Hiroyuki Shimizu

National Institute of Infectious Diseases, Tokyo, Edo, Tōkyō, Japan

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Publications (77)333.67 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Human cardioviruses or Saffold viruses (SAFV) of the family Picornaviridae are newly emerging viruses whose genetic and phenotypic diversity are poorly understood. We report here the full genome sequence of eleven genotypes of SAFV from Pakistan and Afghanistan, along with a re-evaluation of their genetic diversity and recombination. We detected 88 SAFV from stool samples of 943 acute flaccid paralysis cases by RT-PCR targeting the 5'-UTR. Further characterization based on complete VP1 revealed 71 SAFV belonging to eleven genotypes, including three new genotypes. SAFV showed high genetic diversity and recombination based on the phylogenies, pairwise distance distributions and recombination mapping analyses. Phylogenies based on non-structural and UTRs were highly incongruent indicating frequent recombination events among SAFV. We improved the SAFV genotyping classification criteria by determining new VP1 thresholds based on the principles used for the classification of enteroviruses. For genotype assignment, we propose a threshold of 23% and 10% divergence for VP1 nucleotide and amino acid sequences, respectively. Other members of Theilovirus, such as Thera virus and Theiler's murine encephalomyelitis virus, are difficult to classify in the same species as SAFV, because they are genetically distinct from SAFV, with 41-56% amino acid pairwise distances. The new genetic information obtained in this study will improve our understanding of the evolution and classification of SAFV.
    Journal of General Virology 06/2014; · 3.13 Impact Factor
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    ABSTRACT: Aichivirus C is the third species in the genus Kobuvirus, family Picornaviridae, and the virus is circulating in pigs worldwide. Aichivirus A in humans and Aichivirus B in cows have been shown to associate with diarrheal diseases, however, the pathogenesis of Aichivirus C has not been demonstrated clearly. In this study, the full genome nucleotide sequence of the Thai strain, CMP06/2007/THA collected from stool sample of a diarrheal piglet was analyzed and identified as a variant type with a 90-nucleotide deletion in the 2B-coding region. In addition, molecular characterization of nucleotide sequences of the 2B-coding region of Aichivirus C strains from six diarrheal and six healthy piglets in Thailand, and four strains from healthy pigs in Japan revealed that all of the strains in this study were variant types. These findings indicate that variant strains of Aichivirus C are circulating in Asian countries such as China, Thailand and Japan, and deletion of tandem repeat of 2B-region is unlikely to associate with the pathogenesis of the virus.
    Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 05/2014; · 3.22 Impact Factor
  • Hiroyuki Shimizu, Kazutoshi Nakashima
    The Lancet Infectious Diseases 01/2014; · 19.97 Impact Factor
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    ABSTRACT: Aichivirus C is the third species in the genus Kobuvirus, family Picornaviridae, and the virus is circulating in pigs worldwide. Aichivirus A in humans and Aichivirus B in cows have been shown to associate with diarrheal diseases, however, the pathogenesis of Aichivirus C has not been demonstrated clearly. In this study, the full genome nucleotide sequence of the Thai strain, CMP06/2007/THA collected from stool sample of a diarrheal piglet was analyzed and identified as a variant type with a 90-nucleotide deletion in the 2B-coding region. In addition, molecular characterization of nucleotide sequences of the 2B-coding region of Aichivirus C strains from six diarrheal and six healthy piglets in Thailand, and four strains from healthy pigs in Japan revealed that all of the strains in this study were variant types. These findings indicate that variant strains of Aichivirus C are circulating in Asian countries such as China, Thailand and Japan, and deletion of tandem repeat of 2B-region is unlikely to associate with the pathogenesis of the virus.
    Infection, Genetics and Evolution. 01/2014;
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    ABSTRACT: In 2011, a large outbreak of hand-foot-and-mouth disease (HFMD) caused by coxsackievirus A6 (CV-A6) occurred in Japan and other countries. The cutaneous manifestations of CV-A6-associated HFMD (CV-A6-HFMD) are more extensive and variable than those of classic HFMD (1–3). Differential diagnosis of HFMD from chickenpox is occasionally challenging because of its unusual clinical characteristics. For example, the spread of rashes in CV-A6-HFMD is more toward the extremities and body trunk, a manner different from that in typical HFMD in which the rashes are mostly lo-calized to the hands and soles of the feet (1,2). A 24-month-old girl was hospitalized in the pediatric intensive care unit (PICU) on May 16, 2013 (23 days be-fore day 0) due to hypoxemia. The patient had an un-derlying diagnosis of Down syndrome with a ventricular septal defect and pulmonary hypertension but no histo-ry of varicella infection or vaccination against varicella. Before discharge on June 8, 2013 (day 0), she devel-oped a reddish papular rash with some vesicles on her hip, which rapidly spread throughout her entire body and face; she was afebrile. On June 10, 2013 (day 2), the Infection Control Team (ICT) of the Saiseikai Nakatsu Hospital (Osaka, Japan) was notified of this patient as a suspected case of chick-enpox in PICU. Assessment of this case was complicat-ed because the rash spread to her upper and lower ex-tremities; however, it was also observed to a lesser extent on her body trunk but not on the head. Although the papules were comparable to varicella in terms of their size (approximately 5 mm), HFMD was considered to be more likely because there were fewer vesicles than that expected for varicella, and the rash was neither crusted nor pigmented. Infection control policies and measures for varicella-zoster virus (VZV) and enterovirus are different. VZV is transmitted via droplet nuclei, whereas enterovirus is transmitted from person to person via direct contact with the virus shed from the gastrointestinal or upper respiratory tract. To prevent enteroviral transmission, hand hygiene is particularly important (4). Although there was no other case of suspected chickenpox in PICU, the Department of Pediatrics was concerned about the high transmissibility of varicella, which is air-borne. ICT in collaboration with the pediatric staff im-mediately initiated varicella infection control in the pediatric ward and performed laboratory diagnosis for treatment of the present case. ICT decided to implement the following responses: (i) immediate isolation of the infected patient from other children in PICU from June 10, 2013; (ii) immediate restriction on PICU use from June 10, 2013; and (iii) drafting a plan of broad prophylactic administration of antivirals against VZV for children who were housed in the same room depend-ing on the laboratory result for VZV. In addition to a specific laboratory examination for VZV, specimens of pharyngeal swabs, vesicular fluid, and feces were collected during the course of medical care, and laboratory tests were performed for diagnosis and treatment. Informed consent for this study was ob-tained from the patient' s guardian, and the clinical samples were tested to device a treatment plan and in-fection control measures. On June 12, 2013 (day 4), the results of VZV tests in-cluding analysis of IgM, IgG, and specific viral antigen, were negative. On the same day, specimens (vesicle fluid, nasopharyngeal swabs, and feces) were collected, and reverse transcription (RT)-hyper PCR (5) was per-formed to screen for enterovirus in all samples (day 4). RT-hyper PCR was employed because it is faster than previously available PCR methods (5,6). Based on the results obtained by RT-hyper PCR, ICT immediately terminated varicella surveillance and dis-continued the restriction on PICU use and antiviral therapy to the patient. The team also withdrew the broader prophylactic antiviral administration through-out the unit and instead endorsed precautions against contact infections. On June 14, 2013 (day 6), RT-PCR was performed to determine the partial nucleotide sequence of the capsid protein VP1 cording region. Primer pairs were designed
    Japanese journal of infectious diseases 11/2013; 66(6):564-566. · 1.51 Impact Factor
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    ABSTRACT: Enterovirus 71 (EV71) is a picornavirus that causes outbreaks of hand foot and mouth disease (HFMD) primarily in the Asia-Pacific area. Unlike coxsackievirus A16, which also causes HFMD, EV71 induces severe neuropathology leading to high fatalities especially among children under the age of 6 years. Currently, no established vaccines or treatments are available against EV71 infection. The monoclonal antibody (MAb), MA28-7, neutralizes only specific strains of EV71 that have a conserved glycine at amino acid, VP1-145, a surface exposed residue that maps to the five-fold vertex, and has been implicated in receptor binding. The cryo-electron microscopy structure of a complex between EV71 and the Fab fragment of MA28-7 shows that only one Fab occupies each five-fold vertex. A positively-charged patch, which has also been implicated in receptor binding lies within the Fab footprint. We identify the strain-specific epitope of EV71 and discuss the possible neutralization mechanisms of the antibody.
    Journal of Virology 08/2013; · 5.08 Impact Factor
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    ABSTRACT: Some strains of enterovirus 71 (EV71), but not others, infect leukocytes by binding to a specific receptor molecule: the P-selectin glycoprotein ligand-1 (PSGL-1). We find that a single amino acid residue within the capsid protein VP1 determines whether EV71 binds to PSGL-1. Examination of capsid sequences of representative EV71 strains revealed that the PSGL-1-binding viruses had either a G or a Q at residue 145 within the capsid protein VP1 (VP1-145G or Q), whereas PSGL-1-nonbinding viruses had VP1-145E. Using site-directed mutagenesis we found that PSGL-1-binding strains lost their capacity to bind when VP1-145G/Q was replaced by E; conversely, nonbinding strains gained the capacity to bind PSGL-1 when VP1-145E was replaced with either G or Q. Viruses with G/Q at VP1-145 productively infected a leukocyte cell line, Jurkat T-cells, whereas viruses with E at this position did not. We previously reported that EV71 binds to the N-terminal region of PSGL-1, and that binding depends on sulfated tyrosine residues within this region. We speculated that binding depends on interaction between negatively charged sulfate groups and positively charged basic residues in the virus capsid. VP1-145 on the virus surface is in close proximity to conserved lysine residues at VP1-242 and VP1-244. Comparison of recently published crystal structures of EV71 isolates with either Q or E at VP1-145 revealed that VP1-145 controls the orientation of the lysine side-chain of VP1-244: with VP1-145Q the lysine side chain faces outward, but with VP1-145E, the lysine side chain is turned toward the virus surface. Mutation of VP1-244 abolished virus binding to PSGL-1, and mutation of VP1-242 greatly reduced binding. We propose that conserved lysine residues on the virus surface are responsible for interaction with sulfated tyrosine residues at the PSGL-1 N-terminus, and that VP1-145 acts as a switch, controlling PSGL-1 binding by modulating the exposure of VP1-244K.
    PLoS Pathogens 07/2013; 9(7):e1003511. · 8.14 Impact Factor
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    ABSTRACT: Since 2005, a large poliomyelitis outbreak associated with type 2 circulating vaccine-derived poliovirus (cVDPV2) has occurred in northern Nigeria, where immunization coverage with trivalent oral poliovirus vaccine (tOPV) has been low. Phylogenetic analysis of P1/capsid region sequences of isolates from each of the 403 cases reported in 2005-2011 resolved the outbreak into 23 independent VDPV2 emergences, at least seven of which established circulating lineage groups. Virus from one emergence (lineage group 2005-8; 361 isolates) was estimated to have circulated for over six years. The population of the major cVDPV2 lineage group expanded rapidly in early 2009, fell sharply after two tOPV rounds in mid-2009, and gradually expanded again through 2011. The two major determinants of attenuation of the Sabin 2 OPV strain (A(481) in the 5' -untranslated region [5' -UTR] and VP1-Ile(143)) had been replaced in all VDPV2 isolates; most A(481) 5' -UTR replacements occurred by recombination with other enteroviruses. cVDPV2 isolates representing different lineage groups had biological properties indistinguishable from those of wild polioviruses, including efficient growth in neuronal-derived HEK293 cells, the capacity to cause paralytic disease in both humans and PVR-Tg21 transgenic mice, loss of the temperature-sensitive phenotype, and the capacity for sustained person-to-person transmission. We estimate from the poliomyelitis case count and the paralytic case:infection ratio for type 2 wild poliovirus infections that ∼700,000 cVDPV2 infections have occurred during the outbreak. The detection of multiple concurrent cVDPV2 outbreaks in northern Nigeria highlights the risks of cVDPV emergence accompanying tOPV use at low rates of coverage in developing country settings.
    Journal of Virology 02/2013; · 5.08 Impact Factor
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    ABSTRACT: Enviroxime is an anti-picornavirus compound that targets host phosphatidylinositol-4 kinase III beta (PI4KB) activity for its anti-picornavirus activity. To date, several anti-poliovirus (PV) compounds that are associated with a common resistance mutation in viral protein 3A (a G5318A [3A-Ala70Thr] mutation in PV) similar to enviroxime have been identified. Most of these compounds have a direct inhibitory effect on PI4KB activity as well as enviroxime (designated as major enviroxime-like compounds). However, one of the compounds, AN-12-H5, showed no inhibitory effect on PI4KB, and was considered to belong to another group of enviroxime-like compounds (designated as minor enviroxime-like compounds). In the present study, we performed siRNA-sensitization assay targeting PI4KB related genes, and identified oxysterol-binding protein (OSBP) as a target of minor enviroxime-like compounds. Knockdown of OSBP and OSBP2 increased the sensitivity of the cells against PV to AN-12-H5 and a newly identified minor enviroxime-like compound T-00127-HEV2, and also to T-00127-HEV1 to a minor extent. A ligand of OSBP, 25-hydroxycholesterol (25-HC), acted as a minor enviroxime-like compound. Minor enviroxime-like compounds induced relocalization of OSBP to Golgi apparatus in the cells. Treatment of the cells with major or minor enviroxime-like compounds suppressed expression of genes (HMGCS1 and SQLE) in SREBP/SCAP regulatory pathway, and diminished endogenous phosphatidylinositol 4-phosphate (PI4P) at Golgi apparatus. Our results suggested that minor enviroxime-like compounds are phenotypically identical to 25-HC, and that major and minor enviroxime-like compounds suppress production and/or accumulation of PI4P in PV-infected cells by targeting PI4KB and OSBP family I activities, respectively.
    Journal of Virology 01/2013; · 5.08 Impact Factor
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    Japanese journal of infectious diseases 01/2013; 66(3):260-261. · 1.51 Impact Factor
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    ABSTRACT: Saffold virus (SAFV) is a newly discovered human virus in the genus Cardiovirus, family Picornaviridae. The virus was first described from fecal specimens of a child with fever of unknown origin in 2007. A total of 454 fecal specimens were collected from children with diarrhea attended clinics in Japan, 2010-2011, 7 (1.5%) were positive for SAFV. Mixed-infections of SAFV and other enteric viruses (rotavirus, norovirus, and bocavirus) were found in 4 out of 7 cases, while monoinfection by SAFV alone was detected in 3 cases. In addition to diarrhea, fever and vomiting were observed in 3 children and mild dehydration in 1 case. No particular symptoms of cough and rhinorrhea were noted. Analysis of partial VP1 nucleotide sequence of 7 Japanese SAFV strains revealed that 5 SAFV sequences were most closely related with SAFV2 reference strains, but separated into SAFV2-A (3 strains) and SAFV2-B (2 strains). In addition, the other 2 strains were classified as SAFV3. Our results indicated that SAFVs (SAFV2 and SAFV3) were circulated in children with acute gastroenteritis in Japan during 2010 and 2011 epidemic season.
    Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 11/2012; · 3.22 Impact Factor
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    ABSTRACT: Enterovirus 71 (EV71) is the causative agent of hand-foot-and-mouth disease and can trigger neurological disorders. EV71 outbreak is a major public health concern in Asia-Pacific countries. By performing experimental-mathematical investigation, here we demonstrate that viral productivity and transmissibility but not viral cytotoxicity are drastically different among EV71 strains and can be associated with their epidemiological backgrounds. This is the first report demonstrating the dynamics of non-enveloped virus replication in cell culture using mathematical modeling.
    Journal of Virology 10/2012; · 5.08 Impact Factor
  • Hiroyuki Shimizu
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    ABSTRACT: To avoid the risk of vaccine-associated paralytic poliomyelitis (VAPP) and polio outbreaks due to circulating vaccine-derived polioviruses, an inactivated poliovirus vaccine (IPV) was introduced for routine immunization in a number of countries with a low risk of polio outbreaks. Currently, production and marketing of a standalone conventional IPV and two diphtheria-pertussis-tetanus-IPV (Sabin-derived IPV; sIPV) products have been submitted, and it is expected that the IPV products will be introduced in Japan in the autumn of 2012. At the same time, a decline in the OPV immunization rate became apparent in Japan due to serious public concerns about a remaining risk of VAPP and introduction of IPV in the near future. Therefore, the recent development of polio immunity gaps should be carefully monitored, and surveillance of suspected polio cases and laboratory diagnosis of polioviruses have to be intensified for the transition period from OPV to IPV in Japan. The development of sIPV is one of the most realistic options to introduce affordable IPV to developing countries. In this regard, further clinical studies on its efficacy, safety, and interchangeability of sIPV will be needed after the introduction of the sIPV products, which will be licensed in Japan for the first time in the world.
    Uirusu 06/2012; 62(1):57-65.
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    ABSTRACT: This study reports the detection and the genetic characterization of HBoV, a new member in the Parvoviridae family. Among 177 fecal specimens collected from children with diarrhea younger than 5 years in Japan, 11 (6.2%) were positive for HBoV. Co-infection with other enteric viruses (norovirus and adenovirus) was found in nine (81.8%) pediatric patients, while monoinfection by HBoV alone was detected in two (18.2%) cases. Nucleotide sequence analysis of 11 Japanese HBoV strains revealed that seven HBoV sequences were most closely related to other HBoV 1 reference strains, while the other four strains were similar to HBoV 2A. These results indicated that HBoV was one of the viral agents found in stool specimens collected from children with acute gastroenteritis and HBoV 1 and 2A circulated in Japan between 2009 and 2010 epidemic season.
    Journal of Medical Virology 06/2012; 84(6):901-5. · 2.37 Impact Factor
  • Clinical and vaccine Immunology: CVI 03/2012; 19(3):459. · 2.60 Impact Factor
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    Minetaro Arita, Takaji Wakita, Hiroyuki Shimizu
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    ABSTRACT: Poliovirus (PV) modifies membrane-trafficking machinery in host cells for its viral RNA replication. To date, ARF1, ACBD3, BIG1/BIG2, GBF1, RTN3, and PI4KB have been identified as host factors of enterovirus (EV), including PV, involved in membrane traffic. In this study, we performed small interfering RNA (siRNA) screening targeting membrane-trafficking genes for host factors required for PV replication. We identified valosin-containing protein (VCP/p97) as a host factor of PV replication required after viral protein synthesis, and its ATPase activity was essential for PV replication. VCP colocalized with viral proteins 2BC/2C and 3AB/3B in PV-infected cells and showed an interaction with 2BC and 3AB but not with 2C and 3A. Knockdown of VCP did not suppress the replication of coxsackievirus B3 or Aichi virus. A VCP-knockdown-resistant PV mutant had an A4881G (a mutation of E253G in 2C) mutation, which is known as a determinant of a secretion inhibition-negative phenotype. However, knockdown of VCP did not affect the inhibition of cellular protein secretion caused by overexpression of each individual viral protein. These results suggested that VCP is a host factor required for viral RNA replication of PV among membrane-trafficking proteins and provides a novel link between cellular protein secretion and viral RNA replication.
    Journal of Virology 02/2012; 86(10):5541-53. · 5.08 Impact Factor
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    ABSTRACT: A transcription-reverse transcription (RT) concerted reaction (TRCR) method was developed for rapid and specific detection of EV71 from clinical specimens. This method was validated with EV71 strains from all of the known genotypes (genotypes A, B1 to B5, and C1 to C5), with detection limits of 10 to 10(3) copies, and was useful for identification of EV71 from throat swabs of patients with hand, foot, and mouth disease (HFMD).
    Journal of clinical microbiology 02/2012; 50(5):1764-8. · 4.16 Impact Factor
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    Emerging Infectious Diseases 02/2012; 18(2):337-9. · 6.79 Impact Factor
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    Yorihiro Nishimura, Hiroyuki Shimizu
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    ABSTRACT: Human enterovirus species A (HEV-A) is one of the four species of HEV in the genus Enterovirus in the family Picornaviridae. Among HEV-A, coxsackievirus A16 (CVA16) and enterovirus 71 (EV71) are the major causative agents of hand, foot, and mouth disease (HFMD). Some other types of HEV-A are commonly associated with herpangina. Although HFMD and herpangina due to HEV-A are common febrile diseases among infants and children, EV71 can cause various neurological diseases, such as aseptic meningitis and fatal encephalitis. Recently, two human transmembrane proteins, P-selectin glycoprotein ligand-1 (PSGL-1) and scavenger receptor class B, member 2 (SCARB2), were identified as functional receptors for EV71 and CVA16. In in vitro infection experiments using the prototype HEV-A strains, PSGL-1 and SCARB2 could be responsible for the specific receptors for EV71 and CVA16. However, the involvement of both receptors in the in vitro and in vivo infections of clinical isolates of HEV-A has not been clarified yet. To elucidate a diverse array of the clinical outcome of HEV-A-associated diseases, the identification and characterization of HEV-A receptors may provide useful information in understanding the HEV-A pathogenesis at a molecular level.
    Frontiers in Microbiology 01/2012; 3:105. · 3.90 Impact Factor
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    ABSTRACT: Human cosavirus (HCoSV) is a newly discovered virus in Picornaviridae family. At present it is not clear whether HCoSV is associated with diseases, including gastroenteritis in humans, as epidemiological data is limited. Epidemiological surveillance of HCoSV was conducted on 150 fecal specimens collected from children and 150 samples from adults with diarrhea in Thailand by RT-PCR screening. HCoSV was found in a single adult specimen and not in any of the fecal specimens from children. This represents the first report of HCoSV infection in patients with diarrhea in Thailand. Extensive epidemiological surveillance of novel viruses associated with diarrhea in other populations may provide a better understanding of the distribution, genetic diversity, and association of the viral agents associated with acute gastroenteritis in humans.
    Virus Genes 12/2011; 44(2):244-6. · 1.77 Impact Factor

Publication Stats

2k Citations
333.67 Total Impact Points

Institutions

  • 2000–2014
    • National Institute of Infectious Diseases, Tokyo
      Edo, Tōkyō, Japan
  • 2013
    • Osaka Saiseikai Nakatsu Hospital
      Ōsaka, Ōsaka, Japan
    • The Children's Hospital of Philadelphia
      Philadelphia, Pennsylvania, United States
    • Nishimura Pediatric Clinic
      Kioto, Kyōto, Japan
  • 2012
    • Chiang Mai University
      • Department of Microbiology
      Chiang Mai, Chiang Mai Province, Thailand
    • National Institute of Health and Nutrition
      Edo, Tōkyō, Japan
  • 2010
    • Hokkaido Institute of Public Health
      Edo, Tōkyō, Japan
    • The University of Tokyo
      • Faculty & Graduate School of Medicine
      Tokyo, Tokyo-to, Japan
  • 2009
    • Victorian Infectious Diseases Reference Laboratory
      Melbourne, Victoria, Australia
  • 2008
    • Yunnan Center for Disease Control and Prevention
      Yün-nan, Yunnan, China
  • 2006
    • Hyogo Prefectural Institute of Public Health and Consumer Sciences
      Kōbe, Hyōgo, Japan
  • 2004
    • Nagasaki University
      • Institute of Tropical Medicine
      Nagasaki, Nagasaki, Japan