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

抄録

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.