Dataset Information

SARS-COV-2 genomic monitoring in the state of Sao Paulo unveils two emerging AY.43 sublineages.

ABSTRACT: Delta VOC is highly diverse with more than 120 sublineages already described as of November 30, 2021. In this study, through active monitoring of circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants in the state of São Paulo, southeast Brazil, we identified two emerging sublineages from the ancestral AY.43 strain which were classified as AY.43.1 and AY.43.2. These sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for the AY.43.1 and ORF1ab:G1155C for the AY.43.2 and our analysis reveals that they might have a likely-Brazilian origin. Much is still unknown regarding their dissemination in the state of São Paulo and Brazil as well as their potential impact on the ongoing vaccination process. However, the results obtained in this study reinforce the importance of genomic surveillance activity for timely identification of emerging SARS-CoV-2 variants which can impact the ongoing SARS-CoV-2 vaccination and public health policies.

SUBMITTER: Lima ARJ

PROVIDER: S-EPMC9088347 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature

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SARS-COV-2 genomic monitoring in the state of São Paulo unveils two emerging AY.43 sublineages.

Lima Alex Ranieri Jerônimo ARJ Ribeiro Gabriela G Viala Vincent Louis VL de Lima Loyze Paola Oliveira LPO Martins Antonio Jorge AJ Barros Claudia Renata Dos Santos CRDS Marqueze Elaine Cristina EC Bernardino Jardelina de Souza Todao JST Moretti Debora Botequio DB Rodrigues Evandra Strazza ES Santos Elaine Vieira EV Brassaloti Ricardo Augusto RA Cassano Raquel de Lello Rocha Campos RLRC Mariani Pilar Drummond Sampaio Corrêa PDSC Clemente Luan Gaspar LG Assato Patricia Akemi PA Costa Felipe Allan da Silva da FADSD Poleti Mirele Daiana MD Lesbon Jessika Cristina Chagas JCC Mattos Elisangela Chicaroni EC Banho Cecilia Artico CA Sacchetto Lívia L Moraes Marília Mazzi MM Palmieri Melissa M Martininghi Maiara M Caldeira Luiz Artur Vieira LAV Silva Fabiana Erica Vilanova da FEVD Grotto Rejane Maria Tommasini RMT Souza-Neto Jayme A JA Giovanetti Marta M Junior Alcantara Luiz Carlos LC Nogueira Maurício Lacerda ML Fukumasu Heidge H Coutinho Luiz Lehmann LL Kashima Simone S Neto Raul Machado RM Covas Dimas Tadeu DT Slavov Svetoslav Nanev SN Sampaio Sandra Coccuzzo SC Elias Maria Carolina MC

Journal of medical virology 20220312 7

Delta VOC is highly diverse with more than 120 sublineages already described as of November 30, 2021. In this study, through active monitoring of circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants in the state of São Paulo, southeast Brazil, we identified two emerging sublineages from the ancestral AY.43 strain which were classified as AY.43.1 and AY.43.2. These sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a ...[more]

PMID: 35229308

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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

SARS-COV-2 genomic monitoring in the state of Sao Paulo unveils two emerging AY.43 sublineages.

Publications

SARS-COV-2 genomic monitoring in the state of São Paulo unveils two emerging AY.43 sublineages.

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