1887

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.

Funding
This study was supported by the:
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award 313403/2018-0)
    • Principle Award Recipient: MarildaMendonça Siqueira
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award 302317/2017-1)
    • Principle Award Recipient: GonzaloBello
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award 303902/2019)
    • Principle Award Recipient: GabrielLuz wallau
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award 306146/2017-7)
    • Principle Award Recipient: FelipeGomes Naveca
  • Pan American Health Organization Brazil Country Office and by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Award Finance Code 001)
    • Principle Award Recipient: MarildaMendonça Siqueira
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award CNPQ BRICS STI 4 441080/2020-0)
    • Principle Award Recipient: MarildaMendonça Siqueira
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award Covid 10 MCTI 402457/2020-0)
    • Principle Award Recipient: MarildaMendonça Siqueira
  • INCT-FCx (Award 465259/2014-6)
    • Principle Award Recipient: MarildaMendonça Siqueira
  • Inova Fiocruz/Fundação Oswaldo Cruz (Award VPPCB-005- FIO-20-2-87)
    • Principle Award Recipient: MarildaMendonça Siqueira
  • Inova Fiocruz/Fundação Oswaldo Cruz (Award VPPCB-007-FIO-18-2-30)
    • Principle Award Recipient: MarildaMendonça Siqueira
  • FAPERJ (Award E-26/210.196/2020)
    • Principle Award Recipient: MarildaMendonça Siqueira
  • FAPERJ (Award E-203.074/2017)
    • Principle Award Recipient: MarildaMendonça Siqueira
  • FAPEAM (Award 005/2020)
    • Principle Award Recipient: FelipeGomes Naveca
  • MS/FNDCT/SCTIE/Decit (Award 403276/2020-9)
    • Principle Award Recipient: FelipeGomes Naveca
  • MS/FNDCT/SCTIE/Decit (Award 402457/2020-9)
    • Principle Award Recipient: FelipeGomes Naveca
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2022-03-17
2024-04-28
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