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Ixodid ticks, such as Ixodes ovatus and Haemaphysalis flava, are important vectors of tick-borne diseases in Japan, such as Japanese spotted fever caused by Rickettsia japonica. This study describes the Rickettsia infection rates influenced by the population genetic structure of I.ovatus and H. flava along an altitudinal gradient. A total of 346 adult I. ovatus and 243 H. flava were analyzed for the presence of Rickettsia by nested PCR targeting the 17kDA, gltA, rOmpA, and rOmpB genes. The population genetic structure was analyzed utilizing the mitochondrial cytochrome oxidase 1 (cox1) marker. The Rickettsia infection rates were 13.26% in I. ovatus and 6.17% in H. flava. For I. ovatus, the global FST value revealed significant genetic differentiation among the different populations, whereas H. flava showed non-significant genetic differentiation. The cox1 I. ovatus cluster dendrogram showed two cluster groups, while the haplotype network and phylogenetic tree showed three genetic groups. A significant difference was observed in Rickettsia infection rates and mean altitude per group between the two cluster groups and the three genetic groups identified within I. ovatus. No significant differences were found in the mean altitude or Rickettsia infection rates of H. flava. Our results suggest a potential correlation between the low gene flow in I. ovatus populations and the spatially heterogeneous Rickettsia infection rates observed along the altitudinal gradient. This information can be used in understanding the relationship between the tick vector, its pathogen, and environmental factors, such as altitude, and for the control of tick-borne diseases in Japan. [ABSTRACT FROM AUTHOR]

Data are limited on the incidence of coronavirus disease 2019 (COVID-19) reinfection in children. This population-based cohort study in Niigata, Japan from January to November 2022 demonstrated the incidence of reinfection was 1337/48 099 (2.8%), and the hazard ratio for reinfection in vaccinated children was 0.29 (95% confidence interval, 0.20–0.40). [ABSTRACT FROM AUTHOR]

Objective: This study examined the knowledge, attitudes, and practices (KAP) of an at-risk population living in Niigata prefecture regarding tick-borne diseases (TBDs) and preventive strategies. Methods: A cross-sectional questionnaire-based study was conducted to assess the KAP of the community. Results: In total, 186 responses were received. Among the respondents, 130 (69·9%) were men, and the mean age was 51.1 (14·3). Nine (4·8%) respondents reported having experienced tick bites. Of the respondents, 44 (23.7%) knew about both scrub typhus and severe fever with thrombocytopenia syndrome, while 156 (83·9%) and 71 (38·2%) recognized limiting skin exposure and use of insect repellents as preventive measures, respectively. The attitudes towards TBDs: being worried about tick bites (p = 0·018) and interested in preventing TBDs (p = 0·001), were significantly higher among women than men. About 75% of the respondents reported taking preventive measures against tick bites, and limiting skin exposure was the most frequently applied method (69·9%). Insect repellents were used by 58 (31·2%) respondents. Age (p = 0·049), being worried about tick bites (p = 0·046), and knowledge of ticks score (p = 0·024) were the significant independent predictors of practicing countermeasures. Conclusion: We identified gaps in knowledge and practices regarding TBDs. Public health interventions should be implemented to improve public awareness of TBDs. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID-19) has caused a serious disease burden and poses a tremendous public health challenge worldwide. Here, we report a comprehensive epidemiological and genomic analysis of SARS-CoV-2 from 63 patients in Niigata City, a medium-sized Japanese city, during the early phase of the pandemic, between February and May 2020. Among the 63 patients, 32 (51%) were female, with a mean (±standard deviation) age of 47.9 ± 22.3 years. Fever (65%, 41/63), malaise (51%, 32/63), and cough (35%, 22/63) were the most common clinical symptoms. The median C t value after the onset of symptoms lowered within 9 days at 20.9 cycles (interquartile range, 17–26 cycles), but after 10 days, the median C t value exceeded 30 cycles (p < 0.001). Of the 63 cases, 27 were distributed in the first epidemic wave and 33 in the second, and between the two waves, three cases from abroad were identified. The first wave was epidemiologically characterized by a single cluster related to indoor sports activity spread in closed settings, which included mixing indoors with families, relatives, and colleagues. The second wave showed more epidemiologically diversified events, with most index cases not related to each other. Almost all secondary cases were infected by droplets or aerosols from closed indoor settings, but at least two cases in the first wave were suspected to be contact infections. Results of the genomic analysis identified two possible clusters in Niigata City, the first of which was attributed to clade S (19B by Nexstrain clade) with a monophyletic group derived from the Wuhan prototype strain but that of the second wave was polyphyletic suggesting multiple introductions, and the clade was changed to GR (20B), which mainly spread in Europe in early 2020. These findings depict characteristics of SARS-CoV-2 transmission in the early stages in local community settings during February to May 2020 in Japan, and this integrated approach of epidemiological and genomic analysis may provide valuable information for public health policy decision-making for successful containment of chains of infection. [ABSTRACT FROM AUTHOR]

The article discusses a study about predation on the minimal armhook squid by minke whales. The data were obtained from a total of 200 minke whales collected from May to September in 2004 and 2005 during surveys conducted over the entire area between the Pacific coast of northern Japan, and in the International Whaling Commission's defined sub-Areas 7, 8 and 9, excluding Russian Exclusive Economic Zone (EEZ). The study found that the minke whales fed on minimal armhook squid in a relatively restricted area near the Emperor Seamounts, irrespective of the broad research area.

Ixodid ticks (Acari:Ixodidae) are essential vectors of tick-borne diseases in Japan. In this study, we characterized the population genetic structure and inferred genetic divergence in two widespread and abundant ixodid species, Ixodes ovatus and Haemaphysalis flava. Our hypothesis was that genetic divergence would be high in I. ovatus because of the low mobility of their small rodent hosts of immature I. ovatus would limit their gene flow compared to more mobile avian hosts of immature H. flava. We collected 320 adult I. ovatus from 29 locations and 223 adult H. flava from 17 locations across Niigata Prefecture, Japan, and investigated their genetic structure using DNA sequences from fragments of two mitochondrial gene regions, cox1 and the 16S rRNA gene. For I. ovatus , pairwise F ST and analysis of molecular variance (AMOVA) analyses of cox1 and 16S sequences indicated significant genetic variation among populations, whereas both markers showed non-significant genetic variation among locations for H. flava. A cox1 gene tree and haplotype network revealed three genetic groups of I. ovatus. One of these groups consisted of haplotypes distributed at lower altitudes (251–471 m.a.s.l.). The cox1 sequences of I. ovatus from Japan clustered separately from I. ovatus sequences reported from China, suggesting the potential for cryptic species in Japan. Our results support our hypothesis and suggest that the host preference of ticks at the immature stage may influence the genetic structure of the ticks. This information may be important for understanding the tick-host interactions in the field to better understand the tick-borne disease transmission and in designing an effective tick control program. • The study compared the population genetic structure between two Ixodid ticks: Ixodes ovatus and Haemaphysalis flava populations. • A putative I. ovatus species complex was revealed based on the three haplotype clusters in both cox1 and 16S rRNA genes. • Despite the sharing of large mammalian hosts at the adult stage of I. ovatus and H. flava , we observed contrasting population genetic structure. [ABSTRACT FROM AUTHOR]

Background: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has dramatically altered the clinical profile of pediatric coronavirus disease 2019 (COVID-19). In Japan, we experienced a pandemic of omicron subvariant BA.1/BA.2 from January through June 2022. However, after the emergence of BA.5 in early July 2022, the number of children hospitalized with COVID-19 increased dramatically in Japan., Methods: We collected data on monthly numbers of cases and clinical characteristics of hospitalized children with COVID-19 in 13 hospitals, the total number of pediatric COVID-19 cases, and COVID-19 vaccination rates in Niigata, Japan, for the period from January 2020 through August 2022. We compared clinical presentation during the periods of BA.1/BA.2 predominance (January-June 2022) and BA.5 predominance (July-August 2022) and estimated vaccine effectiveness (VE) against hospitalization during the BA.5-predominant period., Results: Between January 1, 2020, and August 31, 2022, 49,387 children (19,085 children/100,000 population) were newly diagnosed as having COVID-19, and 393 were hospitalized for COVID-19. Hospitalization for febrile seizure, especially complex seizure, was significantly higher during BA.5 predominance than during BA.1/BA.2 predominance (27.9% vs. 7.0%, P < 0.01). VE against hospitalization during BA.5 predominance was estimated to be 75% (95% confidence interval, 48%-88%, P < 0.01)., Conclusions: The emergence of BA.5 significantly affected children in Japan; the number with complex febrile seizure who required hospitalization was higher than during BA.1/BA.2 predominance. The COVID-19 vaccination rate in children must be increased to prevent hospitalization for COVID-19 and to prepare for current and future variant outbreaks., Competing Interests: The authors have no funding or conflicts of interest to disclose., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

Background: Spread of variants of concerns (VOCs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an increase in children with coronavirus disease 2019 (COVID-19). In February 2021, clusters of the Alpha variant of SARS-CoV-2 started to be reported in Niigata, Japan, including a large nursery cluster. We investigated the transmission routes and household secondary attack rates (SARs) in this cluster., Methods: Epidemiologic data related to a nursery cluster in Niigata, Japan, particularly child-origin and adult-origin SARs, were analyzed. VOCs were confirmed by whole-genome sequencing of virus from patients., Results: In total, 42 persons (22 children and 20 adults) in the cluster were infected with the Alpha variant. In the nursery, 13 of 81 children (16.0%) and 4 of 24 teachers (16.7%) were infected. SARS-CoV-2 later spread to 25 persons (10 children and 15 adults) outside the nursery. Child-origin and adult-origin household SARs were 27.7% (13/47) and 47.0% (8/17) ( P = 0.11), respectively, which were higher than rates attributable to non-VOCs in previous studies., Conclusions: As compared with non-VOCs, the Alpha variant of SARS-CoV-2 exhibited high transmissibility among children and adults and may pose a high risk for household secondary transmission from SARS-CoV-2-infected children. Increased transmissibility of current or future VOCs could lead to greater transmission from children to adults or other children., Competing Interests: The authors have no funding or conflicts of interest to disclose., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

Background: School closures are a subject of debate during the present coronavirus disease 2019 (COVID-19) pandemic. Because children are not the main driver of COVID-19 transmission in the community, school education must be prioritized in conjunction with appropriate infection prevention and control measures, as determined by local COVID-19 incidence., Methods: We investigated the causes and transmission routes of a primary school cluster of COVID-19 that occurred during November and December 2020 in Niigata, Japan., Results: In the cluster, the virus spread among teachers, then from teachers to students, and then to their family members. This primary school cluster comprised 26 infected patients and included teachers (13/33, 39%), students (9/211, 4%), and family members (4/65, 6%). The secondary attack rate from the 3 index teachers to the remaining 30 teachers was 33%; however, the rate to students was only 4%. Factors contributing to cluster formation include the fact that 2 of the index teachers continued working while symptomatic and that the environment and infection prevention measures in the teachers' room were inadequate., Conclusions: To open schools safely and without interruption, adequate measures to prevent COVID-19 infection in schools should be emphasized not only for children but also for teachers and their environment., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

We performed tick surveys in all regions (Kaetsu, Chuetsu, Joetsu, and Sado) of the Niigata prefecture, Japan. A total of 105 field surveys were done from 2016 to 2018 in 41 sites, from north to south, in the prefecture. All 4806 ticks collected were identified and classified by species, sex, and developmental stage. Twelve species were recorded: Dermacentor taiwanensis, Haemaphysalis flava, Haemaphysalis hystricis, Haemaphysalis japonica, Haemaphysalis longicornis, Haemaphysalis megaspinosa, Ixodes ovatus, Ixodes nipponensis, Ixodes persulcatus, Ixodes monospinosus, Ixodes columnae, and Ixodes turdus. The major tick species in Niigata prefecture were H. flava, H. longicornis, and I. ovatus and they comprised 93.4% of all samples. These three species have one generation per year. Climatic and anthropogenic factors may be involved in the substantial change of the endemic species composition from a previous tick survey (1959) in the Niigata prefecture. These factors include increasing temperatures, introduction of new hosts such as the wild boar, highway construction, and a rural exodus facilitating animal migration and reproduction. Tick hosts suitable for the transmission of Japanese spotted fever, Lyme borreliosis, and SFTS occur in Niigata prefecture. Heightened awareness of these three tick-borne diseases is needed for preparation and disease prevention., (Copyright © 2021 The Author(s). Published by Elsevier GmbH.. All rights reserved.)

Japanese spotted fever, a tick-borne disease caused by Rickettsia japonica, was firstly described in southwestern Japan. There was a suspicion of Rickettsia japonica infected ticks reaching the non-endemic Niigata Prefecture after a confirmed case of Japanese spotted fever in July 2014. Therefore, from 2015 to 2017, 38 sites were surveyed and rickettsial pathogens were investigated in ticks from north to south of Niigata Prefecture including Sado island. A total of 3336 ticks were collected and identified revealing ticks of three genera and ten species: Dermacentor taiwanensis, Haemaphysalis flava, Haemaphysalis hystricis, Haemaphysalis longicornis, Haemaphysalis megaspinosa, Ixodes columnae, Ixodes monospinosus, Ixodes nipponensis, Ixodes ovatus, and Ixodes persulcatus. Investigation of rickettsial DNA showed no ticks infected by R. japonica. However, three species of spotted fever group rickettsiae (SFGR) were found in ticks, R. asiatica, R. helvetica, and R. monacensis, confirming Niigata Prefecture as a new endemic area to SFGR. These results highlight the need for public awareness of the occurrence of this tick-borne disease, which necessitates the establishment of public health initiatives to mitigate its spread.

Bovine torovirus (BToV) is recognized as an enteric pathogen of calves, but its etiological role in diarrhea and epidemiological characterization in adult cows remain unclear. In 2007-2008, three outbreaks of epidemic diarrhea occurred in adult cows at three dairy farms in Niigata Prefecture, Japan. BToV was the only enteric pathogen detected in these outbreaks, as determined by electron microscopy, reverse transcription-PCR, bacteria and parasite tests of fecal samples, and antibody tests with paired sera. The epidemiological features of the three outbreaks were similar to those of bovine coronavirus infection, except for the absence of bloody diarrhea, with diarrhea spreading among most adult cows, but not in calves, within several days and diarrhea lasting for 3-5 days with anorexia. Decreased milk production and mild respiratory symptoms were also observed in two of the outbreaks. Nucleotide sequence analysis of the BToV nucleocapsid, spike, and hemagglutinin-esterase (HE) genes revealed a close relatedness among the detected BToV strains from each outbreak and those of Japanese BToV strain Aichi/2004. Furthermore, we isolated a BToV strain, designated Niigata (TC), from a fecal sample using a human rectal tumor cell line. Sequence analysis of this isolate and Aichi/2004 indicated that both strains have truncated HE genes with deletions in the 3' region that occurred through cell culture-adaptation. The short projections that are believed to be formed by the HE protein on virus particles were not observed in these cultured strains by electron microscopy. Taken together, these results suggest that BToV causes epidemic diarrhea in adult cows and should be included in the differential diagnosis of diarrhea in adult cows. In addition, our findings indicate that the HE protein of BToV may not be necessary for viral replication.

The objective of this study was to characterize the off-seasonal influenza virus A subtype H3N2, which caused an outbreak in an elderly hospital in Niigata, Japan. Virus isolates were subtyped by the hemagglutination-inhibition test and screened for antiviral drug sensitivity by real-time PCR using cycling probe technology the and 50% inhibitory concentration (IC(50)) method. Whole genome sequencing was performed in order to determine the phylogeny of the outbreak virus. Seven virus isolates were analyzed in this study, and the results showed that all belonged to the influenza virus A (H3N2). These viruses exhibited the S31N mutation in M2, which confers resistance to amantadine. The results of the IC(50) analysis showed that these viruses were sensitive to both oseltamivir and zanamivir. Whole genome analysis revealed that the virus was similar to the A/Perth/16/2009 strain and that it is a triple reassortant virus with a 3+3+2 pattern of segment recombination.