Population Genomics Insights into the First Wave of COVID-19

Vasilarou, Maria; Alachiotis, Nikolaos; Garefalaki, Joanna; Beloukas, Apostolos; Pavlidis, Pavlos

doi:10.3390/life11020129

Cited by 17 publications

(18 citation statements)

References 68 publications

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“…But SARS-CoV-2, like related coronaviruses, encodes a proofreading domain (ExoN) that reduces its mutation rate relative to RNA viruses that do not (such as influenza, HIV, and hepatitis C viruses). The pace of change of the SARS-CoV-2 genome has thus been estimated at 1.87 3 10 À6 nucleotide substitutions per site per day 7 , roughly 5-fold lower than influenza A/H3N2 (10.9 3 10 À6 nucleotide substitutions per site per day; https://nextstrain. org 8 ; accessed 22 May 2021).…”

Section: Introductionmentioning

confidence: 99%

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

et al. 2021

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One year into the global COVID-19 pandemic, the focus of attention has shifted to the emergence and spread of SARS-CoV-2 variants of concern (VOCs). After nearly a year of the pandemic with little evolutionary change affecting human health, several variants have now been shown to have substantial detrimental effects on transmission and severity of the virus. Public health officials, medical practitioners, scientists, and the broader community have since been scrambling to understand what these variants mean for diagnosis, treatment, and the control of the pandemic through nonpharmaceutical interventions and vaccines. Here we explore the evolutionary processes that are involved in the emergence of new variants, what we can expect in terms of the future emergence of VOCs, and what we can do to minimise their impact.

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Section: Introductionmentioning

confidence: 99%

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

et al. 2021

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“… 2021 ; Vasilarou et al . 2021 ). A role for NSP14, the proofreading exoribonuclease of this virus that accounts for its unusually high replication fidelity, has been proposed in these postulated recombination events (Gribble et al .…”

Section: Introductionmentioning

confidence: 99%

The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2

Wassenaar

Wanchai

Buzard³

et al. 2022

FEMS Microbiology Reviews

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The genomic diversity of SARS-CoV-2 is the result of a relatively low level of spontaneous mutations introduced during viral replication. With millions of SARS-CoV-2 genome sequences now available, we can begin to assess the overall genetic repertoire of this virus. We find that during 2020 there was a global wave of one variant that went largely unnoticed, possibly because its members were divided over several sub-lineages (B.1.177 and sub-lineages B.1.177.XX). We collectively call this Janus, and it was eventually replaced by the Alpha (B.1.1.7) Variant of Concern (VoC), next replaced by Delta (B.1.617.2), which itself might soon be replaced by a fourth pandemic wave consisting of Omicron (B.1.1.529). We observe that splitting up and redefining variant lineages over time, as was the case with Janus and is now happening with Alpha, Delta, and Omicron, is not helpful to describe the epidemic waves spreading globally. Only about five percent of the 30,000 nucleotides of the SARS-CoV-2 genome are found to be variable. We conclude that a fourth wave of the pandemic with the Omicron variant might not be that different from other VoCs, and that we may already have the tools in hand to effectively deal with this new VoC.

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“…Different researchers prove that the Sars-Cov-2 genome is the result of the recombination between two beta-coronavirus genomes: Pangolin and Bat coronavirus [ 7 , 8 , 29 , 30 ]. Various in silico studies search for the effect of the vaccination, especially with pneumococcal vaccines, to protect against symptomatic cases of SARS-CoV-2 infection and death [ 31 – 36 ].…”

Section: Discussionmentioning

confidence: 99%

Intelligent system based comparative analysis study of SARS-CoV-2 spike protein and antigenic proteins in different types of vaccines

Touati

Elngar

2022

Beni-Suef Univ J Basic Appl Sci

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Background Coronaviruses, members of the Coronavirinae subfamily in the Coronaviridae family, are enveloped and positive-stranded RNA viruses that infect animals and humans, causing intestinal and respiratory infections. Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus, named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This disease appeared, for the first time (December 2019), in China and has spread quickly worldwide causing a large number of deaths. Considering the global threat, the World Health Organization (WHO) has declared, in March 2020, COVID-19 as a pandemic. Many studies suggest the great effect of the existing vaccines to protect against symptomatic cases of death by the COVID-19 virus. This paper, proposes to compare the main antigenic proteins sequences of the existing vaccines with Spike (S) protein of the SARS-CoV-2 genome. Our choice of S protein is justified by the major role that plays it in the receptor recognition and membrane fusion process based on an intelligent system. Herein, we focus on finding a correlation between S protein and compulsory vaccines in the countries that have a less death number by COVID-19 virus. In this work, we have used a combination of coding methods, signal processing, and bioinformatic techniques with the goal to localize the similar patterns between the S gene of the SARS-Cov-2 genome and 14 investigated vaccines. Results A total of 8 similar sequences which have a size more than 6 amino acids were identified. Further, these comparisons propose that these segments can be implicated in the immune response against COVID-19, which may explain the wide variation by country in the severity of this viral threat. Conclusions Our in silico study suggests a possible protective effect of Poliovirus, HIB, Hepatitis B, PCV10, Measles, Mumps, and Rubella (MMR) vaccines against COVID-19.

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Population Genomics Insights into the First Wave of COVID-19

Cited by 17 publications

References 68 publications

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2

Intelligent system based comparative analysis study of SARS-CoV-2 spike protein and antigenic proteins in different types of vaccines

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