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Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil

The year of 2021 was marked by the emergence and dispersal of a number of SARS-CoV-2 lineages, resulting in the “third wave” of COVID-19 in several countries despite the level of vaccine coverage. Soon after the first confirmed cases of COVID-19 by the Delta variant in Brazil, at least seven Delta s...

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Autores principales: Romano, Camila Malta, de Oliveira, Cristina Mendes, da Silva, Luciane Sussuchi, Levi, José Eduardo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9249134/
https://www.ncbi.nlm.nih.gov/pubmed/35783651
http://dx.doi.org/10.3389/fmed.2022.930380
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author Romano, Camila Malta
de Oliveira, Cristina Mendes
da Silva, Luciane Sussuchi
Levi, José Eduardo
author_facet Romano, Camila Malta
de Oliveira, Cristina Mendes
da Silva, Luciane Sussuchi
Levi, José Eduardo
author_sort Romano, Camila Malta
collection PubMed
description The year of 2021 was marked by the emergence and dispersal of a number of SARS-CoV-2 lineages, resulting in the “third wave” of COVID-19 in several countries despite the level of vaccine coverage. Soon after the first confirmed cases of COVID-19 by the Delta variant in Brazil, at least seven Delta sub-lineages emerged, including the globally spread AY.101 and AY.99.2. In this study we performed a detailed analysis of the COVID-19 scenario in Brazil from April to December 2021 by using data collected by the largest private medical diagnostic company in Latin America (Dasa), and SARS-CoV-2 genomic sequences generated by its SARS-CoV-2 genomic surveillance project (GENOV). For phylogenetic and Bayesian analysis, SARS-CoV-2 genomes available at GISAID public database were also retrieved. We confirmed that the Brazilian AY.99.2 and AY.101 were the most prevalent lineages during this period, overpassing the Gamma variant in July/August. We also estimated that AY.99.2 likely emerged a few weeks after the entry of the B.1.617.2 in the country, at some point between late April and May and rapidly spread to other countries. Despite no increased fitness described for the AY.99.2 lineage, a rapid shift in the composition of Delta SARS-CoV-2 lineages prevalence in Brazil took place. Understanding the reasons leading the AY.99.2 to become the dominant lineage in the country is important to understand the process of lineage competitions that may inform future control measures.
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spelling pubmed-92491342022-07-02 Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil Romano, Camila Malta de Oliveira, Cristina Mendes da Silva, Luciane Sussuchi Levi, José Eduardo Front Med (Lausanne) Medicine The year of 2021 was marked by the emergence and dispersal of a number of SARS-CoV-2 lineages, resulting in the “third wave” of COVID-19 in several countries despite the level of vaccine coverage. Soon after the first confirmed cases of COVID-19 by the Delta variant in Brazil, at least seven Delta sub-lineages emerged, including the globally spread AY.101 and AY.99.2. In this study we performed a detailed analysis of the COVID-19 scenario in Brazil from April to December 2021 by using data collected by the largest private medical diagnostic company in Latin America (Dasa), and SARS-CoV-2 genomic sequences generated by its SARS-CoV-2 genomic surveillance project (GENOV). For phylogenetic and Bayesian analysis, SARS-CoV-2 genomes available at GISAID public database were also retrieved. We confirmed that the Brazilian AY.99.2 and AY.101 were the most prevalent lineages during this period, overpassing the Gamma variant in July/August. We also estimated that AY.99.2 likely emerged a few weeks after the entry of the B.1.617.2 in the country, at some point between late April and May and rapidly spread to other countries. Despite no increased fitness described for the AY.99.2 lineage, a rapid shift in the composition of Delta SARS-CoV-2 lineages prevalence in Brazil took place. Understanding the reasons leading the AY.99.2 to become the dominant lineage in the country is important to understand the process of lineage competitions that may inform future control measures. Frontiers Media S.A. 2022-06-17 /pmc/articles/PMC9249134/ /pubmed/35783651 http://dx.doi.org/10.3389/fmed.2022.930380 Text en Copyright © 2022 Romano, de Oliveira, da Silva and Levi. https://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 Medicine
Romano, Camila Malta
de Oliveira, Cristina Mendes
da Silva, Luciane Sussuchi
Levi, José Eduardo
Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil
title Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil
title_full Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil
title_fullStr Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil
title_full_unstemmed Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil
title_short Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil
title_sort early emergence and dispersal of delta sars-cov-2 lineage ay.99.2 in brazil
topic Medicine
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9249134/
https://www.ncbi.nlm.nih.gov/pubmed/35783651
http://dx.doi.org/10.3389/fmed.2022.930380
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