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Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat.
Hannon, William W; Roychoudhury, Pavitra; Xie, Hong; Shrestha, Lasata; Addetia, Amin; Jerome, Keith R; Greninger, Alexander L; Bloom, Jesse D.
  • Hannon WW; Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA.
  • Roychoudhury P; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • Xie H; Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195, USA.
  • Shrestha L; Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195, USA.
  • Addetia A; Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA.
  • Jerome KR; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • Greninger AL; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • Bloom JD; Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA.
Virus Evol ; 8(2): veac052, 2022.
Article in English | MEDLINE | ID: covidwho-1922335
ABSTRACT
The long-term evolution of viruses is ultimately due to viral mutants that arise within infected individuals and transmit to other individuals. Here, we use deep sequencing to investigate the transmission of viral genetic variation among individuals during a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak that infected the vast majority of crew members on a fishing boat. We deep-sequenced nasal swabs to characterize the within-host viral population of infected crew members, using experimental duplicates and strict computational filters to ensure accurate variant calling. We find that within-host viral diversity is low in infected crew members. The mutations that did fix in some crew members during the outbreak are not observed at detectable frequencies in any of the sampled crew members in which they are not fixed, suggesting that viral evolution involves occasional fixation of low-frequency mutations during transmission rather than persistent maintenance of within-host viral diversity. Overall, our results show that strong transmission bottlenecks dominate viral evolution even during a superspreading event with a very high attack rate.
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Full text: Available Collection: International databases Database: MEDLINE Topics: Variants Language: English Journal: Virus Evol Year: 2022 Document Type: Article Affiliation country: Ve

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Full text: Available Collection: International databases Database: MEDLINE Topics: Variants Language: English Journal: Virus Evol Year: 2022 Document Type: Article Affiliation country: Ve