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

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.

Keywords: COVID-19; Diamond Princess; SARS-CoV-2; haplotypes.

Fig. 1.

WGS of SARS-CoV-2 isolates (strains) on the DP cruise ship off Yokohama in Japan. (A) Box plots of the Cq values from RT-qPCR assays that either successfully resulted in WGS or incomplete sequencing. A Cq of at least 32 (∼300 viral copy) is favorable for obtaining a whole-genome sequence by PrimalSeq. (B) The genome position of genetic variations found among DP isolates compared with the isolate Wuhan-Hu-1 (MN908947). (C) The detected nucleotide transition and transversion in all GISAID available SARS-CoV-2 genomes (n = 412, isolation date by February 19, 2020; updated on May 14, 2020) (Dataset S3) and DP isolates (n = 73) compared with the isolate Wuhan-Hu-1 (MN908947). (D) The detected ratio of synonymous/nonsynonymous mutations on coding sequences or intergenic regions in all GISAID available SARS-CoV-2 genomes is described above (n = 412) and DP isolates (n = 73) compared with the isolate Wuhan-Hu-1 (MN908947).

Fig. 2.

Haplotype network using genome-wide SNVs (HN-GSNVs). (A) An ML phylogenetic analysis was conducted using 73 SARS-CoV-2 isolates (February 15 to 17, 2020) from the DP cruise ship off Yokohama in Japan compared with all GISAID-available SARS-CoV-2 genomes (n = 412, isolation date by February 19, 2020; updated on May 14, 2020). In total, 447 SNVs were detected in 482 isolates. The isolate location and G11083T allele information are described in the color schemes on the outside of the phylogenetic tree. (B) Clusters of the DP isolates (n = 73) and Wuhan-Hu-1 were compared with a median-joining SNV network analysis to identify the strain that was first spread (indicated A, n = 29 isolates) and subsequent transmissions (indicated B, n = 5 isolates; indicated C, n = 6 isolates; and the other 33 isolates). Information on each isolate can be obtained in Dataset S1. A possible transmission between partners in the same cabin after the quarantine is shown by thick arrows between isolate nodes.