Citation: Viala, V.L.; Slavov, S.N.; de Lima, L.P.O.; Lima, A.R.J.; Ribeiro, G.; Martins, A.J.; Petry, B.; Banho, C.A.; Barros, C.R.d.S.; Moncau, C.T.; et al. The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela. Viruses 2022, 14, 1481. https://doi.org/10.3390/v14071481 Academic Editor: Lokesh Kumar Sharma Received: 18 April 2022 Accepted: 30 June 2022 Published: 5 July 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). viruses Article The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela Vincent Louis Viala 1, * , Svetoslav Nanev Slavov 2 , Loyze Paola Oliveira de Lima 1 , Alex Ranieri Jeronimo Lima 1 , Gabriela Ribeiro 1 , Antonio Jorge Martins 1 , Bruna Petry 3 , Cecilia Artico Banho 4 , Claudia Renata dos Santos Barros 1 , Cristina Tschorny Moncau 3 , Debora Botequio Moretti 1 , Debora Glenda Lima de La-Roque 2 , Elaine Cristina Marqueze 1 , Elisangela Chicaroni Mattos 5 , Felipe Allan da Silva da Costa 6 , Heidge Fukumasu 5 , Jardelina de Souza Todao Bernardino 1 , Jayme A. Souza-Neto 7 , Jessika Cristina Chagas Lesbon 5 , Lara Passos Kayanoki 8 , Leandro Lombo Bernardo 9 ,Lívia Sacchetto 4 , Luan Gaspar Clemente 3 , Luiz Carlos Júnior Alcantara 10,11 , Luiz Lehmann Coutinho 3 , Beatriz de Carvalho Marques 4 , Marta Giovanetti 12,13 , Maurício Lacerda Nogueira 4 , Mirele Daiana Poleti 5 , Patricia Akemi Assato 6 , Pedro De Queiroz Cattony Neto 1 , Raquel de Lello Rocha Campos Cassano 3 , Raul Machado Neto 1 , Rejane Maria Tommasini Grotto 7,14 , Ricardo Augusto Brassaloti 3 , Simone Kashima 2 , Dimas Tadeu Covas 1,2 , Maria Carolina Elias 1, * and Sandra Coccuzzo Sampaio 1, * 1 Butantan Institute, São Paulo 05503-900, SP, Brazil; loyze.lima@butantan.gov.br (L.P.O.d.L.); alex.lima@butantan.gov.br (A.R.J.L.); gabriela.rribeiro@butantan.gov.br (G.R.); antonio.martins@butantan.gov.br (A.J.M.); claudia.barros@butantan.gov.br (C.R.d.S.B.); debora.moretti@butantan.gov.br (D.B.M.); elaine.marqueze@butantan.gov.br (E.C.M.); jardelina.bernardino@butantan.gov.br (J.d.S.T.B.); pedro.cattony@butantan.gov.br (P.D.Q.C.N.); raul.machado@butantan.gov.br (R.M.N.); dimas.covas@butantan.gov.br (D.T.C.) 2 Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; svetoslav.slavov@hemocentro.fmrp.usp.br (S.N.S.); debora.laroque@usp.br (D.G.L.d.L.-R.); skashima@hemocentro.fmrp.usp.br (S.K.) 3 Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, SP, Brazil; bruna.petry@usp.br (B.P.); crismoncau@gmail.com (C.T.M.); luan.clemente@usp.br (L.G.C.); llcoutinho@usp.br (L.L.C.); raquel_lello@yahoo.com.br (R.d.L.R.C.C.); ricardo.brassaloti@usp.br (R.A.B.) 4 Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil; ceci.abanho@gmail.com (C.A.B.); liviasacchetto@gmail.com (L.S.); bbiacarvalho@outlook.com (B.d.C.M.); mauricio.nogueira@edu.famerp.br (M.L.N.) 5 Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, SP, Brazil; limattos@usp.br (E.C.M.); fukumasu@usp.br (H.F.); jessika.chagas@usp.br (J.C.C.L.); mirelep@usp.br (M.D.P.) 6 Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; felipe.allan@unesp.br (F.A.d.S.d.C.); p.assato@unesp.br (P.A.A.) 7 School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; jayme.souza-neto@unesp.br (J.A.S.-N.); rejane.grotto@unesp.br (R.M.T.G.) 8 Vigilância Epidemiológica de Ilhabela, Ilhabela 11630-000, SP, Brazil; ve.saude@ilhabela.sp.gov.br 9 Hospital Mario Covas Junior, Ilhabela 11630-000, SP, Brazil; leandrobernardo50@gmail.com 10 Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; alcantaraluiz42@gmail.com 11 Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-360, RJ, Brazil 12 Reference Laboratory of Flavivirus, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, RJ, Brazil; marta.giovanetti@ioc.fiocruz.br 13 Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, 00128 Rome, Italy 14 Molecular Biology and Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, Botucatu 18610-034, SP, Brazil * Correspondence: vincent.viala@butantan.gov.br (V.L.V.); carolina.eliassabbaga@butantan.gov.br (M.C.E.); sandra.coccuzzo@butantan.gov.br (S.C.S.) 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) Viruses 2022, 14, 1481. https://doi.org/10.3390/v14071481 https://www.mdpi.com/journal/viruses