Influence of herd immunity on norovirus: a long-term field study of repeated viral gastroenteritis outbreaks at the same facilities.

BACKGROUND: Viral acute gastroenteritis (AG) is detected worldwide annually. Outbreaks caused by viruses associated with gastroenteritis have been reported repeatedly at the same facilities in Yokohama, Japan over several years. We investigated the statuses of these repeated outbreaks to consider herd immunity at the facility level. METHODS: Between September 2007 and August 2017, 1459 AG outbreaks were reported at 1099 facilities. Stool samples were collected for virological testing, and the norovirus gene was amplified and sequenced to determine the genotype using the N-terminal region of the capsid. RESULTS: The outbreaks were caused by norovirus, sapovirus, rotavirus A, and rotavirus C. Norovirus was consistently predominant over the 10-year period. Of 1099 facilities, 227 reported multiple outbreaks, of which norovirus-only combinations accounted for 76.2%. More outbreaks were due to different genotype combinations than the same genotype combinations. For facilities that experienced two norovirus outbreaks, the average interval between outbreaks was longer for groups with the same combinations than for groups with different genogroup or genotype combinations, although no statistically significant differences were observed. At 44 facilities, outbreaks occurred repeatedly during the same AG season, and most exhibited combinations of different norovirus genotypes or viruses. Among 49 combinations with the same norovirus genotype at the same facilities over 10 years, the most prevalent genotypes were combinations of genogroup II genotype 4 (GII.4), followed by GII.2, GII.6, GII.3, GII.14, and GI.3. The mean interval between outbreaks was 31.2 ± 26.8 months for all combinations, and the mean intervals were longer for non-GII.4 genotype cases than for GII.4 cases, and statistically significant differences were observed (t-test, P < 0.05). Additionally, these average intervals were longer for kindergarten/nursery schools and primary schools than for nursing homes for older adults (t-test, P < 0.05). CONCLUSIONS: Repeated AG outbreaks at the same facilities in Yokohama during the 10-year study period included mainly norovirus combinations. Herd immunity at the facility level was maintained for at least the same AG season. Norovirus genotype-specific herd immunity was maintained for an average of 31.2 months during the study period, and these intervals differed depending on genotype.

Increased risk of rhinovirus infection in children during the coronavirus disease-19 pandemic.

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.

Hepatitis A Outbreak Among Men Who Have Sex With Men, Yokohama, Japan, January to May 2018.

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.

Norovirus genotype distribution in outbreaks of acute gastroenteritis among children and older people: an 8-year study.

BACKGROUND: Noroviruses (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. METHODS: Between 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. RESULTS: During 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). CONCLUSIONS: The 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.

Genetic Analysis of Norovirus GII.4 Variant Strains Detected in Outbreaks of Gastroenteritis in Yokohama, Japan, from the 2006-2007 to the 2013-2014 Seasons.

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.

Detection and Genetic Analysis of Noroviruses and Sapoviruses in Sea Snail.

An outbreak of acute gastroenteritis occurred at a restaurant in Yokohama in December 2011. Because many of the customers had consumed raw sea snail, sea snail was suspected to be the source of this outbreak. To determine whether sea snail contains Norovirus (NoV) or Sapovirus (SaV), we analyzed 27 sea snail samples collected over 5 months (May, June, August, October, and December 2012) and 59.3% were positive for NoV and/or SaV. The levels of NoV ranged from 1.5 × 10(3) to 1.5 × 10(5) copies/g tissue, and those of SaV from 1.5 × 10(2) to 1.3 × 10(3) copies/g tissue. The highest levels were observed in sea snails collected in December. A phylogenetic analysis of the NoVs showed that the viral strains were NoV genotypes GI.4, GI.6, GII.4, GII.12, GII.13, and GII.14, and the SaV strains were genotypes GI.2 and GI.3. The NoV GII.4 Sydney 2012 variants were only detected in December. This variant was a major source of gastroenteritis in Japan in the winter of 2012/2013. In contrast, the NoV GII.4 strains detected in May and June 2012 were not the Sydney 2012 variant. This study demonstrates that sea snail contains multiple genogroups and genotypes of NoV and SaV strains. We conclude that the sea snail presents a risk of gastroenteritis when consumed raw.

Nucleotide Correlations Between Rotavirus C Isolates in Clinical Samples from Outbreaks and in Sewage Samples.

Rotavirus C (RVC) is detected in both sporadic cases and outbreaks of gastroenteritis worldwide. However, the epidemic dynamics of RVC in populations remain poorly understood because the detection rate is low. In this study, raw sewage samples were collected from a wastewater treatment plant in Yokohama, Japan, over 5 years, in 12-month period from September to August, to identify the RVC strains in these samples and compare them with the RVC strains circulating in the population. RVC strains were detected in 15 of the 118 raw sewage samples collected between 2007 and 2012. The highest number of positive samples detected per period (seven) was in 2008-2009. A fragment (225 nucleotides) of the VP7 gene of RVC from 14 sewage samples was sequenced. The nucleotide sequences of 11 strains were completely consistent with those of clinical strains identified in Yokohama. A phylogenetic analysis showed that 13 strains from the sewage samples clustered with several Yokohama outbreak strains and were closely related to the clinical strains (except sewage-derived strain Y11-SW0805-C). Our study demonstrates a correlation between clinical and sewage strains of RVC based on a genetic analysis, and shows that monitoring environmental samples is an effective way to study the strains circulating in a population, including in asymptomatic or mildly symptomatic patients, even when these infections are not detected in clinical samples. This is the first report of the surveillance of RVC in sewage samples in Yokohama, Japan, for molecular epidemiological analysis.

Epidemiological and genetic analysis of human group C rotaviruses isolated from outbreaks of acute gastroenteritis in Yokohama, Japan, between 2006 and 2012.

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.

An outbreak of food-borne gastroenteritis due to sapovirus among junior high school students.

The human sapovirus (SaV) causes acute gastroenteritis mainly in infants and young children. A food-borne outbreak of gastroenteritis associated with SaV occurred among junior high school students in Yokohama, Japan, during and after a study trip. The nucleotide sequences of the partial capsid gene derived from the students exhibited 98% homology to a SaV genogroup IV strain, Hu/Angelholm/SW278/2004/SE, which was isolated from an adult with gastroenteritis in Solna, Sweden. An identical nucleotide sequence was detected from a food handler at the hotel restaurant, suggesting that the causative agent of the outbreak was transmitted from the food handler. This is the first description of a food-borne outbreak associated with the SaV genogroup IV strain in Japan.