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Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic

Since the identification of SARS-CoV-2, a large number of genomes have been sequenced with unprecedented speed around the world. This marks a unique opportunity to analyze virus spreading and evolution in a worldwide context. Currently, there is not a useful haplotype description to help to track im...

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Autores principales: Justo Arevalo, Santiago, Zapata Sifuentes, Daniela, Huallpa, César J., Landa Bianchi, Gianfranco, Castillo Chávez, Adriana, Garavito-Salini Casas, Romina, Uceda-Campos, Guillermo, Pineda Chavarria, Roberto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7971176/
https://www.ncbi.nlm.nih.gov/pubmed/33746914
http://dx.doi.org/10.3389/fmicb.2021.612432
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author Justo Arevalo, Santiago
Zapata Sifuentes, Daniela
Huallpa, César J.
Landa Bianchi, Gianfranco
Castillo Chávez, Adriana
Garavito-Salini Casas, Romina
Uceda-Campos, Guillermo
Pineda Chavarria, Roberto
author_facet Justo Arevalo, Santiago
Zapata Sifuentes, Daniela
Huallpa, César J.
Landa Bianchi, Gianfranco
Castillo Chávez, Adriana
Garavito-Salini Casas, Romina
Uceda-Campos, Guillermo
Pineda Chavarria, Roberto
author_sort Justo Arevalo, Santiago
collection PubMed
description Since the identification of SARS-CoV-2, a large number of genomes have been sequenced with unprecedented speed around the world. This marks a unique opportunity to analyze virus spreading and evolution in a worldwide context. Currently, there is not a useful haplotype description to help to track important and globally scattered mutations. Also, differences in the number of sequenced genomes between countries and/or months make it difficult to identify the emergence of haplotypes in regions where few genomes are sequenced but a large number of cases are reported. We propose an approach based on the normalization by COVID-19 cases of relative frequencies of mutations using all the available data to identify major haplotypes. Furthermore, we can use a similar normalization approach to tracking the temporal and geographic distribution of haplotypes in the world. Using 171,461 genomes, we identify five major haplotypes or operational taxonomic units (OTUs) based on nine high-frequency mutations. OTU_3 characterized by mutations R203K and G204R is currently the most frequent haplotype circulating in four of the six continents analyzed (South America, North America, Europe, Asia, Africa, and Oceania). On the other hand, during almost all months analyzed, OTU_5 characterized by the mutation T85I in nsp2 is the most frequent in North America. Recently (since September), OTU_2 has been established as the most frequent in Europe. OTU_1, the ancestor haplotype, is near to extinction showed by its low number of isolations since May. Also, we analyzed whether age, gender, or patient status is more related to a specific OTU. We did not find OTU’s preference for any age group, gender, or patient status. Finally, we discuss structural and functional hypotheses in the most frequently identified mutations, none of those mutations show a clear effect on the transmissibility or pathogenicity.
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spelling pubmed-79711762021-03-19 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic Justo Arevalo, Santiago Zapata Sifuentes, Daniela Huallpa, César J. Landa Bianchi, Gianfranco Castillo Chávez, Adriana Garavito-Salini Casas, Romina Uceda-Campos, Guillermo Pineda Chavarria, Roberto Front Microbiol Microbiology Since the identification of SARS-CoV-2, a large number of genomes have been sequenced with unprecedented speed around the world. This marks a unique opportunity to analyze virus spreading and evolution in a worldwide context. Currently, there is not a useful haplotype description to help to track important and globally scattered mutations. Also, differences in the number of sequenced genomes between countries and/or months make it difficult to identify the emergence of haplotypes in regions where few genomes are sequenced but a large number of cases are reported. We propose an approach based on the normalization by COVID-19 cases of relative frequencies of mutations using all the available data to identify major haplotypes. Furthermore, we can use a similar normalization approach to tracking the temporal and geographic distribution of haplotypes in the world. Using 171,461 genomes, we identify five major haplotypes or operational taxonomic units (OTUs) based on nine high-frequency mutations. OTU_3 characterized by mutations R203K and G204R is currently the most frequent haplotype circulating in four of the six continents analyzed (South America, North America, Europe, Asia, Africa, and Oceania). On the other hand, during almost all months analyzed, OTU_5 characterized by the mutation T85I in nsp2 is the most frequent in North America. Recently (since September), OTU_2 has been established as the most frequent in Europe. OTU_1, the ancestor haplotype, is near to extinction showed by its low number of isolations since May. Also, we analyzed whether age, gender, or patient status is more related to a specific OTU. We did not find OTU’s preference for any age group, gender, or patient status. Finally, we discuss structural and functional hypotheses in the most frequently identified mutations, none of those mutations show a clear effect on the transmissibility or pathogenicity. Frontiers Media S.A. 2021-02-17 /pmc/articles/PMC7971176/ /pubmed/33746914 http://dx.doi.org/10.3389/fmicb.2021.612432 Text en Copyright © 2021 Justo Arevalo, Zapata Sifuentes, Huallpa, Landa Bianchi, Castillo Chávez, Garavito-Salini Casas, Uceda-Campos and Pineda Chavarria. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Justo Arevalo, Santiago
Zapata Sifuentes, Daniela
Huallpa, César J.
Landa Bianchi, Gianfranco
Castillo Chávez, Adriana
Garavito-Salini Casas, Romina
Uceda-Campos, Guillermo
Pineda Chavarria, Roberto
Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic
title Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic
title_full Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic
title_fullStr Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic
title_full_unstemmed Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic
title_short Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic
title_sort global geographic and temporal analysis of sars-cov-2 haplotypes normalized by covid-19 cases during the pandemic
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7971176/
https://www.ncbi.nlm.nih.gov/pubmed/33746914
http://dx.doi.org/10.3389/fmicb.2021.612432
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