense research on its spike protein, which is essential for viral entrance into host cells. Viral reproduction and transmission, host immune response regulation, receptor recognition and host cell entrance mechanisms, as well as structural and functional effects have all been linked to mutations in the spike protein. Spike protein mutations can also result in immune evasion mechanisms that impair vaccine effectiveness and escape, and they are linked to illness severity and clinical consequences. Numerous studies have been conducted to determine the effects of these mutations on the spike protein structure and how it interacts with host factors. These results have important implications for the design and development of medicines and vaccines based on spike proteins as well as for the assessment of those products' efficiency against newly discovered spike protein mutations. The paper gives a general overview of how spike protein mutations are categorized and named, as well as the genomic and phylogenetic techniques that have been used to track their genesis and dissemination. Additionally, it looks at the links between spike protein mutations and clinical outcomes, illness severity, unanswered problems, and future research prospects. Additionally, explored are the effects of these mutations on vaccine effectiveness as well as the possible therapeutic targeting of spike protein mutations.
ARTICLE | doi:10.20944/preprints202207.0358.v1
Subject: Biology And Life Sciences, Virology Keywords: Foot-and-mouth disease virus; safe sample transport; single-stranded positive-sense RNA; TRIzol extraction; naked RNA; infectivity; RNA transfection; lipofectamine; self-transfection; BHK cells
Online: 25 July 2022 (08:14:51 CEST)
Safe sample transport is of great importance for infectious diseases diagnostics. Various treatments and buffers are used to inactivate pathogens in diagnostic samples. At the same time, adequate sample preservation, particularly of nucleic acids, is essential to allow an accurate laboratory diagnosis. For viruses with single-stranded RNA genomes of positive polarity, such as foot-and-mouth disease virus (FMDV), however, naked full-length viral RNA can itself be infectious. In order to assess the risk of infection from inactivated FMDV samples, two animal experiments were performed. In the first trial, six cattle were injected with FMDV RNA (isolate A22/IRQ/24/64) into the tongue epithelium. All animals developed clinical disease within two days and FMDV was reisolated from serum and saliva samples. In the second trial, another group of six cattle was exposed to FMDV RNA by instilling it on the tongue and spraying it into the nose. The animals were observed for 10 days after exposure. All animals remained clinically unremarkable and virus isolation as well as FMDV genome detection in serum and saliva were negative. No transfection reagent was used for any of the animal inoculations. In conclusion, cattle can be infected by injection with naked FMDV RNA, but not by non-invasive exposure to the RNA. Inactivated FMDV samples that contain full-length viral RNA carry only a negligible risk of infecting animals.