Haplotype networks of SARS-CoV-2 infections in the <i>Diamond Princess</i> cruise ship outbreak

Abstract

The <i>Diamond Princess</i> 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 <i>Diamond Princess</i> 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.