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Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak.
Proc Natl Acad Sci U S A. 2020 08 18; 117(33):20198-20201.PN

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.

Authors+Show Affiliations

Pathogen Genomics Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Pathogen Genomics Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Influenza Virus Research Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Influenza Virus Research Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Influenza Virus Research Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Influenza Virus Research Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Department of Virology 3, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Pathogen Genomics Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Pathogen Genomics Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Influenza Virus Research Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.National Institute of Infectious Diseases, 162-8640 Tokyo, Japan.Pathogen Genomics Center, National Institute of Infectious Diseases, 162-8640 Tokyo, Japan; makokuro@niid.go.jp.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32723824

Citation

Sekizuka, Tsuyoshi, et al. "Haplotype Networks of SARS-CoV-2 Infections in the Diamond Princess Cruise Ship Outbreak." Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 33, 2020, pp. 20198-20201.
Sekizuka T, Itokawa K, Kageyama T, et al. Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak. Proc Natl Acad Sci U S A. 2020;117(33):20198-20201.
Sekizuka, T., Itokawa, K., Kageyama, T., Saito, S., Takayama, I., Asanuma, H., Nao, N., Tanaka, R., Hashino, M., Takahashi, T., Kamiya, H., Yamagishi, T., Kakimoto, K., Suzuki, M., Hasegawa, H., Wakita, T., & Kuroda, M. (2020). Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak. Proceedings of the National Academy of Sciences of the United States of America, 117(33), 20198-20201. https://doi.org/10.1073/pnas.2006824117
Sekizuka T, et al. Haplotype Networks of SARS-CoV-2 Infections in the Diamond Princess Cruise Ship Outbreak. Proc Natl Acad Sci U S A. 2020 08 18;117(33):20198-20201. PubMed PMID: 32723824.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak. AU - Sekizuka,Tsuyoshi, AU - Itokawa,Kentaro, AU - Kageyama,Tsutomu, AU - Saito,Shinji, AU - Takayama,Ikuyo, AU - Asanuma,Hideki, AU - Nao,Naganori, AU - Tanaka,Rina, AU - Hashino,Masanori, AU - Takahashi,Takuri, AU - Kamiya,Hajime, AU - Yamagishi,Takuya, AU - Kakimoto,Kensaku, AU - Suzuki,Motoi, AU - Hasegawa,Hideki, AU - Wakita,Takaji, AU - Kuroda,Makoto, Y1 - 2020/07/28/ PY - 2020/7/30/pubmed PY - 2020/9/4/medline PY - 2020/7/30/entrez KW - COVID-19 KW - Diamond Princess KW - SARS-CoV-2 KW - haplotypes SP - 20198 EP - 20201 JF - Proceedings of the National Academy of Sciences of the United States of America JO - Proc Natl Acad Sci U S A VL - 117 IS - 33 N2 - 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. SN - 1091-6490 UR - https://www.unboundmedicine.com/medline/citation/32723824/Haplotype_networks_of_SARS_CoV_2_infections_in_the_Diamond_Princess_cruise_ship_outbreak_ L2 - http://www.pnas.org/cgi/pmidlookup?view=long&pmid=32723824 DB - PRIME DP - Unbound Medicine ER -