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.

Highly specific monoclonal antibodies and epitope identification against SARS-CoV-2 nucleocapsid protein for antigen detection tests.

The ongoing coronavirus disease 2019 (COVID-19) pandemic is a major global public health concern. Although rapid point-of-care testing for detecting viral antigen is important for management of the outbreak, the current antigen tests are less sensitive than nucleic acid testing. In our current study, we produce monoclonal antibodies (mAbs) that exclusively react with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and exhibit no cross-reactivity with other human coronaviruses, including SARS-CoV. Molecular modeling suggests that the mAbs bind to epitopes present on the exterior surface of the nucleocapsid, making them suitable for detecting SARS-CoV-2 in clinical samples. We further select the optimal pair of anti-SARS-CoV-2 nucleocapsid protein (NP) mAbs using ELISA and then use this mAb pair to develop immunochromatographic assay augmented with silver amplification technology. Our mAbs recognize the variants of concern (501Y.V1-V3) that are currently in circulation. Because of their high performance, the mAbs of this study can serve as good candidates for developing antigen detection kits for COVID-19.

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.

Ideal Test Time for Coronavirus Disease 2019 Contact Tracing.

Background: Epidemiological contact tracing is a powerful tool to rapidly detect SARS-CoV-2 infection in persons with a close contact history with COVID-19-affected patients. However, it remains unclear whom and when should be PCR tested among the close contact subjects. Methods: We retrospectively analyzed 817 close contact subjects, including 144 potentially SARS-CoV-2-infected persons. The patient characteristics and contact type, duration between the date of the close contact and specimen sampling, and PCR test results in PCR positive and negative persons were compared. Results: We found that male gender {adjusted odds ratio 1.747 [95% confidence interval (CI) 1.180-2.608]}, age ≥ 60 [1.749 (95% CI 1.07-2.812)], and household contact [2.14 (95% CI 1.388-3.371)] are independent risk factors for close contact SARS-CoV-2 infection. Symptomatic subjects were predicted 6.179 (95% CI 3.985-9.61) times more likely to be infected compared to asymptomatic ones. We could observe PCR test positivity between days 1 and 17 after close contact. However, no subject could be found with a Ct-value <30, considered less infective, after day 14 of close contact. Conclusions: Based on our results, we suggest that contact tracing should be performed on the high-risk subjects between days 3 and 13 after close contacts.

Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains.

Human metapneumovirus (HMPV) is a major etiological agent of acute respiratory infections in humans. HMPV has been circulating worldwide for more than six decades and is currently divided into five agreed-upon subtypes: A1, A2a, A2b, B1, and B2. Recently, the novel HMPV subtypes A2c, A2b1, and A2b2 have been proposed. However, the phylogenetic and evolutionary relationships between these recently proposed HMPV subtypes are unclear. Here, we report a genome-wide phylogenetic and evolutionary analysis of 161 HMPV strains, including unique HMPV subtype A2b strains with a 180- or 111-nucleotide duplication in the G gene (nt-dup). Our data demonstrate that the HMPV A2b subtype contains two distinct subtypes, A2b1 and A2b2, and that the HMPV subtypes A2c and A2b2 may be different names for the same subtype. HMPV A2b strains with a nt-dup also belong to subtype A2b2. Molecular evolutionary analyses indicate that subtypes A2b1 and A2b2 diverged from subtype A2b around a decade after the subtype A2 was divided into the subtypes A2a and A2b. These data support the A2b1 and A2b2 subtypes proposed in 2012 and are essential for the unified classification of HMPV subtype A2 strains, which is important for future HMPV surveillance and epidemiological studies.

Early combination treatment with baloxavir and peramivir for hospitalized adults with influenza A in Yokohama, Japan.

Baloxavir marboxil is a new anti-influenza drug, but data on the clinical efficacy of a combination treatment of baloxavir and peramivir is scarce. We conducted a single-center retrospective analysis comparing the mortality of a combination of baloxavir and peramivir (B & P, n = 10) and peramivir without baloxavir (P-mono, n = 132) in hospitalized adults with influenza A between 2011 and 2019 in Yokohama City, Japan. Sequencing analysis was conducted in the B & P group to check the I38 mutation in polymerase acidic protein which is associated with baloxavir resistance. The 30-day mortality rates were 0 (0%) in the B & P group and 6 (4.5%) in the P-mono group, respectively, which was not statistically significant. The I38 mutation was not detected before and after the combination treatment. A combination treatment of baloxavir and peramivir might be more effective than peramivir without baloxavir and prevent the emergence of baloxavir resistance in hospitalized adults with influenza A.

Environmental Surveillance Can Dynamically Track Ecological Changes in Enteroviruses.

Environmental surveillance can be used to trace enteroviruses shed from human stool using a sewer network that is independent of symptomatic or asymptomatic infection. In this study, the local transmission of enteroviruses was analyzed using two wastewater treatment plants, which were relatively close to each other (15 km), designated as sentinels. Influent was collected at both sentinels once a month from 2013 to 2016, and viruses were isolated. Using neutralizing tests with type-specific polyclonal antisera and molecular typing, 933 isolates were identified as enteroviruses. Our results showed that the frequency of virus isolation varied for each serotype at the two sentinels in a time-dependent manner. Because echovirus 11 (Echo11) and coxsackievirus B5 isolates showed a high frequency and were difficult to distinguish, they were further grouped into various lineages based on the VP1 amino acid sequences. The prevalence of each lineage was visualized using multidimensional scaling. The results showed that Echo11 isolates of the same lineage were isolated continuously, similar to coxsackievirus B5 isolates of three lineages. Conversely, Echo1, Echo13, Echo18, Echo19, Echo20, Echo29, and Echo33 were isolated only once each. Our findings suggested that if an enterovirus is imported into the population, it may result in small-scale transmission, whereas if there are initially many infected individuals, it may be possible for the virus to spread to a wide area, beyond the local community, over time. In addition, our findings could provide insights into risk assessment of transmission for importation of poliovirus in polio-free countries and regions.IMPORTANCE In this study, we showed that environmental enterovirus surveillance can be used to monitor the propagation of nonpolio enteroviruses in addition to poliovirus detection. Since epidemiological studies of virus transmission based on the past were performed using specimens from humans, there were limitations to research design, such as specimen collection for implementation on a large-scale target population. However, environmental monitoring can dynamically track the ecological changes in enteroviruses in the region by monitoring viruses in chronological order and targeting the population within the area by monitoring viruses over time. We observed differences in the transmission of echovirus 11 and coxsackievirus B5 in the region according to lineage in a time-dependent manner and with a multidimensional scaling pattern.

Predominant Detection of the Subgroup A2b Human Metapneumovirus Strain with a 111-Nucleotide Duplication in the G gene in Yokohama City, Japan in 2018.

Human metapneumovirus (HMPV) has been a major causative agent of acute respiratory infections in humans. Recently, two types of variant A2b subtype HMPV strains possessing a 111- or 180-nucleotide duplication (nt-dup) in the G gene (HMPV A2b180nt-dup and HMPV A2b111nt-dup, respectively) were detected in Japan, Spain, Vietnam, and China. Our surveillance for infectious agents in Yokohama City, Japan revealed that the HMPV A2b111nt-dup strain became predominant in Yokohama City in 2018. In contrast, no classic HMPV A2b strain was detected after 2017. These data indicate a beneficial role of the 111nt-dup in the G gene for the transmission of HMPV.

Genetic and antigenic characterisation of influenza A(H3N2) viruses isolated in Yokohama during the 2016/17 and 2017/18 influenza seasons.

BACKGROUND: Influenza A(H3N2) virus rapidly evolves to evade human immune responses, resulting in changes in the antigenicity of haemagglutinin (HA). Therefore, continuous genetic and antigenic analyses of A(H3N2) virus are necessary to detect antigenic mutants as quickly as possible. AIM: We attempted to phylogenetically and antigenically capture the epidemic trend of A(H3N2) virus infection in Yokohama, Japan during the 2016/17 and 2017/18 influenza seasons. METHODS: We determined the HA sequences of A(H3N2) viruses detected in Yokohama, Japan during the 2016/17 and 2017/18 influenza seasons to identify amino acid substitutions and the loss or gain of potential N-glycosylation sites in HA, both of which potentially affect the antigenicity of HA. We also examined the antigenicity of isolates using ferret antisera obtained from experimentally infected ferrets. RESULTS: Influenza A(H3N2) viruses belonging to six clades (clades 3C.2A1, 3C.2A1a, 3C.2A1b, 3C.2A2, 3C.2A3 and 3C.2A4) were detected during the 2016/17 influenza season, whereas viruses belonging to two clades (clades 3C.2A1b and 3C.2A2) dominated during the 2017/18 influenza season. The isolates in clades 3C.2A1a and 3C.2A3 lost one N-linked glycosylation site in HA relative to other clades. Antigenic analysis revealed antigenic differences among clades, especially clade 3C.2A2 and 3C.2A4 viruses, which showed distinct antigenic differences from each other and from other clades in the antigenic map. CONCLUSION: Multiple clades, some of which differed antigenically from others, co-circulated in Yokohama, Japan during the 2016/17 and 2017/18 influenza seasons.

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.

Isolation and Complete Genome Sequencing of Zika Virus Imported from the Dominican Republic to Japan.

Zika virus (ZIKV) infection has been documented within Central and South America, Asia, and Africa. Here we report the isolation of virus from a patient infected with ZIKV returning to Japan from the Dominican Republic. The ZIKV strain was imaged by electron microscopy and its complete genome sequence was analyzed. Phylogenetic analysis and molecular characterization revealed that the strain was of Asian lineage, and carried 2 unique mutations in its NS5 region. These mutations are characteristic of strains that originated in the Dominican Republic and the USA in 2016.

A novel 111-nucleotide duplication in the G gene of human metapneumovirus.

In 2017, novel human metapneumovirus (HMPV) A2b subgroup strains with a 111-nucleotide duplication in the G gene was detected by the present team. These strains were related to previously identified HMPV A2b strains with a 180-nucleotide duplication; however, they appeared to be different strains, produced by an independent duplication event. The recent evolution of HMPV suggests that careful monitoring of this virus is required.

180-Nucleotide Duplication in the G Gene of Human metapneumovirus A2b Subgroup Strains Circulating in Yokohama City, Japan, since 2014.

Human metapneumovirus (HMPV), a member of the family Paramyxoviridae, was first isolated in 2001. Seroepidemiological studies have shown that HMPV has been a major etiological agent of acute respiratory infections in humans for more than 50 years. Molecular epidemiological, genetic, and antigenetic evolutionary studies of HMPV will strengthen our understanding of the epidemic behavior of the virus and provide valuable insight for the control of HMPV and the development of vaccines and antiviral drugs against HMPV infection. In this study, the nucleotide sequence of and genetic variations in the G gene were analyzed in HMPV strains prevalent in Yokohama City, in the Kanto area, Japan, between January 2013 and June 2016. As a part of the National Epidemiological Surveillance of Infectious Diseases, Japan, 1308 clinical specimens (throat swabs, nasal swabs, nasal secretions, and nasal aspirate fluids) collected at 24 hospitals or clinics in Yokohama City were screened for 15 major respiratory viruses with a multiplex reverse transcription-PCR assay. HMPV was detected in 91 specimens, accounting for 7.0% of the total specimens, and the nucleotide sequences of the G genes of 84 HMPV strains were determined. Among these 84 strains, 6, 43, 10, and 25 strains were classified into subgroups A2a, A2b, B1, and B2, respectively. Approximately half the HMPV A2b subgroup strains detected since 2014 had a 180-nucleotide duplication (180nt-dup) in the G gene and clustered on a phylogenic tree with four classical 180nt-dup-lacking HMPV A2b strains prevalent between 2014 and 2015. The 180nt-dup causes a 60-amino-acid duplication (60aa-dup) in the G protein, creating 23-25 additional potential acceptor sites for O-linked sugars. Our data suggest that 180nt-dup occurred between 2011 and 2013 and that HMPV A2b strains with 180nt-dup (A2b180nt-dup HMPV) became major epidemic strains within 3 years. The detailed mechanism by which the A2b180nt-dup HMPV strains gained an advantage that allowed their efficient spread in the community and the effects of 60aa-dup on HMPV virulence must be clarified.

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.

Four Cases of Autochthonous Dengue Infection in Japan and 46 Imported Cases: Characteristics of Japanese Dengue.

OBJECTIVE: A dengue outbreak occurred in Japan 2014. We investigated the characteristics of dengue infection among Japanese. METHODS: We investigated the medical charts retrospectively. Patients The study participants are patients who came to our clinic between 2008 and 2014. RESULTS: We investigated 4 domestic cases and 46 imported cases of Japanese with laboratory confirmation of dengue. Major symptoms were fever (100%), rash (86%), fatigue (84%), headache (81%), joint pain (66%), muscle pain (49%), and bleeding (6%). A late rash that appeared near the time of fever resolution was observed in 37 cases (74%). A total of 38/43 (88%) cases had low WBC count (<3,500 /µL) during the febrile period, 42/48 (88%) cases had a low platelet (PLT) count (<130×10(3)/µL), and 44/50 (88%) cases had a C-reactive protein (CRP) <2.0 mg/dL. CONCLUSION: Patients with a high fever, late rash, fever-associated leukopenia, low PLT count, low CRP, and elevated aminotransferases are generally suspected of having a dengue infection.

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.