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1.
Marta Giovanetti; Svetoslav Nanev Slavov; Vagner Fonseca; Eduan Wilkinson; Houriiyah Tegally; Jose Patane; Vincent Louis Viala; Emmanuel James San; Evandra Strazza Rodrigues; Elaine Vieira Santos; Flavia Aburjaile; Joilson Xavier; Hegger Fritsch; Talita Emile Ribeiro Adelino; Felicidade Pereira; Arabela Leal; Felipe Campos de Melo Iani; Glauco de Carvalho Pereira; Cynthia Vazquez; Gladys Mercedes Estigarribia Sanabria; Elaine Cristina de Oliveira; Luiz Demarchi; Julio Croda; Rafael Dos Santos Bezerra Sr.; Loyze Paola Oliveira de Lima; Antonio Jorge Martins; Claudia Renata dos Santos Barros; Elaine Cristina Marqueze; Jardelina de Souza Todao Bernardino; Debora Botequio Moretti; Ricardo Augusto Brassaloti; Raquel de Lello Rocha Campos Cassano; Pilar Drummond Sampaio Correa Mariani; Joao Paulo Kitajima; Bibiana Santos; Rodrigo Proto Siqueira; Vlademir Vicente Cantarelli; Stephane Tosta; Vanessa Brandao Nardy; Luciana Reboredo de Oliveira da Silva; Marcela Kelly Astete Gomez; Jaqueline Gomes Lima; Adriana Aparecida Ribeiro; Natalia Rocha Guimaraes; Luiz Takao Watanabe; Luana Barbosa Da Silva; Raquel da Silva Ferreira; Mara Patricia F. da Penha; Maria Jose Ortega; Andrea Gomez de la Fuente; Shirley Villalba; Juan Torales; Maria Liz Gamarra; Carolina Aquino; Gloria Patricia Martinez Figueredo; Wellington Santos Fava; Ana Rita C. Motta Castro; James Venturini; Sandra Maria do Vale Leone de Oliveira; Crhistinne Cavalheiro Maymone Goncalves; Maria do Carmo Debur Rossa; Guilherme Nardi Becker; Mayra Marinho Presibella; Nelson Quallio Marques; Irina Nastassja Riediger; Sonia Raboni; Gabriela Mattoso; Allan D. Cataneo; Camila Zanluca; Claudia N Duarte dos Santos; Patricia Akemi Assato; Felipe Allan da Silva da Costa; Mirele Daiana Poleti; Jessika Cristina Chagas Lesbon; Elisangela Chicaroni Mattos; Cecilia Artico Banho; Livia S Sacchetto; Marilia Mazzi Moraes; Rejane Maria Tommasini Grotto; Jayme A. Souza-Neto; Mauricio L Nogueira; Heidge Fukumasu; Luiz Lehmann Coutinho; Rodrigo Tocantins Calado; Raul Machado Neto; Ana Maria Bispo de Filippis; Rivaldo Venancio da Cunha; Carla Freitas; Cassio Roberto Leonel Peterka; Cassia de Fatima Rangel Fernandes; Wildo Navegantes; Rodrigo Fabiano do Carmo Said; Maria Almiron; Carlos F Campelo de A e Melo; Jose Lourenco; Tulio de Oliveira; Edward C Holmes; Ricardo Haddad; Sandra Coccuzzo Sampaio; Maria Carolina Elias; Simone Kashima; Luiz Carlos Junior Alcantara; Dimas Tadeu Covas.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-21264644

Résumé

Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

2.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-21260508

Résumé

We report a genomic surveillance of SARS-CoV-2 lineages circulating in Parana, Southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Parana in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1.1.28 and B.1.1.33 were predominant throughout 2020 until the introduction of the variant P.2 in August 2020 and a variant of concern (VOC), P.1, in January 2021. Phylogenetic analyses of the SARS-CoV-2 genomes that were previously classified as the VOC P.1 lineage by PANGO showed that some genomes from February to April 2021 branched in a monophyletic clade and that these samples grouped together with genomes recently described with the lineage P.1-like-II. An extended phylogenetic analysis, including SARS-CoV-2 genomes from all over Brazil, showed that the P.1-like-II lineage appears at a high frequency in the southern region of the country. The P.1-like-II lineage genomes share some, but not all, defining mutations of the VOC P.1. For instance, it has the previously described ORF1a:D2980H and N:P383 L unique mutations and the newly detected ORF1a:P1213 L and ORF1b:K2340N mutations. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10% of the genomes classified as the VOC P.1 from Parana in March and April 2021. We also report the identification of the S:W152C mutation in one genome from Parana, classified as the N.10 variant. Finally, we analyzed the correlation between the lineage and the P.1 variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Parana. This analysis does not support an association between the P.1 variant prevalence and COVID-19 severity or age strata. Our results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Parana characterized by the dominance of the P.1 strain, as well as a high frequencies of the P.1-like-II lineage and the S:E661D mutations. Epidemiological and genomic surveillance efforts should be continued to unveil the biological relevance of the novel mutations detected in the VOC P.1 in Parana.

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