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Akari Y, Hatazawa R, Kuroki H, Ito H, Negoro M, Tanaka T, Miwa H, Sugiura K, Umemoto M, Tanaka S, Ogawa M, Ito M, Fukuda S, Murata T, Taniguchi K, Suga S, Kamiya H, Nakano T, Taniguchi K, Komoto S. Full genome-based characterization of an Asian G3P[6] human rotavirus strain found in a diarrheic child in Japan: Evidence for porcine-to-human zoonotic transmission. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 115:105507. [PMID: 37757900 DOI: 10.1016/j.meegid.2023.105507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
Human rotavirus strains having the unconventional G3P[6] genotype have been sporadically detected in diarrheic patients in different parts of the world. However, the full genomes of only three human G3P[6] strains from Asian countries (China, Indonesia, and Vietnam) have been sequenced and characterized, and thus the exact origin and evolution of G3P[6] strains in Asia remain to be elucidated. Here, we sequenced and characterized the full genome of a G3P[6] strain (RVA/Human-wt/JPN/SO1199/2020/G3P[6]) found in a stool sample from a 3-month-old infant admitted with acute gastroenteritis in Japan. On full genomic analysis, strain SO1199 was revealed to have a unique Wa-like genogroup configuration: G3-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1. VP6 genotype I5 and NSP1 genotype A8 are commonly found in porcine rotavirus strains. Furthermore, phylogenetic analysis demonstrated that all 11 genes of strain SO1199 were closely related to those of porcine and/or porcine-like human rotaviruses and thus appeared to be of porcine origin. Thus, strain SO1199 was shown to possess a porcine-like genomic backbone and thus is likely to be the result of interspecies transmission of a porcine rotavirus strain. Of note is that all 11 genes of strain SO1199 were phylogenetically located in clusters, distinct from those of the previously identified porcine-like human G3P[6] strains from around the world including Asia, suggesting the occurrence of independent porcine-to-human zoonotic transmission events. To our knowledge, this is the first report on full genome-based characterization of a human G3P[6] strain that has emerged in Japan. Our findings revealed the diversity of unconventional human G3P[6] strains in Asia, and provide important insights into the origin and evolution of G3P[6] strains.
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Affiliation(s)
- Yuki Akari
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Riona Hatazawa
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Haruo Kuroki
- Sotobo Children's Clinic, Isumi, Chiba 299-4503, Japan
| | - Hiroaki Ito
- Department of Pediatrics, Kameda Medical Center, Kamogawa, Chiba 296-8602, Japan
| | - Manami Negoro
- Institute for Clinical Research, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Takaaki Tanaka
- Department of Pediatrics, Kawasaki Medical School, Okayama, Okayama 700-8505, Japan
| | - Haruna Miwa
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Katsumi Sugiura
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | | | - Shigeki Tanaka
- Department of Pediatrics, Mie Chuo Medical Center, Tsu, Mie 514-1101, Japan
| | - Masahiro Ogawa
- Department of Pediatrics, Mie Chuo Medical Center, Tsu, Mie 514-1101, Japan
| | - Mitsue Ito
- Department of Pediatrics, Japanese Red Cross Ise Hospital, Ise, Mie 516-8512, Japan
| | - Saori Fukuda
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Takayuki Murata
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan; Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Kiyosu Taniguchi
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Shigeru Suga
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Hajime Kamiya
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Takashi Nakano
- Department of Pediatrics, Kawasaki Medical School, Okayama, Okayama 700-8505, Japan
| | - Koki Taniguchi
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Satoshi Komoto
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan; Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi 470-1192, Japan; Division of One Health, Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Yufu, Oita 879-5593, Japan.
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Louge Uriarte EL, Badaracco A, Spetter MJ, Miño S, Armendano JI, Zeller M, Heylen E, Späth E, Leunda MR, Moreira AR, Matthijnssens J, Parreño V, Odeón AC. Molecular Epidemiology of Rotavirus A in Calves: Evolutionary Analysis of a Bovine G8P[11] Strain and Spatio-Temporal Dynamics of G6 Lineages in the Americas. Viruses 2023; 15:2115. [PMID: 37896894 PMCID: PMC10611311 DOI: 10.3390/v15102115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Rotavirus A (RVA) causes diarrhea in calves and frequently possesses the G6 and P[5]/P[11] genotypes, whereas G8 is less common. We aimed to compare RVA infections and G/P genotypes in beef and dairy calves from major livestock regions of Argentina, elucidate the evolutionary origin of a G8 strain and analyze the G8 lineages, infer the phylogenetic relationship of RVA field strains, and investigate the evolution and spatio-temporal dynamics of the main G6 lineages in American countries. Fecal samples (n = 422) from diarrheic (beef, 104; dairy, 137) and non-diarrheic (beef, 78; dairy, 103) calves were analyzed by ELISA and semi-nested multiplex RT-PCR. Sequencing, phylogenetic, phylodynamic, and phylogeographic analyses were performed. RVA infections were more frequent in beef (22.0%) than in dairy (14.2%) calves. Prevalent genotypes and G6 lineages were G6(IV)P[5] in beef (90.9%) and G6(III)P[11] (41.2%) or mixed genotypes (23.5%) in dairy calves. The only G8 strain was phylogenetically related to bovine and artiodactyl bovine-like strains. Re-analyses inside the G8 genotype identified G8(I) to G8(VIII) lineages. Of all G6 strains characterized, the G6(IV)P[5](I) strains from "Cuenca del Salado" (Argentina) and Uruguay clustered together. According to farm location, a clustering pattern for G6(IV)P[5] strains of beef farms was observed. Both G6 lineage strains together revealed an evolutionary rate of 1.24 × 10-3 substitutions/site/year, and the time to the most recent common ancestor was dated in 1853. The most probable ancestral locations were Argentina in 1981 for G6(III) strains and the USA in 1940 for G6(IV) strains. The highest migration rates for both G6 lineages together were from Argentina to Brazil and Uruguay. Altogether, the epidemiology, genetic diversity, and phylogeny of RVA in calves can differ according to the production system and farm location. We provide novel knowledge about the evolutionary origin of a bovine G8P[11] strain. Finally, bovine G6 strains from American countries would have originated in the USA nearly a century before its first description.
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Affiliation(s)
- Enrique L. Louge Uriarte
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Alejandra Badaracco
- Instituto Nacional de Tecnología Agropecuaria, EEA Montecarlo, Av. El Libertador Nº 2472, Montecarlo CP3384, Misiones, Argentina;
| | - Maximiliano J. Spetter
- Facultad de Ciencias Veterinarias, Departamento de Fisiopatología, Centro de Investigación Veterinaria de Tandil (CIVETAN), Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil CP7000, Buenos Aires, Argentina; (M.J.S.); (J.I.A.)
| | - Samuel Miño
- Instituto Nacional de Tecnología Agropecuaria, EEA Cerro Azul, Ruta 14, km 836, Cerro Azul CP3313, Misiones, Argentina;
| | - Joaquín I. Armendano
- Facultad de Ciencias Veterinarias, Departamento de Fisiopatología, Centro de Investigación Veterinaria de Tandil (CIVETAN), Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil CP7000, Buenos Aires, Argentina; (M.J.S.); (J.I.A.)
| | - Mark Zeller
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Elisabeth Heylen
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Ernesto Späth
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (E.S.); (A.C.O.)
| | - María Rosa Leunda
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Ana Rita Moreira
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Viviana Parreño
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Virología e Innovaciones Tecnológicas, Nicolas Repetto y de los Reseros s/n, Hurlingham CP1686, Buenos Aires, Argentina
| | - Anselmo C. Odeón
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (E.S.); (A.C.O.)
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Phan T, Hikita T, Okitsu S, Akari Y, Komoto S, Hayakawa S, Ushijima H. Whole genome sequencing and genomic characterization of a DS-1-like G2P[4] group A rotavirus in Japan. Virus Genes 2023; 59:688-692. [PMID: 37405556 DOI: 10.1007/s11262-023-02018-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/26/2023] [Indexed: 07/06/2023]
Abstract
After rotavirus was discovered in 1973, it became the leading pathogen in causing acute gastroenteritis in humans worldwide. In this study, we performed whole genome sequencing and genomic characterization of a DS-1-like G2P[4] group A rotavirus in feces of a Japanese child with acute gastroenteritis who was fully Rotarix® vaccinated. The genomic investigation determined a genomic constellation G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 of this rotavirus strain. Its antigenic epitopes of the VP7 and VP4 proteins had significant mismatches compared with the vaccine strains. Our study is the latest attempt to investigate the evolution of the VP7 and VP4 genes of emerging G2P[4] rotavirus in Japan.
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Affiliation(s)
- Tung Phan
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Shoko Okitsu
- Division of Microbiology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Yuki Akari
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Division of One Health, Research Center for Global and Local Infectious Diseases, Oita University, Yufu, Oita, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan.
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4
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Malakalinga JJ, Misinzo G, Msalya GM, Shayo MJ, Kazwala RR. Genetic diversity and Genomic analysis of G3P[6] and equine-like G3P[8] in Children Under-five from Southern Highlands and Eastern Tanzania. Acta Trop 2023; 242:106902. [PMID: 36948234 DOI: 10.1016/j.actatropica.2023.106902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/12/2023] [Accepted: 03/18/2023] [Indexed: 03/24/2023]
Abstract
Rotavirus group A genomic characterization is critical for understanding the mechanisms of rotavirus diversity, such as reassortment events and possible interspecies transmission. However, little is known about the genetic diversity and genomic relationship of the rotavirus group A strains circulating in Tanzania. The genetic and genomic relationship of RVA genotypes was investigated in children under the age of five. A total of 169 faecal samples were collected from under-five with diarrhea in Mbeya, Iringa and Morogoro regions of Tanzania. The RVA were screened in children under five with diarrhea using reverse transcription PCR for VP7 and VP4, and the G and P genotypes were determined using Sanger dideoxynucleotide cycle sequencing. Whole-genome sequencing was performed on selected genotypes. The overall RVA rate was 4.7% (8/169). The G genotypes were G3 (7/8) and G6 (1/8) among the 8 RVA positives, while the P genotypes were P[6] (4/8) and P[8] (2), and the other two were untypeable. G3P[6] and G3P[8] were the identified genotype combinations. The genomic analysis reveals that the circulating G3P[8] and G3P[6] isolates from children under the age of five with diarrhea had a DS-1-like genome configuration (I2-R2-C2-M2-Ax-N2-T2-E2-H2). The phylogenic analysis revealed that all 11 segments of G3P[6] were closely related to human G3P[6] identified in neighboring countries such as Uganda, Kenya, and other African countries, implying that G3P[6] strains descended from a common ancestor. Whereas, G3P[8] were closely related to previously identified equine-like G3P[P8] from Kenya, Japan, Thailand, Brazil, and Taiwan, implying that this strain was introduced rather than reassortment events. We discovered amino acid differences at antigenic epitopes and N-linked glycosylation sites between the wild type G3 and P[8] compared to vaccine strains, implying that further research into the impact of these differences on vaccine effectiveness is warranted. The phylogenic analysis of VP7 also identified a bovine-like G6. For the first time in Tanzania, we report the emergence of novel equine-like G3 and bovine-like G6 RVA strains, highlighting the importance of rotavirus genotype monitoring and genomic analysis of representative genotypes.
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Affiliation(s)
- Joseph J Malakalinga
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3021, Morogoro, Tanzania; SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro, Tanzania; Food and Microbiology Laboratory, Tanzania Bureau of Standards, Ubungo Area, Morogoro Road/Sam Nujoma Road, P.O. Box 9524, Dar es Salaam, Tanzania.
| | - Gerald Misinzo
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro, Tanzania; Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3019, Morogoro, Tanzania
| | - George M Msalya
- Department of Animal, Aquaculture and Range Sciences, College of Agriculture, Sokoine University of Agriculture, P.O. Box 3004, Morogoro, Tanzania
| | - Mariana J Shayo
- Muhimbili University of Health and Allied sciences, Department of Biological and Pre-clinical Studies, PO Box 65001, Dar es Salaam, Tanzania
| | - Rudovick R Kazwala
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3021, Morogoro, Tanzania
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Prevalence and genomic characterization of rotavirus group A genotypes in piglets from in southern highlands and eastern Tanzania. Heliyon 2022; 8:e11750. [DOI: 10.1016/j.heliyon.2022.e11750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/27/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
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Maina MM, Faneye AO, Motayo BO, Nseabasi-Maina N, Adeniji AJ. Human rotavirus VP4 and VP7 genetic diversity and detection of GII norovirus in Ibadan as Nigeria introduces rotavirus vaccine. J Int Med Res 2022; 50:3000605221121956. [PMID: 36138570 PMCID: PMC9511342 DOI: 10.1177/03000605221121956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objective This cross-sectional study investigated the circulating strains of rotavirus and screened for noravirus in Ibadan, Nigeria as the country introduces the rotavirus vaccine into its national immunization program. Methods Sixty-five stool samples were collected from children younger than 5 years with clinically diagnosed diarrhea and screened for the presence of rotavirus and norovirus using RT-PCR. Rotavirus-positive samples were further analyzed to determine the G and P genotypes using semi-nested multiplex PCR. Results The rates of rotavirus and norovirus positivity were 30.8% and 10.8%, respectively, whereas the rate of rotavirus and norovirus mixed infection was 4.6%. G1 was the predominant VP7 genotype, followed by G2, G9, and G1G2G9, whereas the predominant VP4 genotype was P[4], followed by P[6], P[8], and P[9]. The mixed P types P[4]P[8] and P[4]P[6] were also detected. G1P[4] was the most common VP4 and VP7 combination, followed by G2P[4], G1[P6], G1P[8], G2P[6], G2P[9], G9P[6], G2G9P[4], G2P[4]P[6], G1P[4]P[8], G2G9P[8], G1G2G9P[8], and G1[non-typable] P[non-typable], which were detected in at least 5% of the samples. Four samples had a combination of non-typable G and P types. Conclusions It is essential to monitor the circulation of virus strains prior to and during the implementation of the immunization program.
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Affiliation(s)
- Meshach Maunta Maina
- Department of Veterinary Microbiology, University of Maiduguri, Nigeria.,Department of Virology, College of Medicine, University of Ibadan, Nigeria
| | | | | | | | - Adekunle Johnson Adeniji
- Department of Virology, College of Medicine, University of Ibadan, Nigeria.,WHO National Poliovirus laboratory, Department of Virology, University of Ibadan, Nigeria
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Qin YF, Gong QL, Zhang M, Sun ZY, Wang W, Wei XY, Chen Y, Zhang Y, Zhao Q, Jiang J. Prevalence of bovine rotavirus among Bovidae in China during 1984-2021: A systematic review and meta-analysis. Microb Pathog 2022; 169:105661. [PMID: 35817280 DOI: 10.1016/j.micpath.2022.105661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 06/20/2022] [Accepted: 06/26/2022] [Indexed: 11/28/2022]
Abstract
Bovine rotavirus (BRV) is a potential zoonotic intestinal pathogen that brings a serious threat to calf health, and has resulted in huge economic losses to China's breeding industry. Here, a systematic review and meta-analysis was conducted to estimate the prevalence of BRV among Bovidae from 1984 to 2021 in China. A total of 64 publications on BRV investigation in China were screened from the databases Chinese National Knowledge Infrastructure (CNKI), Wan Fang Database, Technology Periodical Database (VIP), PubMed, and ScienceDirect. The random-effect model was used to calculate the pooled prevalence of BRV, and the analyzed data were derived from 25 provinces in China. The estimated pooled prevalence of BRV in China was 35.7% (8176/17,292). In addition, the prevalence of BRV in Southwestern China (77.1%; 2924/3600) was significantly higher than that in other regions of China. Regarding geographic and climatic factors, the prevalence of BRV in the subgroup of latitude 30-35° (76.8%; 3303/4659) was significantly higher than that in the subgroup of latitude less than 30° (37.0%; 485/1275) or more than 35° (32.6%; 1703/5722), while the prevalence of BRV in the subgroup of longitude 100-105° (75.4%; 2513/3849) was significantly higher than that in the subgroup of longitude less than 100° (32.6%; 619/2255) or more than 105° (48.9%; 2359/5552). Rainfall was positively correlated with the prevalence of BRV, whereas temperature was negatively correlated with the positive rate of BRV (P < 0.05). Our data showed that the prevalence of BRV was strongly correlated with geographical and climatic conditions. Thus, we recommend that the corresponding prevention and control programs should be formulated according to different geographical conditions. The strengthening of BRV surveillance in areas with high altitude, low temperature, and heavy rainfall may contribute to the decrease of the incidence of BRV infection among Bovidae herds in China.
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Affiliation(s)
- Yi-Feng Qin
- College of Life Science, Changchun Sci-Tech University, Shuangyang, Jilin Province, 130600, China; College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, 130118, China
| | - Qing-Long Gong
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, 130118, China
| | - Miao Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Zheng-Yao Sun
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Wei Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, 163319, China
| | - Xin-Yu Wei
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, 163319, China
| | - Yu Chen
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, 163319, China
| | - Yuan Zhang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, 130118, China.
| | - Quan Zhao
- College of Life Science, Changchun Sci-Tech University, Shuangyang, Jilin Province, 130600, China.
| | - Jing Jiang
- College of Life Science, Changchun Sci-Tech University, Shuangyang, Jilin Province, 130600, China.
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Fukuda S, Akari Y, Hatazawa R, Negoro M, Tanaka T, Asada K, Nakamura H, Sugiura K, Umemoto M, Kuroki H, Ito H, Tanaka S, Ito M, Ide T, Murata T, Taniguchi K, Suga S, Kamiya H, Nakano T, Taniguchi K, Komoto S. Rapid spread of unusual G9P[8] human rotavirus strains possessing NSP4 genes of the E2 genotype in Japan. Jpn J Infect Dis 2022; 75:466-475. [DOI: 10.7883/yoken.jjid.2022.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Japan
| | - Yuki Akari
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Japan
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Japan
| | - Manami Negoro
- Institute for Clinical Research, National Mie Hospital, Japan
| | - Takaaki Tanaka
- Department of Pediatrics, Kawasaki Medical School, Japan
| | | | | | | | | | | | - Hiroaki Ito
- Department of Pediatrics, Kameda Medical Center, Japan
| | - Shigeki Tanaka
- Department of Pediatrics, Mie Chuo Medical Center, Japan
| | - Mitsue Ito
- Department of Pediatrics, Japanese Red Cross Ise Hospital, Japan
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Japan
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Japan
| | | | - Shigeru Suga
- Department of Pediatrics, National Mie Hospital, Japan
| | - Hajime Kamiya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Japan
| | - Takashi Nakano
- Department of Pediatrics, Kawasaki Medical School, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Japan
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9
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Sadiq A, Bostan N, Aziz A. Effect of rotavirus genetic diversity on vaccine impact. Rev Med Virol 2022; 32:e2259. [PMID: 34997676 DOI: 10.1002/rmv.2259] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/05/2021] [Indexed: 11/07/2022]
Abstract
Group A rotaviruses (RVAs) are the leading cause of gastroenteritis, causing 0.2 million deaths and several million hospitalisations globally each year. Four rotavirus vaccines (RotarixTM , RotaTeqTM , Rotavac® and ROTASIIL® ) have been pre-qualified by the World Health Organization (WHO), but the two newly pre-qualified vaccines (Rotavac® and ROTASIIL® ) are currently only in use in Palestine and India, respectively. In 2009, WHO strongly proposed that rotavirus vaccines be included in the routine vaccination schedule of all countries around the world. By the end of 2019, a total of 108 countries had administered rotavirus vaccines, and 10 countries have currently been approved by Gavi for the introduction of rotavirus vaccine in the near future. With 39% of global coverage, rotavirus vaccines have had a substantial effect on diarrhoeal morbidity and mortality in different geographical areas, although efficacy appears to be higher in high income settings. Due to the segmented RNA genome, the pattern of RVA genotypes in the human population is evolving through interspecies transmission and/or reassortment events for which the vaccine might be less effective in the future. However, despite the relative increase in some particular genotypes after rotavirus vaccine use, the overall efficacy of rotavirus mass vaccination worldwide has not been affected. Some of the challenges to improve the effect of current rotavirus vaccines can be solved in the future by new rotavirus vaccines and by vaccines currently in progress.
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Affiliation(s)
- Asma Sadiq
- Department of Biosciences, Molecular Virology Laboratory, COMSATS University, Islamabad, Pakistan
| | - Nazish Bostan
- Department of Biosciences, Molecular Virology Laboratory, COMSATS University, Islamabad, Pakistan
| | - Aamir Aziz
- Sarhad University of Science and Information Technology, Institute of Biological Sciences, Sarhad University, Peshawar, Pakistan
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10
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HASAN MA, KABIR MH, MIYAOKA Y, YAMAGUCHI M, TAKEHARA K. G and P genotype profiles of rotavirus A field strains circulating in a vaccinated bovine farm as parameters for assessing biosecurity level. J Vet Med Sci 2022; 84:929-937. [PMID: 35527015 PMCID: PMC9353085 DOI: 10.1292/jvms.22-0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
After improvement of hygiene protocols on boots in a bovine operation (farm A) in Ibaraki, Japan in September 2017, mortality of calves and the detection of 4 viral pathogen indicators,
including bovine rotavirus A (RVA), became significantly low for one year. Subsequently, in the present study, these indicators and mortality were monitored and confirmed all were still low,
except for the detection rate of bovine RVA in calves less than 3 weeks old. The present study aimed to investigate G and P genotypic profiles of RVAs in farm A from 2018 to 2020. Molecular
analysis using semi-nested multiplex RT-PCR of positive RVAs (n=122) and sequencing of selected samples revealed the presence of G6, G8, G10, P[1], P[5] and P[11] genotypes and the
prevalence of G and/or P combination and mixed infections. The most common combination of G and P types was G10P[11] (41.8%), followed by mixed infection with G6+G10P[5] (11.5%).
Phylogenetic analysis of RVAs showed clustering with bovine and other animal-derived RVA strains, suggesting the possibility of multiple reassortant events with strains of bovine and others
animal origins. Noteworthy as well is that vaccinated cattle might fail to provide their offspring with maternal immunity against RVA infections, due to insufficient colostrum feeding. Our
findings further highlight the importance of RVA surveillance in bovine populations, which may be useful to improving effective routine vaccination and hygiene practices on bovine farms.
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Affiliation(s)
- Md. Amirul HASAN
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Md. Humayun KABIR
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Yu MIYAOKA
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Makiko YAMAGUCHI
- Laboratory of Animal Health, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology
| | - Kazuaki TAKEHARA
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology
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11
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Wandera EA, Hatazawa R, Tsutsui N, Kurokawa N, Kathiiko C, Mumo M, Waithira E, Wachira M, Mwaura B, Nyangao J, Khamadi SA, Njau J, Fukuda S, Murata T, Taniguchi K, Ichinose Y, Kaneko S, Komoto S. Genomic characterization of an African G4P[6] human rotavirus strain identified in a diarrheic child in Kenya: Evidence for porcine-to-human interspecies transmission and reassortment. INFECTION GENETICS AND EVOLUTION 2021; 96:105133. [PMID: 34767977 DOI: 10.1016/j.meegid.2021.105133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 01/04/2023]
Abstract
Human rotavirus strains having the unconventional G4P[6] genotype have been sporadically identified in diarrheic patients in different parts of the world. However, the whole genome of only one human G4P[6] strain from Africa (central Africa) has been sequenced and analyzed, and thus the exact origin and evolutionary pattern of African G4P[6] strains remain to be elucidated. In this study, we characterized the full genome of an African G4P[6] strain (RVA/Human-wt/KEN/KCH148/2019/G4P[6]) identified in a stool specimen from a diarrheic child in Kenya. Full genome analysis of strain KCH148 revealed a unique Wa-like genogroup constellation: G4-P[6]-I1-R1-C1-M1-A1-N1-T7-E1-H1. NSP3 genotype T7 is commonly found in porcine rotavirus strains. Furthermore, phylogenetic analysis showed that 10 of the 11 genes of strain KCH148 (VP7, VP4, VP6, VP1-VP3, NSP1, and NSP3-NSP5) appeared to be of porcine origin, the remaining NSP2 gene appearing to be of human origin. Therefore, strain KCH148 was found to have a porcine rotavirus backbone and thus is likely to be of porcine origin. Furthermore, strain KCH148 is assumed to have been derived through interspecies transmission and reassortment events involving porcine and human rotavirus strains. To our knowledge, this is the first report on full genome-based characterization of a human G4P[6] strain from east Africa. Our observations demonstrated the diversity of human G4P[6] strains in Africa, and provide important insights into the origin and evolutionary pattern of zoonotic G4P[6] strains on the African continent.
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Affiliation(s)
- Ernest Apondi Wandera
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Naohisa Tsutsui
- Department of Project Planning and Management, Mitsubishi Tanabe Pharma Corporation, Chuo-ku, Tokyo 103-8405, Japan
| | - Natsuki Kurokawa
- Department of Project Planning and Management, Mitsubishi Tanabe Pharma Corporation, Chuo-ku, Tokyo 103-8405, Japan
| | - Cyrus Kathiiko
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Maurine Mumo
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Eunice Waithira
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Mary Wachira
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Boniface Mwaura
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - James Nyangao
- Center for Virus Research, KEMRI, Nairobi 54840-00200, Kenya
| | | | - Joseph Njau
- Department of Pediatrics, Kiambu County Referral Hospital, Kiambu 39-00900, Kenya
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Yoshio Ichinose
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Satoshi Kaneko
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan.
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12
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Liu X, Yan N, Yue H, Wang Y, Zhang B, Tang C. Detection and molecular characteristics of bovine rotavirus A in dairy calves in China. J Vet Sci 2021; 22:e69. [PMID: 34423605 PMCID: PMC8460460 DOI: 10.4142/jvs.2021.22.e69] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/11/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Abstract
Background Bovine group A rotavirus (BoRVA) is a major cause of severe gastroenteritis in newborn dairy calves. Only one study has investigated the G and P genotypes among dairy calves in a few regions of China, which were G6 and P[5]. Therefore, data on the prevalence and molecular characteristics of BoRVA in dairy calves in China remains limited. Objectives The purpose of this study was to investigate the prevalence and molecular characteristics of BoRVA in dairy calves in China. Methods 269 dairy calves diarrheic samples from 23 farms in six provinces in China were collected to detect BoRVA using reverse transcription polymerase chain reaction. Results 71% of samples were determined to be BoRVA-positive. Two G genotypes (G6, G10) and two P genotypes (P[1], P[5]) were identified, and G6P[1] BoRVA was the predominant strain. Moreover, the VP7 and VP4 gene sequences of these dairy calf BoRVA strains revealed abundant genetic diversity. Interestingly, eight out of 17 complete G6 VP7 sequences were clustered into G6 lineage VI and analysis showed the strains were closely related to Chinese yak BoRVA strains. Conclusions The results of this study show that BoRVA circulates widely among dairy calves in China, and the dominant genotype in circulation is G6P[1], first report on molecular characteristics of complete P[5] VP4 genes in chinese dairy calves. These results will help us to further understand the prevalence and genetic evolution of BoRVA among dairy calves in China and, thus, prevent the disease more effectively.
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Affiliation(s)
- Xiaoying Liu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Nan Yan
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Hua Yue
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu 610041, China
| | - Yuanwei Wang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Bin Zhang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Cheng Tang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu 610041, China.
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13
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Tacharoenmuang R, Guntapong R, Upachai S, Singchai P, Fukuda S, Ide T, Hatazawa R, Sutthiwarakom K, Kongjorn S, Onvimala N, Luechakham T, Ruchusatsawast K, Kawamura Y, Sriwanthana B, Motomura K, Tatsumi M, Takeda N, Yoshikawa T, Murata T, Uppapong B, Taniguchi K, Komoto S. Full genome-based characterization of G4P[6] rotavirus strains from diarrheic patients in Thailand: Evidence for independent porcine-to-human interspecies transmission events. Virus Genes 2021; 57:338-357. [PMID: 34106412 DOI: 10.1007/s11262-021-01851-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/17/2021] [Indexed: 12/18/2022]
Abstract
The exact evolutionary patterns of human G4P[6] rotavirus strains remain to be elucidated. Such strains possess unique and strain-specific genotype constellations, raising the question of whether G4P[6] strains are primarily transmitted via independent interspecies transmission or human-to-human transmission after interspecies transmission. Two G4P[6] rotavirus strains were identified in fecal specimens from hospitalized patients with severe diarrhea in Thailand, namely, DU2014-259 (RVA/Human-wt/THA/DU2014-259/2014/G4P[6]) and PK2015-1-0001 (RVA/Human-wt/THA/PK2015-1-0001/2015/G4P[6]). Here, we analyzed the full genomes of the two human G4P[6] strains, which provided the opportunity to study and confirm their evolutionary origin. On whole genome analysis, both strains exhibited a unique Wa-like genotype constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The NSP1 genotype A8 is commonly found in porcine rotavirus strains. Furthermore, on phylogenetic analysis, each of the 11 genes of strains DU2014-259 and PK2015-1-0001 appeared to be of porcine origin. On the other hand, the two study strains consistently formed distinct clusters for nine of the 11 gene segments (VP4, VP6, VP1-VP3, and NSP2-NSP5), strongly indicating the occurrence of independent porcine-to-human interspecies transmission events. Our observations provide important insights into the origin of zoonotic G4P[6] strains, and into the dynamic interaction between porcine and human rotavirus strains.
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Affiliation(s)
- Ratana Tacharoenmuang
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Ratigorn Guntapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Sompong Upachai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Phakapun Singchai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Karun Sutthiwarakom
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Santip Kongjorn
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Napa Onvimala
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Tipsuda Luechakham
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | | | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Busarawan Sriwanthana
- Medical Sciences Technical Office, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Kazushi Motomura
- Thailand-Japan Research Collaboration Center on Emerging and Re-Emerging Infections, Nonthaburi, 11000, Thailand
- Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Masashi Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-Emerging Infections, Nonthaburi, 11000, Thailand
| | - Naokazu Takeda
- Thailand-Japan Research Collaboration Center on Emerging and Re-Emerging Infections, Nonthaburi, 11000, Thailand
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Ballang Uppapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan.
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14
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Murata T, Sakurai A, Suzuki M, Komoto S, Ide T, Ishihara T, Doi Y. Shedding of Viable Virus in Asymptomatic SARS-CoV-2 Carriers. mSphere 2021; 6:e00019-21. [PMID: 34011679 PMCID: PMC8265619 DOI: 10.1128/msphere.00019-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Information regarding the infectivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in asymptomatic carriers is scarce. In order to determine the duration of infectivity and its correlation with reverse transcription-PCR (RT-PCR) results and time since initial positive PCR test in this population, we evaluated SARS-CoV-2 cell infectivity in nasopharyngeal samples longitudinally obtained from asymptomatic carriers who disembarked from a cruise ship during a COVID-19 outbreak. Of 166 nasopharyngeal samples collected from 39 asymptomatic carriers every 48 h until two consecutive negative PCR test results were obtained, SARS-CoV-2 was successfully isolated from 9 PCR-positive samples which were obtained from 7 persons (18%; 7/39). Viable viruses were isolated predominantly within 7 days after the initial positive PCR test, except for one person who shed viable virus until day 15. The median crossing point (Cp) value of RT-PCR of culture-positive samples was 24.6 (interquartile range [IQR], 20.4 to 25.8; range, 17.9 to 30.3), and Cp values were significantly associated with isolation of viable virus (odds ratio, 0.496; 95% confidence interval [CI], 0.329 to 0.747; P value, 0.001), which was consistent with existing data for symptomatic patients. Genome sequence analysis of SARS-CoV-2 samples consecutively obtained from a person who shed viable virus for 15 days identified the emergence of two novel single nucleotide variants (C8626T transition and C18452T transition) in the sample collected on day 15, with the latter corresponding to an amino acid substitution in nonstructural protein 14. The impact of these mutations on prolonged viable-virus shedding is unclear. These findings underscore the potential role of asymptomatic carriers in transmission.IMPORTANCE A growing number of studies suggest the potential role of asymptomatic SARS-CoV-2 carriers as a major driver of the COVID-19 pandemic; however, virological assessment of asymptomatic infection has largely been limited to reverse transcription-PCR (RT-PCR), which can be persistently positive without necessarily indicating the presence of viable virus (e.g., replication-competent virus). Here, we evaluated the infectivity of asymptomatic SARS-CoV-2 carriers by detecting SARS-CoV-2-induced cytopathic effects on Vero cells using longitudinally obtained nasopharyngeal samples from asymptomatic carriers. We show that asymptomatic carriers can shed viable virus until 7 days after the initial positive PCR test, with one outlier shedding until day 15. The crossing point (Cp) value of RT-PCR was the leading predictive factor for virus viability. These findings provide additional insights into the role of asymptomatic carriers as a source of transmission and highlight the importance of universal source control measures, along with isolation policy for asymptomatic carriers.
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Affiliation(s)
- Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Aki Sakurai
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Center for Joint Research Facilities Support, Research Promotion and Support Headquarters, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Takuma Ishihara
- Innovative and Clinical Research Promotion Center, Gifu University Hospital, Yanagido, Gifu, Japan
| | - Yohei Doi
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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15
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Sircar S, Malik YS, Kumar P, Ansari MI, Bhat S, Shanmuganathan S, Kattoor JJ, Vinodhkumar O, Rishi N, Touil N, Ghosh S, Bányai K, Dhama K. Genomic Analysis of an Indian G8P[1] Caprine Rotavirus-A Strain Revealing Artiodactyl and DS-1-Like Human Multispecies Reassortment. Front Vet Sci 2021; 7:606661. [PMID: 33585597 PMCID: PMC7873603 DOI: 10.3389/fvets.2020.606661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/14/2020] [Indexed: 12/03/2022] Open
Abstract
The surveillance studies for the presence of caprine rotavirus A (RVA) are limited in India, and the data for the whole-genome analysis of the caprine RVA is not available. This study describes the whole-genome-based analysis of a caprine rotavirus A strain, RVA/Goat-wt/IND/K-98/2015, from a goat kid in India. The genomic analysis revealed that the caprine RVA strain K-98, possess artiodactyl-like and DS-1 human-like genome constellation G8P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The three structural genes (VP2, VP4, and VP7) were close to caprine host having nucleotide-based identity range between 97.5 and 98.9%. Apart from them, other gene segments showed similarity with either bovine or human like genes, ultimately pointing toward a common evolutionary origin having an artiodactyl-type backbone of strain K-98. Phylogenetically, the various genes of the current study isolate also clustered inside clades comprising Human-Bovine-Caprine isolates from worldwide. The current findings add to the knowledge on caprine rotaviruses and might play a substantial role in designing future vaccines or different alternative strategies combating such infections having public health significance. To the best of our knowledge, this is the first report on the whole-genome characterization of a caprine RVA G8P[1] strain from India. Concerning the complex nature of the K-98 genome, whole-genome analyses of more numbers of RVA strains from different parts of the country are needed to comprehend the genomic nature and genetic diversity among caprine RVA.
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Affiliation(s)
- Shubhankar Sircar
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
- Amity Institute of Virology and Immunology, J-3 Block, Amity University, Noida, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - Prashant Kumar
- Amity Institute of Virology and Immunology, J-3 Block, Amity University, Noida, India
| | - Mohd Ikram Ansari
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - Sudipta Bhat
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - S. Shanmuganathan
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - Jobin Jose Kattoor
- Animal Disease Diagnsotic Laboratory, Purdue University, West Lafayette, IN, United States
| | - O.R. Vinodhkumar
- Division of Epidemiology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - Narayan Rishi
- Amity Institute of Virology and Immunology, J-3 Block, Amity University, Noida, India
| | - Nadia Touil
- Laboratoire de Recherche et de Biosécurité, Hôpital Militaire d'instruction Med V de Rabat, Rabat, Morocco
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Krisztián Bányai
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
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16
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Elkady G, Zhu J, Peng Q, Chen M, Liu X, Chen Y, Hu C, Chen H, Guo A. Isolation and whole protein characterization of species A and B bovine rotaviruses from Chinese calves. INFECTION GENETICS AND EVOLUTION 2021; 89:104715. [PMID: 33434703 DOI: 10.1016/j.meegid.2021.104715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/14/2020] [Accepted: 01/06/2021] [Indexed: 10/22/2022]
Abstract
Rotaviruses (RVs) account for severe diarrhea in children and young animals globally. In the current study, the fecal samples of diarrheic calves from a beef farm in Inner Mongolia were screened for RVA by ELISA and RT-PCR, followed by culture of three positive RVA samples in the MA-104 cell line. After 10 blind passages, cytopathic effects (CPE) appeared as detachment, granulation, and clustering of the inoculated cells. The virus isolates were identified by RT-PCR (VP6 gene RVA) and ESI-LC-MS/MS for whole protein sequencing. The protein sequences demonstrated the presence of two strains from species A rotavirus and one RVB strain; RVA/Cow-tc/CHN/35333/2019/G6P[5] was mixed with one RVB strain (RVB/Cow-tc/CHN/35334/2019/G5P[3]) in two samples, and RVA/Cow-tc/CHN/10927/2019/G8P[7] was found in one sample. They are of genotype constellations (G6-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3), (G8-P[7]-I5-R1-C1- M2-A1-N1-T1-E1-H1), and (G5-P[3]-I3-R5-C5-A5-N4-H5), respectively. Besides, phylogenetic analysis of the obtained sequences demonstrated viral evolution.
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Affiliation(s)
- Gehad Elkady
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Zhu
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingjie Peng
- Wuhan Keqian Biology Co. Ltd, Wuhan 430023, China
| | - Ming Chen
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Liu
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China; National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China; National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China; National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China.
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17
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Komoto S, Tacharoenmuang R, Guntapong R, Upachai S, Singchai P, Ide T, Fukuda S, Hatazawa R, Sutthiwarakom K, Kongjorn S, Onvimala N, Luechakham T, Sriwanthana B, Murata T, Uppapong B, Taniguchi K. Genomic characterization of a novel G3P[10] rotavirus strain from a diarrheic child in Thailand: Evidence for bat-to-human zoonotic transmission. INFECTION GENETICS AND EVOLUTION 2021; 87:104667. [DOI: 10.1016/j.meegid.2020.104667] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/18/2020] [Accepted: 12/02/2020] [Indexed: 02/04/2023]
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18
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Islam A, Hossain ME, Rostal MK, Ferdous J, Islam A, Hasan R, Miah M, Rahman M, Rahman MZ, Daszak P, Epstein JH. Epidemiology and Molecular Characterization of Rotavirus A in Fruit Bats in Bangladesh. ECOHEALTH 2020; 17:398-405. [PMID: 32876756 PMCID: PMC7464061 DOI: 10.1007/s10393-020-01488-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 07/07/2020] [Accepted: 07/28/2020] [Indexed: 05/06/2023]
Abstract
Rotavirus A (RVA) is the primary cause of acute dehydrating diarrhea in human and numerous animal species. Animal-to-human interspecies transmission is one of the evolutionary mechanisms driving rotavirus strain diversity in humans. We screened fresh feces from 416 bats (201 Pteropus medius, 165 Rousettus leschenaultii and 50 Taphozous melanopogon) for RVA using rRT-PCR. We detected a prevalence of 7% (95% CI 3.5-10.8) and 2% (95% CI 0.4-5.2) in P. medius and R. leschenaultii, respectively. We did not detect RVA in the insectivorous bat (T. melanopogon). We identified RVA strains similar to the human strains of G1 and G8 based on sequence-based genotyping, which underscores the importance of including wildlife species in surveillance for zoonotic pathogens to understand pathogen transmission and evolution better.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, 460 West 34th Street, Suite 17, New York, NY, 10001, USA
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Mohammad Enayet Hossain
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Melinda K Rostal
- EcoHealth Alliance, 460 West 34th Street, Suite 17, New York, NY, 10001, USA
| | - Jinnat Ferdous
- EcoHealth Alliance, 460 West 34th Street, Suite 17, New York, NY, 10001, USA
- Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka, 1212, Bangladesh
| | - Ausraful Islam
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rashedul Hasan
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mojnu Miah
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafizur Rahman
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammed Ziaur Rahman
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Peter Daszak
- EcoHealth Alliance, 460 West 34th Street, Suite 17, New York, NY, 10001, USA
| | - Jonathan H Epstein
- EcoHealth Alliance, 460 West 34th Street, Suite 17, New York, NY, 10001, USA.
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19
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Unusual mono-reassortant of a Wa-like G1P[8] species A rotavirus containing a DS-1-like (genotype 2) NSP4 gene. Virus Genes 2020; 56:638-641. [PMID: 32699936 DOI: 10.1007/s11262-020-01780-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/05/2020] [Indexed: 10/23/2022]
Abstract
Species A rotaviruses are a major cause of acute gastroenteritis in infants and young children worldwide. Reassortment is a common phenomenon due to the segmented nature of the rotavirus genome. The complete coding sequences of a species A rotavirus strain isolated from the feces of a child with acute gastroenteritis in Japan in 2018 were determined using an unbiased viral metagenomics approach. The genetic analysis revealed that the rotavirus strain had an unusual genomic constellation (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1), suggesting reassortment of a genotype 1 with a genotype 2 rotavirus, from which the NSP4-encoding gene was acquired.
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20
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Ihira M, Kawamura Y, Miura H, Hattori F, Higashimoto Y, Sugata K, Ide T, Komoto S, Taniguchi K, Yoshikawa T. Molecular characterization of rotaviruses obtained from patients with rotavirus-associated encephalitis/encephalopathy. Microbiol Immunol 2020; 64:541-555. [PMID: 32511783 DOI: 10.1111/1348-0421.12827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022]
Abstract
Group A rotavirus (RVA) rarely causes severe complications such as encephalitis/encephalopathy. However, the pathophysiology of this specific complication remains unclear. Next-generation sequence analysis was used to compare the entire genome sequences of RVAs detected in patients with encephalitis/encephalopathy and gastroenteritis. This study enrolled eight patients with RVA encephalitis/encephalopathy and 10 with RVA gastroenteritis who were treated between February 2013 and July 2014. Viral RNAs were extracted from patients' stool, and whole-genome sequencing analysis was carried out to identify the specific gene mutations in RVA obtained from patients with severe neurological complications. Among the eight encephalitis/encephalopathy cases, six strains were DS-1-like G1P[8] and the remaining two were Wa-like G1P[8] (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). Meanwhile, eight of the 10 viruses detected in rotavirus gastroenteritis patients were DS-1-like G1P[8], and the remaining two were Wa-like G1P[8]. These strains were further characterized by conducting phylogenetic analysis. No specific clustering was demonstrated in RVAs detected from encephalitis/encephalopathy patients. Although the DS-1-like G1P[8] strain was predominant in both groups, no specific molecular characteristics were detected in RVAs from patients with severe central nervous system complications.
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Affiliation(s)
- Masaru Ihira
- Faculty of Clinical Engineering, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Hiroki Miura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Fumihiko Hattori
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yuki Higashimoto
- Faculty of Medical Technology, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Ken Sugata
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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21
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Fukuda S, Tacharoenmuang R, Guntapong R, Upachai S, Singchai P, Ide T, Hatazawa R, Sutthiwarakom K, Kongjorn S, Onvimala N, Ruchusatsawast K, Rungnopakun P, Mekmallika J, Kawamura Y, Motomura K, Tatsumi M, Takeda N, Murata T, Yoshikawa T, Uppapong B, Taniguchi K, Komoto S. Full genome characterization of novel DS-1-like G9P[8] rotavirus strains that have emerged in Thailand. PLoS One 2020; 15:e0231099. [PMID: 32320419 PMCID: PMC7176146 DOI: 10.1371/journal.pone.0231099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/16/2020] [Indexed: 01/05/2023] Open
Abstract
The emergence and rapid spread of unusual DS-1-like intergenogroup reassortant rotaviruses having G1/3/8 genotypes have been recently reported from major parts of the world (Africa, Asia, Australia, Europe, and the Americas). During rotavirus surveillance in Thailand, three novel intergenogroup reassortant strains possessing the G9P[8] genotype (DBM2017-016, DBM2017-203, and DBM2018-291) were identified in three stool specimens from diarrheic children. In the present study, we determined and analyzed the full genomes of these three strains. On full-genomic analysis, all three strains were found to share a unique genotype constellation comprising both genogroup 1 and 2 genes: G9-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis demonstrated that each of the 11 genes of the three strains was closely related to that of emerging DS-1-like intergenogroup reassortant, human, and/or locally circulating human strains. Thus, the three strains were suggested to be multiple reassortants that had acquired the G9-VP7 genes from co-circulating Wa-like G9P[8] rotaviruses in the genetic background of DS-1-like intergenogroup reassortant (likely equine-like G3P[8]) strains. To our knowledge, this is the first description of emerging DS-1-like intergenogroup reassortant strains having the G9P[8] genotype. Our observations will add to the growing insights into the dynamic evolution of emerging DS-1-like intergenogroup reassortant rotaviruses through reassortment.
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Affiliation(s)
- Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ratana Tacharoenmuang
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ratigorn Guntapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Sompong Upachai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Phakapun Singchai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Center for Research Promotion and Support, Joint Research Support Promotion Facility, Fujita Health University, Toyoake, Aichi, Japan
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Karun Sutthiwarakom
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Santip Kongjorn
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Napa Onvimala
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | | | | | | | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Kazushi Motomura
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
- Osaka Institute of Public Health, Osaka, Japan
| | - Masashi Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Naokazu Takeda
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ballang Uppapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- * E-mail:
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22
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Malakalinga JJ, Misinzo G, Msalya GM, Kazwala RR. Rotavirus Burden, Genetic Diversity and Impact of Vaccine in Children under Five in Tanzania. Pathogens 2019; 8:pathogens8040210. [PMID: 31671824 PMCID: PMC6963457 DOI: 10.3390/pathogens8040210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/27/2019] [Accepted: 10/07/2019] [Indexed: 01/17/2023] Open
Abstract
In Tanzania, rotavirus infections are responsible for 72% of diarrhea deaths in children under five. The Rotarix vaccine was introduced in early 2013 to mitigate rotavirus infections. Understanding the disease burden and virus genotype trends over time is important for assessing the impact of rotavirus vaccine in Tanzania. When assessing the data for this review, we found that deaths of children under five declined after vaccine introduction, from 8171/11,391 (72% of diarrhea deaths) in 2008 to 2552/7087 (36% of diarrhea deaths) in 2013. Prior to vaccination, the prevalence of rotavirus infections in children under five was 18.1–43.4%, 9.8–51%, and 29–41% in Dar es Salaam, Mwanza and Tanga, respectively, and after the introduction of vaccines, these percentages declined to 17.4–23.5%, 16–19%, and 10–29%, respectively. Rotaviruses in Tanzania are highly diverse, and include genotypes of animal origin in children under five. Of the genotypes, 10%, 28%, and 7% of the strains are untypable in Dar es Salaam, Tanga, and Zanzibar, respectively. Mixed rotavirus genotype infection accounts for 31%, 29%, and 12% of genotypes in Mwanza, Tanga and Zanzibar, respectively. The vaccine effectiveness ranges between 53% and 75% in Mwanza, Manyara and Zanzibar. Rotavirus vaccination has successfully reduced the rotavirus burden in Tanzania; however, further studies are needed to better understand the relationship between the wildtype strain and the vaccine strain as well as the zoonotic potential of rotavirus in the post-vaccine era.
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Affiliation(s)
- Joseph J Malakalinga
- Food and Microbiology Laboratory, Tanzania Bureau of Standards, Ubungo Area, Morogoro Road/Sam Nujoma Road, P.O. Box 9524, Dar es Salaam, Tanzania.
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Africa Centre of Excellence for Infectious Diseases of Humans and Animals in Eastern and Southern Africa (ACE), Sokoine University of Agriculture (SUA), P.O. Box 3297, Chuo Kikuu, SUA, Morogoro, Tanzania.
| | - Gerald Misinzo
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Africa Centre of Excellence for Infectious Diseases of Humans and Animals in Eastern and Southern Africa (ACE), Sokoine University of Agriculture (SUA), P.O. Box 3297, Chuo Kikuu, SUA, Morogoro, Tanzania.
| | - George M Msalya
- Department of Animal, Aquaculture and Range Sciences, College of Agriculture, Sokoine University of Agriculture, P.O. Box 3004, Morogoro, Tanzania.
| | - Rudovick R Kazwala
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3021, Morogoro, Tanzania.
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23
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Cordey S, Laubscher F, Hartley MA, Junier T, Pérez-Rodriguez FJ, Keitel K, Vieille G, Samaka J, Mlaganile T, Kagoro F, Boillat-Blanco N, Mbarack Z, Docquier M, Brito F, Eibach D, May J, Sothmann P, Aldrich C, Lusingu J, Tapparel C, D'Acremont V, Kaiser L. Detection of dicistroviruses RNA in blood of febrile Tanzanian children. Emerg Microbes Infect 2019; 8:613-623. [PMID: 30999808 PMCID: PMC6493270 DOI: 10.1080/22221751.2019.1603791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fever is the leading cause of paediatric outpatient consultations in Sub-Saharan Africa. Although most are suspected to be of viral origin, a putative causative pathogen is not identified in over a quarter of these febrile episodes. Using a de novo assembly sequencing approach, we report the detection (15.4%) of dicistroviruses (DicV) RNA in sera collected from 692 febrile Tanzanian children. In contrast, DicV RNA was only detected in 1/77 (1.3%) plasma samples from febrile Tanzanian adults, suggesting that children could represent the primary susceptible population. Estimated viral load by specific quantitative real-time RT–PCR assay ranged from < 1.32E3 to 1.44E7 viral RNA copies/mL serum. Three DicV full-length genomes were obtained, and a phylogenetic analyse on the capsid region showed the presence of two clusters representing tentative novel genus. Although DicV-positive cases were detected throughout the year, a significantly higher positivity rate was observed during the rainy season. This study reveals that novel DicV RNA is frequently detected in the blood of Tanzanian children, paving the way for further investigations to determine if DicV possibly represent a new agent in humans.
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Affiliation(s)
- Samuel Cordey
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland
| | - Florian Laubscher
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland
| | - Mary-Anne Hartley
- c Department of Ambulatory Care and Community Medicine , Lausanne University Hospital Lausanne , Switzerland
| | - Thomas Junier
- d Swiss Institute of Bioinformatics Geneva , Switzerland.,e Global Health Institute, School of Life Sciences , École Polytechnique Fédérale de Lausanne Lausanne , Switzerland
| | | | - Kristina Keitel
- f Swiss Tropical and Public Health Institute , University of Basel Basel , Switzerland
| | - Gael Vieille
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland
| | - Josephine Samaka
- g Ifakara Health Institute , Dar es Salaam , Tanzania.,h Amana Hospital , Dar es Salaam , Tanzania
| | | | - Frank Kagoro
- g Ifakara Health Institute , Dar es Salaam , Tanzania
| | - Noémie Boillat-Blanco
- f Swiss Tropical and Public Health Institute , University of Basel Basel , Switzerland.,i Infectious Diseases Service , Lausanne University Hospital Lausanne , Switzerland
| | | | - Mylène Docquier
- k iGE3 Genomics Platform , University of Geneva Geneva , Switzerland
| | - Francisco Brito
- d Swiss Institute of Bioinformatics Geneva , Switzerland.,l Department of Genetic Medicine and Development , Faculty of Medicine of Geneva Geneva , Switzerland
| | - Daniel Eibach
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,n German Centre for Infection Research (DZIF) , Hamburg , Germany
| | - Jürgen May
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,n German Centre for Infection Research (DZIF) , Hamburg , Germany
| | - Peter Sothmann
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,n German Centre for Infection Research (DZIF) , Hamburg , Germany.,o Division of Tropical Medicine, 1st Department of Medicine , University Medical Center Hamburg-Eppendorf Hamburg , Germany.,p Division of Infectious Diseases and Tropical Medicine , Medical Center of the University of Munich (LMU) Munich , Germany
| | - Cassandra Aldrich
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,p Division of Infectious Diseases and Tropical Medicine , Medical Center of the University of Munich (LMU) Munich , Germany
| | - John Lusingu
- q National Institute for Medical Research , Tanga Research Centre , Tanga , Tanzania
| | | | - Valérie D'Acremont
- c Department of Ambulatory Care and Community Medicine , Lausanne University Hospital Lausanne , Switzerland.,f Swiss Tropical and Public Health Institute , University of Basel Basel , Switzerland
| | - Laurent Kaiser
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland.,r Geneva Centre for Emerging Viral Diseases Geneva , Switzerland
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24
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Generation of Infectious Recombinant Human Rotaviruses from Just 11 Cloned cDNAs Encoding the Rotavirus Genome. J Virol 2019; 93:JVI.02207-18. [PMID: 30728265 DOI: 10.1128/jvi.02207-18] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 01/28/2019] [Indexed: 12/26/2022] Open
Abstract
The generation of recombinant group A rotaviruses (RVAs) entirely from cloned cDNAs has been described only for a single animal RVA strain, simian SA11-L2. We recently developed an optimized RVA reverse genetics system based on only RVA cDNAs (11-plasmid system), in which the concentration of cDNA plasmids containing the NSP2 and NSP5 genes is 3- or 5-fold increased in relation to that of the other plasmids. Based on this approach, we generated a recombinant human RVA (HuRVA)-based monoreassortant virus containing the VP4 gene of the simian SA11-L2 virus using the 11-plasmid system. In addition to this monoreassortant virus, authentic HuRVA (strain KU) was also generated with the 11-plasmid system with some modifications. Our results demonstrate that the 11-plasmid system involving just RVA cDNAs can be used for the generation of recombinant HuRVA and recombinant HuRVA-based reassortant viruses.IMPORTANCE Human group A rotavirus (HuRVA) is a leading pathogen causing severe diarrhea in young children worldwide. In this paper, we describe the generation of recombinant HuRVA (strain KU) from only 11 cloned cDNAs encoding the HuRVA genome by reverse genetics. The growth properties of the recombinant HuRVA were similar to those of the parental RVA, providing a powerful tool for better understanding of HuRVA replication and pathogenesis. Furthermore, the ability to manipulate the genome of HuRVAs "to order" will be useful for next-generation vaccine production for this medically important virus and for the engineering of clinical vectors expressing any foreign genes.
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25
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Yoshikawa T, Ihira M, Higashimoto Y, Hattori F, Miura H, Sugata K, Komoto S, Taniguchi K, Iguchi A, Yamada M, Ariga T. Persistent systemic rotavirus vaccine infection in a child with X‐linked severe combined immunodeficiency. J Med Virol 2019; 91:1008-1013. [DOI: 10.1002/jmv.25410] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/28/2018] [Accepted: 01/21/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Tetsushi Yoshikawa
- Department of PediatricsFujita Health University School of MedicineToyoake Aichi Japan
| | - Masaru Ihira
- Faculty of Clinical EngineeringToyoake Aichi Japan
| | - Yuki Higashimoto
- Faculty of Medical TechnologyFujita Health University School of Health SciencesToyoake Aichi Japan
| | - Fumihiko Hattori
- Department of PediatricsFujita Health University School of MedicineToyoake Aichi Japan
| | - Hiroki Miura
- Department of PediatricsFujita Health University School of MedicineToyoake Aichi Japan
| | - Ken Sugata
- Department of PediatricsFujita Health University School of MedicineToyoake Aichi Japan
| | - Satoshi Komoto
- Department of Virology and ParasitologyFujita Health University School of MedicineToyoake Aichi Japan
| | - Koki Taniguchi
- Department of Virology and ParasitologyFujita Health University School of MedicineToyoake Aichi Japan
| | - Akihiro Iguchi
- Department of PediatricsFaculty of Medicine and Graduate School of Medicine, Hokkaido UniversitySapporo Japan
| | - Masafumi Yamada
- Department of PediatricsFaculty of Medicine and Graduate School of Medicine, Hokkaido UniversitySapporo Japan
| | - Tadashi Ariga
- Department of PediatricsFaculty of Medicine and Graduate School of Medicine, Hokkaido UniversitySapporo Japan
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26
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Wandera EA, Komoto S, Mohammad S, Ide T, Bundi M, Nyangao J, Kathiiko C, Odoyo E, Galata A, Miring'u G, Fukuda S, Hatazawa R, Murata T, Taniguchi K, Ichinose Y. Genomic characterization of uncommon human G3P[6] rotavirus strains that have emerged in Kenya after rotavirus vaccine introduction, and pre-vaccine human G8P[4] rotavirus strains. INFECTION GENETICS AND EVOLUTION 2018; 68:231-248. [PMID: 30543939 DOI: 10.1016/j.meegid.2018.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 10/27/2022]
Abstract
A monovalent rotavirus vaccine (RV1) was introduced to the national immunization program in Kenya in July 2014. There was increased detection of uncommon G3P[6] strains that coincided temporally with the timing of this vaccine introduction. Here, we sequenced and characterized the full genomes of two post-vaccine G3P[6] strains, RVA/Human-wt/KEN/KDH1951/2014/G3P[6] and RVA/Human-wt/KEN/KDH1968/2014/G3P[6], as representatives of these uncommon strains. On full-genomic analysis, both strains exhibited a DS-1-like genotype constellation: G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis revealed that all 11 genes of strains KDH1951 and KDH1968 were very closely related to those of human G3P[6] strains isolated in Uganda in 2012-2013, indicating the derivation of these G3P[6] strains from a common ancestor. Because the uncommon G3P[6] strains that emerged in Kenya are fully heterotypic as to the introduced vaccine strain regarding the genotype constellation, vaccine effectiveness against these G3P[6] strains needs to be closely monitored.
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Affiliation(s)
- Ernest Apondi Wandera
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan.
| | - Shah Mohammad
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Martin Bundi
- National Biosafety Authority, Nairobi 00100, Kenya
| | - James Nyangao
- Center for Virus Research, KEMRI, Nairobi 54840-00200, Kenya
| | - Cyrus Kathiiko
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Erick Odoyo
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Amina Galata
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Gabriel Miring'u
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Yoshio Ichinose
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
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Motayo BO, Faneye AO, Adeniji JA. Epidemiology of Rotavirus A in Nigeria: Molecular Diversity and Current Insights. J Pathog 2018; 2018:6513682. [PMID: 30364038 PMCID: PMC6188771 DOI: 10.1155/2018/6513682] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 08/29/2018] [Indexed: 11/19/2022] Open
Abstract
Rotavirus induced acute gastroenteritis AGE has been a major disease burden in Nigeria, since it was first reported in 1985. Prevalence rates have increased with severe public health consequences particularly among children. The vaccine Rotarix® has been introduced and is commercially available in Nigeria. However routine rotavirus vaccination is yet to be introduced into the National Immunization Program. Molecular epidemiology of rotavirus in Nigeria has shown the presence of various genotypes, with genotype G12P[8] being the most recent introduction. There are however gaps in molecular data on rotavirus in Nigeria. We therefore reviewed molecular data on rotavirus isolated in Nigeria and also analyzed VP4 and VP7 genes of Nigerian rotavirus strains in Genbank. We have shown that there is a distinct trend in rotavirus molecular epidemiology in Nigeria, with new genotype introductions occurring after the year 2010. We also observed from our analysis the emergence of genotype G12 Lineage III as a dominant genotype. This information elucidates rotavirus molecular epidemiology in Nigeria and gives insight to the expanding landscape of rotavirus genotypes. We recommend the institution of molecular surveillance country wide, before considering the inclusion of rotavirus vaccination into the National Immunization Program in Nigeria, in other to monitor evolution of divergent or recombinant strains.
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Affiliation(s)
- Babatunde Olanrewaju Motayo
- Department of Virology, University of Ibadan, Nigeria
- Pathology Department, Federal Medical Centre, Idi-Aba, Abeokuta, Nigeria
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Characterization of a G10P[14] rotavirus strain from a diarrheic child in Thailand: Evidence for bovine-to-human zoonotic transmission. INFECTION GENETICS AND EVOLUTION 2018; 63:43-57. [DOI: 10.1016/j.meegid.2018.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 11/21/2022]
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Komoto S, Ide T, Negoro M, Tanaka T, Asada K, Umemoto M, Kuroki H, Ito H, Tanaka S, Ito M, Fukuda S, Suga S, Kamiya H, Nakano T, Taniguchi K. Characterization of unusual DS-1-like G3P[8] rotavirus strains in children with diarrhea in Japan. J Med Virol 2018; 90:890-898. [PMID: 29315643 DOI: 10.1002/jmv.25016] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 10/30/2017] [Indexed: 12/11/2022]
Abstract
The emergence and rapid spread of novel DS-1-like intergenogroup reassortant rotaviruses having the equine-like G3 genotype (DS-1-like G3P[8] strains) have been recently reported from several countries. During rotavirus surveillance in Japan in 2015-2016, three DS-1-like G3P[8] strains were identified from children with severe diarrhea. In the present study, we sequenced and characterized the full genomes of these three strains. On full-genomic analysis, all three strains showed a unique genotype constellation including both genogroup 1 and 2 genes: G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis revealed that each of the 11 genes of the three strains was closely related to that of Japanese DS-1-like G1P[8] and/or Japanese equine-like G3P[4] human strains. Thus, the three study strains were suggested to be reassortants that acquired the G3-VP7 gene from equine G3 rotaviruses on the genetic background of DS-1-like G1P[8] strains. Our observations will provide important insights into the evolutionary dynamics of emerging DS-1-like G3P[8] strains.
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Affiliation(s)
- Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Manami Negoro
- Institute for Clinical Research, National Mie Hospital, Tsu, Mie, Japan
| | - Takaaki Tanaka
- Department of Pediatrics, Kawasaki Medical School, Okayama, Okayama, Japan
| | - Kazutoyo Asada
- Department of Pediatrics, National Mie Hospital, Tsu, Mie, Japan
| | | | | | - Hiroaki Ito
- Sotobo Children's Clinic, Isumi, Chiba, Japan
| | - Shigeki Tanaka
- Department of Pediatrics, Mie Chuo Medical Center, Tsu, Mie, Japan
| | - Mitsue Ito
- Department of Pediatrics, Japanese Red Cross Ise Hospital, Ise, Mie, Japan
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Shigeru Suga
- Department of Pediatrics, National Mie Hospital, Tsu, Mie, Japan
| | - Hajime Kamiya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Takashi Nakano
- Department of Pediatrics, Kawasaki Medical School, Okayama, Okayama, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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Komoto S, Tacharoenmuang R, Guntapong R, Ide T, Sinchai P, Upachai S, Fukuda S, Yoshikawa T, Tharmaphornpilas P, Sangkitporn S, Taniguchi K. Identification and characterization of a human G9P[23] rotavirus strain from a child with diarrhoea in Thailand: evidence for porcine-to-human interspecies transmission. J Gen Virol 2017; 98:532-538. [PMID: 28382902 DOI: 10.1099/jgv.0.000722] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An unusual rotavirus strain with the G9P[23] genotype (RVA/Human-wt/THA/KKL-117/2014/G9P[23]) was identified in a stool specimen from a 10-month-old child hospitalized with severe diarrhoea. In this study, we sequenced and characterized the complete genome of strain KKL-117. On full-genomic analysis, strain KKL-117 was found to have the following genotype constellation: G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. The non-G/P genotype constellation of this strain (I5-R1-C1-M1-A8-N1-T1-E1-H1) is commonly shared with rotavirus strains from pigs. Furthermore, phylogenetic analysis indicated that each of the 11 genes of strain KKL-117 appeared to be of porcine origin. Our observations provide important insights into the dynamic interactions between human and porcine rotavirus strains.
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Affiliation(s)
- Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Ratana Tacharoenmuang
- Department of Medical Sciences, National Institute of Health, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Ratigorn Guntapong
- Department of Medical Sciences, National Institute of Health, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Phakapun Sinchai
- Department of Medical Sciences, National Institute of Health, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Sompong Upachai
- Department of Medical Sciences, National Institute of Health, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | | | - Somchai Sangkitporn
- Department of Medical Sciences, National Institute of Health, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
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Tacharoenmuang R, Komoto S, Guntapong R, Ide T, Sinchai P, Upachai S, Yoshikawa T, Tharmaphornpilas P, Sangkitporn S, Taniguchi K. Full Genome Characterization of Novel DS-1-Like G8P[8] Rotavirus Strains that Have Emerged in Thailand: Reassortment of Bovine and Human Rotavirus Gene Segments in Emerging DS-1-Like Intergenogroup Reassortant Strains. PLoS One 2016; 11:e0165826. [PMID: 27802339 PMCID: PMC5089778 DOI: 10.1371/journal.pone.0165826] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 10/18/2016] [Indexed: 12/15/2022] Open
Abstract
The emergence and rapid spread of unusual DS-1-like intergenogroup reassortant rotavirus strains have been recently reported in Asia, Australia, and Europe. During rotavirus surveillance in Thailand in 2013-2014, novel DS-1-like intergenogroup reassortant strains having G8P[8] genotypes (i.e., strains KKL-17, PCB-79, PCB-84, PCB-85, PCB-103, SKT-107, SWL-12, NP-130, PCB-656, SKT-457, SSKT-269, and SSL-55) were identified in stool samples from hospitalized children with severe diarrhea. In this study, we determined and characterized the complete genomes of these 12 strains (seven strains, KKL-17, PCB-79, PCB-84, PCB-85, PCB-103, SKT-107, and SWL-12, found in 2013 (2013 strains), and five, NP-130, PCB-656, SKT-457, SSKT-269, and SSL-55, in 2014 (2014 strains)). On full genomic analysis, all 12 strains showed a unique genotype constellation comprising a mixture of genogroup 1 and 2 genes: G8-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. With the exception of the G genotype, the unique genotype constellation of the 12 strains (P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2) was found to be shared with DS-1-like intergenogroup reassortant strains. On phylogenetic analysis, six of the 11 genes of the 2013 strains (VP4, VP2, VP3, NSP1, NSP3, and NSP5) appeared to have originated from DS-1-like intergenogroup reassortant strains, while the remaining four (VP7, VP6, VP1, and NSP2) and one (NSP4) gene appeared to be of bovine and human origin, respectively. Thus, the 2013 strains appeared to be reassortant strains as to DS-1-like intergenogroup reassortant, bovine, bovine-like human, and/or human rotaviruses. On the other hand, five of the 11 genes of the 2014 strains (VP4, VP2, VP3, NSP1, and NSP3) appeared to have originated from DS-1-like intergenogroup reassortant strains, while three (VP7, VP1, and NSP2) and one (NSP4) were assumed to be of bovine and human origin, respectively. Notably, the remaining two genes, VP6 and NSP5, of the 2014 strains appeared to have originated from locally circulating DS-1-like G2P[4] human rotaviruses. Thus, the 2014 strains were assumed to be multiple reassortment strains as to DS-1-like intergenogroup reassortant, bovine, bovine-like human, human, and/or locally circulating DS-1-like G2P[4] human rotaviruses. Overall, the great genomic diversity among the DS-1-like intergenogroup reassortant strains seemed to have been generated through additional reassortment events involving animal and human strains. Moreover, all the 11 genes of three of the 2014 strains, NP-130, PCB-656, and SSL-55, were very closely related to those of Vietnamese DS-1-like G8P[8] strains that emerged in 2014-2015, indicating the derivation of these DS-1-like G8P[8] strains from a common ancestor. To our knowledge, this is the first report on full genome-based characterization of DS-1-like G8P[8] strains that have emerged in Thailand. Our observations will add to our growing understanding of the evolutionary patterns of emerging DS-1-like intergenogroup reassortant strains.
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Affiliation(s)
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ratigorn Guntapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Phakapun Sinchai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Sompong Upachai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | | | - Somchai Sangkitporn
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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