Dataset Information

Genomic monitoring of the SARS-CoV-2 B1.1.7 (WHO VOC Alpha) in the Sao Paulo state, Brazil.

ABSTRACT: The SARS-CoV-2 alpha VOC (also known as lineage B.1.1.7) initially described in the autumn, 2020 in UK, rapidly became the dominant lineage across much of Europe. Despite multiple studies reporting molecular evidence suggestive of its circulation in Brazil, much is still unknown about its genomic diversity in the state of São Paulo, the main Brazilian economic and transportation hub. To get more insight regarding its transmission dynamics into the State we performed phylogenetic analysis on all alpha VOC strains obtained between February and August 2021 from the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants. The performed phylogenetic analysis showed that most of the alpha VOC genomes were interspersed with viral strains sampled from different Brazilian states and other countries suggesting that multiple independent Alpha VOC introductions from Brazil and overseas have occurred in the São Paulo State over time. Nevertheless, large monophyletic clusters were also observed especially from the Central-West part of the São Paulo State (the city of Bauru) and the metropolitan region of the São Paulo city. Our results highlight the Alpha VOC molecular epidemiology in the São Paulo state and reinforce the need for continued genomic surveillance strategies for the real-time monitoring of potential emerging SARS-CoV-2 variants during the ever-growing vaccination process.

SUBMITTER: Slavov SN

PROVIDER: S-EPMC8636783 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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Publications

Genomic monitoring of the SARS-CoV-2 B1.1.7 (WHO VOC Alpha) in the Sao Paulo state, Brazil.

Slavov Svetoslav Nanev SN Bezerra Rafael Dos Santos RDS Rodrigues Evandra Strazza ES Santos Elaine Vieira EV Borges Joseane Serrano JS de la Roque Débora Glenda Lima DGL Patané José Salvatore Leister JSL Lima Alex Ranieri Jerônimo ARJ Ribeiro Gabriela G Viala Vincent Louis VL de Lima Loyze Paola Oliveira LPO Martins Antonio Jorge AJ Dos Santos Barros Claudia Renata CR Marqueze Elaine Cristina EC Bernardino Jardelina de Souza Todão JST Moretti Debora Botequio DB Brassaloti Ricardo Augusto RA Cassano Raquel de Lello Rocha Campos RLRC Mariani Pilar Drummond Sampaio Corrêa PDSC Kitajima João Paulo JP Santos Bibiana B Assato Patricia Akemi PA da Silva da Costa Felipe Allan FA Poleti Mirele Daiana MD Lesbon Jessika Cristina Chagas JCC Mattos Elisangela Chicaroni EC Banho Cecilia Artico CA Sacchetto Lívia L Moraes Marília Mazzi MM Grotto Rejane Maria Tommasini RMT Souza-Neto Jayme A JA Giovanetti Marta M de Alcantara Luiz Carlos Junior LCJ Nogueira Maurício Lacerda ML Fukumasu Heidge H Coutinho Luiz Lehmann LL Calado Rodrigo Tocantins RT Neto Raul Machado RM Covas Dimas Tadeu DT Coccuzzo Sampaio Sandra S Elias Maria Carolina MC Kashima Simone S

Virus research 20211127

The SARS-CoV-2 alpha VOC (also known as lineage B.1.1.7) initially described in the autumn, 2020 in UK, rapidly became the dominant lineage across much of Europe. Despite multiple studies reporting molecular evidence suggestive of its circulation in Brazil, much is still unknown about its genomic diversity in the state of São Paulo, the main Brazilian economic and transportation hub. To get more insight regarding its transmission dynamics into the State we performed phylogenetic analysis on all ...[more]

PMID: 34848213

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Project description:Roadkill estimates for different species and species groups are available for many countries and regions. However, there is a lack of information from tropical countries, including from Latin America. In this study, we analyzed medium and large-sized mammal roadkill data from 18 toll road companies (TRC) in São Paulo State (6,580 km of monitored toll roads), Brazil. We extrapolated these roadkill numbers to the entire system of major paved roads in the State (36,503 km). The TRC collected mammal-road- mortality data both before (2-lanes) and after (4-lanes) road reconstruction. We used the "before" data from the TRC to estimate annual mammal-road-mortality along 2-lane roads that remained public roads. Combined with the data for the new 4-lane highways, this allowed us to estimate annual mammal road mortality for all the paved roads in the State. During 10 years of roadkill monitoring along toll roads, a total of 37,744 roadkilled mammals were recorded, representing a total of 32 medium to large-sized mammal species (average number of roadkilled individuals/year = 3,774 ± 1,159; min = 1,932; max = 5,369; 0.6 individuals roadkilled/km/year). Most roadkilled species were common generalists, but there were also relatively high roadkill numbers of threatened and endangered species (4.3% of the data), which is a serious conservation concern. Most of the roadkill was reported occurred during the nocturnal period (66%, n = 14,189) and in the rainy months (October-March) (55%, n = 15,318). Reported mammal roadkill tended to increase between 2009 and 2014 (R2 = 0.614; p = 0.065), with an average increase of 313.5 individuals/year. Extrapolation of the results to the entire São Paulo State, resulted in an average estimate of 39,605 medium and large-sized mammals roadkilled per year. Our estimates of the number of roadkilled individuals can be used as one of the input parameters in population viability analyses to understand the extinction or extirpation risk, especially for threatened and endangered species.

Dataset Information

Genomic monitoring of the SARS-CoV-2 B1.1.7 (WHO VOC Alpha) in the Sao Paulo state, Brazil.

Publications

Genomic monitoring of the SARS-CoV-2 B1.1.7 (WHO VOC Alpha) in the Sao Paulo state, Brazil.

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