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Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine.
Yeh, Ting-Yu; Contreras, Gregory P.
  • Yeh TY; Auxergen Inc., Columbus Center, 701 East Pratt Street, Baltimore, MD 21202, United States of America.
  • Contreras GP; Auxergen Inc., Columbus Center, 701 East Pratt Street, Baltimore, MD 21202, United States of America.
Bull World Health Organ ; 99(7): 486-495, 2021 Jul 01.
Article in English | MEDLINE | ID: covidwho-1305609
ABSTRACT

OBJECTIVE:

To examine transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in shipboard quarantine of the Diamond Princess cruise ship.

METHODS:

We obtained the full SARS-CoV-2 genome sequences of 28 samples from the Global Initiative on Sharing All Influenza Data database. The samples were collected between 10 and 25 February 2020 and came for individuals who had been tested for SARS-CoV-2 during the quarantine on the cruise ship. These samples were later sequenced in either Japan or the United States of America. We analysed evolution dynamics of SARS-CoV-2 using computational tools of phylogenetics, natural selection pressure and genetic linkage.

FINDINGS:

The SARS-CoV-2 outbreak in the cruise most likely originated from either a single person infected with a virus variant identical to the WIV04 isolates, or simultaneously with another primary case infected with a virus containing the 11083G > T mutation. We identified a total of 24 new viral mutations across 64.2% (18/28) of samples, and the virus evolved into at least five subgroups. Increased positive selection of SARS-CoV-2 were statistically significant during the quarantine (Tajima's D -2.03, P < 0.01; Fu and Li's D -2.66, P < 0.01; and Zeng's E -2.37, P < 0.01). Linkage disequilibrium analysis confirmed that ribonucleic acid (RNA) recombination with the11083G > T mutation also contributed to the increase of mutations among the viral progeny.

CONCLUSION:

The findings indicate that the 11083G > T mutation of SARS-CoV-2 spread during shipboard quarantine and arose through de novo RNA recombination under positive selection pressure.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: Asia Language: English Journal: Bull World Health Organ Year: 2021 Document Type: Article Affiliation country: BLT.20.255752

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: Asia Language: English Journal: Bull World Health Organ Year: 2021 Document Type: Article Affiliation country: BLT.20.255752