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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.
- Received:
- Accepted:
- Published Online:
Funding
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
(Award 313403/2018-0)
- Principle Award Recipient: MarildaMendonça Siqueira
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
(Award 302317/2017-1)
- Principle Award Recipient: GonzaloBello
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
(Award 303902/2019)
- Principle Award Recipient: GabrielLuz wallau
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
(Award 306146/2017-7)
- Principle Award Recipient: FelipeGomes Naveca
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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
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
(Award CNPQ BRICS STI 4 441080/2020-0)
- Principle Award Recipient: MarildaMendonça Siqueira
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
(Award Covid 10 MCTI 402457/2020-0)
- Principle Award Recipient: MarildaMendonça Siqueira
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INCT-FCx
(Award 465259/2014-6)
- Principle Award Recipient: MarildaMendonça Siqueira
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Inova Fiocruz/Fundação Oswaldo Cruz
(Award VPPCB-005- FIO-20-2-87)
- Principle Award Recipient: MarildaMendonça Siqueira
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Inova Fiocruz/Fundação Oswaldo Cruz
(Award VPPCB-007-FIO-18-2-30)
- Principle Award Recipient: MarildaMendonça Siqueira
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FAPERJ
(Award E-26/210.196/2020)
- Principle Award Recipient: MarildaMendonça Siqueira
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FAPERJ
(Award E-203.074/2017)
- Principle Award Recipient: MarildaMendonça Siqueira
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FAPEAM
(Award 005/2020)
- Principle Award Recipient: FelipeGomes Naveca
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MS/FNDCT/SCTIE/Decit
(Award 403276/2020-9)
- Principle Award Recipient: FelipeGomes Naveca
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MS/FNDCT/SCTIE/Decit
(Award 402457/2020-9)
- Principle Award Recipient: FelipeGomes Naveca