Genomic epidemiology of SARS-CoV-2 in large university hospital cohort: the UnCoVER-Brazil project

This work aimed to study the role of different SARS-CoV-2 lineages in the epidemiology of multiple waves of the COVID-19 pandemic in Ribeirão Preto (São Paulo state), with comparison within Brazil and globally. Viral genomic sequencing was combined with clinical and sociodemographic information of 2...

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Published in	Epidemiology and infection Vol. 151; p. e126
Main Authors	de Carvalho, Felipe Santos, Slack, Sarah Danielle, Barbosa-Júnior, Francisco, de Campos, Mateus Rennó, Castro, Guilherme Silveira, Baroni, Sabrina, Bueno, Livia Mara Torres, Coeli, Fernanda Borchers, Yamamoto, Aparecida Yulie, Silva, Jorgete Maria, Calado, Rodrigo do Tocantins, Fonseca, Benedito Antônio Lopes, Colli, Leandro Machado, Bellissimo-Rodrigues, Fernando
Format	Journal Article
Language	English
Published	Cambridge, UK Cambridge University Press 20.07.2023
Subjects	Brazil - epidemiology COVID-19 COVID-19 - epidemiology COVID-19 vaccines Disease transmission Epidemiology Genomes Genomics Health surveillance Herd immunity Hospitalization Hospitals Hospitals, University Humans Infections Missing data Pandemics SARS-CoV-2 - genetics Severe acute respiratory syndrome coronavirus 2 Short Paper Sociodemographics Vaccination Viral diseases Whole genome sequencing Brazil COVID-19 epidemiology genome SARS-CoV-2 variants
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Abstract	This work aimed to study the role of different SARS-CoV-2 lineages in the epidemiology of multiple waves of the COVID-19 pandemic in Ribeirão Preto (São Paulo state), with comparison within Brazil and globally. Viral genomic sequencing was combined with clinical and sociodemographic information of 2,379 subjects at a large Brazilian hospital. On the whole 2,395 complete SARS-CoV-2 genomes were obtained from April 2020 to January 2022. We report variants of concern (VOC) and interest (VOI) dynamics and the role of Brazilian lineages. We identified three World Health Organization VOCs (Gamma, Delta, Omicron) and one VOI (Zeta), which caused distinct waves in this cohort. We also identified 47 distinct Pango lineages. Consistent with the high prevalence of Gamma in Brazil, Pango lineage P.1 dominated infections in this cohort for half of 2021. Each wave of infection largely consisted of a single variant group, with each new group quickly and completely rising to dominance. Despite increasing vaccination in Brazil starting in 2021, this pattern was observed throughout the study and is consistent with the hypothesis that herd immunity tends to be SARS-CoV-2 variant-specific and does not broadly protect against COVID-19.
AbstractList	This work aimed to study the role of different SARS-CoV-2 lineages in the epidemiology of multiple waves of the COVID-19 pandemic in Ribeirão Preto (São Paulo state), with comparison within Brazil and globally. Viral genomic sequencing was combined with clinical and sociodemographic information of 2,379 subjects at a large Brazilian hospital. On the whole 2,395 complete SARS-CoV-2 genomes were obtained from April 2020 to January 2022. We report variants of concern (VOC) and interest (VOI) dynamics and the role of Brazilian lineages. We identified three World Health Organization VOCs (Gamma, Delta, Omicron) and one VOI (Zeta), which caused distinct waves in this cohort. We also identified 47 distinct Pango lineages. Consistent with the high prevalence of Gamma in Brazil, Pango lineage P.1 dominated infections in this cohort for half of 2021. Each wave of infection largely consisted of a single variant group, with each new group quickly and completely rising to dominance. Despite increasing vaccination in Brazil starting in 2021, this pattern was observed throughout the study and is consistent with the hypothesis that herd immunity tends to be SARS-CoV-2 variant-specific and does not broadly protect against COVID-19. This work aimed to study the role of different SARS-CoV-2 lineages in the epidemiology of multiple waves of the COVID-19 pandemic in Ribeirão Preto (São Paulo state), with comparison within Brazil and globally. Viral genomic sequencing was combined with clinical and sociodemographic information of 2,379 subjects at a large Brazilian hospital. On the whole 2,395 complete SARS-CoV-2 genomes were obtained from April 2020 to January 2022. We report variants of concern (VOC) and interest (VOI) dynamics and the role of Brazilian lineages. We identified three World Health Organization VOCs (Gamma, Delta, Omicron) and one VOI (Zeta), which caused distinct waves in this cohort. We also identified 47 distinct Pango lineages. Consistent with the high prevalence of Gamma in Brazil, Pango lineage P.1 dominated infections in this cohort for half of 2021. Each wave of infection largely consisted of a single variant group, with each new group quickly and completely rising to dominance. Despite increasing vaccination in Brazil starting in 2021, this pattern was observed throughout the study and is consistent with the hypothesis that herd immunity tends to be SARS-CoV-2 variant-specific and does not broadly protect against COVID-19.This work aimed to study the role of different SARS-CoV-2 lineages in the epidemiology of multiple waves of the COVID-19 pandemic in Ribeirão Preto (São Paulo state), with comparison within Brazil and globally. Viral genomic sequencing was combined with clinical and sociodemographic information of 2,379 subjects at a large Brazilian hospital. On the whole 2,395 complete SARS-CoV-2 genomes were obtained from April 2020 to January 2022. We report variants of concern (VOC) and interest (VOI) dynamics and the role of Brazilian lineages. We identified three World Health Organization VOCs (Gamma, Delta, Omicron) and one VOI (Zeta), which caused distinct waves in this cohort. We also identified 47 distinct Pango lineages. Consistent with the high prevalence of Gamma in Brazil, Pango lineage P.1 dominated infections in this cohort for half of 2021. Each wave of infection largely consisted of a single variant group, with each new group quickly and completely rising to dominance. Despite increasing vaccination in Brazil starting in 2021, this pattern was observed throughout the study and is consistent with the hypothesis that herd immunity tends to be SARS-CoV-2 variant-specific and does not broadly protect against COVID-19.
ArticleNumber	e126
Author	Calado, Rodrigo do Tocantins Silva, Jorgete Maria Fonseca, Benedito Antônio Lopes Castro, Guilherme Silveira Barbosa-Júnior, Francisco de Carvalho, Felipe Santos Yamamoto, Aparecida Yulie de Campos, Mateus Rennó Slack, Sarah Danielle Coeli, Fernanda Borchers Bellissimo-Rodrigues, Fernando Colli, Leandro Machado Baroni, Sabrina Bueno, Livia Mara Torres
AuthorAffiliation	4 Oncology and Imaging Department, Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil 6 Virology Laboratory, University Hospital of Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil 2 Infectious Diseases Division, Internal Medicine Department, Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil 5 Epidemiological Surveillance Service, University Hospital of Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil 3 Medicine Department, Federal University of São Carlos , São Carlos , Brazil 1 Social Medicine Department, Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
AuthorAffiliation_xml	– name: 3 Medicine Department, Federal University of São Carlos , São Carlos , Brazil – name: 6 Virology Laboratory, University Hospital of Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil – name: 5 Epidemiological Surveillance Service, University Hospital of Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil – name: 2 Infectious Diseases Division, Internal Medicine Department, Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil – name: 4 Oncology and Imaging Department, Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil – name: 1 Social Medicine Department, Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
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Cites_doi	10.1093/ve/veac064 10.3390/v13050724 10.1080/22221751.2021.2011617 10.3201/eid2803.212020 10.1016/S0140-6736(22)00484-6
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References	2021; 13 2021; 6 2022; 28 2022; 8 2022; 399 2022; 11 Andrés (S095026882300119X_r6) 2022; 11 Barber (S095026882300119X_r7) 2022; 399 Fonseca (S095026882300119X_r10) 2022; 8 cr-split#-S095026882300119X_r4.2 Bonifácio (S095026882300119X_r3) 2022; 28 O’Toole (S095026882300119X_r8) 2021; 6 cr-split#-S095026882300119X_r1.1 cr-split#-S095026882300119X_r1.2 Resende (S095026882300119X_r9) 2021; 13 cr-split#-S095026882300119X_r4.1 S095026882300119X_r2 S095026882300119X_r5
References_xml	– volume: 13 start-page: 724 issue: 5 year: 2021 article-title: A potential SARS-CoV-2 variant of interest (VOI) harboring mutation E484K in the spike protein was identified within lineage B.1.1.33 circulating in Brazil publication-title: Viruses – volume: 6 start-page: 121 year: 2021 article-title: Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch publication-title: Wellcome Open Research – volume: 8 start-page: veac064 issue: 2 year: 2022 article-title: Tracking the turnover of SARS-CoV-2 VOCs gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status publication-title: Virus Evolution – volume: 399 start-page: 2351 issue: 10344 year: 2022 end-page: 2380 article-title: Estimating global, regional, and national daily and cumulative infections with SARS-CoV-2 through Nov 14, 2021: A statistical analysis publication-title: The Lancet – volume: 28 start-page: 730 issue: 3 year: 2022 end-page: 733 article-title: Long-term symptoms among COVID-19 survivors in prospective cohort study, Brazil publication-title: Emerging Infectious Diseases – volume: 11 start-page: 172 issue: 1 year: 2022 end-page: 181 article-title: A year living with SARS-CoV-2: An epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain) publication-title: Emerging Microbes & Infections – volume: 8 start-page: veac064 year: 2022 ident: S095026882300119X_r10 article-title: Tracking the turnover of SARS-CoV-2 VOCs gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status publication-title: Virus Evolution doi: 10.1093/ve/veac064 – ident: S095026882300119X_r5 – volume: 13 start-page: 724 year: 2021 ident: S095026882300119X_r9 article-title: A potential SARS-CoV-2 variant of interest (VOI) harboring mutation E484K in the spike protein was identified within lineage B.1.1.33 circulating in Brazil publication-title: Viruses doi: 10.3390/v13050724 – ident: #cr-split#-S095026882300119X_r1.2 – volume: 11 start-page: 172 year: 2022 ident: S095026882300119X_r6 article-title: A year living with SARS-CoV-2: An epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain) publication-title: Emerging Microbes and Infections doi: 10.1080/22221751.2021.2011617 – volume: 28 start-page: 730 year: 2022 ident: S095026882300119X_r3 article-title: Long-term symptoms among COVID-19 survivors in prospective cohort study, Brazil publication-title: Emerging Infectious Diseases doi: 10.3201/eid2803.212020 – ident: #cr-split#-S095026882300119X_r1.1 – ident: S095026882300119X_r2 – ident: #cr-split#-S095026882300119X_r4.1 – ident: #cr-split#-S095026882300119X_r4.2 – volume: 399 start-page: 2351 year: 2022 ident: S095026882300119X_r7 article-title: Estimating global, regional, and national daily and cumulative infections with SARS-CoV-2 through Nov 14, 2021: A statistical analysis publication-title: The Lancet doi: 10.1016/S0140-6736(22)00484-6 – volume: 6 start-page: 121 year: 2021 ident: S095026882300119X_r8 article-title: Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch publication-title: Wellcome Open Research
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SubjectTerms	Brazil - epidemiology COVID-19 COVID-19 - epidemiology COVID-19 vaccines Disease transmission Epidemiology Genomes Genomics Health surveillance Herd immunity Hospitalization Hospitals Hospitals, University Humans Infections Missing data Pandemics SARS-CoV-2 - genetics Severe acute respiratory syndrome coronavirus 2 Short Paper Sociodemographics Vaccination Viral diseases Whole genome sequencing
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Title	Genomic epidemiology of SARS-CoV-2 in large university hospital cohort: the UnCoVER-Brazil project
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