Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection

• DOI: 10.1099/mgen.0.000751
• Publication Date: 2022-03-17T14:20:44Z
• Authors: Filipe Zimmer Dez...; Paola Cristina Re...; Felipe Gomes Naveca; Valdinete Alves d...; Victor Costa de S...; Anna Carolina Dia...; Luciana Appolinario; Renata Serrano Lopes; Ana Carolina da F...; Alice Sampaio Bar...; Taina Moreira Mar...; Elisa Cavalcante ...; Marcelo Henrique ...; Cassia Docena; Matheus Filgueira...; Laís Ceschini Mac...; Richard Steiner S...; Tatiana Schäffer ...; Leticia Garay Mar...; Felicidade Mota P...; Darcita Buerger R...; Sandra Bianchini ...; Rodrigo Ribeiro-R...; Thais Oliveira Costa; Joaquim Cesar Sousa; Fabio Miyajima; Edson Delatorre; Tiago Gräf; Gonzalo Bello; Marilda Mendonça ...; Gabriel Luz Wallau
• Keywords: Lineage (genetic); Superinfection; Pandemic

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has infected almost 200 million people worldwide by July 2021 and the pandemic been characterized infection waves of viral lineages showing distinct fitness profiles. The simultaneous a single individual two SARS-CoV-2 may impact COVID-19 disease progression provides window opportunity for recombination emergence new with differential phenotype. Several hundred are currently well phylogenetically defined, but main factors have precluded major coinfection/codetection analysis thus far: (i) low diversity during first year pandemic, which limited identification lineage defining mutations necessary to distinguish coinfecting/recombining lineages; (ii) availability raw sequencing data where abundance distribution intrasample/intrahost variability can be accessed. Here, we assembled large dataset from Brazilian samples covering period 18 May 2020 30 April probed it unexpected patterns high variability. This approach enabled us detect nine cases coinfection lineage-defining mutations, representing 0.61 % all investigated. In addition, matched these coinfections spatio-temporal epidemiological confirming its plausibility cocirculating at timeframe Our suggests that is rare phenomenon, although certainly lower bound estimate considering difficulty very similar number sequenced total infections.