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medrxiv; 2021.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2021.12.27.21268309


The COVID-19 epidemic in Brazil was driven mainly by the spread of Gamma (P.1), a locally emerged Variant of Concern (VOC) that was first detected in early January 2021. This variant was estimated to be responsible for more than 96% of cases reported between January and June 2021, being associated with increased transmissibility and disease severity, a reduction in neutralization antibodies and effectiveness of treatments or vaccines, as well as diagnostic detection failure. Here we show that, following several importations predominantly from the USA, the Delta variant rapidly replaced Gamma after July 2021. However, in contrast to what was seen in other countries, the rapid spread of Delta did not lead to a large increase in the number of cases and deaths reported in Brazil. We suggest that this was likely due to the relatively successful early vaccination campaign coupled with natural immunity acquired following prior infection with Gamma. Our data reinforces reports of the increased transmissibility of the Delta variant and, considering the increasing concern due to the recently identified Omicron variant, argues for the necessity to strengthen genomic monitoring on a national level to quickly detect and curb the emergence and spread of other VOCs that might threaten global health.

COVID-19 , Death
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.
medrxiv; 2021.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2021.10.07.21264644


Brazil has experienced some of the highest numbers of COVID-19 infections and deaths globally and made Latin America a pandemic epicenter from May 2021. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of local virus transmission dynamics. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and an adjacent 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, the absence of effective restriction measures led to the local emergence and international spread of Variants of Concern (VOC) and under monitoring (VUM), including the Gamma (P.1) and Zeta (P.2) variants. In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring and providing a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

medrxiv; 2020.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2020.05.05.20091611


The recent emergence of a previously unknown coronavirus (SARS-CoV-2), first confirmed in the city of Wuhan in China in December 2019, has caused serious public health and economic issues due to its rapid dissemination worldwide. Although 61,888 confirmed cases had been reported in Brazil by 28 April 2020, little was known about the SARS-CoV-2 epidemic in the country. To better understand the recent epidemic in the second most populous state in southeast Brazil (Minas Gerais, MG), we looked at existing epidemiological data from 3 states and sequenced 40 complete genomes from MG cases using Nanopore. We found evidence of multiple independent introductions from outside MG, both from genome analyses and the overly dispersed distribution of reported cases and deaths. Epidemiological estimates of the reproductive number using different data sources and theoretical assumptions all suggest a reduction in transmission potential since the first reported case, but potential for sustained transmission in the near future. The estimated date of introduction in Brazil was consistent with epidemiological data from the first case of a returning-traveler from Lombardia, Italy. These findings highlight the unique reality of MGs epidemic and reinforce the need for real-time and continued genomic surveillance strategies as a way of understanding and therefore preparing against the epidemic spread of emerging viral pathogens.

biorxiv; 2020.
Preprint in English | bioRxiv | ID: ppzbmed-10.1101.2020.04.30.069039


Genomic surveillance has become a useful tool for better understanding virus pathogenicity, origin and spread. Obtaining accurately assembled, complete viral genomes directly from clinical samples is still a challenging. Here, we describe three protocols using a unique primer set designed to recover long reads of SARS-CoV-2 directly from total RNA extracted from clinical samples. This protocol is useful, accessible and adaptable to laboratories with varying resources and access to distinct sequencing methods: Nanopore, Illumina and/or Sanger.