Open AccessUnusual SARS-CoV-2 intrahost diversity reveals lineage superinfection
Author(s) -
Filipe Zimmer Dezordi,
Paola Cristina Resende,
Felipe Gomes Naveca,
Valdinete Alves do Nascimento,
Victor Costa de Souza,
Ariane Gomes Paixão,
Luciana Appolinario,
Renata Serrano Lopes,
Ana Carolina da Fonseca Mendonça,
Alice Sampaio Barreto da Rocha,
Tainá Moreira Martins Venas,
Elisa Cavalcante Pereira,
Marcelo Henrique Santos Paiva,
Cássia Docena,
Matheus Filgueira Bezerra,
Laís Ceschini Machado,
Richard Steiner Salvato,
Tatiana Schäffer Gregianini,
Letícia Garay Martins,
Felicidade Mota Pereira,
Darcita Büerger Rovaris,
Sandra Bianchini Fernandes,
Rodrigo RibeiroRodrigues,
Thais Oliveira Costa,
Joaquim Cesar Sousa,
Fábio Miyajima,
Edson Delatorre,
Tiago Gräf,
Gonzalo Bello,
Marilda Mendonça Siqueira,
Gabriel Luz Wallau
Publication year - 2022
Publication title -
microbial genomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.476
H-Index - 28
ISSN - 2057-5858
DOI - 10.1099/mgen.0.000751
Subject(s) - lineage (genetic) , coinfection , biology , evolutionary biology , superinfection , pandemic , phylogenetics , covid-19 , genetics , virology , disease , virus , gene , infectious disease (medical specialty) , medicine , pathology
Severe Acute Respiratory Syndrome Coronavirus 2 (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 may impact COVID-19 disease progression and 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 phylogenetically defined, but two main factors have precluded major coinfection/codetection and recombination 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/recombining viral lineages; and the (ii) limited availability of raw sequencing data where abundance and distribution of intrasample/intrahost variability can be accessed. Here, we assembled 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. This approach enabled us to detect nine cases of SARS-CoV-2 coinfection with well characterized lineage-defining mutations, representing 0.61 % of all samples investigated. In addition, we matched these SARS-CoV-2 coinfections with spatio-temporal epidemiological data confirming its plausibility with the cocirculating lineages at the timeframe investigated. Our data suggests that coinfection with distinct SARS-CoV-2 lineages is a rare phenomenon, although it is certainly a lower bound estimate considering the difficulty to detect coinfections with very similar SARS-CoV-2 lineages and the low number of samples sequenced from the total number of infections.