tetano
Editor, Senior Moderator
PeerJ
. 2020 May 21;8:e9255.
doi: 10.7717/peerj.9255. eCollection 2020.
Insights on Early Mutational Events in SARS-CoV-2 Virus Reveal Founder Effects Across Geographical Regions
Carlos Farkas[SUP] 1 2 [/SUP], Francisco Fuentes-Villalobos[SUP] 3 [/SUP], Jose Luis Garrido[SUP] 4 [/SUP], Jody Haigh[SUP] 1 2 [/SUP], Mar?a In?s Barr?a[SUP] 3 [/SUP]
Affiliations
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.
Keywords: COVID-19; Coronavirus; Founder effect; Mutations; RT-qPCR; SARS-CoV-2; SNVs; Viral genetic drift.
. 2020 May 21;8:e9255.
doi: 10.7717/peerj.9255. eCollection 2020.
Insights on Early Mutational Events in SARS-CoV-2 Virus Reveal Founder Effects Across Geographical Regions
Carlos Farkas[SUP] 1 2 [/SUP], Francisco Fuentes-Villalobos[SUP] 3 [/SUP], Jose Luis Garrido[SUP] 4 [/SUP], Jody Haigh[SUP] 1 2 [/SUP], Mar?a In?s Barr?a[SUP] 3 [/SUP]
Affiliations
- PMID: 32509472
- PMCID: PMC7246029
- DOI: 10.7717/peerj.9255
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.
Keywords: COVID-19; Coronavirus; Founder effect; Mutations; RT-qPCR; SARS-CoV-2; SNVs; Viral genetic drift.