Genomic Epidemiology Reveals Multiple Introductions of Severe Acute Respiratory Syndrome Coronavirus 2 in Niigata City, Japan, Between February and May 2020

Dissemination of local sub-variants of SARS-CoV-2 detected by detailed mutation analysis in wastewater-based epidemiology

Wastewater-based epidemiology (WBE) is effective for identifying the predominant SARS-CoV-2 variants within specific populations as well as early warning of disease outbreaks. The variant analysis in WBE has been limited to quantifying the proportion of variants, and it has been unable to trace their origins and dissemination pathways. This study aims to elucidate the emergence and transmission of locally predominant SARS-CoV-2 sub-variants through detailed mutation analysis in wastewater genomic surveillance. Genome mutations at each nucleotide position in the S region were examined to identify locally unique sub-variants in geographically distinct cities of Komatsu and Hamamatsu. Notably, the XBT variant, which had never been reported in clinical samples from Japan, was detected in wastewater in Komatsu. Moreover, a unique sub-variant of BA.5 was detected in Komatsu for a duration of 17 weeks whereas it was absent in Hamamatsu. Mutation analysis also revealed significant differences in the duration of the common BA.2.75 sub-variant's prevalence in Komatsu for 35 weeks, in contrast to only one week in Hamamatsu. These findings underscore the efficacy of wastewater-based genomic epidemiology in identifying the timing of variant entry and prevalence duration, enhancing our understanding of the origins, transmission pathways, and evolutionary trajectories of epidemically important variants.

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

We studied 226 patients in Toyama Prefecture who were notified of COVID-19 during the first wave between March 30 and May 18, 2020. Of the 226 patients, 22 (9.7%) died, most (95%) of whom 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 staff members; however, 12 of the 41 residents (29%) died. Although the threshold cycle (Ct) values were significantly lower in the 20-64 and ≥65 years age groups than in the <20 years age group, no correlation was found between the Ct values and 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 the SARS-CoV-2 strains, which were initially introduced into Toyama Prefecture in late March and early April 2020, and their closely related strains, identified as lineage B.1.1, circulated during the first wave. The reduced inter-prefectural mobility of local residents may support the lack of strain diversity in SARS-CoV-2 during the first wave of the state of emergency.

Assessing the Pre-Vaccination Anti-SARS-CoV-2 IgG Seroprevalence among Residents and Staff in Nursing Home in Niigata, Japan, November 2020

An outbreak of coronavirus disease 2019 (COVID-19) occurred in a nursing home in Niigata, Japan, November 2020, with an attack rate of 32.0% (63/197). The present study was aimed at assessing the pre-vaccination seroprevalence almost half a year after the COVID-19 outbreak in residents and staff in the facility, along with an assessment of the performance of the enzyme-linked immunosorbent assay (ELISA) and the chemiluminescent immunoassay (CLIA), regarding test seropositivity and seronegativity in detecting immunoglobulin G (IgG) anti-severe acute respiratory syndrome 2 (SARS-CoV-2) antibodies (anti-nucleocapsid (N) and spike (S) proteins). A total of 101 people (30 reverse transcription PCR (RT-PCR)-positive and 71 RT-PCR-negative at the time of the outbreak in November 2020) were tested for anti-IgG antibody titers in April 2021, and the seroprevalence was approximately 40.0-60.0% for residents and 10.0-20.0% for staff, which was almost consistent with the RT-PCR test results that were implemented during the outbreak. The seropositivity for anti-S antibodies showed 90.0% and was almost identical to the RT-PCR positives even after approximately six months of infections, suggesting that the anti-S antibody titer test is reliable for a close assessment of the infection history. Meanwhile, seropositivity for anti-N antibodies was relatively low, at 66.7%. There was one staff member and one resident that were RT-PCR-negative but seropositive for both anti-S and anti-N antibody, indicating overlooked infections despite periodical RT-PCR testing at the time of the outbreak. Our study indicated the impact of transmission of SARS-CoV-2 in a vulnerable elderly nursing home in the pre-vaccination period and the value of a serological study to supplement RT-PCR results retrospectively.