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

Farkas, Carlos; Fuentes-Villalobos, Francisco; Garrido, Jose Luis; Haigh, Jody; Ines Barria, Maria

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 ORF lab 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.

Más información

Título según WOS: ID WOS:000534427100010 Not found in local WOS DB
Título de la Revista: PEERJ
Volumen: 8
Editorial: PEERJ INC
Fecha de publicación: 2020
DOI:

10.7717/peerj.9255

Notas: ISI