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

PeerJ

article

Carlos Farkas¹  Francisco Fuentes-Villalobos³  Jose Luis Garrido⁴  Jody Haigh¹  María Inés Barría³ 

[1] Oncology and Hematology;Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba;Faculty of Biological Sciences, Department of Microbiology, Center of Biotechnology, Universidad de Concepción, Universidad de Concepción;Ichor Biologics LLC

关键词: SARS-CoV-2;    Founder effect;    Mutations;    RT-qPCR;    Coronavirus;    COVID-19;    SNVs;    Viral genetic drift;   

DOI  :  10.7717/peerj.9255

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY