Dataset Information

The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela.

ABSTRACT: Our effort in SARS-CoV-2 genomic surveillance in Brazil has detected the Alpha Variant of Concern with a predominance higher than 75% in the population of Ilhabela island (São Paulo State) at a time when the Gamma VOC was already predominating the mainland raised concerns for closer surveillance on this island. Therefore, we intensified the surveillance for 24 weeks by generating data from 34% of local positive cases. Our data show that the patterns of VOC predominance dynamics and infection rates were in general distinct from the mainland. We report here the first known case of Alpha predominance in a Brazilian population, a delay greater than 3 months for the Gamma to dominate the previous variants compared to the mainland, and a faster dispersion rate of Gamma and Delta VOCs compared to the mainland. Phylogenetic analysis revealed the SARS-CoV-2 transmission dynamics in Ilhabela were characterized by multiple independent introduction events of Gamma and Delta, with a few events of Alpha introduction, two of them followed by community transmission. This study evidenced the peculiar behavior of SARS-CoV-2 variants in an isolated population and brought to light the importance of specific programs for SARS-CoV-2 genomic surveillance in isolated populations.

SUBMITTER: Viala VL

PROVIDER: S-EPMC9323713 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature

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The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela.

Viala Vincent Louis VL Slavov Svetoslav Nanev SN de Lima Loyze Paola Oliveira LPO Lima Alex Ranieri Jeronimo ARJ Ribeiro Gabriela G Martins Antonio Jorge AJ Petry Bruna B Banho Cecilia Artico CA Barros Claudia Renata Dos Santos CRDS Moncau Cristina Tschorny CT Moretti Debora Botequio DB de La-Roque Debora Glenda Lima DGL Marqueze Elaine Cristina EC Mattos Elisangela Chicaroni EC Costa Felipe Allan da Silva da FADSD Fukumasu Heidge H Bernardino Jardelina de Souza Todao JST Souza-Neto Jayme A JA Lesbon Jessika Cristina Chagas JCC Kayanoki Lara Passos LP Bernardo Leandro Lombo LL Sacchetto Lívia L Clemente Luan Gaspar LG Alcantara Luiz Carlos Júnior LCJ Coutinho Luiz Lehmann LL Marques Beatriz de Carvalho BC Giovanetti Marta M Nogueira Maurício Lacerda ML Poleti Mirele Daiana MD Assato Patricia Akemi PA Cattony Neto Pedro De Queiroz PQ Cassano Raquel de Lello Rocha Campos RLRC Neto Raul Machado RM Grotto Rejane Maria Tommasini RMT Brassaloti Ricardo Augusto RA Kashima Simone S Covas Dimas Tadeu DT Elias Maria Carolina MC Sampaio Sandra Coccuzzo SC

Viruses 20220705 7

Our effort in SARS-CoV-2 genomic surveillance in Brazil has detected the Alpha Variant of Concern with a predominance higher than 75% in the population of Ilhabela island (São Paulo State) at a time when the Gamma VOC was already predominating the mainland raised concerns for closer surveillance on this island. Therefore, we intensified the surveillance for 24 weeks by generating data from 34% of local positive cases. Our data show that the patterns of VOC predominance dynamics and infection rat ...[more]

PMID: 35891460

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Project description:IntroductionAfter three years since the beginning of the pandemic, the new coronavirus continues to raise several questions regarding its infectious process and host response. Several mutations occurred in different regions of the SARS-CoV-2 genome, such as in the spike gene, causing the emergence of variants of concern and interest (VOCs and VOIs), of which some present higher transmissibility and virulence, especially among patients with previous comorbidities. It is essential to understand its spread dynamics to prevent and control new biological threats that may occur in the future. In this population_based retrospective observational study, we generated data and used public databases to understand SARS-CoV-2 dynamics.MethodsWe sequenced 1,003 SARS-CoV-2 genomes from naso-oropharyngeal swabs and saliva samples from Pará from May 2020 to October 2022. To gather epidemiological data from Brazil and the world, we used FIOCRUZ and GISAID databases.ResultsRegarding our samples, 496 (49.45%) were derived from female participants and 507 (50.55%) from male participants, and the average age was 43 years old. The Gamma variant presented the highest number of cases, with 290 (28.91%) cases, followed by delta with 53 (5.28%). Moreover, we found seven (0.69%) Omicron cases and 651 (64.9%) non-VOC cases. A significant association was observed between sex and the clinical condition (female, p = 8.65e-08; male, p = 0.008961) and age (p = 3.6e-10).DiscussionAlthough gamma had been officially identified only in December 2020/January 2021, we identified a gamma case from Belém (capital of Pará State) dated May 2020 and three other cases in October 2020. This indicates that this variant was circulating in the North region of Brazil several months before its formal identification and that Gamma demonstrated its actual transmission capacity only at the end of 2020. Furthermore, the public data analysis showed that SARS-CoV-2 dispersion dynamics differed in Brazil as Gamma played an important role here, while most other countries reported a new infection caused by the Delta variant. The genetic and epidemiological information of this study reinforces the relevance of having a robust genomic surveillance service that allows better management of the pandemic and that provides efficient solutions to possible new disease-causing agents.

Dataset Information

The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela.

Publications

The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela.

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