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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2020
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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. |
format | Online Article Text |
id | pubmed-7246029 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
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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