Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak

The Diamond Princess cruise ship was put under quarantine off-shore 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 respira-tory syndrome coronavirus 2 (SARS-CoV-2) directly from PCR+ clin-ical 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 Prin-cess originated from a single introduction event before the quar-antine 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 cab-ins during the quarantine. This study demonstrates the usefulness of haplotype network/phylogeny analysis in identifying potential infection routes.