Draft genome sequence of Yersinia pseudotuberculosis isolated from a wild rat in Japan.

We report a draft genome sequence of Yersinia pseudotuberculosis isolated from the spleen of a wild rat from Mikura-shima Island, Japan. The bacterium was identified as serotype O:4b using PCR-based O-genotyping. These genomic data provide insights into the pathogenic potential of this strain in spontaneous outbreaks among wild animals.

High Seroprevalence of Severe Fever with Thrombocytopenia Syndrome Virus Infection among the Dog Population in Thailand.

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne zoonotic disease caused by the SFTS virus (SFTSV). In Thailand, three human cases of SFTS were reported in 2019 and 2020, but there was no report of SFTSV infection in animals. Our study revealed that at least 16.6% of dogs in Thailand were seropositive for SFTSV infection, and the SFTSV-positive dogs were found in several districts in Thailand. Additionally, more than 70% of the serum samples collected at one shelter possessed virus-neutralization antibodies against SFTSV and the near-complete genome sequences of the SFTSV were determined from one dog in the shelter. The dog SFTSV was genetically close to those from Thailand and Chinese patients and belonged to genotype J3. These results indicated that SFTSV has already spread among animals in Thailand.

Simple and rapid detection of severe fever with thrombocytopenia syndrome virus in cats by reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay using a dried reagent.

Severe fever with thrombocytopenia syndrome virus (SFTSV) causes lethal hemorrhagic diseases in human, cats, and dogs. Several human cases involving direct transmission of SFTSV from diseased animals have been reported. Therefore, rapid diagnosis in veterinary clinics is important for preventing animal-to-human transmission. Previously, we developed a simplified reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for human that does not require RNA extraction for detecting the SFTSV genome. In this study, we improved the simplified RT-LAMP assay for cats by introducing a dried reaction reagent and investigated the applicability of this method for diagnosing SFTS in cats. SFTSV RNA was detected in 11 of 12 cats naturally infected with SFTSV by RT-LAMP assay using both liquid and dried reagents. The RT-LAMP assay using liquid and dried reagents was also applicable to the detection of SFTSV genes 3-4 days after challenge in cats experimentally infected with SFTSV. The minimum copy number of SFTSV genes for 100% detection using the RT-LAMP assay with liquid and dried reagents was 4.3 × 104 and 9.6 × 104 copies/mL, respectively. Although the RT-LAMP assay using the dried reagent was less sensitive than that using the liquid reagent, it was sufficiently sensitive to detect SFTSV genes in cats with acute-phase SFTS. As the simplified RT-LAMP assay using a dried reagent enables detection of SFTSV genes more readily than the assay using a liquid reagent, it is applicable for use in veterinary clinics.

Lethal Disease in Dogs Naturally Infected with Severe Fever with Thrombocytopenia Syndrome Virus.

Severe fever with the thrombocytopenia syndrome virus (SFTSV) causes fatal disease in humans, cats, and cheetahs. In this study, the information on seven dogs with SFTS was summarized. All dogs showed anorexia, high fever, leukopenia, and thrombocytopenia, two dogs showed vomiting and loose stool, and five dogs had tick parasites. All dogs also had a history of outdoor activity. The SFTSV gene was detected in all dogs. Remarkably, three dogs (43%) died. SFTSV was isolated from six dogs and the complete genomes were determined. A significant increase in anti-SFTSV-IgG antibodies was observed in two dogs after recovery, and anti-SFTSV-IgM antibodies were detected in four dogs in the acute phase. Using an ELISA cut-off value of 0.410 to discriminate between SFTSV-negative and positive dogs, the detection of anti-SFTSV-IgM antibodies was useful for the diagnosis of dogs with acute-phase SFTS. Four out of the ninety-eight SFTSV-negative dogs possessed high anti-SFTSV IgG antibody titers, indicating that some dogs can recover from SFTSV infection. In conclusion, SFTSV is lethal in some dogs, but many dogs recover from SFTSV infection.

Risk assessment of infection with severe fever with thrombocytopenia syndrome virus based on a 10-year serosurveillance in Yamaguchi Prefecture.

In Japan, the first patient with severe fever with thrombocytopenia syndrome was reported in Yamaguchi in 2012. To understand the severe fever with thrombocytopenia syndrome virus (SFTSV) infection in this region, a retrospective surveillance in sika deer and wild boars in Yamaguchi was conducted using a virus-neutralizing (VN) test. The result revealed that 510 of the 789 sika deer and 199 of the 517 wild boars were positive for anti-SFTSV antibodies. Interestingly, seroprevalence in sika deer increased significantly from 2010-2013 to 2015-2020. The SFTSV gene was detected in one of the 229 serum samples collected from sika deer, but not from wild boars. In conclusion, SFTSV had spread among wild animals before 2012 and expanded gradually around 2013-2015 in Yamaguchi.

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan.

After the first case of coronavirus disease 2019 (COVID-19) in Japan on 15 January 2020, multiple nationwide COVID-19 clusters were identified by the end of February. The Japanese government focused on mitigating the emerging COVID-19 clusters by conducting active nationwide epidemiological surveillance. However, an increasing number of cases continued to appear until early April 2020, many with unclear infection routes and no recent history of travel outside Japan. We aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from the COVID-19 cases that appeared until early April 2020 and to characterize their genealogical networks in order to demonstrate possible routes of spread in Japan. Nasopharyngeal specimens were collected from patients, and reverse transcription-quantitative PCR tests for SARS-CoV-2 were performed. Positive RNA samples were subjected to whole-genome sequencing, and a haplotype network analysis was performed. Some of the primary clusters identified during January and February 2020 in Japan descended directly from the Wuhan-Hu-1-related isolates from China and other distinct clusters. Clusters were almost contained until mid-March; the haplotype network analysis demonstrated that the COVID-19 cases from late March through early April may have created an additional large cluster related to the outbreak in Europe, leading to additional spread within Japan. In conclusion, genome surveillance has suggested that there were at least two distinct SARS-CoV-2 introductions into Japan from China and other countries.IMPORTANCE This study aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from COVID-19 cases and to characterize their genealogical networks to demonstrate possible routes of spread in Japan. We found that there were at least two distinct SARS-CoV-2 introductions into Japan, initially from China and subsequently from other countries, including Europe. Our findings can help understand how SARS-CoV-2 entered Japan and contribute to increased knowledge of SARS-CoV-2 in Asia and its association with implemented stay-at-home/shelter-in-place/self-restraint/lockdown measures. This study suggested that it is necessary to formulate a more efficient containment strategy using real-time genome surveillance to support epidemiological field investigations in order to highlight potential infection linkages and mitigate the next wave of COVID-19 in Japan.

Associations between Japanese spotted fever (JSF) cases and wildlife distribution on the Boso Peninsula, Central Japan (2006-2017).

Populations of large mammals have been dramatically increasing in Japan, resulting in damage to agriculture, forestry, and ecosystems. However, their effects on tick-borne diseases have been poorly studied. Here, we focused on the relationship between Japanese spotted fever (JSF), a tick-borne disease caused by Rickettsia japonica, and populations of large mammals. To explore factors that affected the area in which JSF cases occur, we used generalized linear mixed models (GLMMs). We demonstrated that the expansion of the area of JSF occurrence can be predicted by deer density and geographical factors, which is likely due to differences in landscape structure. However, the associated models have limitations because of the lack of information about the distribution of vectors and reservoirs. To reduce the risk of humans contracting JSF, potential reservoirs should be confirmed.

First record of infestation of a pet sloth in Japan with the exotic tick Amblyomma geayi (Acari: Ixodidae).

On December 11, 2018, a single unengorged adult tick was found on the body surface of the trunk of an imported wild-caught Linnaeus's two-toed sloth (Choloepus didactylus) during a routine health check in an animal clinic in Tokyo, Japan. The tick was identified as Amblyomma geayi based on the morphological and molecular characteristics. This is the first case of the introduction of an Amblyomma species to Japan via an imported pet sloth. The present study highlights the current loopholes in Japan's regulatory system for animal imports.

SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise.

Japan has reported 26 cases of coronavirus disease 2019 (COVID-19) linked to cruise tours on the River Nile in Egypt between March 5 and 15, 2020. Here, we characterized the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome of isolates from 10 travelers who returned from Egypt and from patients possibly associated with these travelers. We performed haplotype network analysis of SARS-CoV-2 isolates using genome-wide single-nucleotide variations. Our analysis identified two potential Egypt-related clusters from these imported cases, and these clusters were related to globally detected viruses in different countries.

Rickettsia japonica Infection after Land Leech Bite, Japan.

We report a case of Rickettsia japonica infection in an 81-year-old man in central Japan. The patient had fever, rash, and an eschar but no evidence of a tick bite. His symptoms began 8 days after a land leech bite. The land leech is a potential vector of R. japonica.

Isolation and molecular detection of Ehrlichia species from ticks in western, central, and eastern Japan.

Ehrlichiosis is a tick-borne bacterial disease caused by pathogens of the Ehrlichia genus. Although human ehrlichiosis has not been reported in Japan, Ehrlichia spp., which are closely related to Ehrlichia chaffeensis, were detected in several species of ixodid ticks. In this study, the presence of Ehrlichia spp. in ticks in Japan was studied by using isolation and molecular detection methods. In total, 1237 ticks were collected from vegetation in western, central, and eastern parts of Japan. The ticks were tested for detection of ehrlichial DNA with a nested polymerase chain reaction and/or isolation by inoculation of mice with the homogenate. Ehrlichial DNA was detected in 29 of these ticks. The ehrlichial DNAs, groEL and 16S rRNA genes, detected in Ixodes turdus showed a high similarity to those of E. chaffeensis with 94.7% and 99.2% identity, respectively. Ehrlichia sp. HF and Candidatus Neoehrlichia mikurensis were also detected in I. ovatus. Furthermore, Ehrlichia sp. HF was isolated from laboratory mice that were intraperitoneal inoculated with I. ovatus tick homogenate. Some ehrlichial agents detected in Ixodes ticks might be a previously unknown Ehrlichia species. In this study, Candidatus N. mikurensis was detected in I. ovatus ticks. Because I. ovatus is distributed widely and cases of its tick bite in humans are ubiquitously reported in Japan, there is a potential for ehrlichiosis to be endemic to Japan, necessitating intensive surveillance of this infectious disease.

Case Report: Concurrent Sympatric Scrub Typhus and Japanese Spotted Fever in Japan.

Scrub typhus and Japanese spotted fever-both rickettsial diseases-are endemic and notifiable in Japan and may cause a fatal outcome without prompt treatment. Here we present the first case of a concurrent sympatric infection of both diseases with grade II evidence. A 67-year-old woman, after a single event of potential exposure to the pathogens, presented with a 12-day history of fever, pharyngeal pain, papulo-erythematous rash, and pronounced fatigue. Her erythematous rash was distributed on her trunk and extremities, palms, and soles and eventually progressed to purpura. Fever persisted until doxycycline was administered on day 12. A significant > 4-fold increase in immunoglobulin G and immunoglobulin M titers against multiple serotypes of Orientia tsutsugamushi and Rickettsia japonica were revealed by indirect immunoperoxidase assays. These clinical and serological data, even in the absence of molecular or isolation evidence, provided grade II evidence that this was a concurrent infection of sympatric scrub typhus and Japanese spotted fever.

Distinguishing Japanese Spotted Fever and Scrub Typhus, Central Japan, 2004- 2015.

Japanese spotted fever (JSF) and scrub typhus (ST) are endemic to Japan and share similar clinical features. To document the clinical and epidemiologic characteristics that distinguish these 2 rickettsial diseases, during 2004-2015 we recruited 31 JSF patients, 188 ST patients, and 97 nonrickettsial disease patients from the southern Boso Peninsula of Japan. JSF occurred during April-October and ST during November-December. Patients with JSF and ST were significantly older and more likely to reside in wooded areas than were patients with nonrickettsial diseases. Spatial analyses revealed that JSF and ST clusters rarely overlapped. Clinical findings more frequently observed in JSF than in ST patients were purpura, palmar/plantar rash, hyponatremia, organ damage, and delayed defervescence after treatment. Although their clinical features are similar, JSF and ST differ in seasonality, geographic distribution, physical signs, and severity. Because a considerable percentage of patients did not notice rash and eschar, many rickettsial diseases might be underdiagnosed in Japan.

Prevalence and characteristics of human parechovirus and enterovirus infection in febrile infants.

BACKGROUND: Human parechovirus (HPeV) and human non-polio enterovirus (EV) are important causes of fever without source (FWS) in young infants. Their prevalence and clinical characteristics are largely unknown in Asian countries. This study was conducted to elucidate the epidemiology and clinical characteristics of HPeV and EV infection in febrile young infants in Japan. METHODS: During February 2010-August 2015, we obtained 53 stool, 44 throat swab, and 20 cerebrospinal fluid samples from 56 infants (<3 months) with FWS at a single hospital. To each sample, we applied reverse transcription-polymerase chain reaction for HPeV and EV. We compared the clinical characteristics of HPeV and EV patients. RESULTS: HPeV was detected in 11 and EV in 17 patients. HPeV was detected during July-September. HPeV patients, compared with EV patients, had lower age (32 vs 47 days; P = n.s.), higher prevalence of exclusive breast-feeding (81.8 vs 29.4%; P = 0.024), and lower prevalence of sick contacts (36.4 vs 88.2%; P = 0.010). More HPeV than EV patients met the systemic inflammatory response syndrome criteria (90.9 vs 52.9%; P = 0.049). In the HPeV group, leukopenia, thrombopenia, and elevated deviation enzyme were observed, although the prevalence of abnormal cerebrospinal fluid was significantly lower than in the EV group. HPeV patients had longer hospital stay (7 vs 5 days; P = 0.025). CONCLUSION: HPeV and EV are important causal viruses of FWS. Characteristic clinical pictures exist in these virus infections, but further research is needed to accumulate more cases to produce a comprehensive picture of these virus infections.

Characterization of large and small-plaque variants in the Zika virus clinical isolate ZIKV/Hu/S36/Chiba/2016.

An Asian/American lineage Zika virus (ZIKV) strain ZIKV/Hu/S36/Chiba/2016 formed 2 types in plaque size, large and small. Genomic analysis of the plaque-forming clones obtained from the isolate indicated that the clones forming small plaques commonly had an adenine nucleotide at position 796 (230Gln in the amino acid sequence), while clones forming large plaques had a guanine nucleotide (230Arg) at the same position, suggesting that this position was associated with the difference in plaque size. Growth kinetics of a large-plaque clone was faster than that of a small-plaque clone in Vero cells. Recombinant ZIKV G796A/rZIKV-MR766, which carries a missense G796A mutation, was produced using an infectious molecular clone of the ZIKV MR766 strain rZIKV-MR766/pMW119-CMVP. The plaque size of the G796A mutant was significantly smaller than that of the parental strain. The G796A mutation clearly reduced the growth rate of the parental virus in Vero cells. Furthermore, the G796A mutation also decreased the virulence of the MR766 strain in IFNAR1 knockout mice. These results indicate that the amino acid variation at position 230 in the viral polyprotein, which is located in the M protein sequence, is a molecular determinant for plaque morphology, growth property, and virulence in mice of ZIKV.

The First Case of Zika Virus Isolated from a Japanese Patient Who Returned to Japan from Fiji in 2016.

Outbreaks of Zika virus (ZIKV) infection in tropical and subtropical regions are a cause of worldwide concern and represent a public health emergency. ZIKV was isolated from a 17-year-old patient with fever and maculopapular rash. The patient returned to Japan from the Republic of Fiji in late April 2016. The complete genome sequence of the ZIKV isolate (ZIKV/Hu/S36/Chiba/2016), which might be the first strain to be isolated in Japan, was identified and reported.

Extremely Low Genomic Diversity of Rickettsia japonica Distributed in Japan.

Rickettsiae are obligate intracellular bacteria that have small genomes as a result of reductive evolution. Many Rickettsia species of the spotted fever group (SFG) cause tick-borne diseases known as "spotted fevers". The life cycle of SFG rickettsiae is closely associated with that of the tick, which is generally thought to act as a bacterial vector and reservoir that maintains the bacterium through transstadial and transovarial transmission. Each SFG member is thought to have adapted to a specific tick species, thus restricting the bacterial distribution to a relatively limited geographic region. These unique features of SFG rickettsiae allow investigation of how the genomes of such biologically and ecologically specialized bacteria evolve after genome reduction and the types of population structures that are generated. Here, we performed a nationwide, high-resolution phylogenetic analysis of Rickettsia japonica, an etiological agent of Japanese spotted fever that is distributed in Japan and Korea. The comparison of complete or nearly complete sequences obtained from 31 R. japonica strains isolated from various sources in Japan over the past 30 years demonstrated an extremely low level of genomic diversity. In particular, only 34 single nucleotide polymorphisms were identified among the 27 strains of the major lineage containing all clinical isolates and tick isolates from the three tick species. Our data provide novel insights into the biology and genome evolution of R. japonica, including the possibilities of recent clonal expansion and a long generation time in nature due to the long dormant phase associated with tick life cycles.

Isolation and characterization of Toxoplasma gondii genotypes from goats at an abattoir in Okinawa.

Toxoplasma gondii genotypes were isolated and characterized from cephalic muscle samples collected from 24 goats slaughtered at an abattoir in Okinawa between 2008 and 2009. Of the 24 samples assayed using latex agglutination, 18 were seropositive, 2 were pseudo-positive, and 4 were seronegative against T. gondii antibodies. The samples were then inoculated into laboratory mice to isolate the parasite. Among the isolated samples, 13 (72.2% of the 18 seropositive strains in the latex agglutination assay) were seropositive, 1 (50%) was pseudo-positive, and none were seronegative. However, after being frozen and stored at -20ºC, all samples were found to be T. gondii-free. Of the 14 isolates of the GRA6 genotype, 6 were of type I, 7 were of type II, and 1 was of type III; the genotype distribution ratio was similar to that of T. gondii strains isolated from locally raised pigs. Moreover, no sulfonamide-tolerant dhps gene mutant of T. gondii was detected.

Hepatitis E virus infection in wild mongooses of Okinawa, Japan: Demonstration of anti-HEV antibodies and a full-genome nucleotide sequence.

Hepatitis E virus (HEV), a single-strand RNA virus, has been recovered not only from human beings but also from various species of animals. Here we report our results suggesting that mongoose should be added to the list of reservoir animals of HEV. Of 100 mongooses we examined in Okinawa, Japan, 21 were thought to be positive for anti-HEV antibodies, among which one was definitely positive for HEV RNA. Full-genome sequencing of the HEV isolate revealed that it segregates to a unique subgroup within genotype III. Interestingly, this mongoose strain was closely related to a swine isolate previously reported from Okinawa, implicating the possibility of interspecies transmission between these animals.