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

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 datase...

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Autores principales: Farkas, Carlos, Fuentes-Villalobos, Francisco, Garrido, Jose Luis, Haigh, Jody, Barría, María Inés
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246029/
https://www.ncbi.nlm.nih.gov/pubmed/32509472
http://dx.doi.org/10.7717/peerj.9255
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author Farkas, Carlos
Fuentes-Villalobos, Francisco
Garrido, Jose Luis
Haigh, Jody
Barría, María Inés
author_facet Farkas, Carlos
Fuentes-Villalobos, Francisco
Garrido, Jose Luis
Haigh, Jody
Barría, María Inés
author_sort Farkas, Carlos
collection PubMed
description 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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spelling pubmed-72460292020-06-04 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 Barría, María Inés PeerJ Bioinformatics 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. PeerJ Inc. 2020-05-21 /pmc/articles/PMC7246029/ /pubmed/32509472 http://dx.doi.org/10.7717/peerj.9255 Text en © 2020 Farkas et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Farkas, Carlos
Fuentes-Villalobos, Francisco
Garrido, Jose Luis
Haigh, Jody
Barría, María Inés
Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions
title Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions
title_full Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions
title_fullStr Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions
title_full_unstemmed Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions
title_short Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions
title_sort insights on early mutational events in sars-cov-2 virus reveal founder effects across geographical regions
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246029/
https://www.ncbi.nlm.nih.gov/pubmed/32509472
http://dx.doi.org/10.7717/peerj.9255
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