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

Lamarca, Alessandra P; Almeida, Luiz Gonzaga Paula de; Francisco, Ronaldo da Silva; Cavalcante, Liliane Tavares de Faria; Brustolini, Otávio J. B.; Gerber, Alexandra Lehmkuhl; Guimarães, Ana P.; Oliveira, Thiago Henrique de; Nascimento, Érica Ramos dos Santos; Policarpo, Cíntia; Souza, Isabelle Vasconcellos de; Carvalho, Erika Martins de; Ribeiro, Mário Sérgio; Carvalho, Silvia; Silva, Flávio Dias da; Garcia, Márcio Henrique de Oliveira; Souza, Leandro Magalhães de; Silva, Cristiane Gomes da; Ribeiro, Caio Luiz Pereira; Cavalcanti, Andréa Cony; Mello, Claudia Maria Braga de; Tanuri, Amílcar; Vasconcelos, Ana Tereza Ribeiro de

doi:10.1099/mgen.0.000859

Cited by 4 publications

(1 citation statement)

References 66 publications

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“…The first case of Delta variant infection was documented on 17 June (EW 24) in a patient from Garibaldi city, within the Vinhedos e Basalto health microregion. This finding diverges from the typical pattern of introducing new variants, which often happens in capital cities, metropolitan areas, or cities with major airports [77]. In RS, the introduction of the Delta variant occurred within the Vinhedos e Basalto region, a tourist destination, primarily during the winter season.…”

Section: Discussionmentioning

confidence: 66%

Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis

y Castro,

Piccoli,

Vieira

et al. 2023

Microorganisms

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Mutations in the SARS-CoV-2 genome can alter the virus’ fitness, leading to the emergence of variants of concern (VOC). In Brazil, the Gamma variant dominated the pandemic in the first half of 2021, and from June onwards, the first cases of Delta infection were documented. Here, we investigate the introduction and dispersal of the Delta variant in the RS state by sequencing 1077 SARS-CoV-2-positive samples from June to October 2021. Of these samples, 34.7% were identified as Gamma and 65.3% as Delta. Notably, 99.2% of Delta sequences were clustered within the 21J lineage, forming a significant Brazilian clade. The estimated clock rate was 5.97 × 10−4 substitutions per site per year. The Delta variant was first reported on 17 June in the Vinhedos Basalto microregion and rapidly spread, accounting for over 70% of cases within nine weeks. Despite this, the number of cases and deaths remained stable, possibly due to vaccination, prior infections, and the continued mandatory mask use. In conclusion, our study provides insights into the Delta variant circulating in the RS state, highlighting the importance of genomic surveillance for monitoring viral evolution, even when the impact of new variants may be less severe in a given region.

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Section: Discussionmentioning

confidence: 66%

Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis

y Castro,

Piccoli,

Vieira

et al. 2023

Microorganisms

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How Did Latin America Face the SARS-CoV-2 Variants?

Jaspe,

Zambrano,

Loureiro

et al. 2024

The Latin American Studies Book Series

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Environmental genomic surveillance of SARS-CoV-2 in wastewater in Rio de Janeiro, Brazil

Gonçalves-Brito,

Magaldi,

Farias

et al. 2023

Journal of Water and Health

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Wastewater-based epidemiology can be a useful tool for monitoring SARS-CoV-2 prevalence and epidemiology to help prevent further disease spreading among the population. Being a complementary approach regarding its prevalence and diversity, and geographic distribution. The study aimed to evaluate the genetic diversity of the SARS-CoV-2 in two wastewater treatment plants (WWTPs) in Rio de Janeiro, Brazil. Samples were collected over a period of January to December 2021 and were concentrated with PEG8000 and the presence of the SARS-CoV-2 was detected using E and N1 genes. Partial sequencing of the SARS-CoV-2 genomes resulted in the identification of variants of concern and variants of interest throughout the collection period. It was possible to identify the Mu, Delta, Gamma and Omicron variants in WWTP1, on the contrary, no variants were observed in WWTP2. To the best of our knowledge, we detected the variant Mu (B.1.621) containing characteristic mutations (S:E484K, S:N501Y) from WWTP, for the first time, in Brazil. Another Mu variant detected from clinical surveillance was announced one month after our finding. The detection of SARS-CoV-2 in wastewater can serve as a tool to monitor the prevalence and epidemiology in each community, helping to understand the spread of the virus among the population.

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

Cited by 4 publications

References 66 publications

Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis

Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis

How Did Latin America Face the SARS-CoV-2 Variants?

Environmental genomic surveillance of SARS-CoV-2 in wastewater in Rio de Janeiro, Brazil

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