Impact of COVID-19 and closed transmission of SARS-CoV-2 during the first wave in Toyama Prefecture, Japan, March 30 to May 18, 2020

Kosuke Tamura; Noriko Inasaki; Masae Itamochi; Yumiko Saga; Takahisa Shimada; Shunsuke Yazawa; Hitoshi Sasajima; Chikako Kawashiri; Emiko Yamazaki; Tomomi Ichikawa; Hiroyasu Kaya; Yoshihiro Yamamoto; Yoshitomo Morinaga; Seiji Yamashiro; Satoshi Nomura; Shinichi Takeda; Hiroyuki Itoh; Koujiro Hirota; Yukio Horie; Norikazu Hirano; Tsuyoshi Sekizuka; Makoto Kuroda; Hideki Tani; Kazunori Oishi

doi:10.7883/yoken.JJID.2023.210

This article has now been updated. Please use the final version.

Impact of COVID-19 and closed transmission of SARS-CoV-2 during the first wave in Toyama Prefecture, Japan, March 30 to May 18, 2020

Kosuke Tamura, Noriko Inasaki, Masae Itamochi, Yumiko Saga, Takahisa Shimada, Shunsuke Yazawa, Hitoshi Sasajima, Chikako Kawashiri, Emiko Yamazaki, Tomomi Ichikawa, Hiroyasu Kaya, Yoshihiro Yamamoto, Yoshitomo Morinaga, Seiji Yamashiro, Satoshi Nomura, Shinichi Takeda, Hiroyuki Itoh, Koujiro Hirota, Yukio Horie, Norikazu Hirano, Tsuyoshi Sekizuka, Makoto Kuroda, Hideki Tani, Kazunori Oishi

Author information

Kosuke Tamura
Department of Research Planning, Toyama Institute of Health, Japan
Noriko Inasaki
Department of Virology, Toyama Institute of Health, Japan
Masae Itamochi
Department of Virology, Toyama Institute of Health, Japan
Yumiko Saga
Department of Virology, Toyama Institute of Health, Japan
Takahisa Shimada
Department of Virology, Toyama Institute of Health, Japan
Shunsuke Yazawa
Department of Virology, Toyama Institute of Health, Japan
Hitoshi Sasajima
Toyama Institute of Health, Japan
Chikako Kawashiri
Toyama Institute of Health, Japan
Emiko Yamazaki
Osaka Institute of Public Health, Japan
Tomomi Ichikawa
Toyama Red Cross Hospital, Japan
Hiroyasu Kaya
Department of Infectious Disease, Toyama Prefectural Central Hospital, Japan
Yoshihiro Yamamoto
Department of Clinical Infectious Diseases, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Japan
Yoshitomo Morinaga
Department of Microbiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Japan
Seiji Yamashiro
Department of Internal Medicine, Asahi General Hospital, Japan
Satoshi Nomura
Toyama City Hospital, Japan
Shinichi Takeda
Kurobe City Hospital, Japan
Hiroyuki Itoh
Takaoka City Hospital, Japan
Koujiro Hirota
Tonami General Hospital, Japan
Yukio Horie
Saiseikai Toyama Hospital, Japan
Norikazu Hirano
Toyama Rosai Hospital, Japan
Tsuyoshi Sekizuka
Pathogen Genomic Center, National Institute of Infectious Diseases, Japan
Makoto Kuroda
Pathogen Genomic Center, National Institute of Infectious Diseases, Japan
Hideki Tani
Department of Virology, Toyama Institute of Health, Japan
Kazunori Oishi
Toyama Institute of Health, Japan

Keywords: SARS-CoV-2, COVID-19, First wave, Genomic analysis, Case fatality rate

JOURNAL FREE ACCESS Advance online publication

Article ID: JJID.2023.210

DOI https://doi.org/10.7883/yoken.JJID.2023.210

The final version of this article is now available: Vol. 77 (2024), No. 2 pp. 75-82

Details

Abstract

We studied 226 patients in Toyama Prefecture, notified with COVID-19 during the first wave between March 30 and May 18, 2020. Of the 226 patients, 22 (9.7%) died, of whom most (95%) were aged ≥65 years. A large cluster comprising 59 patients (41 residents and 18 staff members) was identified in a nursing home on April 17. No deaths occurred among the staff members, but 12 of the 41 cases in residents (29%) died. Although the Ct values were significantly lower in the 20–64 and the ≥65 years age-groups than in the age <20 years age-group, no correlation was found between the Ct values and the severity, fatal outcome, or secondary infection. The haplotype network of 145 SARS-CoV-2 isolates (64%) from 226 patients was analyzed. The viral genomes of the case groups differed by less than five nucleotide bases. These data suggest that SARS-CoV-2 strains, which were initially introduced into Toyama Prefecture during late March and early April 2020, and their closely related strains, identified as the lineage B.1.1, circulated during the first wave. The reduced inter-prefectural mobility of local residents may support a lack of strain diversity in SARS-CoV-2 during a state of emergency in the first wave.

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