Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions

PeerJ
C. FarkasM. I. Barria

Abstract

Here we aim to describe early mutational events across samples from publicly available SARS-CoV-2 sequences from the sequence read archive and GenBank repositories. Up until 27 March 2020, we downloaded 50 illumina datasets, mostly from China, USA (WA State) and Australia (VIC). A total of 30 datasets (60%) contain at least a single founder mutation and most of the variants are missense (over 63%). Five-point mutations with clonal (founder) effect were found in USA next-generation sequencing samples. Sequencing samples from North America in GenBank (22 April 2020) present this signature with up to 39% allele frequencies among samples (n = 1,359). Australian variant signatures were more diverse than USA samples, but still, clonal events were found in these samples. Mutations in the helicase, encoded by the ORF1ab gene in SARS-CoV-2 were predominant, among others, suggesting that these regions are actively evolving. Finally, we firmly urge that primer sets for diagnosis be carefully designed, since rapidly occurring variants would affect the performance of the reverse transcribed quantitative PCR (RT-qPCR) based viral testing.

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Citations

Aug 23, 2020·Pathogens·Sameer MohammadShuja Shafi Malik
Oct 30, 2020·Infection and Drug Resistance·Raphael B Stricker, Melissa C Fesler
Dec 3, 2020·Canadian Journal of Microbiology·Raquel L RussellBrian L Mark
Feb 20, 2021·Genome Research·Nicolae SapovalTodd J Treangen
Sep 10, 2021·Laboratory Investigation; a Journal of Technical Methods and Pathology·Yuan ZhouJian Wu

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Datasets Mentioned

BETA
PRJNA607948
PRJNA610428
PRJNA612578
PRJNA231221
SRR11397716
SRR11397721
SRR11397719

Methods Mentioned

BETA
amplicon sequencing
PCR

Software Mentioned

bcftools mpileup
bowtie2 aligner
Minimap2
Strelka2
htslib
blast
illumina
Fasttree
samtools
Interactive Tree of Life server ( iTOL )

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