Retrospective Analysis of Omicron in Minas Gerais, Brazil: Emergence, Dissemination, and Diversification

Brazil is one of the countries most affected by COVID-19, with the highest number of deaths recorded. Brazilian Health Institutions have reported four main peaks of positive COVID-19 cases. The last two waves were characterized by the emergence of the VOC Omicron and its sublineages. This study aimed to conduct a retrospective surveillance study illustrating the emergence, dissemination, and diversification of the VOC Omicron in 15 regional health units (RHUs) in MG, the second most populous state in Brazil, by combining epidemiological and genomic data. A total of 5643 confirmed positive COVID-19 samples were genotyped using the panels TaqMan SARS-CoV-2 Mutation and 4Plex SC2/VOC Bio-Manguinhos to define mutations classifying the BA.1, BA.2, BA.4, and BA.5 sublineages. While sublineages BA.1 and BA.2 were more prevalent during the third wave, BA.4 and BA.5 dominated the fourth wave in the state. Epidemiological and viral genome data suggest that age and vaccination with booster doses were the main factors related to clinical outcomes, reducing the number of deaths, irrespective of the Omicron sublineages. Complete genome sequencing of 253 positive samples confirmed the circulation of the BA.1, BA.2, BA.4, and BA.5 subvariants, and phylogenomic analysis demonstrated that the VOC Omicron was introduced through multiple international events, followed by transmission within the state of MG. In addition to the four subvariants, other lineages have been identified at low frequency, including BQ.1.1 and XAG. This integrative study reinforces that the evolution of Omicron sublineages was the most significant factor driving the highest peaks of positive COVID-19 cases without an increase in more severe cases, prevented by vaccination boosters.

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Journal
Microorganisms
Published
2024-08-23
DOI
https://doi.org/10.3390/microorganisms12091745
Primary Topic
SARS-CoV-2 and COVID-19 Research
Type
article
Field-Weighted Citation Impact
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article

Retrospective Analysis of Omicron in Minas Gerais, Brazil: Emergence, Dissemination, and Diversification

Filipe Romero Rebello Moreira, Mariane Talon de Menezes, Luíza Campos Guerra de Araújo e Santos, Hugo José Alves et al.
Microorganisms
SARS-CoV-2 and COVID-19 Research
article

Retrospective Analysis of Omicron in Minas Gerais, Brazil: Emergence, Dissemination, and Diversification

Filipe Romero Rebello Moreira, Mariane Talon de Menezes, Luíza Campos Guerra de Araújo e Santos, Hugo José Alves, Marisa de Oliveira Ribeiro, Renato Santana Aguiar, Adriano de Paula Sabino, Natália Virtude Carobin, Jorge G. Ferreira, Rillery Calixto Dias, João Locke Ferreira de Araújo, Daniel Costa Queiroz, José Nélio Januário, Rennan Garcias Moreira, Jaqueline Silva de Oliveira, Renan P. Souza, Paula Luize Camargos Fonseca, Ludmila Oliveira Lamounier, Carolina Zaniboni Ferrari, Diego Menezes, Eneida Santos de Oliveira, Talita Adelino, Nara de Oliveira Carvalho, Aryel Beatriz Paz e Silva, Isabela Braga-Paz, Natália Rocha Guimarães, Fernanda Gil de Souza, Patrícia Álvarez, André Felipe Leal Bernardes, Mônica Barcellos Arruda, Carolina Senra Alves de Souza, Renée Silva Carvalho, Felipe Campos de Melo Iani, Luisa Aimeé Vargas
article en

Abstract

Brazil is one of the countries most affected by COVID-19, with the highest number of deaths recorded. Brazilian Health Institutions have reported four main peaks of positive COVID-19 cases. The last two waves were characterized by the emergence of the VOC Omicron and its sublineages. This study aimed to conduct a retrospective surveillance study illustrating the emergence, dissemination, and diversification of the VOC Omicron in 15 regional health units (RHUs) in MG, the second most populous state in Brazil, by combining epidemiological and genomic data. A total of 5643 confirmed positive COVID-19 samples were genotyped using the panels TaqMan SARS-CoV-2 Mutation and 4Plex SC2/VOC Bio-Manguinhos to define mutations classifying the BA.1, BA.2, BA.4, and BA.5 sublineages. While sublineages BA.1 and BA.2 were more prevalent during the third wave, BA.4 and BA.5 dominated the fourth wave in the state. Epidemiological and viral genome data suggest that age and vaccination with booster doses were the main factors related to clinical outcomes, reducing the number of deaths, irrespective of the Omicron sublineages. Complete genome sequencing of 253 positive samples confirmed the circulation of the BA.1, BA.2, BA.4, and BA.5 subvariants, and phylogenomic analysis demonstrated that the VOC Omicron was introduced through multiple international events, followed by transmission within the state of MG. In addition to the four subvariants, other lineages have been identified at low frequency, including BQ.1.1 and XAG. This integrative study reinforces that the evolution of Omicron sublineages was the most significant factor driving the highest peaks of positive COVID-19 cases without an increase in more severe cases, prevented by vaccination boosters.

MicroorganismsVol. 12(9)
Universidade Federal de Minas Gerais (BR), Universidade Federal do Rio de Janeiro (BR), Ezequiel Dias Foundation (BR), D’Or Institute for Research and Education (BR), Secretaria da Saúde (BR), Secretaria Municipal de Saúde (BR), Fundação Oswaldo Cruz (BR)
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Ministério da Ciência, Tecnologia e Inovação, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Financiadora de Estudos e Projetos, Fundação de Amparo à Pesquisa do Estado de Minas Gerais
Good health and well-being
Openalex Percentile: Top 83%
SARS-CoV-2 and COVID-19 Research
DOIOpen Access PDFOpenAlex
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