Background Coronavirus disease (COVID‐19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), was first detected in Japan in January 2020 and has spread throughout the country. Previous studies have reported that viral interference among influenza virus, rhinovirus, and other respiratory viruses can affect viral infections at the host and population level. Methods To investigate the impact of COVID‐19 on influenza and other respiratory virus infections, we analyzed clinical specimens collected from 2244 patients in Japan with respiratory diseases between January 2018 and September 2020. Results The frequency of influenza and other respiratory viruses (coxsackievirus A and B; echovirus; enterovirus; human coronavirus 229E, HKU1, NL63, and OC43; human metapneumovirus; human parainfluenza virus 1, 2, 3, and 4; human parechovirus; human respiratory syncytial virus; human adenovirus; human bocavirus; human parvovirus B19; herpes simplex virus type 1; and varicella‐zoster virus) was appreciably reduced among all patients during the COVID‐19 pandemic except for that of rhinovirus in children younger than 10 years, which was appreciably increased. COVID‐19 has not spread among this age group, suggesting an increased risk of rhinovirus infection in children. Conclusions Rhinovirus infections should be continuously monitored to understand their increased risk during the COVID‐19 pandemic and viral interference with SARS‐CoV‐2.

Noroviruses (NoVs) are the leading cause of acute gastroenteritis, both in sporadic cases and outbreaks. Since the 1990s, the emergence of several GII.4 variants has been reported worldwide. To investigate the epidemic status of NoV, 6,724 stool samples collected from outbreaks in Yokohama, Japan, from the 2006–2007 to 2013–2014 seasons were assessed for NoVs. We genotyped one specimen from each GII outbreak and conducted a sequence analysis of the VP1 gene for several GII.4 strains. Of the 947 NoV outbreaks during our study, GII was detected in 835, and GII.4 was the predominant genotype of GII. Five different GII.4 variants, Yerseke 2006a, Den Haag 2006b (2006b), Apeldoorn 2007, New Orleans 2009, and Sydney 2012, were detected. During this study period, the most prevalent variant of GII.4 was 2006b, and in each individual season, either 2006b or Sydney 2012 was the predominant variant. Out of the 16 detected 2006b strains, 12 had some amino acid substitutions in their blockade epitope, and these substitutions were concentrated in three residues. Two of the 2006b strains detected in the 2012–2013 season had a S368E substitution, which is consistent with the amino acid residues at same site of NSW0514 (Sydney 2012 prototype). Among the 16 detected strains of Sydney 2012, a phylogenetic analysis showed that all five strains detected in Yokohama during the 2011–2012 season clustered away from the other Sydney 2012 strains that were detected in the 2012–2013 and 2013–2014 seasons. These five strains and other Sydney 2012 strains in Yokohama had a few amino acid differences in the blockade epitopes compared with NSW0514. The amino acid substitutions observed in this study provide informative data about the evolution of a novel GII.4 variant.

Group C rotavirus (GCRV) infection has been described in several parts of the world, predominantly as sporadic cases of acute gastroenteritis. Little is known about the yearly changes in the GCRV strains from diarrheal outbreaks. Stool samples collected from outbreaks of acute gastroenteritis in Yokohama, Japan, between 2006 and 2012 that were negative for norovirus, sapovirus, and group A rotavirus, were screened for GCRV using a reverse passive hemagglutination method. The GCRV strains were characterized by nucleotide sequence and phylogenetic analysis of their VP6, VP7, VP4, and NSP4 genes. Samples from nine of 735 outbreaks in Yokohama (1 %) contained GCRV, and eight of these outbreaks occurred in primary schools. The nucleotide sequences of the strains detected in this study were more closely related to Asian strains than to those from other regions of the world. The nucleotide sequences of the VP7 gene in these nine strains differed, and yearly changes were observed in the amino acid sequences of the VP4 genes. Phylogenetic trees constructed using the nucleotide sequences of the VP6, VP7, VP4, and NSP4 genes showed that sublineage S1 has divided into S1-1 and S1-2 in the VP4 gene only. Our results confirm that the prevalent strains of GCRV change yearly in Yokohama. This is the first study to demonstrate GCRV-associated gastroenteritis outbreaks in Yokohama, Japan.

BackgroundNoroviruses (NoVs) are the most frequent cause of acute gastroenteritis worldwide among people of all ages and the leading cause of gastrointestinal disease outbreaks in various settings. To clarify the differences in epidemic situations among different settings, we investigated epidemiological trends and the distribution of NoV genotypes in Yokohama, Japan.MethodsBetween September 2007 and August 2015, 746 outbreaks of NoV gastroenteritis were reported in kindergarten/nursery schools (K/Ns), primary schools (PSs), and nursing homes for the aged (NHs). Stool samples were collected for NoV testing, and the NoV gene was amplified and sequenced to determine the genotype.ResultsDuring the eight seasons, 248 NoV outbreaks occurred in K/Ns, 274 outbreaks in PSs, and 224 outbreaks in NHs. These outbreaks occurred throughout the year, except in August, and the number increased in November and peaked in December. The number of outbreaks that occurred from November to February comprised 76.8 % of all outbreaks. The outbreaks originated in K/Ns or PSs in every season, except for one season. Five genogroup (G)I and nine GII genotypes in K/Ns, six GI and 10 GII genotypes in PSs, and three GI and six GII genotypes in NHs were detected during the eight seasons. GII.4 was the most prevalent genotype in K/Ns and NHs. However, GII.6 was the most prevalent genotype in PSs. The epidemic genotypes in K/Ns and PSs changed by NoV season, although GII.4 was always predominant in NHs. Moreover, the distribution of genotypes was significantly different between epidemic and non-epidemic periods in each facility (p < 0.01 for all).ConclusionsThe epidemic situation of NoV outbreaks differs by facility, NoV season, and month. The genotype distribution is likely dependent on the facility and is significantly different between epidemic and non-epidemic periods.

Between January and May in 2018, 17 male cases of hepatitis A were reported in Yokohama, Japan. Of these, 14 identified as men who have sex with men. The viral sequence in this outbreak was same as that of the recent European and Taiwanese outbreaks strain.