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Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak.
Sekizuka, Tsuyoshi; Itokawa, Kentaro; Kageyama, Tsutomu; Saito, Shinji; Takayama, Ikuyo; Asanuma, Hideki; Nao, Naganori; Tanaka, Rina; Hashino, Masanori; Takahashi, Takuri; Kamiya, Hajime; Yamagishi, Takuya; Kakimoto, Kensaku; Suzuki, Motoi; Hasegawa, Hideki; Wakita, Takaji; Kuroda, Makoto.
  • Sekizuka T; Pathogen Genomics Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Itokawa K; Pathogen Genomics Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Kageyama T; Influenza Virus Research Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Saito S; Influenza Virus Research Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Takayama I; Influenza Virus Research Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Asanuma H; Influenza Virus Research Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Nao N; Department of Virology 3, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Tanaka R; Pathogen Genomics Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Hashino M; Pathogen Genomics Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Takahashi T; Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Kamiya H; Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Yamagishi T; Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Kakimoto K; Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Suzuki M; Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Hasegawa H; Influenza Virus Research Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Wakita T; National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.
  • Kuroda M; Pathogen Genomics Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan; makokuro@niid.go.jp.
Proc Natl Acad Sci U S A ; 117(33): 20198-20201, 2020 08 18.
Article in English | MEDLINE | ID: covidwho-691088
Preprint
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ABSTRACT
The Diamond Princess cruise ship was put under quarantine offshore Yokohama, Japan, after a passenger who disembarked in Hong Kong was confirmed as a coronavirus disease 2019 case. We performed whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly from PCR+ clinical specimens and conducted a phylogenetic analysis of the outbreak. All tested isolates exhibited a transversion at G11083T, suggesting that SARS-CoV-2 dissemination on the Diamond Princess originated from a single introduction event before the quarantine started. Although further spreading might have been prevented by quarantine, some progeny clusters could be linked to transmission through mass-gathering events in the recreational areas and direct transmission among passengers who shared cabins during the quarantine. This study demonstrates the usefulness of haplotype network/phylogeny analysis in identifying potential infection routes.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Pneumonia, Viral / Ships / Haplotypes / Genome, Viral / Coronavirus Infections / Betacoronavirus Type of study: Observational study / Prognostic study / Randomized controlled trials Limits: Humans Language: English Journal: Proc Natl Acad Sci U S A Year: 2020 Document Type: Article Affiliation country: Pnas.2006824117

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Pneumonia, Viral / Ships / Haplotypes / Genome, Viral / Coronavirus Infections / Betacoronavirus Type of study: Observational study / Prognostic study / Randomized controlled trials Limits: Humans Language: English Journal: Proc Natl Acad Sci U S A Year: 2020 Document Type: Article Affiliation country: Pnas.2006824117