tetano
Editor, Senior Moderator
Microb Genom
. 2022 Mar;8(3).
doi: 10.1099/mgen.0.000751.
Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection
Filipe Zimmer Dezordi[SUP] 1 2 [/SUP], Paola Cristina Resende[SUP] 3 [/SUP], Felipe Gomes Naveca[SUP] 4 [/SUP], Valdinete Alves do Nascimento[SUP] 4 [/SUP], Victor Costa de Souza[SUP] 4 [/SUP], Anna Carolina Dias Paixão[SUP] 3 [/SUP], Luciana Appolinario[SUP] 3 [/SUP], Renata Serrano Lopes[SUP] 3 [/SUP], Ana Carolina da Fonseca Mendonça[SUP] 3 [/SUP], Alice Sampaio Barreto da Rocha[SUP] 3 [/SUP], Taina Moreira Martins Venas[SUP] 3 [/SUP], Elisa Cavalcante Pereira[SUP] 3 [/SUP], Marcelo Henrique Santos Paiva[SUP] 1 5 [/SUP], Cassia Docena[SUP] 6 [/SUP], Matheus Filgueira Bezerra[SUP] 7 [/SUP], Laís Ceschini Machado[SUP] 1 [/SUP], Richard Steiner Salvato[SUP] 8 [/SUP], Tatiana Schäffer Gregianini[SUP] 8 [/SUP], Leticia Garay Martins[SUP] 9 [/SUP], Felicidade Mota Pereira[SUP] 10 [/SUP], Darcita Buerger Rovaris[SUP] 11 [/SUP], Sandra Bianchini Fernandes[SUP] 11 [/SUP], Rodrigo Ribeiro-Rodrigues[SUP] 12 [/SUP], Thais Oliveira Costa[SUP] 13 [/SUP], Joaquim Cesar Sousa[SUP] 13 [/SUP], Fabio Miyajima[SUP] 13 [/SUP], Edson Delatorre[SUP] 14 [/SUP], Tiago Gräf[SUP] 15 [/SUP], Gonzalo Bello[SUP] 16 [/SUP], Marilda Mendonça Siqueira[SUP] 3 [/SUP], Gabriel Luz Wallau[SUP] 1 2 [/SUP]
Affiliations
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.
Keywords: COVID-19; codetection; coinfection; genomics.
. 2022 Mar;8(3).
doi: 10.1099/mgen.0.000751.
Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection
Filipe Zimmer Dezordi[SUP] 1 2 [/SUP], Paola Cristina Resende[SUP] 3 [/SUP], Felipe Gomes Naveca[SUP] 4 [/SUP], Valdinete Alves do Nascimento[SUP] 4 [/SUP], Victor Costa de Souza[SUP] 4 [/SUP], Anna Carolina Dias Paixão[SUP] 3 [/SUP], Luciana Appolinario[SUP] 3 [/SUP], Renata Serrano Lopes[SUP] 3 [/SUP], Ana Carolina da Fonseca Mendonça[SUP] 3 [/SUP], Alice Sampaio Barreto da Rocha[SUP] 3 [/SUP], Taina Moreira Martins Venas[SUP] 3 [/SUP], Elisa Cavalcante Pereira[SUP] 3 [/SUP], Marcelo Henrique Santos Paiva[SUP] 1 5 [/SUP], Cassia Docena[SUP] 6 [/SUP], Matheus Filgueira Bezerra[SUP] 7 [/SUP], Laís Ceschini Machado[SUP] 1 [/SUP], Richard Steiner Salvato[SUP] 8 [/SUP], Tatiana Schäffer Gregianini[SUP] 8 [/SUP], Leticia Garay Martins[SUP] 9 [/SUP], Felicidade Mota Pereira[SUP] 10 [/SUP], Darcita Buerger Rovaris[SUP] 11 [/SUP], Sandra Bianchini Fernandes[SUP] 11 [/SUP], Rodrigo Ribeiro-Rodrigues[SUP] 12 [/SUP], Thais Oliveira Costa[SUP] 13 [/SUP], Joaquim Cesar Sousa[SUP] 13 [/SUP], Fabio Miyajima[SUP] 13 [/SUP], Edson Delatorre[SUP] 14 [/SUP], Tiago Gräf[SUP] 15 [/SUP], Gonzalo Bello[SUP] 16 [/SUP], Marilda Mendonça Siqueira[SUP] 3 [/SUP], Gabriel Luz Wallau[SUP] 1 2 [/SUP]
Affiliations
- PMID: 35297757
- DOI: 10.1099/mgen.0.000751
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.
Keywords: COVID-19; codetection; coinfection; genomics.