SARS-CoV-2 worldwide replication drives rapid rise and selection of mutations across the viral genome: a time-course study - potential challenge for vaccines and therapies.

Stefanie Weber,Christina M Ramirez,Barbara Weiser,Walter Doerfler,Harold Burger

doi:10.15252/emmm.202114062

Abstract

Scientists and the public were alarmed at the first large viral variant of SARS‐CoV‐2 reported in December 2020. We have followed the time course of emerging viral mutants and variants during the SARS‐CoV‐2 pandemic in ten countries on four continents. We examined > 383,500 complete SARS‐CoV‐2 nucleotide sequences in GISAID (Global Initiative of Sharing All Influenza Data) with sampling dates extending until April 05, 2021. These sequences originated from ten different countries: United Kingdom, South Africa, Brazil, United States, India, Russia, France, Spain, Germany, and China. Among the 77 to 100 novel mutations, some previously reported mutations waned and some of them increased in prevalence over time. VUI2012/01 (B.1.1.7) and 501Y.V2 (B.1.351), the so‐called UK and South Africa variants, respectively, and two variants from Brazil, 484K.V2, now called P.1 and P.2, increased in prevalence. Despite lockdowns, worldwide active replication in genetically and socio‐economically diverse populations facilitated selection of new mutations. The data on mutant and variant SARS‐CoV‐2 strains provided here comprise a global resource for easy access to the myriad mutations and variants detected to date globally. Rapidly evolving new variant and mutant strains might give rise to escape variants, capable of limiting the efficacy of vaccines, therapies, and diagnostic tests.

Highlights

Between December 2019 and January 28, 2021, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic has expanded world-wide to 219 countries and territories; about 101.9 million people have been infected, and about 2.2 million (2.16 %) have lost their lives according to Johns Hopkins[3].In our laboratory, we have set out to follow the rapid rise of new mutations in the SARS-CoV-2 genome as Covid-19 cases soared worldwide
We examined mutations from the US, India, Brazil, Russia, the UK, France, Spain, Germany, South Africa and China that were deposited in the GISAID (Global Initiative of Sharing All Influenza Data) database[4]
Nucleotide sequences from the UK, South Africa, Brazil, the US, India, Russia, France, Spain, Germany and China were compared to the reference genome of the SARSCoV-2 isolate from Wuhan-Hu-1, NCBI Reference Sequence: NC_045512.2

Summary

Introduction

Between December 2019 and January 28, 2021, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic has expanded world-wide to 219 countries and territories; about 101.9 million people have been infected, and about 2.2 million (2.16 %) have lost their lives according to Johns Hopkins[3].In our laboratory, we have set out to follow the rapid rise of new mutations in the SARS-CoV-2 genome as Covid-19 cases soared worldwide. We analyzed SARS-CoV-2 sequences that had been deposited in data bases between January and May/June of 2020. At least 10 prevalent sites of sequence mutations were observed and up to 80% of nucleotides at the mutated site were changed[1] Several of these mutations led to non-synonymous amino acid changes in different open reading frames across the viral genome. These alterations in functional viral proteins were selected during active worldwide replication of SARS-CoV-2. We examined mutations from the US, India, Brazil, Russia, the UK, France, Spain, Germany, South Africa and China that were deposited in the GISAID (Global Initiative of Sharing All Influenza Data) database[4]

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Results

Conclusion