Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection. Issue 3 (17th March 2022)

• Record Type: Journal Article
• Authors: Dezordi, Filipe Zimmer; Resende, Paola Cristina; Naveca, Felipe Gomes; do Nascimento, Valdinete Alves; de Souza, Victor Costa; Dias Paixão, Anna Carolina; Appolinario, Luciana; Lopes, Renata Serrano; da Fonseca Mendonça, Ana Carolina; Barreto da Rocha, Alice Sampaio; Martins Venas, Taina Moreira; Pereira, Elisa Cavalcante; Paiva, Marcelo Henrique Santos; Docena, Cassia; Bezerra, Matheus Filgueira; Machado, Laís Ceschini; Salvato, Richard Steiner; Gregianini, Tatiana Schäffer; Martins, Leticia Garay; Pereira, Felicidade Mota; Rovaris, Darcita Buerger; Fernandes, Sandra Bianchini; Ribeiro-Rodrigues, Rodrigo; Costa, Thais Oliveira; Sousa, Joaquim Cesar; Miyajima, Fabio; Delatorre, Edson; Gräf, Tiago; Bello, Gonzalo; Siqueira, Marilda Mendonça; Wallau, Gabriel Luz;
• Is Part Of: Microbial genomics. Volume 8:Issue 3(2022)
• Publication Date: 2022-03-17
• Subjects: codetection -- coinfection -- COVID-19 -- genomics; Microbial genomics -- Periodicals; 572.8629
• DOI: 10.1099/mgen.0.000751
• Languages: English
• ISSNs: 2057-5858

Abstract

Abstract : 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.