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

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 G(11083)T, 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.