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/preprints202305.1749.v1
Subject: Biology And Life Sciences, Virology Keywords: Marine sulfated glycans; SARS-CoV-2; Omicron XBB.1.5; Spike protein; Heparin
Online: 25 May 2023 (07:12:52 CEST)
Keywords: Marine sulfated glycans; SARS-CoV-2; Omicron XBB.1.5, Spike protein; Heparin
ARTICLE | doi:10.20944/preprints202212.0202.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Omicron BA.5; Omicron BE.1; animal model
Online: 12 December 2022 (13:12:15 CET)
A new variant of the SARS-CoV-2 Omicron BA.5 virus has displaced all previous variants of the virus around the world. Preliminary assessment of the effectiveness of drugs for the prevention and treatment of COVID-19 requires the availability of infection models in animals. In this study, we characterize the infection model SARS-CoV-2 Omicron BA.5 and its progeny sublineage BE.1 in hACE2-transgenic mice and in Syrian hamsters. Both sublineages turned out to be pathogenic for animals – the challenged animals showed weight loss, a high level of viral load and acute inflammation in the lungs. Part of BA.5-infected mice died after virus challenge, indicating that this virus variant is more pathogenic than the previous BA.1 variant but less pathogenic than Wuhan variant.
ARTICLE | doi:10.20944/preprints202305.2238.v1
Subject: Public Health And Healthcare, Public Health And Health Services Keywords: reinfection; COVID-19; vaccination; Omicron
Online: 31 May 2023 (11:38:23 CEST)
Reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants due to immune escape challenges the global response to the pandemic. We estimated the Omicron reinfection prevalence among people who had previous SARS-CoV-2 infections in Shanghai, China. We conducted a telephone survey in December 2022 for those who were previously infected with Omicron between March and May 2022. Information on demographics, coronavirus disease 2019 (COVID-19) testing, and vaccination history was collected. The overall and subgroup reinfection rates were estimated and compared. Among the 1981 respondents who were infected between March and May 2022, 260 had positive nucleic acid or rapid antigen tests in December 2022, with an estimated reinfection rate of 13.1% (95% confidence interval [95% CI]: 11.6-14.6). The reinfection rate for those who had a booster vaccination was 11.4% (95% CI: 9.2-13.7), which was significantly lower than that for those with an incomplete vaccination series (15.2%, 95% CI: 12.3-18.1) (adjusted odds ratio [aOR]: 0.579; 95% CI: 0.412–0.813). Reinfection with the Omicron variant was lower among individuals with previous SARS-CoV-2 infection and had completed a booster vaccination, suggesting that hybrid immunity can offer better protection against reinfection with Omicron sublineages.
COMMUNICATION | doi:10.20944/preprints202204.0196.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; Omicron; Sublineages; Ecuador
Online: 21 April 2022 (08:24:19 CEST)
The Omicron variant of SARS-CoV-2 is the latest pandemic lineage causing COVID-19. Despite having a vaccination rate ≥ 85% Ecuador recorded a high incidence of Omicron from December 2021 to March 2022. Since Omicron emerged it is evolving into multiple sublineages with distinct prevalence in different regions. In this work, we use all Omicron sequences from Ecuador available at GISAID until March 2022 and the software Nextclade and Pangolin to identify which lineages circulate in this country. We detected 12 different sublineages (BA.1, BA.1.1, BA.1.1.1, BA.1.1.14, BA.1.1.2, BA.1.14, BA.1.15, BA.1.16, BA.1.17, BA.1.6, BA.2, BA.2.3), which has been reported in Africa, America, Europe, and Asia suggesting multiple introduction events. Sublineages BA.1.1 and BA.1 were the most prevalent. Genomic surveillance must continue to evaluate the dynamic of current sublineages, early introduction of new ones and vaccine efficacy against evolving SARS-CoV-2.
ARTICLE | doi:10.20944/preprints202203.0076.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: COVID-19; Omicron; inactivated vaccines
Online: 4 March 2022 (09:10:15 CET)
The COVID-19 pandemic has now become very severe as never before due to the overwhelming spread of Omicron. We found that Omicron outbreak can be effectively prevented by inactivated vaccines, which averted an outbreak of more than 1.6 million people in Hangzhou, China. The 36 mutations in the target spike protein of Omicron neutralizing antibody enable it to evade the immune protection afforded by vaccines. This is because that mRNA and adenovirus-vector vaccines are designed to recognize the spike (S) glycoprotein of the SARS-CoV-2 wild-type (WT) strain. However, Inactivated vaccines contain the whole viral antigens and remain stable in their recognition of newly emerging variants of SARS-CoV-2. Our study confirmed the advantage of inactivated vaccines in the face of highly mutated Omicron variant and provided a basis for the development of effective vaccines to prevent future long-term transmission, mutation and recurrence of SARS-CoV-2.
REVIEW | doi:10.20944/preprints202207.0051.v1
Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: SARS-CoV-2; Omicron; variant of concern
Online: 4 July 2022 (10:28:04 CEST)
For the first time in history, we have witnessed the origin and development of a pandemic. To handle the accelerated accumulation of viral mutations and to comprehend the virus' evolutionary adaptation in humans, an unparalleled program of genetic sequencing and monitoring of SARS-CoV-2 variants has been undertaken. Several scientists have theorized that, with the Omicron surge producing a more contagious but less severe disease, the end of COVID-19 is near. However, by analyzing the behavior shown by this virus for 2 years, we have noted that pandemic viruses do not always show a decreased virulence. Instead, it appears there is an evolutionary equilibrium between transmissibility and virulence. We have termed this concept “intermittent virulence”. The present work analyzes the temporal and epidemiological behavior of SARS-CoV-2 and suggests that there is a high possibility that new virulent variants will arise in the near future, although it is improbable that SARS-CoV-2´s virulence will be the same as was seen during the pandemic phase.
ARTICLE | doi:10.20944/preprints202208.0516.v1
Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: SARS-CoV-2; COVID-19; Omicron; children; hospitalization
Online: 30 August 2022 (09:00:24 CEST)
(1) Background: When the Omicron variant of SARS-CoV-2 first emerged in Germany in January 2022, data on related disease severity among children and adolescents was not yet available. Given Omicron’s high transmissibility, the ability to assess its impact on admission and hospitalization rates in children’s hospitals is critical for the purpose of understanding the scope of its burden on the German health care system. (2) Methods: From January 24, 2022 to July 31, 2022, SARS-CoV-2 cases admitted to German pediatric hospitals were monitored via a national, clinician-led reporting system (CLRS) established by the German Society for Pediatric Infectious Diseases (DGPI). Cases treated on general wards and intensive care units, as well as patient age and need for respiratory support were recorded. (3) Results: From January to July 2022, a median of 1.7 cases (range 0.4–3) per reporting pediatric hospital per day were hospitalized on general wards, whereas a median of 0.1 cases (range 0–0.4 cases) were on intensive care units. Of all hospitalized patients, 4.2% received respiratory support. (4) Conclusions: Despite the high incidence rates documented in connection with the Omicron variant in early 2022, the number of pediatric hospital admissions, and especially the number of cases with need for intensive care treatment and respiratory support due to a symptomatic SARS-CoV-2 infection, remained relatively low. Higher Omicron incidence rates had only a modest impact on SARS-CoV-2-related admissions and hospitalization in German children’s hospitals.
ARTICLE | doi:10.20944/preprints202207.0223.v1
Subject: Biology And Life Sciences, Virology Keywords: Monoclonal antibodies; Sotrovimab; COVID-19; Omicron; BA.2
Online: 14 July 2022 (12:22:21 CEST)
Coronavirus disease 19 (COVID-19) continues to spread worldwide as a severe pandemic. The Omicron BA.2 became the predominant variant and the protagonist of the ongoing surge. As the virus continues to mutate, using of approved drugs or developing new therapeutic or prophylactic therapies against COVID-19 could be more complex. Sotrovimab is a monoclonal antibody (mAb) targeting the conserved epitope on the spike protein receptor; the most recent studies observed that it has substantially decreased in vitro activity against the Omicron BA.2 subvariant, but real-life data are still scarce. We describe the outcome of a case series of outpatients with BA.1 or BA.2 infection treated with sotrovimab. We conducted a retrospective observational study including all non-hospitalized adult patients treated with sotrovimab, for which a Sanger sequencing of SARS-CoV-2 was performed within a regional genomic surveillance program. Eleven (50%) patients with BA.1 infection and eleven (50%) with BA.2 infection were considered. Most patients were immunocompromised. During the follow-up period, no patient died and only one with BA.1 infection was hospitalized for severe COVID-19 pneumonia onset. One month after treatment, 90.9% of patients were completely asymptomatic in each group. We demonstrated that patients carrying the BA.2 variant treated with sotrovimab did not evolve to severe COVID-19, showing a similar outcome to BA.1 infected patients. Further studies are needed to prove that vaccination or the presumably high doses of mAbs used can protect this group of patients at high risk of progression.
ARTICLE | doi:10.20944/preprints202302.0126.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Omicron; SARS-CoV-2; piRNAs; coronavirus genome; translation; replication
Online: 7 February 2023 (08:54:49 CET)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused the COVID-19 pandemic still able to infect the population in many countries. The Omicron strain is the most mutated variant of SARS-CoV-2. The high transmissibility of the strain and the ability to evade immunity require a priority study of its properties in order to quickly create effective means of preventing it. The present work is devoted to the study of in silico interaction of piRNAs with the genome of the SARS-CoV-2 (gRNA) in order to identify endogenous piRNAs and propose synthetic piRNAs with high antiviral activity for drug development. The studies were carried out using proven bioinformatic methods of interaction of the entire SARS-CoV-2 genome with more than eight million piRNAs. Binding sites (BSs) of piRNAs in the 5'UTR were located with overlapping nucleotide sequences called clusters of BSs. Several clusters of BSs were found in the nsp3, nsp7, RNA-dependent RNA polymerase, endoRNAse, S surface glycoprotein, ORF7a and nucleocapsid. 16 synthetic piRNAs have been proposed that interact with gRNA with free binding energy from -170 kJ/mol to -175 kJ/mol, which can be used to create drugs that suppress the reproduction of SARS-CoV-2.
REVIEW | doi:10.20944/preprints202210.0292.v1
Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: Omicron; Covid-19; SARS-CoV-2; Variants of concern
Online: 20 October 2022 (02:16:05 CEST)
Since the beginning of the coronavirus disease 2019 (Covid-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the viral genome, which have led to changes in the pathogenicity, transmissibility, and morbidity. The Omicron variant is the most recent variant of concern (VOC) to emerge and was recognized by the World Health Organization (WHO) on November 26, 2021. The Omicron lineage is phylogenetically distinct from earlier variants, including the previously dominant Delta SARS-CoV-2 variant. Previous research has reported the most common clinical manifestations of the Omicron variant to be fever, runny nose, sore throat, severe headache, and fatigue. The reverse transcription-polymerase chain reaction (RT-PCR) test, rapid antigen assays, and chest computed tomography (CT) scans can help diagnose those with the Omicron variant. Furthermore, many agents are expected to have therapeutic benefits for those infected with the Omicron variant, including TriSb92, molnupiravir, nirmatrelvir, and their combination, corticosteroids, and interleukin-6 (IL-6) receptor blockers. Despite being milder than previous variants, the Omicron variant threatens many lives, particularly among the unvaccinated, due to its higher transmissibility, pathogenicity, and infectivity. This review summarizes the essential features of the Omicron variant, including its history, genome, transmissibility, clinical manifestations, diagnosis, management, and the effectiveness of existing vaccines against this VOC.
ARTICLE | doi:10.20944/preprints202201.0315.v2
Subject: Medicine And Pharmacology, Dentistry And Oral Surgery Keywords: SARS-CoV-2; Omicron; biosafety protocol; dentistry; orthodontics; sustainability
Online: 8 April 2022 (03:58:00 CEST)
With arrival of highly transmissible Omicron variants in global pandemic, dentistry is facing another challenge to preserve biosafety of dental care. With a mission to protect both patients and healthcare workers, adaptability to the changing epidemiologic situation is required from dental professionals. This work presents a prospective sustainable biosafety setting for routine orthodontic care. The protocol is composed from combination of available technologies focused on the air-borne part of a virus pathway. Introduced biosafety protocol has been clinically evaluated after 18 months of application in the real clinical environment. The protocol has three fundamental pillars: (1) UVC air disinfection; (2) air saturation with certified virucidal oils through nebulizing diffusers; (3) complementary solutions. As a method of evaluation pseudonymous on-line smart form was used. Protocol operates with premise that everybody as a hypothetical asymptomatic carrier. Results from 115 patient feedbacks imply that with this protocol in place, there was no observed or reported translation of virus from patient to another patient or from patient to doctor or nurse and vice versa, albeit nine patients have retrospectively admitted visiting the clinic as probably infectious. Despite promising results, a larger clinical sample and exposition to current mutated strains is necessary for reliable conclusions about protocol virucidal efficiency.
COMMUNICATION | doi:10.20944/preprints202203.0010.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; variant; Omicron; Delta; antigen; RT-qPCR
Online: 1 March 2022 (09:01:19 CET)
Rapid antigen detection tests (RAD) are commonly used for the diagnosis of SARS-CoV-2 infections. However, with the continuous emergence of new variants of concern (VOC) presenting various mutations potentially affecting the nucleocapsid protein, the analytical performances of these assays should be frequently reevaluated. One-hundred and twenty samples were selected and tested with both RT-qPCR and five commercial RAD commonly sold in Belgian pharmacies. Of these, direct whole genome sequencing identified the strains present in 116 samples, of which 70 were Delta and 46 were Omicron. Sensitivity across a wide range of Ct values (13.5 to 35.7; median = 21.3) were comparable and ranged from 70.0% to 77.1% for Delta strains and from 69.6% to 78.3% for Omicron strains. When taking swabs with a low viral load (Ct > 25), poor performances were observed for the Delta strains (20.0 to 40.0%) and, even more so, for Omicron strains (0.0 to 23.1%). Two devices failed to detect all samples (n = 13) containing Omicron strains with a low viral load. The poor performance observed with low viral loads is an important limitation of RAD, which is not sufficiently highlighted in the instruction for use of these devices.
ARTICLE | doi:10.20944/preprints202204.0266.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS CoV-2; Variant of Concern; Omicron; mutation; genomic surveillance
Online: 28 April 2022 (03:28:50 CEST)
Genomic surveillance represents an important strategy for understanding evolutionary mechanisms, transmission profile, and infectivity of different SARS-CoV-2 variants. We assessed the epidemiological profile of 366 individuals who tested positive for SARS-CoV-2 from 29 municipalities in Rondônia between December 2021 to March 2022. Samples were collected, RNA was ex-tracted and screened using RT-qPCR for Alpha, Beta, Gamma, Delta and Omicron VOCs and viral quantification was performed. Sequences were analyzed for phylogeny, mutations and lineages. Of the samples analyzed, 93.71% were positive for the Omicron variant and 6.28% were positive for the Delta variant. The symptoms observed were cough, sore throat, and fever, with a mean duration of 5 days; no hospitalizations or deaths were reported. We noted that among the positive individuals, 51% had been immunized with two doses, 22% received three doses, 13% received one dose, and 13% were not immunized. Just 242 samples were amenable to analysis for alignment and phylogenetic characterization; corresponding to variants BA.1 and BA.1.1; a total of 120 mutations were identified, 36% of which were found in the S gene. In conclusion, there was a high frequency of mutations in the SARS-CoV-2 genome, but no record of clinical severity, demonstrating the positive effect of vaccination.
ARTICLE | doi:10.20944/preprints202203.0155.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; Omicron variant; Monoclonal antibody; Neutralization; Spike protein
Online: 10 March 2022 (14:30:25 CET)
SARS-CoV-2 Omicron variants contain many mutations in its spike receptor binding domain, the target of all authorized monoclonal antibodies (mAbs). Determining the extent to which Omicron variants reduced mAb susceptibility is critical to preventing and treating COVID-19. We systematically reviewed PubMed and three preprint servers, last updated February 22, 2022, of the in vitro activity of authorized mAbs against the Omicron variants. Thirty-three studies were eligible including 33 containing Omicron BA.1 susceptibility data and five that also contained Omicron BA.2 susceptibility data. The first two authorized mAb combinations, bamlanivimab/etesevimab and casirivimab/imdevimab, were inactive against the Omicron BA.1 and BA.2 variants. In 24 studies, sotrovimab (third authorized mAb) displayed a median 4.1-fold (IQR: 2.4-7.6) reduced activity against Omicron BA.1 and, in four studies, a median 26-fold (IQR:16-35) reduced activity against Omicron BA.2. In 18 studies, cilgavimab and tixagevimab independently displayed median reductions in activity of >300-fold against Omicron BA.1, while in ten studies, the cilgavimab/tixagevimab combination (fourth authorized mAb preparation) displayed a median 63-fold (IQR: 26-145) reduced activity against Omicron BA.1. In two studies, cilgavimab was approximately 100-fold more susceptible to BA.2 than to BA.1. In two studies, bebtelovimab, the most recently authorized mAb, was fully active against both the Omicron variants. Disparate results between assays were common as evidenced by a median 42-fold range (IQR: 25-625) in IC50 between assays for the eight authorized individual mAbs and three authorized mAb combinations. Highly disparate results between published assays indicates a need for improved mAb susceptibility test standardization or inter-assay calibration.
ARTICLE | doi:10.20944/preprints202305.1361.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Omicron Variant of Concern; Mutations; Lineages
Online: 19 May 2023 (03:00:56 CEST)
The emergence of the SARS-CoV-2 Variant of Concern (VOC) Omicron has been characterized by an explosive number of cases in almost every part of the world. The dissemination of different sub-lineages and recombinant genomes also led to several posterior waves in many countries. The circulation of this VOC and its major sub-lineages (BA.1 to BA.5) was monitored in community cases and in international travelers returning to Venezuela, by a rapid partial sequencing method. The specific sub-lineage assignment was performed by complete genome sequencing. Epidemic waves of SARS-CoV-2 cases were observed among international travelers during 2022, a situation not seen before December 2021. The succession of the Omicron VOC sub-lineages BA.1 to BA.5 occurred sequentially, except for BA.3, which was almost not detected. However, the sub-lineages generally circulated two months earlier in international travelers than in community cases. The diversity of Omicron sub-lineages found in international travelers was related to the one found in the USA, consistent with the most frequent destination of international travel from Venezuela this year. These differences are compatible with the delay observed in Latin American countries in the circulation of the different lineages of the Omicron VOC.
REVIEW | doi:10.20944/preprints202305.0103.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; antiviral agents; Omicron variant; mutant; vaccines; clinical studies
Online: 3 May 2023 (06:04:36 CEST)
Since the onset of coronavirus disease 2019 (COVID-19) pandemic, the virus kept developing and mutating into different variants over time that also gained increased transmissibility and spread in populations at a higher pace, culminating in successive waves of COVID-19 cases. The scientific community has developed vaccines and antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease. Realizing that growing SARS-CoV-2 variations significantly impact the efficacy of antiviral therapies and vaccines, we have summarized the appearance and attributes of SARS-CoV-2 variants for future perspectives in drug design, bringing up-to-date hints for developing therapeutic agents targeting the variants. The Omicron variant is among the most mutated form; its strong transmissibility and immune resistance capacity have prompted international worry. Most mutation sites currently being studied are located in the BCOV_S1_CTD of the S protein. Despite this, several hurdles remain, such as developing vaccination and pharmacological treatment efficacies for emerging mutants of SARS-CoV-2 strains. In this review, we present an updated viewpoint on the current issues faced by the emergence of various SARS-CoV-2 variants. Furthermore, we discuss the clinical studies conducted to assist the development and dissemination of vaccines, small molecule therapeutics, and therapeutic antibodies having broad-spectrum action against SARS-CoV-2 strains.
COMMUNICATION | doi:10.20944/preprints202210.0361.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Omicron variants; BQ.1; BQ.1.1
Online: 24 October 2022 (11:42:07 CEST)
Currently SARS-CoV-2 is spreading around the world as an Omicron strain. Recently, the Omicron variants (BQ.1 and BQ.1.1) were identified as novel Variants of Concern. UpToDate, there is little information about the Omicron Variants BQ.1 and BQ.1.1. The widely altered Omicron variants are spread globally, providing a high risk of infection surges with devastating consequences in some areas. The Omicron type of SARS-CoV-2 has a harm risk of reinfection, according to early reported findings. COVID-19 Variants particularly, BQ.1 and BQ.1.1 have gained global attention and caused a worldwide sensation since their discovery. Therefore, this communication discusses the present status of COVID-19 Variants BQ.1 and BQ.1.1, and their consequences.
ARTICLE | doi:10.20944/preprints202303.0219.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2 pandemic; PCR positivity; Aleph Delta Omicron waves; Mumbai; India
Online: 13 March 2023 (06:31:08 CET)
Background: The SARS-CoV-2 laboratory PCR tests were generally reported only as binary positive or negative outcomes. Instead test positivity, these results contain a great deal of epidemiological information related to viral transmission patterns in populations. These transmission patterns during India’s SARS-CoV-2 viral waves remain largely undocumented. Methods: We analysed 2.7 million real-time polymerase chain reaction (PCR) testing records collected in Mumbai, a bellwether for other Indian cities. We used the inverse of cycle threshold (Ct) values to determine community-level viral load. We quantified wave-specific differences by age, sex and slum population density. Results: Overall PCR positivity was 3.4% during non-outbreak periods, rising to 23.2% and 42.8% during the Aleph (June-November 2020) and Omicron waves (January 2022), respectively, but only 9.9% during the Delta wave (March-June 2021). The community-level median Ct values fell and rose ~7-14 days prior to PCR positivity rates. Viral loads were 4-fold higher during the Delta and Omicron waves than during non-outbreak months. The Delta wave had high viral loads at older ages, in women and in areas of higher slum density. During the Omicron wave, differences in viral load by sex and for slum density had disappeared, but older adults continued to show higher viral load. Conclusions: Mumbai’s viral waves had markedly high viral loads representing an early signal of pandemic trajectory. Continue the vaccination in elderly Indians could reduce viral load in subsequent waves. Ct values are practicable monitoring tools.
ARTICLE | doi:10.20944/preprints202209.0390.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; asymptomatic; seroprevalence; Delta variant; Omicron variant; vaccination
Online: 26 September 2022 (09:41:01 CEST)
A significant proportion of SARS-CoV-2 infections in Africa are identified as asymptomatic, facilitating the silent spread of the virus especially in populated urban cities. With the surge of the highly transmissible Omicron variant, the inclusion of asymptomatics in epidemiological surveys is key in estimating true infections and seroprevalence in the population. The aim of the study was to determine seroprevalence, active infection and circulating variants in Accra, the capital city of Ghana during the Omicron wave. The study was a cross-sectional survey conducted in 22 municipalities in December 2021. Naso-oropharyngeal swabs and serum samples were collected from 1027 individuals aged 5 years and above, for detection of infection by RT-qPCR and estimation of total antibodies using the WANTAI ELISA kit. Our results show 10% SARS-CoV-2 prevalence, with the Omicron and Delta variants accounting for 44.1% and 8.8% of infections, respectively. Omicron was most prevalent (48.9.%) among the 20–39-year-olds. Asymptomatic individuals accounted for 75.2% of infections. Seropositivity within the population was 86.8%, with the 60+ year group having significantly higher likelihood of exposure (OR 10.22: 95% CI: 3.51-29.73; p<0.001). This high seroprevalence appears to have been as a result of increased vaccination among this group (OR 2.7: 95% CI 1.78-4.09, p < 0.001). The high seropositivity of SARS-CoV-2 in the capital could be a good indication of herd immunity among the population and while the low infection rate supports the role of vaccination in reducing viral transmission.
ARTICLE | doi:10.20944/preprints202206.0255.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: coronaviruses; SARS-CoV-2; variant; Omicron; SLiMs; spike protein; motifs; covid-19
Online: 17 June 2022 (13:49:02 CEST)
Short Linear Motifs (SLiMs) are short linear sequences that can mediate protein-protein interaction. Mimicking eukaryotic SLiMs to compete with extra or intracellular binding partners or to sequester host proteins is the crucial strategy of viruses to pervert the host system. The evolved proteins in viruses facilitate minimal protein-protein interactions that significantly affect intracellular signaling networks. Unfortunately, very little information about the SARS-CoV-2 SLiMs is known, especially across the SARS-CoV-2 variants. Through ELM database-based sequence analysis of spike protein from all the major SARS-CoV-2 variants, we identified four overriding SLiMs in the SARS-CoV-2 Omicron variant including LIG_TRFH_1, LIG_REV1ctd_RIR_1, LIG_CaM_NSCaTE_8, and MOD_LATS_1. These SLiMs are highly likely to interfere with various immune functions, interact with host intracellular proteins, regulate cellular pathways, and lubricate viral infection and transmission. These cellular interactions possibly serve as potential therapeutic targets for these variants, and this approach can be further exploited to combat emerging SARS-CoV-2 variants.
ARTICLE | doi:10.20944/preprints202204.0120.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Viruses; Omicron BA.1; BA.2; Delta
Online: 13 April 2022 (08:31:45 CEST)
BA.2, a sublineage of Omicron BA.1, is now prominent in many parts of the world. Early reports indicate that BA.2 is more infectious than BA.1. To gain insight into BA.2 mutation profile and the resulting impact of mutations on interaction with receptor and/or monoclonal antibodies, we analyzed available se-quences, structures of Spike/receptor, and Spike/antibody complexes, and conducted molecular dynamics simulations. The results showed that BA.2 has 50 high-prevalent mutations compared to 48 in BA.1. Seventeen BA.1 mutations are not present in BA.2. Instead, BA.2 has 19 unique mutations and a signature Delta variant mutation (G142D). Intriguingly, the BA.2 has 28 signature mutations in Spike, compared to 30 in BA.1. This is due to two revertant mutations S446G and S496G in the receptor-binding domain (RBD), making BA.2 somewhat similar to Wuhan-Hu-1 (WT), which has G446 and G496. The molecular dynamics simulations showed that the RBD consisting of G446/G496 is more stable than S446/S496 containing RBD. Thus, our analyses suggest that BA.2 has evolved with novel mutations (i) to maintain receptor binding similar to WT, (ii) evade the antibody binding greater than BA.1, and (iii) acquire mutation of the Delta variant that may be associated with the high infectivity.
ARTICLE | doi:10.20944/preprints202210.0404.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2 Omicron; tMRCA; evolutionary rate; mutational profiling; selection pressure
Online: 26 October 2022 (08:15:25 CEST)
The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence of a highly divergent variant of concern (VOC) defined as Omicron or B.1.1.529. This VOC is of particular concern because it has the potential to evade most therapeutic antibodies and has undergone a sustained genetic evolution, resulting in the emergence of five distinct sub-lineages. However, the evolutionary dynamics of initially identified Omicron BA.1 and BA.2 sub-lineages remain poorly understood. Herein, we combined Bayesian phylogenetic analysis, mutational profiling, and selection pressure analysis to track virus genetic changes that drive the early evolutionary dynamics of the Omicron. Based on the Omicron dataset chosen for the improved temporal signals and sampled globally between November 2021 and January 2022, most recent common ancestor (tMRCA) and substitution rates for BA.1 were estimated to be 18 September 2021 (95% highest posterior density (HPD) 04 August – 22 October 2021) and 1.435×10-3 (95% HPD = 1.021×10-3 – 1.869×10-3) substitution/site/year, respectively, whereas 03 November 2021 (95% highest posterior density (HPD) 26 September – 28 November 2021) and 1.074×10-3 (95% HPD = 6.444×10-4 – 1.586×10-3) substitution/site/year for BA.2 sub-lineage. The findings of this study suggest that the Omicron BA.1 and BA.2 sub-lineages originated independently and evolved over time. Furthermore, we identified multiple sites in spike protein undergoing continued diversifying selection that may alter the neutralization profile of BA.1. This study shed light on the ongoing global genomic surveillance and Bayesian molecular dating analyses to better understand the evolutionary dynamics the virus and, as a result, mitigate the impact of emerging variants on public health.
REVIEW | doi:10.20944/preprints202206.0022.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Omicron; bioinformatics; immune escape; RBD mutations; vaccine development
Online: 1 June 2022 (14:12:36 CEST)
The evolution and the emergence of new mutations of viruses affect their transmissibility and/or pathogenicity features, depending on different evolutionary scenarios of virus adaptation to the host. A typical trade-off scenario of SARS-CoV-2 evolution has been proposed, which leads to the appearance of an Omicron strain with lowered lethality, yet enhanced transmissibility. This direction of evolution might be partly explained by virus adaptation to therapeutic agents and enhanced escape from vaccine-induced and natural immunity formed by other SARS-CoV-2 strains. Omicron’s high mutation rate in the Spike protein, as well as its previously described high genome mutation rate (Kandeel et al., 2021), revealed a gap between it and other SARS-CoV-2 strains, indicating the absence of a transitional evolutionary form to the Omicron strain. Therefore, Omicron has emerged as a new serotype and divergent from the evolutionary lineage of other SARS-CoV-2 strains. Omicron is a rapidly evolving variant of high concern, whose new subvariants continue to manifest. Its further understanding and the further monitoring of key mutations that provide virus immune escape and/or high affinity towards the receptor could be useful for vaccine and therapeutic development in order to control the evolutionary direction of the COVID-19 pandemic.
REVIEW | doi:10.20944/preprints202303.0097.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Bivalent COVID-19 vaccine; COVID-19 vaccination booster; COVID-19; Omicron; SARS-CoV-2
Online: 6 March 2023 (07:00:00 CET)
The severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) Omicron variant of concern has been the dominant cause of worldwide COVID-19 cases since 2022. All the Omicron sublineage viruses have demonstrated high transmissibility and an ability to escape vaccine-induced immunity. While first-generation vaccines, including monovalent vaccines, continue to provide protection against severe disease, hospitalization and mortality, their efficacy against Omicron sub variants remains sparse. These vaccines have also been associated with rapidly waning protection against primary COVID-19 and COVID-19 reinfections conferred by evolving Omicron sublineages.. This led to the development and deployment of updated vaccines and the introduction of the bivalent booster. Through this review, we highlight the brief journey of the variants of concern leading to the dominance of Omicron and the effectiveness of the key vaccines against these variants, including the updated (bivalent) boosters.
REVIEW | doi:10.20944/preprints202207.0250.v1
Subject: Biology And Life Sciences, Virology Keywords: Emergence of Omicron and its mechanism; mutation and sub-lineages; Monoclonal antibodies; Antiviral drugs
Online: 18 July 2022 (07:48:00 CEST)
With the ongoing COVID pandemic, the emergence of a novel omicron variant in November 2021 has chaos the world. Despite mass vaccination, this omicron has spread rapidly raising concerns around the globe. The Omicron variant has a vast array of mutations as compared to another variant of concern with overall 50 mutations where 30 mutations are present in its spike protein. This mutation has led to immune escape and more transmissibility compared to other variants, including Delta. A cluster of mutations (H655Y, N679K, and P681H) present at the omicron spike protein could aid in transmission. Currently, no virus-specific data are available to predict the efficacy of anti-viral and mAbs drugs. However, two monoclonal antibody drugs: Sotrovimab and Evusheld are authorized for emergency use in COVID patients. This virus is not fading away soon. The easiest solution and less expensive measure to fight against this pandemic are following COVID appropriate protocols.There is need to strengthen the level of research for development of potential vaccines and anti-viral drugs. It is also important to monitor and expand genomic surveillance to keep track of the emergence of new variants thus avoiding the spread of new diseases worldwide. This article highlights the emergence of omicron and vast number of mutation in its protein. In addition, recent advancement in drugs approved by FDA to treat COVID patients has been listed and focused in this paper.
ARTICLE | doi:10.20944/preprints202205.0381.v1
Subject: Biology And Life Sciences, Virology Keywords: Sars-Cov-2; mAbs; Paxlovid; Remdesivir; Molnupiravir; Microneutralization assay; Cell-based assay; Omicron sublineages
Online: 27 May 2022 (10:45:19 CEST)
Newly emerging SARS-CoV-2 variants may escape monoclonal antibodies (mAbs) and antiviral drugs. By using live virus assays, we assessed the ex vivo inhibition of the B.1 wild type (WT), delta and omicron BA.1 and BA.2 lineages by post-infusion sera from 40 individuals treated with bamlanivimab/etesevimab (BAM/ETE), casirivimab/imdevimab (CAS/IMD) and sotrovimab (SOT) as well as the activity of remdesivir, nirmatrelvir and molnupiravir. mAbs and drug activity were defined as the serum dilution (ID50) and drug concentration (IC50), respectively, showing 50% protection of virus-induced cytopathic effect. All pre-infusion sera were negative for SARS-CoV-2 neutralizing activity. BAM/ETE, CAS/IMD and SOT showed activity against the WT (ID50 6,295 [4,355-8,075] for BAM/ETE; 18,214 [16,248-21,365] for CAS/IMD and 456 [265-592] for SOT) and the delta (14,780 [ID50 10,905-21,020] for BAM/ETE, 63,937 [47,211-79,971] for CAS/IMD and 1,103 [843-1,334] for SOT). Notably, only SOT was active against BA.1 (ID50 200 [37-233]) while BA.2 was neutralized by CAS/IMD (ID50 174 [134-209] ID50) and SOT (ID50 20 [9-31] ID50) but not by BAM/ETE. No significant inter-variant IC50 differences were observed for molnupiravir (1.5±0.1/1.5±0.7/1.0±0.5/0.8±0.01 μM for WT/delta/BA.1/BA.2, respectively); nirmatrelvir (0.05±0.02/0.06±0.01/0.04±0.02/0.04±0.01 μM) and remdesivir (0.08±0.04/0.11±0.08/0.05±0.04/0.08±0.01 μM). Continued evolution of SARS-CoV-2 requires updating the mAbs arsenal, however antivirals have so far remained unaffected.
REVIEW | doi:10.20944/preprints202207.0100.v1
Subject: Biology And Life Sciences, Virology Keywords: omicron; alpha; delta; deltacron; recombination; RNA editing; intra-host variants; tropisms; ox-idative damage; Wuhan
Online: 6 July 2022 (15:27:32 CEST)
The successive waves of the Covid-19 pandemic are driven by SARS-CoV-2 variants that reached critical detection levels in different parts of the world. But how evolved the Wuhan virus since its detection in December 2019 into the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529) variants of concern? This is a story of mice and men, of up to 1,000,000 infected cells in one person, where each cell produces between 105 and 106 viral RNAs, of immune-compromised patients, the digestive tract and viral recombination.
REVIEW | doi:10.20944/preprints202203.0376.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2; Mutations; Omicron; Delta; Variants of Concern; Variants of Interest; Immunity Escape; Mechanisms
Online: 29 March 2022 (08:44:09 CEST)
With the emergence of COVID-19 pandemic in 2019, the world saw a humungous loss of human life and economic resources globally but also the rapid appearance of SARS-CoV-2 variants which have exhibited a higher transmissibility and/or virulence and which also evade immune system to such an extent that it raises a big question mark on the efficacy of current diagnostics, vaccines and convalescent plasma and mAb therapies. This has been attributed to the emergence of huge spectrum of mutations, especially in the virus’s spike (S) protein, occurring in regions harboring high concentration of B cell epitopes thus allowing neutralizing antibody escape. The mutations resulting in ACE 2 receptor recognition failure (T19R), unfavorable electrostatic interactions (E484K), structural change (∆69-70), disruption of hydrogen bonds, salt bridges or hydrophobic interactions (K417N, N501Y, ∆Y145) and change in orientation (N501Y) cause strong immune evasion by these variants. Further, the recent emergence of Omicron with more than 30 mutations in the S protein VOC allows it to escape and fail diagnosis as well as immune system and the protection generated by different vaccination regimes. Yet Omicron may not be the end of the story. This review presents an insight of the immunity escape and its mechanisms followed by different SARS-CoV-2 variant of concerns.
REVIEW | doi:10.20944/preprints202202.0224.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; pandemic; SARS-CoV-2; Omicron variant; emerging disease; global health; virus; genome; mutation
Online: 18 February 2022 (05:23:18 CET)
The 2019 Coronavirus Disease (COVID-19) is a major cause of morbidity and mortality worldwide. Since late November 2021, Omicron variant has emerged as the primary cause of COVID-19 and caused a huge increase in the reported incidence around the world. To date, 32-34 spike mutations have been reported, 15 of which were located in the receptor-binding domain that interacts with the cell surface of the host cells, while the rest were located in the N-terminal domain and around the Furin cleavage site. At present, both the genomic and clinical profiles of this novel variant are being investigated. Here, we aim to discuss the recent reports on the transmissibility and severity of Omicron variant from both the genetic and clinical perspectives. Afterward, we also take the chance to deliver our personal view on the topic.
REVIEW | doi:10.20944/preprints202209.0429.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: COVID-19; Sars-CoV-2; Natural immunity; Cellular immunity; Vaccine-induced immunity; Hybrid immunity; Cross-reactivity; Omicron
Online: 28 September 2022 (03:38:36 CEST)
Background: Both natural immunity and vaccine-induced immunity to COVID-19 may be useful to reduce the mortality/morbidity of this disease, but still a lot of controversy exists. Aims: This narrative review analyzes the literature about: a) the duration of natural immunity; b) cellular immunity; c) cross-reactivity; d) the duration of post-vaccination immune protection; e) the probability of reinfection and its clinical manifestations in the recovered patients; f) comparisons between vaccinated and unvaccinated in the possible reinfections; g) the role of hybrid immunity; h) the effectiveness of natural and vaccine-induced immunity against Omicron variant; i) comparative incidence of adverse effects after vaccination in recovered individuals vs. COVID-19-naïve subjects. Material and Methods: through multiple search engines we investigated COVID-19 literature related to the aims of the review, published since April 2020 through July 2022, including also the previous articles pertinent to the investigated topics. Results: nearly 900 studies were collected and 238 pertinent articles were included. It was highlighted that the vast majority of individuals after COVID-19 develop a natural immunity both of cell-mediated and humoral type, which is effective over time and provides protection against both reinfection and serious illness. Vaccine-induced immunity was shown to decay faster than natural immunity. In general, the severity of the symptoms of reinfection is significantly lower than in the primary infection, with a lower degree of hospitalizations (0.06%) and an extremely low mortality. Conclusions: this narrative review regarding a vast number of articles highlighted the valuable protection induced by the natural immunity after COVID-19, which seems comparable or superior to the one induced by anti-SARS-CoV-2 vaccination. Vaccination of the unvaccinated COVID-19-recovered subjects may not be indicated. Further research is needed in order to: a) measure the durability of immunity over time; b) evaluate both the impacts of Omicron-5 on vaccinated and healed subjects and of hybrid immunity.
DATA DESCRIPTOR | doi:10.20944/preprints202206.0146.v2
Subject: Computer Science And Mathematics, Information Systems Keywords: COVID-19; COVID; Omicron; online learning; remote learning; online education; Twitter; dataset; Tweets; social media; Big Data
Online: 21 July 2022 (08:05:19 CEST)
ARTICLE | doi:10.20944/preprints202207.0286.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2; Omicron variant of concern; homologous boosting; heterologous boosting; Coro-naVac; BNT162b2; healthcare worker; return-to-work
Online: 19 July 2022 (10:15:39 CEST)
Immune escape is observed with SARS-CoV-2 Omicron (Pango lineage B.1.1.529), the predominant circulating strain worldwide. Booster dose was shown to restore immunity against Omicron infection, however, real world data comparing mRNA (BNT162b2; Comirnaty) and inactivated vaccine (CoronaVac; Sinovac) homologous and heterologous boosting is lacking. A retrospective study was performed to compare the rate and outcome of COVID-19 in healthcare workers (HCWs) with various vaccination regime during a territory-wide Omicron outbreak in Hong Kong. During the study period 1 Feb – 31 Mar 2022, 3167 HCWs were recruited, 871 HCWs reported 746 and 183 episodes of significant household and non-household close contact. 737 HCWs acquired COVID-19 which were all clinically mild. Time dependent Cox regression showed that, comparing with 2-dose vaccination, 3-dose vaccination reduced infection risk by 31.7% and 89.3% in household contact and non-household close contact respectively. Using 2-dose BNT162b2 as reference, 2-dose CoronaVac recipient had significantly higher risk of being infected (HR 1.69 P<0.0001). Three-dose BNT162b2 (HR 0.4778 P<0.0001) and 2-dose CoronaVac + BNT162b2 booster (HR 0.4862 P=0.0157) were associated with lower risk of infection. Three-dose CoronaVac and 2-dose BNT162b2 + CoronaVac booster were not significantly different from 2-dose BNT162b2. The mean time to achieve negative RT-PCR or E gene cycle threshold 31 or above was not affected by age, number of vaccine dose taken, vaccine type and timing of the last dose. In summary, we have demonstrated lower risk of breakthrough SARS-CoV-2 infection in HCWs given BNT162b2 as booster after 2 doses of BNT162b2 or CoronaVac.
ARTICLE | doi:10.20944/preprints202205.0238.v2
Subject: Computer Science And Mathematics, Information Systems Keywords: COVID-19; SARS-CoV-2; Omicron; Twitter; tweets; sentiment analysis; big data; Natural Language Processing; Data Science; Data Analysis
Online: 7 July 2022 (08:36:40 CEST)
This paper presents the findings of an exploratory study on the continuously generating Big Data on Twitter related to the sharing of information, news, views, opinions, ideas, knowledge, feedback, and experiences about the COVID-19 pandemic, with a specific focus on the Omicron variant, which is the globally dominant variant of SARS-CoV-2 at this time. A total of 12028 tweets about the Omicron variant were studied, and the specific characteristics of tweets that were analyzed include - sentiment, language, source, type, and embedded URLs. The findings of this study are manifold. First, from sentiment analysis, it was observed that 50.5% of tweets had the ‘neutral’ emotion. The other emotions - ‘bad’, ‘good’, ‘terrible’, and ‘great’ were found in 15.6%, 14.0%, 12.5%, and 7.5% of the tweets, respectively. Second, the findings of language interpretation showed that 65.9% of the tweets were posted in English. It was followed by Spanish or Castillian, French, Italian, Japanese, and other languages, which were found in 10.5%, 5.1%, 3.3%, 2.5%, and <2% of the tweets, respectively. Third, the findings from source tracking showed that “Twitter for Android” was associated with 35.2% of tweets. It was followed by “Twitter Web App”, “Twitter for iPhone”, “Twitter for iPad”, “TweetDeck”, and all other sources that accounted for 29.2%, 25.8%, 3.8%, 1.6%, and <1% of the tweets, respectively. Fourth, studying the type of tweets revealed that retweets accounted for 60.8% of the tweets, it was followed by original tweets and replies that accounted for 19.8% and 19.4% of the tweets, respectively. Fifth, in terms of embedded URL analysis, the most common domains embedded in the tweets were found to be twitter.com, which was followed by biorxiv.org, nature.com, wapo.st, nzherald.co.nz, recvprofits.com, science.org, and other URLs. Finally, to support similar research and development in this field centered around the analysis of tweets, we have developed an open-access Twitter dataset that comprises tweets about the SARS-CoV-2 omicron variant since the first detected case of this variant on November 24, 2021.
ARTICLE | doi:10.20944/preprints202206.0192.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: eCDC; WHO; Sanger sequencing; Omicron variant; minor subvariants; BA.4/BA.5; BA.2; mul-ti-allelic; SNPs; recombinant
Online: 14 June 2022 (04:30:41 CEST)
Large population passages of the SARS-CoV-2 in the past two and a half years have allowed the circulating virus to accumulate an increasing number of mutations in its genome. The most recently emerging Omicron subvariants have the highest number of mutations in the Spike (S) protein gene and these mutations mainly occur in the receptor-binding domain (RBD) and the N-terminal domain (NTD) of the S gene. The eCDC and the WHO recommend partial Sanger sequencing of the SARS-CoV-2 S gene RBD and NTD on the PCR-positive samples in diagnostic laboratories as a practical means of determining the variants of concern to monitor a possible increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them. The author’s diagnostic laboratory has implemented the eCDC/WHO recommendation by sequencing a 398-base segment of the N gene for the definitive detection of SARS-CoV-2 in clinical samples, and sequencing a 445-base segment of the RBD and a 490-509-base segment of the NTD for variant determination. This paper presents 5 selective cases to illustrate the challenges of using Sanger sequencing to diagnose Omicron subvariant when the samples harbor a high level of co-existing minor subvariant sequences with multi-allelic single nucleotide polymorphisms (SNPs) or possible recombinant Omicron subvariants containing a BA.1 NTD and a BA.2 RBD, which can only be detected by using specially designed PCR primers. The current large-scale surveillance programs using next-generation sequencing (NGS) do not face similar problems because NGS focuses on deriving consensus sequence.
ARTICLE | doi:10.20944/preprints202204.0091.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; SARS-CoV; RT-PCR; Sanger sequencing; RT-qPCR; receptor-binding domain (RBD); N-terminal domain (NTD); Omicron; multi-allelic SNPs; false-positive
Online: 12 April 2022 (03:57:29 CEST)
Both SARS-CoV-2 and SARS-CoV initially appeared in China and spread to other parts of the world. SARS-CoV-2 has generated a COVID-19 pandemic causing more than 6 million human deaths worldwide while the SARS outbreak quickly ended in six months with a global total of 774 reported deaths. One of the factors contributing to this stunning difference in the outcome between these two outbreaks is the inaccuracy of the RT-qPCR tests for SARS-CoV-2, which generated a large number of false-negative and false-positive test results that have misled patient management and public health policy-makers. This article presented Sanger sequencing evidence to show that the RT-PCR diagnostic protocol established in 2003 for SARS-CoV can in fact detect SARS-CoV-2 accurately due to the well-known nonspecific PCR amplification of DNAs with similar sequences. Using nested RT-PCR followed by Sanger sequencing to retest 50 patient samples collected in January, 2022 and sold as RT-qPCR positive reference confirmed 21 (42%) were false-positive. Although the other 29 positive isolates were categorized as Omicron variant by partial sequencing of the N gene, and the RBD and the NTD of the S gene, 9 (31%) showed focal to complete sequencing failure in the S gene segments due to multi-allelic SNPs. During the course of the study, an Omicron variant isolate containing a BA.1 NTD and a BA.2 RBD in its S gene was also detected. Routine partial S gene sequencing of all PCR-positive samples can timely discover multi-allelic SNPs and viral recombination in the circulating variants for investigation of their impacts on vaccine efficacies, therapeutics and diagnostics.