Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil

The introduction of SARS-CoV-2 variants of concern (VOCs) in Brazil has been associated with major impacts on the epidemiological and public health scenario. In this study, 291,571 samples were investigated for SARS-CoV-2 variants from August 2021 to March 2022 (the highest peak of positive cases) i...

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Main Authors: Joice do Prado Silva, Aline Brito de Lima, Luige Biciati Alvim, Frederico Scott Varella Malta, Cristiane Pinheiro Toscano Brito Mendonça, André Henrique Barbosa de Carvalho, Jéssica Silqueira Hickson Rios, Paula Luize Camargos Fonseca, Daniel Costa Queiroz, Luíza Campos Guerra de Araújo e Santos, Alessandro Clayton de Souza Ferreira, Renan Pedra de Souza, Renato Santana de Aguiar, Danielle Alves Gomes Zauli
Format: Article
Language:English
Published: MDPI AG 2023-04-01
Series:Viruses
Subjects:
Online Access:https://www.mdpi.com/1999-4915/15/4/1017
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author Joice do Prado Silva
Aline Brito de Lima
Luige Biciati Alvim
Frederico Scott Varella Malta
Cristiane Pinheiro Toscano Brito Mendonça
André Henrique Barbosa de Carvalho
Jéssica Silqueira Hickson Rios
Paula Luize Camargos Fonseca
Daniel Costa Queiroz
Luíza Campos Guerra de Araújo e Santos
Alessandro Clayton de Souza Ferreira
Renan Pedra de Souza
Renato Santana de Aguiar
Danielle Alves Gomes Zauli
author_facet Joice do Prado Silva
Aline Brito de Lima
Luige Biciati Alvim
Frederico Scott Varella Malta
Cristiane Pinheiro Toscano Brito Mendonça
André Henrique Barbosa de Carvalho
Jéssica Silqueira Hickson Rios
Paula Luize Camargos Fonseca
Daniel Costa Queiroz
Luíza Campos Guerra de Araújo e Santos
Alessandro Clayton de Souza Ferreira
Renan Pedra de Souza
Renato Santana de Aguiar
Danielle Alves Gomes Zauli
author_sort Joice do Prado Silva
collection DOAJ
description The introduction of SARS-CoV-2 variants of concern (VOCs) in Brazil has been associated with major impacts on the epidemiological and public health scenario. In this study, 291,571 samples were investigated for SARS-CoV-2 variants from August 2021 to March 2022 (the highest peak of positive cases) in four geographical regions of Brazil. To identify the frequency, introduction, and dispersion of SARS-CoV-2 variants in 12 Brazilian capitals, VOCs defining spike mutations were identified in 35,735 samples through genotyping and viral genome sequencing. Omicron VOC was detected in late November 2021 and replaced the Delta VOC in approximately 3.5 weeks. We estimated viral load differences between SARS-CoV-2 Delta and Omicron through the evaluation of the RT-qPCR cycle threshold (Ct) score in 77,262 samples. The analysis demonstrated that the Omicron VOC has a lower viral load in infected patients than the Delta VOC. Analyses of clinical outcomes in 17,586 patients across the country indicated that individuals infected with Omicron were less likely to need ventilatory support. The results of our study reinforce the importance of surveillance programs at the national level and showed the introduction and faster dispersion of Omicron over Delta VOC in Brazil without increasing the numbers of severe cases of COVID-19.
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spelling doaj.art-b6257a5b72e64722a758e970723f3e462023-11-17T21:47:01ZengMDPI AGViruses1999-49152023-04-01154101710.3390/v15041017Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in BrazilJoice do Prado Silva0Aline Brito de Lima1Luige Biciati Alvim2Frederico Scott Varella Malta3Cristiane Pinheiro Toscano Brito Mendonça4André Henrique Barbosa de Carvalho5Jéssica Silqueira Hickson Rios6Paula Luize Camargos Fonseca7Daniel Costa Queiroz8Luíza Campos Guerra de Araújo e Santos9Alessandro Clayton de Souza Ferreira10Renan Pedra de Souza11Renato Santana de Aguiar12Danielle Alves Gomes Zauli13Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, BrazilDepartamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, BrazilDepartamento de Produtos e Inovação, Instituto Hermes Pardini, Belo Horizonte 31270-901, BrazilDepartamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, BrazilDepartamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, BrazilDepartamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, BrazilDepartamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, BrazilLaboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, BrazilLaboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, BrazilLaboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, BrazilDepartamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, BrazilLaboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, BrazilLaboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, BrazilDepartamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, BrazilThe introduction of SARS-CoV-2 variants of concern (VOCs) in Brazil has been associated with major impacts on the epidemiological and public health scenario. In this study, 291,571 samples were investigated for SARS-CoV-2 variants from August 2021 to March 2022 (the highest peak of positive cases) in four geographical regions of Brazil. To identify the frequency, introduction, and dispersion of SARS-CoV-2 variants in 12 Brazilian capitals, VOCs defining spike mutations were identified in 35,735 samples through genotyping and viral genome sequencing. Omicron VOC was detected in late November 2021 and replaced the Delta VOC in approximately 3.5 weeks. We estimated viral load differences between SARS-CoV-2 Delta and Omicron through the evaluation of the RT-qPCR cycle threshold (Ct) score in 77,262 samples. The analysis demonstrated that the Omicron VOC has a lower viral load in infected patients than the Delta VOC. Analyses of clinical outcomes in 17,586 patients across the country indicated that individuals infected with Omicron were less likely to need ventilatory support. The results of our study reinforce the importance of surveillance programs at the national level and showed the introduction and faster dispersion of Omicron over Delta VOC in Brazil without increasing the numbers of severe cases of COVID-19.https://www.mdpi.com/1999-4915/15/4/1017SARS-CoV-2variantsepidemiologic surveillanceCOVID-19viral loadsymptoms
spellingShingle Joice do Prado Silva
Aline Brito de Lima
Luige Biciati Alvim
Frederico Scott Varella Malta
Cristiane Pinheiro Toscano Brito Mendonça
André Henrique Barbosa de Carvalho
Jéssica Silqueira Hickson Rios
Paula Luize Camargos Fonseca
Daniel Costa Queiroz
Luíza Campos Guerra de Araújo e Santos
Alessandro Clayton de Souza Ferreira
Renan Pedra de Souza
Renato Santana de Aguiar
Danielle Alves Gomes Zauli
Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil
Viruses
SARS-CoV-2
variants
epidemiologic surveillance
COVID-19
viral load
symptoms
title Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil
title_full Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil
title_fullStr Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil
title_full_unstemmed Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil
title_short Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil
title_sort epidemiological surveillance reveals the rise and establishment of the omicron sars cov 2 variant in brazil
topic SARS-CoV-2
variants
epidemiologic surveillance
COVID-19
viral load
symptoms
url https://www.mdpi.com/1999-4915/15/4/1017
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