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Shirai T, Phadungsombat J, Ushikai Y, Yoshikaie K, Shioda T, Sakon N. Epidemiological Features of Human Norovirus Genotypes before and after COVID-19 Countermeasures in Osaka, Japan. Viruses 2024; 16:654. [PMID: 38675994 PMCID: PMC11055107 DOI: 10.3390/v16040654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
We investigated the molecular epidemiology of human norovirus (HuNoV) in all age groups using samples from April 2019 to March 2023, before and after the COVID-19 countermeasures were implemented. GII.2[P16] and GII.4[P31], the prevalent strains in Japan before COVID-19 countermeasures, remained prevalent during the COVID-19 pandemic, except from April to November 2020; in 2021, the prevalence of GII.2[P16] increased among children. Furthermore, there was an increase in the prevalence of GII.4[P16] after December 2022. Phylogenetic analysis of GII.P31 RdRp showed that some strains detected in 2022 belonged to a different cluster of other strains obtained during the present study period, suggesting that HuNoV strains will evolve differently even if they have the same type of RdRp. An analysis of the amino acid sequence of VP1 showed that some antigenic sites of GII.4[P16] were different from those of GII.4[P31]. The present study showed high infectivity of HuNoV despite the COVID-19 countermeasures and revealed changes in the prevalent genotypes and mutations of each genotype. In the future, we will investigate whether GII.4[P16] becomes more prevalent, providing new insights by comparing the new data with those analyzed in the present study.
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Affiliation(s)
- Tatsuya Shirai
- Department of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan; (T.S.)
| | | | - Yumi Ushikai
- Department of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan; (T.S.)
| | - Kunihito Yoshikaie
- Department of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan; (T.S.)
| | - Tatsuo Shioda
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan;
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan; (T.S.)
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2
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Matsumoto N, Kurokawa S, Tamiya S, Nakamura Y, Sakon N, Okitsu S, Ushijima H, Yuki Y, Kiyono H, Sato S. Replication of Human Sapovirus in Human-Induced Pluripotent Stem Cell-Derived Intestinal Epithelial Cells. Viruses 2023; 15:1929. [PMID: 37766335 PMCID: PMC10536750 DOI: 10.3390/v15091929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Sapoviruses, like noroviruses, are single-stranded positive-sense RNA viruses classified in the family Caliciviridae and are recognized as a causative pathogen of diarrhea in infants and the elderly. Like human norovirus, human sapovirus (HuSaV) has long been difficult to replicate in vitro. Recently, it has been reported that HuSaV can be replicated in vitro by using intestinal epithelial cells (IECs) derived from human tissues and cell lines derived from testicular and duodenal cancers. In this study, we report that multiple genotypes of HuSaV can sufficiently infect and replicate in human-induced pluripotent stem cell-derived IECs. We also show that this HuSaV replication system can be used to investigate the conditions for inactivation of HuSaV by heat and alcohol, and the effects of virus neutralization of antisera obtained by immunization with vaccine antigens, under conditions closer to the living environment. The results of this study confirm that HuSaV can also infect and replicate in human normal IECs regardless of their origin and are expected to contribute to future virological studies.
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Affiliation(s)
- Naomi Matsumoto
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Shiho Kurokawa
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba 260-8670, Japan
| | - Shigeyuki Tamiya
- Department of Microbiology and Immunology, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama 640-8156, Japan
| | - Yutaka Nakamura
- Department of Microbiology and Immunology, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama 640-8156, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Yoshikazu Yuki
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba 260-8670, Japan
| | - Hiroshi Kiyono
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba 260-8670, Japan
- Future Medicine Education and Research Organization, Chiba University, Chiba 263-8522, Japan
- CU-UCSD Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Departments of Medicine and Pathology, University of California, San Diego, CA 92093-0956, USA
| | - Shintaro Sato
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
- Department of Microbiology and Immunology, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama 640-8156, Japan
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Doan YH, Yamashita Y, Shinomiya H, Motoya T, Sakon N, Suzuki R, Shimizu H, Shigemoto N, Harada S, Yahiro S, Tomioka K, Sakagami A, Ueki Y, Komagome R, Saka K, Okamoto-Nakagawa R, Shirabe K, Mizukoshi F, Arita Y, Haga K, Katayama K, Kimura H, Muramatsu M, Oka T. Distribution of Human Sapovirus Strain Genotypes over the last four Decades in Japan: a Global Perspective. Jpn J Infect Dis 2023. [PMID: 37005271 DOI: 10.7883/yoken.jjid.2022.704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Sapovirus (SaV) infections are a public health problem because they cause acute gastroenteritis in humans of all ages both as outbreaks and in sporadic cases. However, publicly-available SaV sequence information, especially whole genome sequences for all the SaV genotypes, is still limited. Therefore, in this study, we determined the full/near-full-length genomic sequences of 138 SaVs from the 2001-2015 seasons in 13 prefectures across Japan. The GI genogroup was predominant (67%, n = 92), followed by GII (18%, n = 25), GIV (9%, n = 12), and GV (6%, n = 9). Within the GI genogroup, four different genotypes were identified, as follows: GI.1 (n=44), GI.2 (n=40), GI.3 (n=7), and GI.5 (n=1). We then compared these Japanese SaV sequences with a total of 3119 public human SaV sequences from 49 countries over the last 46 years. The results indicated that GI.1 and GI.2 have been the predominant genotypes in Japan as well as in other countries over at least four decades. Together with public SaV sequences, the 138 newly determined Japanese SaV sequences could facilitate a better understanding of the evolutionary patterns of SaV genotypes.
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Affiliation(s)
- Yen Hai Doan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Japan
| | - Yasutaka Yamashita
- Department of Microbiology, Ehime Prefectural Institute of Public Health and Environmental Science, Japan
| | - Hiroto Shinomiya
- Department of Microbiology, Ehime Prefectural Institute of Public Health and Environmental Science, Japan
| | - Takumi Motoya
- Division of Virology, Ibaraki Prefectural Institute of Public Health, Japan
| | - Naomi Sakon
- Department of Microbiology, Virology Section, Osaka Prefectural Institute of Public Health, Japan
| | - Rieko Suzuki
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Japan
| | - Hideaki Shimizu
- Division of Virology, Kawasaki City Institute for Public Health, Japan
| | - Naoki Shigemoto
- Public Health Research Division, Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Japan
| | - Seiya Harada
- Department of Microbiology, Kumamoto Prefectural Institute of Public Health and Environmental Science, Japan
| | - Shunsuke Yahiro
- Department of Microbiology, Kumamoto Prefectural Institute of Public Health and Environmental Science, Japan
| | - Kyoko Tomioka
- Virus Group, Saitama Prefectural Institute of Public Health, Japan
| | - Akie Sakagami
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Japan
| | - Yo Ueki
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Japan
| | - Rika Komagome
- Division of Virology, Department of Infectious Diseases, Hokkaido Institute of Public Health, Japan
| | - Kyohei Saka
- Microbiology Department, Aomori Prefectural Public Health and Environment Center, Japan
| | - Reiko Okamoto-Nakagawa
- Division of Virology, Yamaguchi Prefectural Institute of Public Health and Environment, Japan
| | - Komei Shirabe
- Division of Virology, Yamaguchi Prefectural Institute of Public Health and Environment, Japan
| | - Fuminori Mizukoshi
- Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Japan
| | - Yono Arita
- Department of Microbiology, Shizuoka Institute of Environment and Hygiene, Japan
| | - Kei Haga
- Laboratory of Viral Infection, Department of Infection Control and Immunology,Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection, Department of Infection Control and Immunology,Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Japan
| | - Hirokazu Kimura
- Department of Health Science, Graduate School of Health Science, Gunma Paz University, Japan
| | | | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Japan
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Yoshida T, Mimura M, Sakon N. Exposure to organophosphorus compounds of Japanese children and the indoor air quality in their residences. Sci Total Environ 2022; 850:158020. [PMID: 35973537 DOI: 10.1016/j.scitotenv.2022.158020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Several organophosphorus compounds such as organophosphate pesticides (OPPs) and trialkylphosphates (TAPs) are suspected to inhibit cholinesterase activities, to affect endocrine systems or to possibly be carcinogenic. To evaluate their adverse effects on health with chronic exposure in the general population, especially in children, we measured the household exposure to OPPs and TAPs by Japanese children via all exposure pathways and the contribution of indoor air quality. First-morning void urine was collected from subjects aged 6 to 15 years (n = 132), and airborne organophosphorus compounds were sampled in the subject's bedroom for 24 h. Airborne levels of nine OPPs and three TAPs and their urinary metabolites were determined. No significant correlations were detected for any compounds between their airborne concentrations and the urinary excretion amounts of their corresponding metabolites. The estimated daily intakes were as follows (median, μg/kg b.w./d): chlorpyrifos, 0.042; diazinon, 0.067; tri-n-butylphosphate, 0.094. The 95th percentiles of the intakes for fenthion, fenitrothion and the above three compounds did not exceed their reference limit values, although one subject had a daily intake of tri-n-butylphosphate that was about twice its reference limit value. The concentration levels of the urinary metabolite of tri-n-butylphosphate in our subjects tended to be higher than those for children in many other countries. The fractions of the amounts absorbed by inhalation to the amounts absorbed via all of the exposure pathways was only 2.3 % (median) for tri-n-butylphosphate. Inhalation did not seem to contribute very much as an absorption pathway of the organophosphorus compounds in these Japanese children while they were at home. The exposure amounts of OPPs were not suggested to be high enough to adversely affect the health of these children at present on the basis of their daily intakes compared to their reference limit values.
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Affiliation(s)
- Toshiaki Yoshida
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan.
| | - Mayumi Mimura
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan
| | - Naomi Sakon
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan
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Sakon N, Takahashi T, Yoshida T, Shirai T, Komano J. Impact of COVID-19 Countermeasures on Pediatric Infections. Microorganisms 2022; 10:microorganisms10101947. [PMID: 36296222 PMCID: PMC9608675 DOI: 10.3390/microorganisms10101947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/24/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022] Open
Abstract
(1) Background: General infection control measures have been implemented at the societal level against COVID-19 since the middle of 2020, namely, hand hygiene, universal masking, and social distancing. The suppressive effect of the social implementation of general infection control measures on pediatric infections has not been systematically assessed. (2) Methods: We addressed this issue based on publicly available data on 11 pediatric infections reported weekly by sentinel sites in Osaka and Iwate prefectures in Japan since 2010. We obtained the 5-year average for 2015-2019 and compared it to the weekly report for 2020-2021. (3) Results: The rate of 6 of the 11 pediatric infections decreased significantly during 2020-2021, regardless of the magnitude of the prevalence of COVID-19 in both areas. However, only RSV infection, one of the six infections, was endemic in 2021. Exanthem subitum was not as affected by COVID-19 countermeasures as other diseases. (4) Conclusions: The social implementation of infectious disease control measures was effective in controling certain infectious diseases in younger age groups, where compliance with the countermeasures should not be as high as that of adults.
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Affiliation(s)
- Naomi Sakon
- Osaka Institute of Public Health, Osaka 5370025, Japan
- Correspondence: (N.S.); (J.K.); Tel.: +81-6-6972-1321 (N.S.)
| | - Tomoko Takahashi
- Iwate Prefectural Research Institute for Environmental Science and Public Health, Morioka 0200857, Japan
| | | | | | - Jun Komano
- Department of Microbiology and Infection Control, Faculty of Fharmacy, Osaka Medical and Pharmaceutical University, Takatsuki 5691041, Japan
- Correspondence: (N.S.); (J.K.); Tel.: +81-6-6972-1321 (N.S.)
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Yoshida T, Mimura M, Sakon N. Estimating household exposure to moth repellents p-dichlorobenzene and naphthalene and the relative contribution of inhalation pathway in a sample of Japanese children. Sci Total Environ 2021; 783:146988. [PMID: 34088142 DOI: 10.1016/j.scitotenv.2021.146988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
p-Dichlorobenzene (DCB) and naphthalene (NP) used as moth repellents in indoor environments are suspected to be carcinogenic. To evaluate their adverse effects on health with chronic exposure in the general population, especially children, we need to know their amounts absorbed by the body and the relationships between their amounts and air quality in residences. At present, little is known worldwide about them. This study examined the daily intakes of DCB and NP by Japanese children via all exposure pathways and the contribution of indoor air quality to the intakes. First-morning void urine samples from the subjects aged 6 to 15 years and air samples in their bedrooms were collected. Airborne NP and DCB and their urinary metabolites were measured. Significant correlations were detected between their airborne concentrations and the urinary excretion amounts of their corresponding metabolites. The absorption amounts of DCB and NP by inhalation of the children while at home were calculated to be 26 and 2.0 ng/kg b.w./h, respectively, as median values. The daily intake was estimated to be 2.4 and 0.90 μg/kg b.w./d (median), respectively. The fractions (median) of inhalation absorption amounts to overall absorption amounts for DCB and NP were 30% and 5%, respectively. In children living in residences where the indoor air concentrations of these compounds were more than half the level of each guideline value for indoor air quality, the main exposure route for their absorption was considered to be inhalation while at home. The indoor concentrations of DCB exceeded the lifetime excess cancer risk level of 10-4 in 22% of the residences and 10-3 in 9% of them. Our findings indicate the need to further reduce airborne concentrations of DCB in Japanese residences to prevent its adverse effects on the health of Japanese children.
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Affiliation(s)
- Toshiaki Yoshida
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan.
| | - Mayumi Mimura
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan
| | - Naomi Sakon
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan
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Cannon JL, Bonifacio J, Bucardo F, Buesa J, Bruggink L, Chan MCW, Fumian TM, Giri S, Gonzalez MD, Hewitt J, Lin JH, Mans J, Muñoz C, Pan CY, Pang XL, Pietsch C, Rahman M, Sakon N, Selvarangan R, Browne H, Barclay L, Vinjé J. Global Trends in Norovirus Genotype Distribution among Children with Acute Gastroenteritis. Emerg Infect Dis 2021; 27:1438-1445. [PMID: 33900173 PMCID: PMC8084493 DOI: 10.3201/eid2705.204756] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Noroviruses are a leading cause of acute gastroenteritis (AGE) among adults and children worldwide. NoroSurv is a global network for norovirus strain surveillance among children <5 years of age with AGE. Participants in 16 countries across 6 continents used standardized protocols for dual typing (genotype and polymerase type) and uploaded 1,325 dual-typed sequences to the NoroSurv web portal during 2016-2020. More than 50% of submitted sequences were GII.4 Sydney[P16] or GII.4 Sydney[P31] strains. Other common strains included GII.2[P16], GII.3[P12], GII.6[P7], and GI.3[P3] viruses. In total, 22 genotypes and 36 dual types, including GII.3 and GII.20 viruses with rarely reported polymerase types, were detected, reflecting high strain diversity. Surveillance data captured in NoroSurv enables the monitoring of trends in norovirus strains associated childhood AGE throughout the world on a near real-time basis.
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Yoshida T, Mimura M, Sakon N. Estimating household exposure to pyrethroids and the relative contribution of inhalation pathway in a sample of Japanese children. Environ Sci Pollut Res Int 2021; 28:19310-19324. [PMID: 33394402 DOI: 10.1007/s11356-020-12060-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Several synthetic pyrethroids are suspected to have carcinogenicity or reproductive toxicity. However, there is little knowledge about indoor air pollution in residences or the extent of intake by the residents of the newly developed pyrethroids, transfluthrin, profluthrin, and metofluthrin, although they have been widely used indoors as mosquito repellents and mothproof repellents in recent years. In the present study, the household exposure to pyrethroids through all exposure pathways and the contribution of inhalation pathway in Japanese children were examined by measuring urinary pyrethroid metabolites in the children and the airborne pyrethroids in their residences. Urine excreted first after waking up was collected from subjects aged 6 to 15 years (n = 132), and airborne pyrethroids were sampled in the subjects' bedrooms for 24 h. Nineteen pyrethroids and their nine urinary metabolites were measured. Their daily intakes estimated were as follows (median, ng/kg b.w./d): bifenthrin, 56; transfluthrin, 22; metofluthrin, 11; profluthrin, 0.86. The contribution rates of the amounts absorbed by inhalation to the amounts absorbed via all of the exposure pathways while at home tended to decrease in the following order: profluthrin (median 15%) ≈ transfluthrin (14%) > metofluthrin (1%) > bifenthrin (0.1%). Transfluthrin was considered to be the most notable pyrethroid as an indoor air pollutant. Our study demonstrated widespread exposure to transfluthrin, metofluthrin, profluthrin, and bifenthrin in a sample of Japanese children.
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Affiliation(s)
- Toshiaki Yoshida
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan.
| | - Mayumi Mimura
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan
| | - Naomi Sakon
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan
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Sasou A, Yuki Y, Kurokawa S, Sato S, Goda Y, Uchida M, Matsumoto N, Sagara H, Watanabe Y, Kuroda M, Sakon N, Sugiura K, Nakahashi-Ouchida R, Ushijima H, Fujihashi K, Kiyono H. Development of Antibody-Fragment-Producing Rice for Neutralization of Human Norovirus. Front Plant Sci 2021; 12:639953. [PMID: 33868338 PMCID: PMC8047661 DOI: 10.3389/fpls.2021.639953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Human norovirus is the leading cause of acute nonbacterial gastroenteritis in people of all ages worldwide. Currently, no licensed norovirus vaccine, pharmaceutical drug, or therapy is available for the control of norovirus infection. Here, we used a rice transgenic system, MucoRice, to produce a variable domain of a llama heavy-chain antibody fragment (VHH) specific for human norovirus (MucoRice-VHH). VHH is a small heat- and acid-stable protein that resembles a monoclonal antibody. Consequently, VHHs have become attractive and useful antibodies (Abs) for oral immunotherapy against intestinal infectious diseases. MucoRice-VHH constructs were generated at high yields in rice seeds by using an overexpression system with RNA interference to suppress the production of the major rice endogenous storage proteins. The average production levels of monomeric VHH (7C6) to GII.4 norovirus and heterodimeric VHH (7C6-1E4) to GII.4 and GII.17 noroviruses in rice seed were 0.54 and 0.28% (w/w), respectively, as phosphate buffered saline (PBS)-soluble VHHs. By using a human norovirus propagation system in human induced pluripotent stem-cell-derived intestinal epithelial cells (IECs), we demonstrated the high neutralizing activity of MucoRice expressing monomeric VHH (7C6) against GII.4 norovirus and of heterodimeric VHH (7C6-1E4) against both GII.4 and GII.17 noroviruses. In addition, MucoRice-VHH (7C6-1E4) retained neutralizing activity even after heat treatment at 90°C for 20 min. These results build a fundamental platform for the continued development of MucoRice-VHH heterodimer as a candidate for oral immunotherapy and for prophylaxis against GII.4 and GII.17 noroviruses in not only healthy adults and children but also immunocompromised patients and the elderly.
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Affiliation(s)
- Ai Sasou
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshikazu Yuki
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Mucosal Vaccines, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shiho Kurokawa
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shintaro Sato
- Division of Mucosal Vaccines, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Mucosal Vaccine Project, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Immunology and Genomics, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Yuki Goda
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masao Uchida
- Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Japan
| | - Naomi Matsumoto
- Mucosal Vaccine Project, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Hiroshi Sagara
- Medical Proteomics Laboratory, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yuji Watanabe
- Medical Proteomics Laboratory, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Masaharu Kuroda
- The National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Kotomi Sugiura
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Rika Nakahashi-Ouchida
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Mucosal Vaccines, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Kohtaro Fujihashi
- Division of Clinical Vaccinology, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Pediatric Dentistry, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Hiroshi Kiyono
- Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Mucosal Vaccines, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Gastroenterology, Department of Medicine, Chiba University – University of California San Diego Center for Mucosal Immunology, Allergy, and Vaccine, University of California, San Diego, San Diego, CA, United States
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Yuki Y, Kurokawa S, Sato S, Sasou A, Matsumoto N, Suzuki A, Sakon N, Goda Y, Takeyama N, Miyoshi T, Marcotte H, Tanaka T, Hammarstrom L, Kiyono H. A Heterodimeric Antibody Fragment for Passive Immunotherapy Against Norovirus Infection. J Infect Dis 2021; 222:470-478. [PMID: 32211769 DOI: 10.1093/infdis/jiaa115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/21/2020] [Indexed: 11/14/2022] Open
Abstract
Human noroviruses cause an estimated 685 million infections and 200 000 deaths annually worldwide. Although vaccines against GII.4 and GI.1 genotypes are under development, no information is available regarding vaccines or monoclonal antibodies to other noroviral genotypes. Here, we developed 2 variable-domain llama heavy-chain antibody fragment (VHHs) clones, 7C6 and 1E4, against GII.4 and GII.17 human noroviruses, respectively. Although 7C6 cross-reacted with virus-like particles (VLPs) of GII.17, GII.6, GII.3, and GII.4, it neutralized only GII.4 norovirus. In contrast, 1E4 reacted with and neutralized only GII.17 VLPs. Both VHHs blocked VLP binding to human induced pluripotent stem cell-derived intestinal epithelial cells and carbohydrate attachment factors. Using these 2 VHHs, we produced a heterodimeric VHH fragment that neutralized both GII.4 and GII.17 noroviruses. Because VHH fragments are heat- and acid-stable recombinant monoclonal antibodies, the heterodimer likely will be useful for oral immunotherapy and prophylaxis against GII.4 and GII.17 noroviruses in young, elderly, or immunocompromised persons.
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Affiliation(s)
- Yoshikazu Yuki
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Shiho Kurokawa
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Shintaro Sato
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,BIKEN Center for Innovative Vaccine Research and Development, Research Foundation for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Ai Sasou
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Naomi Matsumoto
- BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Akio Suzuki
- BIKEN Center for Innovative Vaccine Research and Development, Research Foundation for Microbial Diseases, Osaka University, Osaka, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yuki Goda
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Natsumi Takeyama
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | | | - Harold Marcotte
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | | | - Lennart Hammarstrom
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Hiroshi Kiyono
- Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Division of Mucosal Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Chiba University-University of California San Diego Center for Mucosal Immunology, Allergy, and Vaccine, University of California, San Diego, California, USA
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11
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Yoshida T, Mimura M, Sakon N. Intakes of phthalates by Japanese children and the contribution of indoor air quality in their residences. Environ Sci Pollut Res Int 2020; 27:19577-19591. [PMID: 32219650 DOI: 10.1007/s11356-020-08397-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/11/2020] [Indexed: 06/10/2023]
Abstract
Some phthalates, which are used mainly as plasticizers, are suspected to be endocrine disruptors. In the present study, daily intakes of phthalates by Japanese children through all exposure pathways and the contribution of indoor air quality to the intakes were examined by measuring urinary phthalate metabolites in the children and the airborne phthalates in their residences. Spot urine samples excreted first after waking up in the morning were collected from the subjects aged 6 to 15 years (n = 132), and airborne phthalates were sampled in the subjects' bedrooms for 24 h. Eight airborne phthalates and their urinary metabolites were determined by gas chromatography/mass spectrometry. The daily intakes of the phthalates estimated were as follows (median, μg/kg b.w./day): dimethyl phthalate (DMP), 0.15; diethyl phthalate (DEP), 0.42; diisobutyl phthalate (DiBP), 1.1; di-n-butyl phthalate (DnBP), 2.2; dicyclohexyl phthalate (DcHP), 0.026; benzylbutyl phthalate (BBzP), 0.032; di(2-ethylhexyl) phthalate (DEHP), 6.3. The 95th percentile (21 μg/kg b.w./day) of the DEHP intakes exceeded the reference doses (RfD, 20 μg/kg b.w./day) of the US Environmental Protection Agency (EPA). DEHP was suggested to be the most notable phthalate from the perspective of adverse effects on the health of Japanese children. On the other hand, DcHP and di-n-hexyl phthalate were not considered to be very important as indoor air pollutants and as internal contaminants for the children. The contribution rates of the amounts absorbed by inhalation to the amounts absorbed via all of the exposure pathways were only 7.9, 4.4, 6.6, 3.2, 0.22, and 1.0% as the median for DMP, DEP, DiBP, DnBP, BBzP, and DEHP, respectively. Therefore, inhalation did not seem to contribute very much as an absorption pathway of the phthalates for Japanese children while at home.
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Affiliation(s)
- Toshiaki Yoshida
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan.
| | - Mayumi Mimura
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan
| | - Naomi Sakon
- Osaka Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan
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12
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Matsushima Y, Mizukoshi F, Sakon N, Doan YH, Ueki Y, Ogawa Y, Motoya T, Tsukagoshi H, Nakamura N, Shigemoto N, Yoshitomi H, Okamoto-Nakagawa R, Suzuki R, Tsutsui R, Terasoma F, Takahashi T, Sadamasu K, Shimizu H, Okabe N, Nagasawa K, Aso J, Ishii H, Kuroda M, Ryo A, Katayama K, Kimura H. Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013-2017. Front Microbiol 2019; 10:2189. [PMID: 31611853 PMCID: PMC6777354 DOI: 10.3389/fmicb.2019.02189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/05/2019] [Indexed: 01/05/2023] Open
Abstract
Human norovirus (HuNoV) GII.P17-GII.17 (Kawasaki2014 variant) reportedly emerged in 2014 and caused gastroenteritis outbreaks worldwide. To clarify the evolution of both VP1 and RNA-dependent RNA polymerase (RdRp) regions of GII.P17-GII.17, we analyzed both global and novel Japanese strains detected during 2013–2017. Time-scaled phylogenetic trees revealed that the ancestral GII.17 VP1 region diverged around 1949, while the ancestral GII.P17 RdRp region diverged around 2010. The evolutionary rates of the VP1 and RdRp regions were estimated at ~2.7 × 10−3 and ~2.3 × 10−3 substitutions/site/year, respectively. The phylogenetic distances of the VP1 region exhibited no overlaps between intra-cluster and inter-cluster peaks in the GII.17 strains, whereas those of the RdRp region exhibited a unimodal distribution in the GII.P17 strains. Conformational epitope positions in the VP1 protein of the GII.P17-GII.17 strains were similar, although some substitutions, insertions and deletions had occurred. Strains belonging to the same cluster also harbored substitutions around the binding sites for the histo-blood group antigens of the VP1 protein. Moreover, some amino acid substitutions were estimated to be near the interface between monomers and the active site of the RdRp protein. These results suggest that the GII.P17-GII.17 virus has produced variants with the potential to alter viral antigenicity, host-binding capability, and replication property over the past 10 years.
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Affiliation(s)
- Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Fuminori Mizukoshi
- Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Utsunomiya, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Yo Ueki
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Sendai, Japan
| | - Yasutaka Ogawa
- Division of Virology, Saitama Institute of Public Health, Saitama, Japan
| | - Takumi Motoya
- Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi, Japan
| | | | - Naoki Shigemoto
- Hiroshima Prefectural Technology Research Institute Public Health and Environment Center, Hiroshima, Japan
| | - Hideaki Yoshitomi
- Fukuoka Institute of Health and Environmental Sciences, Dazaifu, Japan
| | | | - Rieko Suzuki
- Kanagawa Prefectural Institute of Public Health, Chigasaki, Japan
| | - Rika Tsutsui
- Aomori Prefecture Public Health and Environment Center, Aomori, Japan
| | - Fumio Terasoma
- Wakayama Prefectural Research Center of Environment and Public Health, Wakayama, Japan
| | - Tomoko Takahashi
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health, Morioka, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku, Japan
| | - Hideaki Shimizu
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Nobuhiko Okabe
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | | | - Jumpei Aso
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan.,Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka, Japan
| | - Haruyuki Ishii
- Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Kitasato University, Minato, Japan
| | - Hirokazu Kimura
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan.,Department of Microbiology, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
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13
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Abstract
The number of person-to-person transmitted norovirus cases (n = 4,712) in school children in Osaka, Japan, during 2016/17 was the largest since 2012/13. Norovirus outbreaks were reported by 101 schools including 53 nursery schools (1,927 cases), 18 kindergartens (1,086 cases) and 30 elementary schools (1,699 cases). The dominant genotype among outbreaks was GII.P16-GII.2 (57.4%; 58/101), followed by GII.P2-GII.2 (8.9%; 9/101) and GII.P7-GII.6 (5.9%; 6/101). GII.4 was not detected despite dominance in previous years.
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Affiliation(s)
- Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Japan
| | - Jun Komano
- Department of Clinical Laboratory, Nagoya Medical Center, Japan
| | - Heidi L Tessmer
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ryosuke Omori
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.,Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
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14
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Sakon N, Sadamasu K, Shinkai T, Hamajima Y, Yoshitomi H, Matsushima Y, Takada R, Terasoma F, Nakamura A, Komano J, Nagasawa K, Shimizu H, Katayama K, Kimura H. Foodborne Outbreaks Caused by Human Norovirus GII.P17-GII.17-Contaminated Nori, Japan, 2017. Emerg Infect Dis 2019; 24:920-923. [PMID: 29664371 PMCID: PMC5938760 DOI: 10.3201/eid2405.171733] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Seven foodborne norovirus outbreaks attributable to the GII.P17-GII.17 strain were reported across Japan in 2017, causing illness in a total of 2,094 persons. Nori (dried shredded seaweed) was implicated in all outbreaks and tested positive for norovirus. Our data highlight the stability of norovirus in dehydrated food products.
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15
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Sato S, Hisaie K, Kurokawa S, Suzuki A, Sakon N, Uchida Y, Yuki Y, Kiyono H. Human Norovirus Propagation in Human Induced Pluripotent Stem Cell-Derived Intestinal Epithelial Cells. Cell Mol Gastroenterol Hepatol 2018; 7:686-688.e5. [PMID: 30543870 PMCID: PMC6477164 DOI: 10.1016/j.jcmgh.2018.11.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/04/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Shintaro Sato
- Mucosal Vaccine Project, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan,Mucosal Vaccine Project, BIKEN Center for Innovative Vaccine Research and Development, Research Foundation for Microbial Diseases, Osaka University, Osaka, Japan,Graduate School of Medicine, Osaka University, Osaka, Japan,Division of Mucosal Vaccine, Research and Development Center for Mucosal Vaccines, Institute of Medical Science, The University of Tokyo, Tokyo, Japan,Division of Mucosal Barriology, Research and Development Center for Mucosal Vaccines, Institute of Medical Science, The University of Tokyo, Tokyo, Japan,Corresponding author:
| | - Kota Hisaie
- Mucosal Vaccine Project, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan,Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shiho Kurokawa
- Division of Mucosal Vaccine, Research and Development Center for Mucosal Vaccines, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akio Suzuki
- Mucosal Vaccine Project, BIKEN Center for Innovative Vaccine Research and Development, Research Foundation for Microbial Diseases, Osaka University, Osaka, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yohei Uchida
- Division of Mucosal Vaccine, Research and Development Center for Mucosal Vaccines, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshikazu Yuki
- Division of Mucosal Vaccine, Research and Development Center for Mucosal Vaccines, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Kiyono
- Division of Mucosal Vaccine, Research and Development Center for Mucosal Vaccines, Institute of Medical Science, The University of Tokyo, Tokyo, Japan,Division of Mucosal Barriology, Research and Development Center for Mucosal Vaccines, Institute of Medical Science, The University of Tokyo, Tokyo, Japan,Division of Mucosal Immunology, IMSUT Distinguished Professor Unit, Institute of Medical Science, The University of Tokyo, Tokyo, Japan,Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan,Department of Medicine, School of Medicine and CU-UCSD Center for Mucosal Immunology, Allergy and Vaccine, University of California, San Diego, San Diego, California
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16
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Nagasawa K, Matsushima Y, Motoya T, Mizukoshi F, Ueki Y, Sakon N, Murakami K, Shimizu T, Okabe N, Nagata N, Shirabe K, Shinomiya H, Suzuki W, Kuroda M, Sekizuka T, Ryo A, Fujita K, Oishi K, Katayama K, Kimura H. Phylogeny and Immunoreactivity of Norovirus GII.P16-GII.2, Japan, Winter 2016-17. Emerg Infect Dis 2018; 24:144-148. [PMID: 29260675 PMCID: PMC5749477 DOI: 10.3201/eid2401.170284] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
During the 2016–17 winter season in Japan, human norovirus GII.P16-GII.2 strains (2016 strains) caused large outbreaks of acute gastroenteritis. Phylogenetic analyses suggested that the 2016 strains derived from the GII.2 strains detected during 2010–12. Immunochromatography between 2016 strains and the pre-2016 GII.2 strains showed similar reactivity.
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17
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Kariya N, Sakon N, Komano J, Tomono K, Iso H. Current prevention and control of health care-associated infections in long-term care facilities for the elderly in Japan. J Infect Chemother 2018; 24:347-352. [DOI: 10.1016/j.jiac.2017.12.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/06/2017] [Indexed: 11/27/2022]
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18
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Chan MCW, Hu Y, Chen H, Podkolzin AT, Zaytseva EV, Komano J, Sakon N, Poovorawan Y, Vongpunsawad S, Thanusuwannasak T, Hewitt J, Croucher D, Collins N, Vinjé J, Pang XL, Lee BE, de Graaf M, van Beek J, Vennema H, Koopmans MPG, Niendorf S, Poljsak-Prijatelj M, Steyer A, White PA, Lun JH, Mans J, Hung TN, Kwok K, Cheung K, Lee N, Chan PKS. Global Spread of Norovirus GII.17 Kawasaki 308, 2014-2016. Emerg Infect Dis 2018; 23:1359-1354. [PMID: 28726618 PMCID: PMC5547775 DOI: 10.3201/eid2308.161138] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Analysis of complete capsid sequences of the emerging norovirus GII.17 Kawasaki 308 from 13 countries demonstrated that they originated from a single haplotype since the initial emergence in China in late 2014. Global spread of a sublineage SL2 was identified. A new sublineage SL3 emerged in China in 2016.
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19
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Nagasawa K, Matsushima Y, Motoya T, Mizukoshi F, Ueki Y, Sakon N, Murakami K, Shimizu T, Okabe N, Nagata N, Shirabe K, Shinomiya H, Suzuki W, Kuroda M, Sekizuka T, Suzuki Y, Ryo A, Fujita K, Oishi K, Katayama K, Kimura H. Genetic Analysis of Human Norovirus Strains in Japan in 2016-2017. Front Microbiol 2018; 9:1. [PMID: 29403456 PMCID: PMC5778136 DOI: 10.3389/fmicb.2018.00001] [Citation(s) in RCA: 282] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/03/2018] [Indexed: 11/18/2022] Open
Abstract
In the 2016/2017 winter season in Japan, HuNoV GII.P16-GII.2 strains (2016 strains) emerged and caused large outbreaks of acute gastroenteritis. To better understand the outbreaks, we examined the molecular evolution of the VP1 gene and RdRp region in 2016 strains from patients by studying their time-scale evolutionary phylogeny, positive/negative selection, conformational epitopes, and phylodynamics. The time-scale phylogeny suggested that the common ancestors of the 2016 strains VP1 gene and RdRp region diverged in 2006 and 1999, respectively, and that the 2016 strain was the progeny of a pre-2016 GII.2. The evolutionary rates of the VP1 gene and RdRp region were around 10-3 substitutions/site/year. Amino acid substitutions (position 341) in an epitope in the P2 domain of 2016 strains were not found in pre-2016 GII.2 strains. Bayesian skyline plot analyses showed that the effective population size of the VP1 gene in GII.2 strains was almost constant for those 50 years, although the number of patients with NoV GII.2 increased in 2016. The 2016 strain may be involved in future outbreaks in Japan and elsewhere.
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Affiliation(s)
- Koo Nagasawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Japan.,Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Takumi Motoya
- Division of Virology, Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Fuminori Mizukoshi
- Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Utsunomiya, Japan
| | - Yo Ueki
- Division of Virology, Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Sendai, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Tomomi Shimizu
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Nobuhiko Okabe
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Noriko Nagata
- Division of Virology, Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Hiroto Shinomiya
- Department of Microbiology, Ehime Prefectural Institute of Public Health and Environmental Science, Matsuyama, Japan
| | - Wataru Suzuki
- Eiken Chemical Co., Ltd., Biochemical Research Laboratory I Department-I, Shimotsuga, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku, Japan
| | - Yoshiyuki Suzuki
- Division of Biological Science, Department of Information and Basic Science, Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Kiyotaka Fujita
- School of Medical Technology, Faculty of Health Science, Gunma Paz University, Takasaki, Japan
| | - Kazunori Oishi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Kitasato University, Minato, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Japan.,Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan.,School of Medical Technology, Faculty of Health Science, Gunma Paz University, Takasaki, Japan
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20
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Mizukoshi F, Nagasawa K, Doan YH, Haga K, Yoshizumi S, Ueki Y, Shinohara M, Ishikawa M, Sakon N, Shigemoto N, Okamoto-Nakagawa R, Ochi A, Murakami K, Ryo A, Suzuki Y, Katayama K, Kimura H. Molecular Evolution of the RNA-Dependent RNA Polymerase and Capsid Genes of Human Norovirus Genotype GII.2 in Japan during 2004-2015. Front Microbiol 2017; 8:705. [PMID: 28487679 PMCID: PMC5403926 DOI: 10.3389/fmicb.2017.00705] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/05/2017] [Indexed: 12/22/2022] Open
Abstract
The RNA-dependent RNA polymerase (RdRp) and capsid (VP1) genes of 51 GII.2 human norovirus (HuNoV) strains collected during the period of 2004-2015 in Japan were analyzed. Full-length analyses of the genes were performed using next-generation sequencing. Based on the gene sequences, we constructed the time-scale evolutionary trees by Bayesian Markov chain Monte Carlo methods. Time-scale phylogenies showed that the RdRp and VP1 genes evolved uniquely and independently. Four genotypes of GII.2 (major types: GII.P2-GII.2 and GII.P16-GII.2) were detected. A common ancestor of the GII.2 VP1 gene existed until about 1956. The evolutionary rates of the genes were high (over 10-3 substitutions/site/year). Moreover, the VP1 gene evolution may depend on the RdRp gene. Based on these results, we hypothesized that transfer of the RdRp gene accelerated the VP1 gene evolution of HuNoV genotype GII.2. Consequently, recombination between ORF1 (polymerase) and ORF2 (capsid) might promote changes of GII.2 antigenicity.
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Affiliation(s)
- Fuminori Mizukoshi
- Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental ScienceUtsunomiya-shi, Japan
| | - Koo Nagasawa
- Infectious Disease Surveillance Center, National Institute of Infectious DiseasesMusashimurayama-shi, Japan
| | - Yen H Doan
- Department of Virology II, National Institute of Infectious DiseasesMusashimurayama-shi, Japan
| | - Kei Haga
- Laboratory of Viral infection I, Kitasato Institute for Life Sciences Graduate School of Infection Control Sciences, Kitasato UniversityMinato-ku, Japan
| | - Shima Yoshizumi
- Department of Infectious Diseases, Hokkaido Institute of Public HealthSapporo-shi, Japan
| | - Yo Ueki
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and EnvironmentSendai-shi, Japan
| | | | - Mariko Ishikawa
- Division of Virology, Kawasaki City Institute for Public HealthKawasaki-shi, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Prefectural Institute of Public HealthOsaka-shi, Japan
| | - Naoki Shigemoto
- Hiroshima Prefectural Technology Research Institute Public Health and Environment CenterHiroshima-shi, Japan
| | - Reiko Okamoto-Nakagawa
- Department of Health Science, Yamaguchi Prefectural Institute of Public Health and EnvironmentYamaguchi-shi, Japan
| | - Akie Ochi
- Department of Microbiology, Ehime Prefectural Institute of Public Health and Environmental ScienceMatsuyama-shi, Japan
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious DiseasesMusashimurayama-shi, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of MedicineYokohama-shi, Japan
| | - Yoshiyuki Suzuki
- Division of Biological Science, Nagoya City UniversityNagoya-shi, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral infection I, Kitasato Institute for Life Sciences Graduate School of Infection Control Sciences, Kitasato UniversityMinato-ku, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious DiseasesMusashimurayama-shi, Japan.,Department of Microbiology, Yokohama City University Graduate School of MedicineYokohama-shi, Japan
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21
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Doan YH, Haga K, Fujimoto A, Fujii Y, Takai-Todaka R, Oka T, Kimura H, Yoshizumi S, Shigemoto N, Okamoto-Nakagawa R, Shirabe K, Shinomiya H, Sakon N, Katayama K. Genetic analysis of human rotavirus C: The appearance of Indian-Bangladeshi strain in Far East Asian countries. Infect Genet Evol 2016; 41:160-173. [PMID: 27071530 DOI: 10.1016/j.meegid.2016.03.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/17/2016] [Accepted: 03/25/2016] [Indexed: 11/30/2022]
Abstract
Rotaviruses C (RVCs) circulate worldwide as an enteric pathogen in both humans and animals. Most studies of their genetic diversity focus on the VP7 and VP4 genes, but the complete genomes of 18 human RVCs have been described in independent studies. The genetic background of the Far East Asian RVCs is different than other human RVCs that were found in India and Bangladesh. Recently, a RVC detected in 2010 in South Korea had genetic background similar to the Indian-Bangladeshi RVCs. This study was undertaken to determine the whole genome of eight Japanese RVCs detected in 2005-2012, and to compare them with other human and animal global RVCs to better understand the genetic background of contemporary Far East Asian RVC. By phylogenetic analysis, the human RVCs appeared to be distinct from animal RVCs. Among human RVCs, three lineage constellations had prolonged circulation. The genetic background of the Far East Asian RVC was distinguished from Indian-Bangladeshi RVC as reported earlier. However, we found one Japanese RVC in 2012 that carried the genetic background of Indian-Bangladeshi RVC, whereas the remaining seven Japanese RVCs carried the typical genetic background of Far East Asian RVC. This is the first report of the Indian-Bangladeshi RVC in Japan. With that observation and the reassortment event of human RVCs in Hungary, our study indicates that the RVCs are spreading from one region to another.
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Affiliation(s)
- Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Fujimoto
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Takai-Todaka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Naoki Shigemoto
- Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan
| | | | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Hiroto Shinomiya
- Ehime Prefectural Institute of Public Health and Environmental Science, Ehime, Japan
| | - Naomi Sakon
- Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
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22
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Pongsuwanna Y, Tacharoenmuang R, Prapanpoj M, Sakon N, Komoto S, Guntapong R, Taniguchi K. Monthly Distribution of Norovirus and Sapovirus Causing Viral Gastroenteritis in Thailand. Jpn J Infect Dis 2016; 70:84-86. [PMID: 27000453 DOI: 10.7883/yoken.jjid.2015.440] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A total of 1,141 rotavirus-negative stool specimens collected from diarrheic children in 4 distinct regions under sentinel surveillance in Thailand between 2006 and 2008 were examined by reverse-transcription (RT)-PCR for norovirus (NoV) and sapovirus (SaV). Three hundred 3 specimens (26.6%) were positive for NoV, with 34 and 269 belonging to genogroup I (GI) and genogroup II (GII), respectively. Twelve specimens (1.1%) were positive for SaV. Mixed infections were found in 5 specimens: 3 samples indicated the presence of both NoV GI and GII, and 2 samples indicated the presence of both NoV GII and SaV. Analysis of the monthly distribution of NoV and SaV revealed that NoV GII was clustered between September and February, while NoV GI was detected mainly in June and July; SaV was found in May, June, and July. In addition, 3 outbreaks of acute gastroenteritis at 2 junior high schools in Phichit and Bangkok, and at a university in Phitsanulok, Thailand in 2006 were found to have been caused by NoV infection. Sequence analysis of NoVs from sporadic cases and outbreaks showed them to be genotypes GII.4 and GII.6.
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23
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Chapellier B, Tange S, Tasaki H, Yoshida K, Zhou Y, Sakon N, Katayama K, Nakanishi A. Examination of a plasmid-based reverse genetics system for human astrovirus. Microbiol Immunol 2015; 59:586-96. [PMID: 26272702 DOI: 10.1111/1348-0421.12317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/26/2015] [Accepted: 08/11/2015] [Indexed: 12/29/2022]
Abstract
A plasmid-based reverse genetics system for human astrovirus type 1 (HAstV1) is examined. Upon transfection into 293T cells, the plasmid vector, which harbors a HAstV1 expression cassette, expressed astroviral RNA that appeared to be capable of viral RNA replication, as indicated by the production of subgenomic RNA and capsid protein expression irrespective of the heterologous 5' ends of the transcribed RNA. Particles infectious to Caco-2 cells were made in this system; however, their infectivity was much lower than would be expected from the amount of particles apparently produced. Using Huh-7 cells as the transfection host with the aim of improving viral capsid processing for virion maturation partially restored the efficiency of infectious particle formation. Our results support the possibility that the DNA transfection process induces a cellular response that targets late, but not early, stages of HAstV1 infection.
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Affiliation(s)
- Benoit Chapellier
- Laboratory of Gene Therapy, Department of Aging Intervention, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8522
| | - Shoichiro Tange
- Laboratory of Gene Therapy, Department of Aging Intervention, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8522
| | - Hidetaka Tasaki
- Laboratory of Gene Therapy, Department of Aging Intervention, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8522
| | - Kazuhiro Yoshida
- Laboratory of Gene Therapy, Department of Aging Intervention, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8522
| | - Yan Zhou
- Laboratory of Gene Therapy, Department of Aging Intervention, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8522
| | - Naomi Sakon
- Osaka Prefectural Institute of Public Health, Osaka, Osaka, 537-0025
| | - Kazuhiko Katayama
- National Institute for Infectious Diseases, Department of Virology 2, Laboratory of Gastroenteritis Viruses, Musashi-Murayama, Tokyo, 208-0011, Japan
| | - Akira Nakanishi
- Laboratory of Gene Therapy, Department of Aging Intervention, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8522
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24
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Sakon N, Yamazaki K, Nakata K, Kanbayashi D, Yoda T, Mantani M, Kase T, Takahashi K, Komano J. Impact of genotype-specific herd immunity on the circulatory dynamism of norovirus: a 10-year longitudinal study of viral acute gastroenteritis. J Infect Dis 2014; 211:879-88. [PMID: 25210139 DOI: 10.1093/infdis/jiu496] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Human norovirus is a major cause of viral acute gastroenteritis worldwide. However, the transition of endemic norovirus genotypes remains poorly understood. The characteristics of natural immunity against norovirus are unclear because few studies have been performed in the natural infection setting. This prospective 10-year surveillance study of acute gastroenteritis in the province of Osaka, Japan, revealed that norovirus spread shows temporal, geographic, and age group-specific features in the humans. Genogroup II genotype 4 (GII.4) was detected in most sporadic pediatric cases, as well as in foodborne and nursing home outbreaks, respectively. The dominant genotypes in outbreaks at childcare facilities and schools shifted every season and involved GI, GII.2, GII.3, GII.4, and GII.6. Evidence at both the facility and individual levels indicated that genotype-specific herd immunity lasted long enough to influence the endemic norovirus genotype in the next season. Thus, norovirus circulates through human populations in a uniquely dynamic fashion.
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Affiliation(s)
- Naomi Sakon
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health
| | - Kenji Yamazaki
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health
| | - Keiko Nakata
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health
| | - Daiki Kanbayashi
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health
| | - Tomoko Yoda
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health
| | | | - Tetsuo Kase
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health
| | - Kazuo Takahashi
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health
| | - Jun Komano
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health Department of Clinical Laboratory, Nagoya Medical Center, Japan
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25
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Yoda T, Suzuki Y, Yamazaki K, Sakon N, Kanki M, Kase T, Takahashi K, Inoue K. Application of a modified loop-mediated isothermal amplification kit for detecting Norovirus genogroups I and II. J Med Virol 2010; 81:2072-8. [PMID: 19856470 PMCID: PMC7166440 DOI: 10.1002/jmv.21626] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Norovirus is a major etiologic agent in worldwide outbreaks of gastroenteritis associated with food as well as person‐to‐person transmission. The ubiquitous nature of Norovirus necessitates simple and rapid detection methods with high accuracy and sensitivity. To this end, several investigators have evaluated the usefulness of commercial reverse‐transcription loop‐mediated isothermal amplification (RT‐LAMP) kits for detecting Norovirus genogroups I (GI) and II (GII). In previous studies, the conventional Loopamp kit for Norovirus GII showed a relatively high detection rate, while that for Norovirus GI showed a relatively low detection rate. In the present study, clinical Norovirus specimens were used to compare the detection rate of a modified Loopamp kit for Norovirus GI with the rates of the conventional Loopamp kit for Norovirus GI and an “in‐house” RT‐LAMP GI primer set, methods which had a high detection rate. Results from the present study showed that the modified Loopamp kit for Norovirus GI had a higher detection rate for two viral genotypes (GI.3, GI.11). On comparison with an “in‐house” GII primer set using genotype GII.4 viruses circulating recently, the detection rate by the Loopamp kit for Norovirus GII was found to be higher, with a 98% detection rate. These results indicate the applicability of the modified LAMP kit for GI and the conventional LAMP kit for GII for detection of Noroviruses in clinical samples. J. Med. Virol. 81:2072–2078, 2009. © 2009 Wiley‐Liss, Inc.
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Affiliation(s)
- Tomoko Yoda
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka, Japan.
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26
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Yamazaki K, Sakon N, Nakata K, Kase T. Prevalence of Enterovirus in Osaka, Japan, between April and September 2008. Jpn J Infect Dis 2009. [DOI: 10.7883/yoken.jjid.2009.80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Affiliation(s)
| | - Naomi Sakon
- Osaka Prefectural Institute of Public Health, Japan
| | - Keiko Nakata
- Osaka Prefectural Institute of Public Health, Japan
| | - Tetsuo Kase
- Osaka Prefectural Institute of Public Health, Japan
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27
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Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T, Yamashita A, Goto N, Takahashi K, Yasunaga T, Ikuta K, Mizutani T, Okamoto Y, Tagami M, Morita R, Maeda N, Kawai J, Hayashizaki Y, Nagai Y, Horii T, Iida T, Nakaya T. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One 2009; 4:e4219. [PMID: 19156205 PMCID: PMC2625441 DOI: 10.1371/journal.pone.0004219] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 12/01/2008] [Indexed: 12/27/2022] Open
Abstract
With the severe acute respiratory syndrome epidemic of 2003 and renewed attention on avian influenza viral pandemics, new surveillance systems are needed for the earlier detection of emerging infectious diseases. We applied a “next-generation” parallel sequencing platform for viral detection in nasopharyngeal and fecal samples collected during seasonal influenza virus (Flu) infections and norovirus outbreaks from 2005 to 2007 in Osaka, Japan. Random RT-PCR was performed to amplify RNA extracted from 0.1–0.25 ml of nasopharyngeal aspirates (N = 3) and fecal specimens (N = 5), and more than 10 µg of cDNA was synthesized. Unbiased high-throughput sequencing of these 8 samples yielded 15,298–32,335 (average 24,738) reads in a single 7.5 h run. In nasopharyngeal samples, although whole genome analysis was not available because the majority (>90%) of reads were host genome–derived, 20–460 Flu-reads were detected, which was sufficient for subtype identification. In fecal samples, bacteria and host cells were removed by centrifugation, resulting in gain of 484–15,260 reads of norovirus sequence (78–98% of the whole genome was covered), except for one specimen that was under-detectable by RT-PCR. These results suggest that our unbiased high-throughput sequencing approach is useful for directly detecting pathogenic viruses without advance genetic information. Although its cost and technological availability make it unlikely that this system will very soon be the diagnostic standard worldwide, this system could be useful for the earlier discovery of novel emerging viruses and bioterrorism, which are difficult to detect with conventional procedures.
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Affiliation(s)
- Shota Nakamura
- Department of Genome Informatics, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Cheng-Song Yang
- International Research Center for Infectious Diseases, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Department of Virology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Naomi Sakon
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Higashinari, Osaka, Japan
| | - Mayo Ueda
- International Research Center for Infectious Diseases, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Department of Virology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Takahiro Tougan
- Department of Molecular Protozoology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Akifumi Yamashita
- Department of Genome Informatics, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Naohisa Goto
- Department of Genome Informatics, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Kazuo Takahashi
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Higashinari, Osaka, Japan
| | - Teruo Yasunaga
- Department of Genome Informatics, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Kazuyoshi Ikuta
- Department of Virology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Tetsuya Mizutani
- Department of Virology 1, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Yoshiko Okamoto
- Center of Research Network for Infectious Diseases, RIKEN, Chiyoda, Tokyo, Japan
| | | | - Ryoji Morita
- Omics Science Center (OSC), RIKEN, Yokohama, Kanagawa, Japan
| | - Norihiro Maeda
- Omics Science Center (OSC), RIKEN, Yokohama, Kanagawa, Japan
| | - Jun Kawai
- Omics Science Center (OSC), RIKEN, Yokohama, Kanagawa, Japan
| | | | - Yoshiyuki Nagai
- Center of Research Network for Infectious Diseases, RIKEN, Chiyoda, Tokyo, Japan
| | - Toshihiro Horii
- International Research Center for Infectious Diseases, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Department of Molecular Protozoology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Tetsuya Iida
- International Research Center for Infectious Diseases, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Takaaki Nakaya
- International Research Center for Infectious Diseases, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- * E-mail:
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28
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Yamazaki K, Sakon N, Nakata K, Kase T. Prevalence of enterovirus in Osaka, Japan, between April and September 2008. Jpn J Infect Dis 2009; 62:80-81. [PMID: 19168970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Kenji Yamazaki
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan.
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29
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Abstract
Sapovirus (SaV) is a causative agent of gastroenteritis. On the basis of capsid protein (VP1) nucleotide sequences, SaV can be divided into 5 genogroups (GI-GV), of which the GI, GII, GIV, and GV strains infect humans. SaV is uncultivable, but expression of recombinant VP1 in insect cells results in formation of viruslike particles (VLPs) that are antigenically similar to native SaV. In this study, we newly expressed SaV GII and GIV VLPs to compare genetic and antigenic relationships among all human SaV genogroups. Hyperimmune antiserum samples against VLPs reacted strongly with homologous VLPs. However, several antiserum samples weakly cross-reacted against heterologous VLPs in an antibody ELISA. Conversely, an antigen ELISA showed that VLPs of SaV in all human genogroups were antigenically distinct. These findings indicate a likely correspondence between SaV antigenicity and VP1 genogrouping and genotyping.
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30
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Sakon N, Yamazaki K, Yoda T, Tsukamoto T, Kase T, Taniguchi K, Takahashi K, Otake T. Norovirus storm in Osaka, Japan, last winter (2006/2007). Jpn J Infect Dis 2007; 60:409-410. [PMID: 18032849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Naomi Sakon
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka 537-0025, Japan.
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Yoda T, Suzuki Y, Yamazaki K, Sakon N, Kanki M, Aoyama I, Tsukamoto T. Evaluation and application of reverse transcription loop-mediated isothermal amplification for detection of noroviruses. J Med Virol 2007; 79:326-34. [PMID: 17245722 PMCID: PMC7166943 DOI: 10.1002/jmv.20802] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of norovirus (NV) was developed. In order to design primer sets for the detection of a wide range of NVs, NVs were categorized into three groups, that is, genogroup I (GI), prevalent GII, and minor GII; three sets of primers were developed for each group. Clinical specimens of patients suffering from enteric RNA viruses, such as NV, group A and C rotavirus, and sapovirus were examined using these primer sets. Various genotypes of NVs were detected in clinical specimens from patients infected with NV where no false positive reaction was observed with other enteric RNA viruses. Additionally, 88 samples of acute gastroenteritis outbreaks were analyzed by an RT-LAMP assay and compared with the results of routine RT-PCR. The results of the RT-LAMP assay corresponded well to that of RT-PCR. These findings suggest the practical application of the RT-LAMP assay for the detection of NVs in clinical specimens. Consequently, the RT-LAMP system and conventional detection kits (NVGI and NVGII detection kits; Eiken Chemical Co., Ltd., Japan) were compared. The detection rate of the prevalent and minor GII primer sets was similar to that of the conventional NVGII kit, while the detection rate of the GI primer set is different because it can detect several genotypes better than the conventional NVGI kit. This is an initial report that the RT-LAMP system is able to detect NVs in clinical specimens within a wide range.
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Affiliation(s)
- Tomoko Yoda
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka, Japan.
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32
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Sakon N, Yamazaki K, Yoda T, Kanki M, Takahashi K, Tsukamoto T, Otake T. Norovirus outbreaks at nursing homes in osaka, Japan. Jpn J Infect Dis 2005; 58:254-5. [PMID: 16116265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Naomi Sakon
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan.
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33
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Sakon N, Yamazaki K, Yoda T, Kanki M, Otake T, Tsukamoto T. A norovirus outbreak of gastroenteritis linked to packed lunches. Jpn J Infect Dis 2005; 58:253. [PMID: 16116264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Naomi Sakon
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan.
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34
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Yoda T, Suzuki Y, Terano Y, Yamazaki K, Sakon N, Kuzuguchi T, Oda H, Tsukamoto T. Precise characterization of norovirus (Norwalk-like virus)-specific monoclonal antibodies with broad reactivity. J Clin Microbiol 2003; 41:2367-71. [PMID: 12791850 PMCID: PMC156499 DOI: 10.1128/jcm.41.6.2367-2371.2003] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have been characterizing monoclonal antibodies against Norovirus (Norwalk-like virus). In the course of our study, two monoclonal antibodies generated against Norovirus genogroup II capsid protein were found to react not only to genogroup II but also to genogroup I recombinant capsid proteins. In addition, we showed that these two monoclonal antibodies reacted to a 40-amino-acid-fragment located close to the N-terminal region of genogroup II Norovirus. Similar reactivity was observed with the equivalent region of genogroup I Norovirus. In this study, we confirmed that the epitopes of the two monoclonal antibodies existed within an 11-amino-acid peptide. To obtain an idea of the reactive ranges of the two monoclonal antibodies toward different strains of Norovirus, their reactivities were investigated using 16 types of peptide constructed according to the data in GenBank and 8 recombinant capsid proteins (7 whole capsid proteins and 1 short [80-amino-acid] protein fragment). A characteristic broad reactivity of the two monoclonal antibodies is clearly shown by the results of this study. Thus, these monoclonal antibodies could be useful tools for detecting a broad range of Norovirus strains.
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Affiliation(s)
- Tomoko Yoda
- Division of Food Microbiology, Osaka Prefectural Institute of Public Health, Japan.
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35
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Oishi I, Sakon N. [Astroviruses]. Uirusu 2000; 50:197-207. [PMID: 11276809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- I Oishi
- Laboratory of Pathology, and Virology, Osaka Prefectural Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan.
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36
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Sakon N, Yamazaki K, Utagawa E, Okuno Y, Oishi I. Genomic characterization of human astrovirus type 6 Katano virus and the establishment of a rapid and effective reverse transcription-polymerase chain reaction to detect all serotypes of human astrovirus. J Med Virol 2000; 61:125-31. [PMID: 10745244 DOI: 10.1002/(sici)1096-9071(200005)61:1<125::aid-jmv20>3.0.co;2-b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We previously reported that human astrovirus type 6 (HAstV T6) was the etiologic agent of a large-scale outbreak of acute gastroenteritis that occurred in 1991 in Katano City, Osaka, Japan [Oishi et al., 1994]. The two representative strains, Katano virus K23 and K24, have been analyzed by sequencing the open reading frame 2 (ORF2) region after amplification by reverse transcription-polymerase chain reaction (RT-PCR). The ORF2 region of HAstV T6 strains, including K23, was found to be about 20 bp smaller than those of other types. There was 94% nucleotide sequence identity and 95% amino acid sequence identity between K23 and K24, with the Oxford strains belonging to HAstV T6. The high homology of the ORF2 region between the Katano and Oxford strains shows intratype genomic stability, irrespective of time and place of virus isolation. Comparing sequences of ORF2 of different HAstV serotypes, we established a rapid and highly sensitive detection system for HAstV types using RT-PCR with the AC230/AC1' primer set designed from the 5'-terminal end region of ORF2. This RT-PCR system seems very useful in detecting at least two different viruses in a single PCR test tube using AC230/AC1' in addition to the NV81/82, SM82 primer sets. Thus, our rapid and effective detection system may contribute to the epidemiologic characterization of astrovirus infections as well as Norwalk-like viruses.
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Affiliation(s)
- N Sakon
- Laboratory of Virology, Osaka Prefectural Institute of Public Health, Osaka, Japan.
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Yoda T, Terano Y, Shimada A, Suzuki Y, Yamazaki K, Sakon N, Oishi I, Utagawa ET, Okuno Y, Shibata T. Expression of recombinant Norwalk-like virus capsid proteins using a bacterial system and the development of its immunologic detection. J Med Virol 2000; 60:475-81. [PMID: 10686033 DOI: 10.1002/(sici)1096-9071(200004)60:4<475::aid-jmv17>3.0.co;2-b] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The capsid protein of Norwalk-like virus (NLV) isolates NLV-36 (Mexico virus type, genogroup II [GII]), NLV-21 (Lordsdale virus type, GII), NLV-114 (untyped GII virus), and NLV-96-908 (KY89 virus type, GI) have been expressed in an Escherichia coli system. The expressed recombinant NLV capsid proteins, fused with maltose binding protein (MBP-rV) and thioredoxin (TRX-rV) in E. coli lysate, were analyzed using sodium dodecyl sulfate-polyacrylamide gel eletrophoresis. Rabbit IgG (R-IgG) in hyperimmune serum has been raised against MBP-rV-36 capsid protein and was purified before further study. Detection of TRX-rVs using an enzyme-linked immunosorbent assay (ELISA) showed that R-IgG had immunologic reactivity to GII as well as to the GI rV capsid proteins TRX-rV-36, TRX-rV-21, TRX-rV-114, and TRX-rV-96-908. Results of Western immunoblot (WB) analysis showed the same broad recognition of R-IgG when using the same samples. The results of the ELISA tests on serum samples obtained from patients involved in confirmed outbreaks of NLV proved that expressed NLV capsid proteins in E. coli can be detected by NLV-infected human serum. In addition, purified NLVs (LD virus types) derived from patients' stool could be detected using anti-NLV R-IgG, whereas normal R-IgG did not react when using WB. Our results strongly suggest that the immunologic detection of NLV antigens using anti-rV R-IgG is possible and seems a significant step toward simplification of an NLV detection test.
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Affiliation(s)
- T Yoda
- Division of Food Microbiology, Osaka Prefectural Institute of Public Health, Osaka, Japan.
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Abstract
While group A and C rotaviruses have been grown in cell culture, group B rotavirus has never been cultured. In this study we successfully isolated porcine group B rotavirus in swine kidney cells. Pancreatin treatment is essential for the propagation of group B rotavirus.
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Affiliation(s)
- T Sanekata
- Department of Veterinary Microbiology, Faculty of Agriculture, Tottori University, Japan.
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