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Article

SARS-CoV-2 Lineage P.4 Detection in Southeast Brazil: A Retrospective Genomic and Clinical Overview

by
Mirele Daiana Poleti
1,
Jéssika Cristina Chagas Lesbon
1,
Elisângela Chicaroni de Mattos Oliveira
1,
José Salvatore Leister Patané
2,
Luan Gaspar Clemente
3,
Vincent Louis Viala
2,
Gabriela Ribeiro
2,
Jéssica Fernanda Perissato Pinheiro
4,
Marta Giovanetti
5,6,
Luiz Carlos Junior Alcantara
5,6,
Loyze Paola Oliveira de Lima
2,
Antonio Jorge Martins
2,
Claudia Renata dos Santos Barros
2,
Elaine Cristina Marqueze
2,
Jardelina de Souza Todão Bernardino
2,
Debora Botequio Moretti
2,
Ricardo Augusto Brassaloti
3,
Raquel de Lello Rocha Campos Cassano
3,
Pilar Drummond Sampaio Corrêa Mariani
7,
Svetoslav Nanev Slavov
8,
Rafael dos Santos Bezerra
8,
Evandra Strazza Rodrigues
8,
Elaine Vieira Santos
8,
Josiane Serrano Borges
8,
Debora Glenda Lima de La Roque
8,
João Paulo Kitajima
9,
Bibiana Santos
9,
Patrícia Akemi Assato
10,
Felipe Allan da Silva da Costa
10,
Cecília Ártico Banho
11,
Lívia Sacchetto
11,
Beatriz de Carvalho Marques
11,
Rejane Maria Tommasini Grotto
10,
Jayme A. Souza-Neto
10,
Maurício Lacerda Nogueira
11,
Luiz Lehmann Coutinho
3,
Rodrigo Tocantins Calado
8,
Raul Machado Neto
2,
Dimas Tadeu Covas
2,
Simone Kashima
8,
Maria Carolina Elias
2,
Sandra Coccuzzo Sampaio
2 and
Heidge Fukumasu
1,*add Show full author list remove Hide full author list
1
Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, SP, Brazil
2
Butantan Institute, Sao Paulo 05503-000, SP, Brazil
3
Functional Genomic Center, Department of Animal Science, Luiz de Queiroz School of Agriculture, University of Sao Paulo, Piracicaba 13418-900, SP, Brazil
4
Municipal Epidemiological Surveillance, Araras 13601-111, SP, Brazil
5
Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
6
Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
7
NGS Soluções Genômicas, Piracicaba 13416-030, SP, Brazil
8
Blood Center of Ribeirao Preto, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto 14051-060, SP, Brazil
9
Mendelics Genomic Analysis, Sao Paulo 02511-000, SP, Brazil
10
School of Agricultural Sciences, Sao Paulo State University, Botucatu 18618-970, SP, Brazil
11
Laboratório de Pesquisas em Virologia, Medicine School of São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
 
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*
Author to whom correspondence should be addressed.
COVID 2022, 2(12), 1768-1777; https://doi.org/10.3390/covid2120127
Submission received: 14 October 2022 / Revised: 24 November 2022 / Accepted: 29 November 2022 / Published: 5 December 2022
(This article belongs to the Special Issue The Genetic Diversity, Evolution and Epidemiology of SARS-CoV-2)
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Abstract

São Paulo state has been the epicenter of the Coronavirus Disease 2019 (COVID-19) in Brazil, ranking first by state with over six million reported cases. In February 2021, the P.4 lineage was reported in 21 cities across the state by public health authorities due to the L452R mutation. Here, by analyzing 17,304 genome sequences of SARS-CoV-2 sampled between February and August of 2021 in 476 distinct cities in São Paulo, we assess the transmission dynamics of the P.4 lineage and other SARS-CoV-2 variants that were, at the time of the study, co-circulating in the state. Additionally, clinical parameters from the city of Araras, São Paulo (N = 251) were considered to estimate the potential risk and mortality rate associated with the P.4 lineage since its higher prevalence was observed in that city. Our data suggest a low frequency (0.55%) of the P.4 lineage across the state, with the gamma variant being the dominant form in all regions (90%) at that time. Furthermore, no evidence of increased transmissibility and disease severity related to the P.4 lineage was observed. The displacement through the time of different lineages in São Paulo highlights how challenging genomic surveillance appears to track the emergence of new SARS-CoV-2 lineages, which could better guide the implementation of control measures.
Keywords: COVID-19; genomic surveillance; mutations; São Paulo COVID-19; genomic surveillance; mutations; São Paulo

Share and Cite

MDPI and ACS Style

Poleti, M.D.; Lesbon, J.C.C.; de Mattos Oliveira, E.C.; Patané, J.S.L.; Clemente, L.G.; Viala, V.L.; Ribeiro, G.; Pinheiro, J.F.P.; Giovanetti, M.; Alcantara, L.C.J.; et al. SARS-CoV-2 Lineage P.4 Detection in Southeast Brazil: A Retrospective Genomic and Clinical Overview. COVID 2022, 2, 1768-1777. https://doi.org/10.3390/covid2120127

AMA Style

Poleti MD, Lesbon JCC, de Mattos Oliveira EC, Patané JSL, Clemente LG, Viala VL, Ribeiro G, Pinheiro JFP, Giovanetti M, Alcantara LCJ, et al. SARS-CoV-2 Lineage P.4 Detection in Southeast Brazil: A Retrospective Genomic and Clinical Overview. COVID. 2022; 2(12):1768-1777. https://doi.org/10.3390/covid2120127

Chicago/Turabian Style

Poleti, Mirele Daiana, Jéssika Cristina Chagas Lesbon, Elisângela Chicaroni de Mattos Oliveira, José Salvatore Leister Patané, Luan Gaspar Clemente, Vincent Louis Viala, Gabriela Ribeiro, Jéssica Fernanda Perissato Pinheiro, Marta Giovanetti, Luiz Carlos Junior Alcantara, and et al. 2022. "SARS-CoV-2 Lineage P.4 Detection in Southeast Brazil: A Retrospective Genomic and Clinical Overview" COVID 2, no. 12: 1768-1777. https://doi.org/10.3390/covid2120127

APA Style

Poleti, M. D., Lesbon, J. C. C., de Mattos Oliveira, E. C., Patané, J. S. L., Clemente, L. G., Viala, V. L., Ribeiro, G., Pinheiro, J. F. P., Giovanetti, M., Alcantara, L. C. J., de Lima, L. P. O., Martins, A. J., dos Santos Barros, C. R., Marqueze, E. C., de Souza Todão Bernardino, J., Moretti, D. B., Brassaloti, R. A., de Lello Rocha Campos Cassano, R., Mariani, P. D. S. C., ... Fukumasu, H. (2022). SARS-CoV-2 Lineage P.4 Detection in Southeast Brazil: A Retrospective Genomic and Clinical Overview. COVID, 2(12), 1768-1777. https://doi.org/10.3390/covid2120127

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