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Unusual SARS-CoV-2 intra-host diversity reveals lineages superinfection
Filipe Zimmer Dezordi; Paola Cristina Resende; Felipe Gomes Naveca; Valdinete Alves do Nascimento; Victor Costa de Souza; Anna Carolina Dias Paixao; Luciana Appolinario; Renata Serrano Lopes; Ana Carolina da Fonseca Mendonca; Alice Sampaio Barreto da Rocha; Taina Moreira Martins Venas; Elisa Cavalcante Pereira; Richard Steiner Salvato; Tatiana Schaffer Gregianini; Leticia Garay Martins; Felicidade Mota Pereira; Darcita Buerger Rovaris; Sandra Bianchini Fernandes; Rodrigo Ribeiro-Rodrigues; Thais Oliveira Costa; Joaquim Cesar Sousa Jr.; Fabio Miyajima; Edson Delatorre; Tiago Graf; Gonzalo Bello; Marilda Mendonca Siqueira; Gabriel Luz Wallau.
  • Filipe Zimmer Dezordi; Departamento de Entomologia e Nucleo de Bioinformatica, Instituto Aggeu Magalhaes (IAM), FIOCRUZ-Pernambuco, Recife, Brasil.
  • Paola Cristina Resende; Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brasil.
  • Felipe Gomes Naveca; Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia (EDTA), Leonidas e Maria Deane Institute, Fiocruz, Manaus, Amazonas, Brazil.
  • Valdinete Alves do Nascimento; Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia (EDTA), Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil.
  • Victor Costa de Souza; Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia (EDTA), Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil.
  • Anna Carolina Dias Paixao; Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brasil.
  • Luciana Appolinario; Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brasil.
  • Renata Serrano Lopes; Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brasil.
  • Ana Carolina da Fonseca Mendonca; Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brasil.
  • Alice Sampaio Barreto da Rocha; Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brasil.
  • Taina Moreira Martins Venas; Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brasil.
  • Elisa Cavalcante Pereira; Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brasil.
  • Richard Steiner Salvato; Laboratorio Central de Saude Publica, Centro Estadual de Vigilancia em Saude da Secretaria de Saude do Estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Al
  • Tatiana Schaffer Gregianini; Laboratorio Central de Saude Publica, Centro Estadual de Vigilancia em Saude da Secretaria de Saude do Estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Al
  • Leticia Garay Martins; Centro Estadual de Vigilancia em Saude da Secretaria de Saude do Estado do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil.
  • Felicidade Mota Pereira; Laboratorio Central de Saude Publica do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brasil.
  • Darcita Buerger Rovaris; Laboratorio Central de Saude Publica do Estado de Santa Catarina (LACEN-SC), Florianopolis, Santa Catarina, Brasil.
  • Sandra Bianchini Fernandes; Laboratorio Central de Saude Publica do Estado de Santa Catarina (LACEN-SC), Florianopolis, Santa Catarina, Brasil.
  • Rodrigo Ribeiro-Rodrigues; Laboratorio Central de Saude Publica do Estado do Espirito Santo (LACEN-ES), Vitoria, Espirito Santo, Brasil.
  • Thais Oliveira Costa; Analytical Competence Molecular Epidemiology Laboratory (ACME), FIOCRUZ-Ceara, Fortaleza, Ceara, Brasil.
  • Joaquim Cesar Sousa Jr.; Analytical Competence Molecular Epidemiology Laboratory (ACME), FIOCRUZ-Ceara, Fortaleza, Ceara, Brasil.
  • Fabio Miyajima; Analytical Competence Molecular Epidemiology Laboratory (ACME), FIOCRUZ-Ceara, Fortaleza, Ceara, Brasil.
  • Edson Delatorre; Departamento de Biologia. Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, Espirito Santo, Alegre, Brasil.
  • Tiago Graf; Instituto Goncalo Moniz (IGM), Fundacao Oswaldo Cruz, Salvador, Bahia, Brasil.
  • Gonzalo Bello; Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brasil.
  • Marilda Mendonca Siqueira; Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brasil.
  • Gabriel Luz Wallau; Departamento de Entomologia e Nucleo de Bioinformatica, Instituto Aggeu Magalhaes (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brasil.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-21263755
ABSTRACT
The SARS-CoV-2 has infected almost 200 million people worldwide by July 2021 and the pandemic has been characterized by infection waves of viral lineages showing distinct fitness profiles. The simultaneous infection of a single individual by two distinct SARS-CoV-2 lineages provides a window of opportunity for viral recombination and the emergence of new lineages with differential phenotype. Several hundred SARS-CoV-2 lineages are currently well characterized but two main factors have precluded major coinfection/codetection analysis thus far i) the low diversity of SARS-CoV-2 lineages during the first year of the pandemic which limited the identification of lineage defining mutations necessary to distinguish coinfecting viral lineages; and the ii) limited availability of raw sequencing data where abundance and distribution of intrasample/intrahost variability can be accessed. Here, we have put together a large sequencing dataset from Brazilian samples covering a period of 18 May 2020 to 30 April 2021 and probed it for unexpected patterns of high intrasample/intrahost variability. It enabled us to detect nine cases of SARS-CoV-2 coinfection with well characterized lineage-defining mutations. In addition, we matched these SARS-CoV-2 coinfections with spatio-temporal epidemiological data confirming their plausibility with the co-circulating lineages at the timeframe investigated. These coinfections represent around 0.61% of all samples investigated. Although our data suggests that coinfection with distinct SARS-CoV-2 lineages is a rare phenomenon, it is likely an underestimation and coinfection rates warrants further investigation. DATA SUMMARYThe raw fastq data of codetection cases are deposited on gisaid.org and correlated to gisaid codes EPI_ISL_1068258, EPI_ISL_2491769, EPI_ISL_2491781, EPI_ISL_2645599, EPI_ISL_2661789, EPI_ISL_2661931, EPI_ISL_2677092, EPI_ISL_2777552, EPI_ISL_3869215. Supplementary data are available on https//doi.org/10.6084/m9.figshare.16570602.v1. The workflow code used in this study is publicly available on https//github.com/dezordi/IAM_SARSCOV2.
Texte intégral: Disponible Collection: Preprints Base de données: medRxiv Type d'étude: Étude pronostique langue: Anglais Année: 2021 Type de document: Preprint

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Texte intégral: Disponible Collection: Preprints Base de données: medRxiv Type d'étude: Étude pronostique langue: Anglais Année: 2021 Type de document: Preprint