Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil

Souza, Ueric José Borges de; Santos, Raíssa Nunes dos; Melo, Fernando Lucas; Belmok, Aline; Galvão, Jucimária Dantas; Rezende, Tereza Cristina Vieira de; Cardoso, Franciano Dias Pereira; Carvalho, Rogério Fernandes; Oliveira, Monike da Silva; Júnior, José Carlos Ribeiro; Gabev, Evgeni Evgeniev; Sabino, Éster Cerdeira; Arns, Clarice Weis; Ribeiro, Bergmann Morais; Spilki, Fernando Rosado; Campos, Fabrício Souza

doi:10.3390/v14040659

Cited by 11 publications

(10 citation statements)

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“…Within the state, it has diverged into lineages AY.99.1 and AY.99.2 between May and June of 2021 ( Fig. 3 ), a result supported by the study of [ 47 ]. Both lineages have spread across the state from this point onwards, with AY.99.2 being dominant.…”

Section: Resultssupporting

confidence: 66%

Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants

et al. 2022

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During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyse more than 1 600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has initially spread mostly in the homonymous city of Rio de Janeiro, the most populous of the state. In a second stage, dispersal occurred to mid- and long-range cities, which acted as new close-range hubs for spread. We observed that the substitution of Gamma by Delta was possibly caused by its higher viral load, a proxy for transmissibility. This variant turnover prompted a new surge in cases, but with lower lethality than was observed during the peak caused by Gamma. We reason that high vaccination rates in the state of Rio de Janeiro were possibly what prevented a higher number of deaths.

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Section: Resultssupporting

confidence: 66%

Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants

et al. 2022

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“…We also found evidence of dispersal from Rio de Janeiro to the Tocantins, mediated from the Northeast Region. The strategic location of the Tocantins state was previously demonstrated as a transmission virus corridor between the North and South Regions of Brazil [ 17 ]. We agreed that the dispersion of the CHIKV is influenced by multiple factors, including the geographic parameters and traffic metrics that contribute to the vector transport.…”

Section: Discussionmentioning

confidence: 99%

“…The Tocantins is a Brazilian state located in the North Region, bordering six states, being a corridor for the transmission of pathogens between the North and the Northeast and Central-West Regions [ 17 ]. According to the Brazilian Institute of Geography and Statistics (IBGE; , accessed on 1 September 2022), in 2021, the state had an estimated population of 1,607,363 inhabitants, and its human development index was 0.699.…”

Section: Introductionmentioning

confidence: 99%

Genomic Epidemiology Reveals the Circulation of the Chikungunya Virus East/Central/South African Lineage in Tocantins State, North Brazil

Souza

Santos

Giovanetti

et al. 2022

Viruses

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The chikungunya virus (CHIKV) is a mosquito-borne virus of the family Togaviridae transmitted to humans by Aedes spp. mosquitoes. In Brazil, imported cases have been reported since June 2014 through two independent introductions, one caused by Asian Lineage in Oiapoque, Amapá state, North Region, and another caused by East/Central/South African (ECSA) in Feira de Santana, Bahia state, Northeast Region. Moreover, there is still limited information about the genomic epidemiology of the CHIKV from surveillance studies. The Tocantins state, located in Northern Brazil, reported an increase in the number of CHIKV cases at the end of 2021 and the beginning of 2022. Thus, to better understand the dispersion dynamics of this viral pathogen in the state, we generated 27 near-complete CHIKV genome sequences from four cities, obtained from clinical samples. Our results showed that the newly CHIKV genomes from Tocantins belonged to the ECSA lineage. Phylogenetic reconstruction revealed that Tocantins’ strains formed a single well-supported clade, which appear to be closely related to isolates from the Rio Grande do Norte state (Northeast Brazil) and the Rio de Janeiro state (Southeast Brazil), that experienced an explosive ECSA epidemic between 2016–2019. Mutation analyses showed eleven frequent non-synonymous mutations in the structural and non-structural proteins, indicating the autochthonous transmission of the CHIKV in the state. None of the genomes recovered within the Tocantins samples carry the A226V mutation in the E1 protein associated with increased transmission in A. albopictus. The study presented here highlights the importance of continued genomic surveillance to provide information not only on recording mutations along the viral genome but as a molecular surveillance tool to trace virus spread within the country, to predict events of likely occurrence of new infections, and, as such, contribute to an improved public health service.

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“…Also, Peru was the main country in which the AY.25.1.1 and AY.26.1 genotypes (Delta sublineages) were documented. Brazil reported 97% of the 22,815 cases of lineage AY.99.2 (firstly reported in Colombia), that was demonstrated to successfully disseminate among different locations in the country (34,35). Lineages derived from the Gamma variant were also reported frequently in Brazil (e.g., P.1.4, P.1.7, P.4, and others).…”

Section: Resultsmentioning

confidence: 99%

Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021

Molina-Mora

Reales-González

Camacho

et al. 2023

Front. Public Health

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Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia, and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1,534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.

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Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil

Cited by 11 publications

References 50 publications

Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants

Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants

Genomic Epidemiology Reveals the Circulation of the Chikungunya Virus East/Central/South African Lineage in Tocantins State, North Brazil

Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021

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