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Fujii Y, Tsugawa T, Fukuda Y, Adachi S, Honjo S, Akane Y, Kondo K, Sakai Y, Tanaka T, Sato T, Higasidate Y, Kubo N, Mori T, Kato S, Hamada R, Kikuchi M, Tahara Y, Nagai K, Ohara T, Yoshida M, Nakata S, Noguchi A, Kikuchi W, Hamada H, Tokutake-Hirose S, Fujimori M, Muramatsu M. Molecular evolutionary analysis of novel NSP4 mono-reassortant G1P[8]-E2 rotavirus strains that caused a discontinuous epidemic in Japan in 2015 and 2018. Front Microbiol 2024; 15:1430557. [PMID: 39050631 PMCID: PMC11266183 DOI: 10.3389/fmicb.2024.1430557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/17/2024] [Indexed: 07/27/2024] Open
Abstract
In the 2010s, several unusual rotavirus strains emerged, causing epidemics worldwide. This study reports a comprehensive molecular epidemiological study of rotaviruses in Japan based on full-genome analysis. From 2014 to 2019, a total of 489 rotavirus-positive stool specimens were identified, and the associated viral genomes were analyzed by next-generation sequencing. The genotype constellations of those strains were classified into nine patterns (G1P[8] (Wa), G1P[8]-E2, G1P[8] (DS-1), G2P[4] (DS-1), G3P[8] (Wa), G3P[8] (DS-1), G8P[8] (DS-1), G9P[8] (Wa), and G9P[8]-E2). The major prevalent genotype differed by year, comprising G8P[8] (DS-1) (37% of that year's isolates) in 2014, G1P[8] (DS-1) (65%) in 2015, G9P[8] (Wa) (72%) in 2016, G3P[8] (DS-1) (66%) in 2017, G1P[8]-E2 (53%) in 2018, and G9P[8] (Wa) (26%) in 2019. The G1P[8]-E2 strains (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1) isolated from a total of 42 specimens in discontinuous years (2015 and 2018), which were the newly-emerged NSP4 mono-reassortant strains. Based on the results of the Bayesian evolutionary analyses, G1P[8]-E2 and G9P[8]-E2 were hypothesized to have been generated from distinct independent inter-genogroup reassortment events. The G1 strains detected in this study were classified into multiple clusters, depending on the year of detection. A comparison of the predicted amino acid sequences of the VP7 epitopes revealed that the G1 strains detected in different years encoded VP7 epitopes harboring distinct mutations. These mutations may be responsible for immune escape and annual changes in the prevalent strains.
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Affiliation(s)
- Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Yuya Fukuda
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Shuhei Adachi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Saho Honjo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Yusuke Akane
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Yoshiyuki Sakai
- Department of Pediatrics, Hakodate Municipal Hospital, Hokkaido, Japan
| | - Toju Tanaka
- Department of Pediatrics, National Hospital Organization Hokkaido Medical Center, Hokkaido, Japan
| | - Toshiya Sato
- Department of Pediatrics, Iwamizawa Municipal General Hospital, Hokkaido, Japan
| | - Yoshihito Higasidate
- Department of Pediatrics, Japan Community Health Care Organization Sapporo Hokushin Hospital, Hokkaido, Japan
| | - Noriaki Kubo
- Department of Pediatrics, Japan Red Cross Urakawa Hospital, Hokkaido, Japan
| | - Toshihiko Mori
- Department of Pediatrics, NTT Medical Center Sapporo, Hokkaido, Japan
| | - Shinsuke Kato
- Department of Pediatrics, Rumoi City Hospital, Hokkaido, Japan
| | - Ryo Hamada
- Department of Pediatrics, Rumoi City Hospital, Hokkaido, Japan
| | - Masayoshi Kikuchi
- Department of Pediatrics, Sunagawa City Medical Center, Hokkaido, Japan
| | - Yasuo Tahara
- Department of Pediatrics, Steel Memorial Muroran Hospital, Hokkaido, Japan
| | - Kazushige Nagai
- Department of Pediatrics, Takikawa Municipal Hospital, Hokkaido, Japan
| | - Toshio Ohara
- Department of Pediatrics, Tomakomai City Hospital, Hokkaido, Japan
| | - Masaki Yoshida
- Department of Pediatrics, Yakumo General Hospital, Hokkaido, Japan
| | | | - Atsuko Noguchi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, Japan
| | - Wakako Kikuchi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiromichi Hamada
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, Chiba, Japan
| | - Shoko Tokutake-Hirose
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, Chiba, Japan
| | - Makoto Fujimori
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, Chiba, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Infectious Disease Research, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Hyogo, Japan
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Hoa-Tran TN, Nakagomi T, Vu HM, Nguyen TTT, Dao ATH, Nguyen AT, Bines JE, Thomas S, Grabovac V, Kataoka-Nakamura C, Taichiro T, Hasebe F, Kodama T, Kaneko M, Dang HTT, Duong HT, Anh DD, Nakagomi O. Evolution of DS-1-like G8P[8] rotavirus A strains from Vietnamese children with acute gastroenteritis (2014-21): Adaptation and loss of animal rotavirus-derived genes during human-to-human spread. Virus Evol 2024; 10:veae045. [PMID: 38952820 PMCID: PMC11215986 DOI: 10.1093/ve/veae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/27/2024] [Accepted: 06/21/2024] [Indexed: 07/03/2024] Open
Abstract
Animal rotaviruses A (RVAs) are considered the source of emerging, novel RVA strains that have the potential to cause global spread in humans. A case in point was the emergence of G8 bovine RVA consisting of the P[8] VP4 gene and the DS-1-like backbone genes that appeared to have jumped into humans recently. However, it was not well documented what evolutionary changes occurred on the animal RVA-derived genes during circulation in humans. Rotavirus surveillance in Vietnam found that DS-1-like G8P[8] strains emerged in 2014, circulated in two prevalent waves, and disappeared in 2021. This surveillance provided us with a unique opportunity to investigate the whole process of evolutionary changes, which occurred in an animal RVA that had jumped the host species barrier. Of the 843 G8P[8] samples collected from children with acute diarrhoea in Vietnam between 2014 and 2021, fifty-eight strains were selected based on their distinctive electropherotypes of the genomic RNA identified using polyacrylamide gel electrophoresis. Whole-genome sequence analysis of those fifty-eight strains showed that the strains dominant during the first wave of prevalence (2014-17) carried animal RVA-derived VP1, NSP2, and NSP4 genes. However, the strains from the second wave of prevalence (2018-21) lost these genes, which were replaced with cognate human RVA-derived genes, thus creating strain with G8P[8] on a fully DS-1-like human RVA gene backbone. The G8 VP7 and P[8] VP4 genes underwent some point mutations but the phylogenetic lineages to which they belonged remained unchanged. We, therefore, propose a hypothesis regarding the tendency for the animal RVA-derived genes to be expelled from the backbone genes of the progeny strains after crossing the host species barrier. This study underlines the importance of long-term surveillance of circulating wild-type strains in order to better understand the adaptation process and the fate of newly emerging, animal-derived RVA among the human population. Further studies are warranted to disclose the molecular mechanisms by which spillover animal RVAs become readily transmissible among humans, and the roles played by the expulsion of animal-derived genes and herd immunity formed in the local population.
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Affiliation(s)
- Thi Nguyen Hoa-Tran
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Toyoko Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Hung Manh Vu
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Trang Thu Thi Nguyen
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Anh Thi Hai Dao
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Anh The Nguyen
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Julie E Bines
- Enteric Diseases Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria 3052, Australia
| | - Sarah Thomas
- Enteric Diseases Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria 3052, Australia
| | - Varja Grabovac
- Vaccine-Preventable Diseases and Immunization Unit, Division of Programmes for Disease Control, World Health Organization Regional Office for the Western Pacific, Manila 1000, Philippines
| | - Chikako Kataoka-Nakamura
- Center Surveillance Division, The Research Foundation for Microbial Diseases of Osaka University, Osaka 768-0065, Japan
| | - Takemura Taichiro
- Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
- Vietnam Research Station, National Institute of Hygiene and Epidemiology-Nagasaki University, Hanoi 100000, Vietnam
| | - Futoshi Hasebe
- Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
- Vietnam Research Station, National Institute of Hygiene and Epidemiology-Nagasaki University, Hanoi 100000, Vietnam
| | - Toshio Kodama
- Department of Bacteriology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Miho Kaneko
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Huyen Thi Thanh Dang
- National office for Expanded Program on Immunization, National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Hong Thi Duong
- National office for Expanded Program on Immunization, National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Dang Duc Anh
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Osamu Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
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Le LKT, Chu MNT, Tate JE, Jiang B, Bowen MD, Esona MD, Gautam R, Jaimes J, Pham TPT, Huong NT, Anh DD, Trang NV, Parashar U. Genetic diversity of G9, G3, G8 and G1 rotavirus group A strains circulating among children with acute gastroenteritis in Vietnam from 2016 to 2021. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105566. [PMID: 38316245 DOI: 10.1016/j.meegid.2024.105566] [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: 12/15/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Rotavirus group A (RVA) is the most common cause of severe childhood diarrhea worldwide. The introduction of rotavirus vaccination programs has contributed to a reduction in hospitalizations and mortality caused by RVA. From 2016 to 2021, we conducted surveillance to monitor RVA prevalence and genotype distribution in Nam Dinh and Thua Thien Hue (TT Hue) provinces where a pilot Rotavin-M1 vaccine (Vietnam) implementation took place from 2017 to 2020. Out of 6626 stool samples, RVA was detected in 2164 (32.6%) by ELISA. RT-PCR using type-specific primers were used to determine the G and P genotypes of RVA-positive specimens. Whole genome sequences of a subset of 52 specimens randomly selected from 2016 to 2021 were mapped using next-generation sequencing. From 2016 to 2021, the G9, G3 and G8 strains dominated, with detected frequencies of 39%, 23%, and 19%, respectively; of which, the most common genotypes identified were G9P[8], G3P[8] and G8P[8]. G1 strains re-emerged in Nam Dinh and TT Hue (29.5% and 11.9%, respectively) from 2020 to 2021. G3 prevalence decreased from 74% to 20% in TT Hue and from 21% to 13% in Nam Dinh province between 2017 and 2021. The G3 strains consisted of 52% human typical G3 (hG3) and 47% equine-like G3 (eG3). Full genome analysis showed substantial diversity among the circulating G3 strains with different backgrounds relating to equine and feline viruses. G9 prevalence decreased sharply from 2016 to 2021 in both provinces. G8 strains peaked during 2019-2020 in Nam Dinh and TT Hue provinces (68% and 46%, respectively). Most G8 and G9 strains had no genetic differences over the surveillance period with very high nucleotide similarities of 99.2-99.9% and 99.1-99.7%, respectively. The G1 strains were not derived from the RVA vaccine. Changes in the genotype distribution and substantial diversity among circulating strains were detected throughout the surveillance period and differed between the two provinces. Determining vaccine effectiveness against circulating strains over time will be important to ensure that observed changes are due to natural secular variation and not from vaccine pressure.
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Affiliation(s)
- Ly K T Le
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Viet Nam
| | - Mai N T Chu
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Viet Nam
| | - Jacqueline E Tate
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Baoming Jiang
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Michael D Bowen
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Mathew D Esona
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Rashi Gautam
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Jose Jaimes
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Thao P T Pham
- Center for Research and Production of Vaccines and Biologicals, Hanoi 100000, Viet Nam
| | - Nguyen T Huong
- Center for Research and Production of Vaccines and Biologicals, Hanoi 100000, Viet Nam
| | - Dang D Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Viet Nam
| | - Nguyen V Trang
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Viet Nam.
| | - Umesh Parashar
- United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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Sashina TA, Velikzhanina EI, Morozova OV, Epifanova NV, Novikova NA. Detection and full-genotype determination of rare and reassortant rotavirus A strains in Nizhny Novgorod in the European part of Russia. Arch Virol 2023; 168:215. [PMID: 37524885 DOI: 10.1007/s00705-023-05838-y] [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: 02/01/2023] [Accepted: 06/13/2023] [Indexed: 08/02/2023]
Abstract
Reassortant DS-1-like rotavirus A strains have been shown to circulate widely in many countries around the world. In Russia, the prevalence of such strains remains unclear due to the preferred use of the traditional binary classification system. In this work, we obtained partial sequence data from all 11 genome segments and determined the full-genotype constellations of rare and reassortant rotaviruses circulating in Nizhny Novgorod in 2016-2019. DS-1-like G3P[8] and G8P[8] strains were found, reflecting the global trend. Most likely, these strains were introduced into the territory of Russia from other countries but subsequently underwent further evolutionary changes locally. G3P[8], G9P[8], and G12P[8] Wa-like strains of subgenotypic lineages that are unusual for the territory of Russia were also identified. Reassortant G2P[8], G4P[4], and G9P[4] strains with one Wa-like gene (VP4 or VP7) on a DS-1-like backbone were found, and these apparently had a local origin. Feline-like G3P[9] and G6P[9] strains were found to be phylogenetically close to BA222 isolated from a cat in Italy but carried some traces of reassortment with human strains from Russia and other countries. Thus, full-genotype determination of rotavirus A strains in Nizhny Novgorod has clarified some questions related to their origin and evolution.
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Affiliation(s)
- Tatiana A Sashina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation.
| | - E I Velikzhanina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - O V Morozova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N V Epifanova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N A Novikova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
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Zhou X, Wang Y, Chen N, Pang B, Liu M, Cai K, Kobayashi N. Surveillance of Human Rotaviruses in Wuhan, China (2019-2022): Whole-Genome Analysis of Emerging DS-1-like G8P[8] Rotavirus. Int J Mol Sci 2023; 24:12189. [PMID: 37569563 PMCID: PMC10419309 DOI: 10.3390/ijms241512189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Group A rotaviruses (RVAs) are major etiologic agents of gastroenteritis in infants and young children worldwide. To study the prevalence and genetic characteristics of RVAs, a hospital-based surveillance study was conducted in Wuhan, China from June 2019 through May 2022. The detection rates of RVAs were 19.40% (142/732) and 3.51% (8/228) in children and adults, respectively. G9P[8] was the predominant genotype, followed by G8P[8] and G3P[8]. G8P[8] emerged and was dominant in the 2021-2022 epidemic season. The genome constellation of six G8P[8] strains was assigned to G8-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis revealed that the VP7, VP4, VP2, VP3, NSP1, NSP2, NSP3, and NSP5 genes of these G8P[8] strains clustered closely with those of the G8P[8] strains in Asia and were distant from those of the P[8] and G2P[4] strains simultaneously detected in Wuhan. In contrast, the VP1, VP6, and NSP4 genes were closely related to the typical G2P[4] rotavirus, including those of G2P[4] strains simultaneously detected in Wuhan. The detection rate of RVAs decreased in the COVID-19 pandemic era. It was deduced that the G8P[8] rotaviruses that emerged in China may be reassortants, carrying the VP6, VP1, and NSP4 genes derived from the G2P[4] rotavirus in the backbone of the neighboring DS-1-like G8P[8] strains represented by CAU17L-103.
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Affiliation(s)
- Xuan Zhou
- Division of Microbiology, Wuhan Center for Disease Control and Prevention, Wuhan 430024, China; (X.Z.); (B.P.); (M.L.)
| | - Yuanhong Wang
- Division of Microbiology, Wuhan Center for Disease Control and Prevention, Wuhan 430024, China; (X.Z.); (B.P.); (M.L.)
| | - Nan Chen
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China;
| | - Beibei Pang
- Division of Microbiology, Wuhan Center for Disease Control and Prevention, Wuhan 430024, China; (X.Z.); (B.P.); (M.L.)
| | - Manqing Liu
- Division of Microbiology, Wuhan Center for Disease Control and Prevention, Wuhan 430024, China; (X.Z.); (B.P.); (M.L.)
| | - Kun Cai
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China;
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan;
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Genomic Constellation of Human Rotavirus G8 Strains in Brazil over a 13-Year Period: Detection of the Novel Bovine-like G8P[8] Strains with the DS-1-like Backbone. Viruses 2023; 15:v15030664. [PMID: 36992373 PMCID: PMC10056101 DOI: 10.3390/v15030664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Rotavirus (RVA) G8 is frequently detected in animals, but only occasionally in humans. G8 strains, however, are frequently documented in nations in Africa. Recently, an increase in G8 detection was observed outside Africa. The aims of the study were to monitor G8 infections in the Brazilian human population between 2007 and 2020, undertake the full-genotype characterization of the four G8P[4], six G8P[6] and two G8P[8] RVA strains and conduct phylogenetic analysis in order to understand their genetic diversity and evolution. A total of 12,978 specimens were screened for RVA using ELISA, PAGE, RT-PCR and Sanger sequencing. G8 genotype represented 0.6% (15/2434) of the entirely RVA-positive samples. G8P[4] comprised 33.3% (5/15), G8P[6] 46.7% (7/15) and G8P[8] 20% (3/15). All G8 strains showed a short RNA pattern. All twelve selected G8 strains displayed a DS-1-like genetic backbone. The whole-genotype analysis on a DS-1-like backbone identified four different genotype-linage constellations. According to VP7 analysis, the Brazilian G8P[8] strains with the DS-1-like backbone strains were derived from cattle and clustered with newly DS-1-like G1/G3/G9/G8P[8] strains and G2P[4] strains. Brazilian IAL-R193/2017/G8P[8] belonged to a VP1/R2.XI lineage and were grouped with bovine-like G8P[8] strains with the DS-1-like backbone strains detected in Asia. Otherwise, the Brazilian IAL-R558/2017/G8P[8] possess a “Distinct” VP1/R2 lineage never previously described and grouped apart from any of the DS-1-like reference strains. Collectively, our findings suggest that the Brazilian bovine-like G8P[8] strains with the DS-1-like backbone strains are continuously evolving and likely reassorting with local RVA strains rather than directly relating to imports from Asia. The Brazilian G8P[6]-DS-1-like strains have been reassorted with nearby co-circulating American strains of the same DS-1 genotype constellation. However, phylogenetic analyses revealed that these strains have some genetic origin from Africa. Finally, rather than being African-born, Brazilian G8P[4]-DS-1-like strains were likely imported from Europe. None of the Brazilian G8 strains examined here exhibited signs of recent zoonotic reassortment. G8 strains continued to be found in Brazil according to their intermittent and localized pattern, thus, does not suggest that a potential emergence is taking place in the country. Our research demonstrates the diversity of G8 RVA strains in Brazil and adds to the understanding of G8P[4]/P[6]/P[8] RVA genetic diversity and evolution on a global scale.
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Kozawa K, Higashimoto Y, Kawamura Y, Miura H, Negishi T, Hattori F, Ihira M, Komoto S, Taniguchi K, Yoshikawa T. Rotavirus genotypes and clinical outcome of natural infection based on vaccination status in the post-vaccine era. Hum Vaccin Immunother 2022; 18:2037983. [PMID: 35240934 PMCID: PMC9009920 DOI: 10.1080/21645515.2022.2037983] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Rotavirus (RV) is a leading cause of gastroenteritis in children. In Japan, Rotarix (RV1; GlaxoSmithKline), which is a monovalent vaccine derived from human RV (G1P[8]), has been introduced since November 2011, and RotaTeq (RV5; MSD) which is an pentavalent, human-bovine mono-reassortant vaccine (G1, G2, G3, G4, and P1A[8]), has been introduced since July 2012. Long-term follow-up on vaccine efficacy and RV genotypical change should be carried out in order to control RV infection. The RV gastroenteritis (RVGE) outbreak occurred during the 2018/2019 season in Aichi prefecture, Japan. Therefore, the molecular epidemiology of RV among three different groups of RVGE, which were outpatients who received RV1, those who received RV5, and those without vaccination, was explored. Clinical features of RVGE patients were compared among the three patient groups. Children less than 15 years of age with gastroenteritis who visited any of seven pediatric practices between January and June 2019 were enrolled in the study. G, P, and E genotypes were determined by direct sequencing of reverse transcription-polymerase chain reaction products amplified from stool samples. Among 110 patients, there were 27, 28, and 55 in the RV1-vaccinated, RV5-vaccinated, and unvaccinated groups, respectively. The most frequent genotype was G8P[8] (92/110 patients, 83.6%). Genotype distributions did not significantly differ among the three patient groups (P = .125). Mean Vesikari score was significantly lower among RV1-vaccinated (7.1) and RV5-vaccinated patients (6.4) than among unvaccinated patients (10.2) (P < .001). Even in RVGE patients treated in an outpatient clinic, RV vaccine reduced the severity of the disease in this cohort.
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Affiliation(s)
- Kei Kozawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Yuki Higashimoto
- Faculty of Medical Technology, Fujita Health University School of Health Sciences, Toyoake, Japan
| | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiroki Miura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Takumi Negishi
- Department of Clinical Laboratory, Fujita Health University Hospital, Toyoake, Japan
| | - Fumihiko Hattori
- Department of Pediatrics, Kariya Toyota General Hospital, Kariya, Japan
| | - Masaru Ihira
- Faculty of Clinical Engineering, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
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8
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Degiuseppe JI, Torres C, Mbayed VA, Stupka JA. Phylogeography of Rotavirus G8P[8] Detected in Argentina: Evidence of Transpacific Dissemination. Viruses 2022; 14:v14102223. [PMID: 36298778 PMCID: PMC9609476 DOI: 10.3390/v14102223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 01/25/2023] Open
Abstract
Rotavirus is one of the leading causes of diarrhea in children. In 2018, G8P[8], an unusual association of genotypes, was detected with moderate frequency in symptomatic children in Argen-tina, unlike a previous sporadic identification in 2016. The aim of this study was to analyze the dissemination pattern of the G8P[8]-lineage IV strains detected in Argentina. Nucleotide sequences of the VP7 gene of Argentine G8P[8] strains (2016, 2018 and 2019) were studied by discrete phylodynamic analyses, together with other worldwide relevant G8-lineage IV strains. Bayes Factor (BF) was used to assess the strength of the epidemiological association between countries. Phylodynamic analyses determined an evolutionary rate of 3.7 × 10-3 (HDP95%: 1.4 × 10-3-8.2 × 10-3) substitutions/site/year. Likewise, the most recent common ancestor was 32.2 years old, dating back to 1986 (HDP95% = 1984-1988). The spatiotemporal dynamics analysis revealed South Korea as being the country of origin of the Argentine strains (posterior probability of the ancestral state: 0.8471), which was also evidenced by a significant rate of diffusion from South Korea to Argentina (BF: 55.1). The detection of G8 in South America in 2016-2017 was not related to the cases detected in 2018-2019, revealing a new G8 introduction to the region and supporting a transpacific dissemination.
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Affiliation(s)
- Juan Ignacio Degiuseppe
- Laboratorio de Gastroenteritis Virales, INEI-ANLIS “Dr. Carlos G. Malbrán”, Avenida Vélez Sarsfield 563, Ciudad de Buenos Aires 1281, Argentina
- Correspondence: ; Tel.: +54-9-11-5804-6039; Fax: +54-11-4301-7428
| | - Carolina Torres
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Bacteriología y Virología Molecular (IBAViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina Junín 954, Ciudad de Buenos Aires 1113, Argentina
| | - Viviana Andrea Mbayed
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Bacteriología y Virología Molecular (IBAViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina Junín 954, Ciudad de Buenos Aires 1113, Argentina
| | - Juan Andrés Stupka
- Laboratorio de Gastroenteritis Virales, INEI-ANLIS “Dr. Carlos G. Malbrán”, Avenida Vélez Sarsfield 563, Ciudad de Buenos Aires 1281, Argentina
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9
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Miura T, Kadoya SS, Takino H, Sano D, Akiba M. Temporal variations of human and animal Rotavirus A genotypes in surface water used for drinking water production. Front Microbiol 2022; 13:912147. [PMID: 36016785 PMCID: PMC9395708 DOI: 10.3389/fmicb.2022.912147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Rotavirus is a major cause of gastroenteritis among infants and children. In this study, nested PCR assays were developed to amplify partial regions of the VP7, VP4, and VP6 genes of Rotavirus A (RVA) for amplicon-based Illumina MiSeq sequencing to investigate RVA genotypes in environmental water samples. Eight sets of inner primers were first designed and screened for use in the nested PCR assays, and four sets of them could produce amplicons. Six sets of outer primers were then designed and combined with the four sets of inner primers that worked. The assays were evaluated for sensitivity using raw water samples collected from one drinking water treatment plant between April 2019 and March 2020 (Sample Set 1; N = 12) and seven DWTPs between 2018 and 2020 (Sample Set 2; N = 18). In total, 43 amplicons from Set 1 were sequenced and diverse sequences from human, porcine, bovine, equine, and feline RVA were observed. Human G8, G3, and G2 genotypes were obtained, with G8 predominant (relative abundance, 36–87%) in samples taken during the rotavirus epidemic season between April and June. Porcine G5, G11, and G4, and bovine G10 and G6 genotypes were also detected. VP4 sequence analysis revealed that the human P[8] genotype was present throughout the year, whereas P[4] and P[9] were present only in the epidemic season. The vaccine strains P[5] and P[8] (RotaTeq®) were also detected. Our approach enables the identification of prevalent human and animal RVA genotypes and their host species that potentially caused fecal contamination in water sources.
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Affiliation(s)
- Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
- *Correspondence: Takayuki Miura,
| | - Syun-suke Kadoya
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
- Department of Urban Engineering, The University of Tokyo, Bunkyo, Japan
| | - Hiroyuki Takino
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
| | - Michihiro Akiba
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
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10
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Wang SJ, Chen LN, Wang SM, Zhou HL, Qiu C, Jiang B, Qiu TY, Chen SL, von Seidlein L, Wang XY. Genetic characterization of two G8P[8] rotavirus strains isolated in Guangzhou, China, in 2020/21: evidence of genome reassortment. BMC Infect Dis 2022; 22:579. [PMID: 35764948 PMCID: PMC9238253 DOI: 10.1186/s12879-022-07542-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
Background The G8 rotavirus genotype has been detected frequently in children in many countries and even became the predominant strain in sub-Saharan African countries, while there are currently no reports from China. In this study we described the genetic characteristics and evolutionary relationship between rotavirus strains from Guangzhou in China and the epidemic rotavirus strains derived from GenBank, 2020–2021. Methods Virus isolation and subsequent next-generation sequencing were performed for confirmed G8P[8] specimens. The genetic characteristics and evolutionary relationship were analyzed in comparison with epidemic rotavirus sequences obtained from GenBank. Results The two Guangzhou G8 strains were DS-1-like with the closest genetic distance to strains circulating in Southeast Asia. The VP7 genes of the two strains were derived from a human, not an animal G8 rotavirus. Large genetic distances in several genes suggested that the Guangzhou strains may not have been transmitted directly from Southeast Asian countries, but have emerged following reassortment events. Conclusions We report the whole genome sequence information of G8P[8] rotaviruses recently detected in China; their clinical and epidemiological significance remains to be explored further. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07542-9.
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Affiliation(s)
- Si-Jie Wang
- Shanghai Institute of Infectious Disease and Biosecurity, and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Medical Molecular Virology of MoE & MoH, Fudan University, Shanghai, People's Republic of China
| | - Li-Na Chen
- Key Laboratory of Medical Molecular Virology of MoE & MoH, Fudan University, Shanghai, People's Republic of China
| | - Song-Mei Wang
- Laboratory of Molecular Biology, Training Center of Medical Experiments, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Hong-Lu Zhou
- Shanghai Institute of Infectious Disease and Biosecurity, and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Chao Qiu
- Shanghai Institute of Infectious Disease and Biosecurity, and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Baoming Jiang
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tian-Yi Qiu
- Zhongshan Hospital, Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China.
| | - Sheng-Li Chen
- Pediatric Center, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue Central, Guangzhou, People's Republic of China.
| | - Lorenz von Seidlein
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Xuan-Yi Wang
- Shanghai Institute of Infectious Disease and Biosecurity, and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China. .,Key Laboratory of Medical Molecular Virology of MoE & MoH, Fudan University, Shanghai, People's Republic of China. .,Children's Hospital, Fudan University, Shanghai, People's Republic of China.
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11
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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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12
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Whole genome sequencing and evolutionary analysis of G8P [8] rotaviruses emerging in Japan. Virusdisease 2022; 33:215-218. [DOI: 10.1007/s13337-022-00765-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 04/03/2022] [Indexed: 10/18/2022] Open
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13
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Amit LN, Mori D, John JL, Chin AZ, Mosiun AK, Jeffree MS, Ahmed K. Emergence of equine-like G3 strains as the dominant rotavirus among children under five with diarrhea in Sabah, Malaysia during 2018-2019. PLoS One 2021; 16:e0254784. [PMID: 34320003 PMCID: PMC8318246 DOI: 10.1371/journal.pone.0254784] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/03/2021] [Indexed: 12/12/2022] Open
Abstract
Rotavirus infection is a dilemma for developing countries, including Malaysia. Although commercial rotavirus vaccines are available, these are not included in Malaysia's national immunization program. A scarcity of data about rotavirus genotype distribution could be partially to blame for this policy decision, because there are no data for rotavirus genotype distribution in Malaysia over the past 20 years. From January 2018 to March 2019, we conducted a study to elucidate the rotavirus burden and genotype distribution in the Kota Kinabalu and Kunak districts of the state of Sabah. Stool specimens were collected from children under 5 years of age, and rotavirus antigen in these samples was detected using commercially available kit. Electropherotypes were determined by polyacrylamide gel electrophoresis of genomic RNA. G and P genotypes were determined by RT-PCR using type specific primers. The nucleotide sequence of the amplicons was determined by Sanger sequencing and phylogenetic analysis was performed by neighbor-joining method. Rotavirus was identified in 43 (15.1%) children with watery diarrhea. The male:female ratio (1.9:1) of the rotavirus-infected children clearly showed that it affected predominantly boys, and children 12-23 months of age. The genotypes identified were G3P[8] (74% n = 31), followed by G1P[8] (14% n = 6), G12P[6](7% n = 3), G8P[8](3% n = 1), and GxP[8] (3% n = 1). The predominant rotavirus circulating among the children was the equine-like G3P[8] (59.5% n = 25) with a short electropherotype. Eleven electropherotypes were identified among 34 strains, indicating substantial diversity among the circulating strains. The circulating genotypes were also phylogenetically diverse and related to strains from several different countries. The antigenic epitopes present on VP7 and VP4 of Sabahan G3 and equine-like G3 differed considerably from that of the RotaTeq vaccine strain. Our results also indicate that considerable genetic exchange is occurring in Sabahan strains. Sabah is home to a number of different ethnic groups, some of which culturally are in close contact with animals, which might contribute to the evolution of diverse rotavirus strains. Sabah is also a popular tourist destination, and a large number of tourists from different countries possibly contributes to the diversity of circulating rotavirus genotypes. Considering all these factors which are contributing rotavirus genotype diversity, continuous surveillance of rotavirus strains is of utmost importance to monitor the pre- and post-vaccination efficacy of rotavirus vaccines in Sabah.
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Affiliation(s)
- Lia Natasha Amit
- Faculty of Medicine and Health Sciences, Department of Pathobiology and Medical Diagnostics, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Daisuke Mori
- Faculty of Medicine and Health Sciences, Department of Pathobiology and Medical Diagnostics, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Jecelyn Leaslie John
- Faculty of Medicine and Health Sciences, Borneo Medical and Health Research Centre, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Abraham Zefong Chin
- Faculty of Medicine and Health Sciences, Department of Community and Family Medicine, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Andau Konodan Mosiun
- Kunak District Health Office, Ministry of Health Malaysia, Kunak, Sabah, Malaysia
| | - Mohammad Saffree Jeffree
- Faculty of Medicine and Health Sciences, Department of Community and Family Medicine, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Kamruddin Ahmed
- Faculty of Medicine and Health Sciences, Department of Pathobiology and Medical Diagnostics, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
- Faculty of Medicine and Health Sciences, Borneo Medical and Health Research Centre, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
- * E-mail:
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14
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Tsugawa T, Akane Y, Honjo S, Kondo K, Kawasaki Y. Rotavirus vaccination in Japan: Efficacy and safety of vaccines, changes in genotype, and surveillance efforts. J Infect Chemother 2021; 27:940-948. [PMID: 33867267 DOI: 10.1016/j.jiac.2021.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/25/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
In Japan, a monovalent rotavirus vaccine (RV1) and a pentavalent rotavirus vaccine (RV5) were launched as voluntary vaccinations in November 2011 and July 2012, respectively. Rotavirus (RV) vaccine coverage in Japan increased from 30.0% in 2012 to 78.4% in 2019. The number of RV gastroenteritis hospitalizations decreased after 2014 in Japan, and is expected to decrease further following the introduction of RV vaccines into the national immunization program in October 2020. The incidence rates of intussusception (IS) among children aged <1 year were 102.8 and 94.0 per 100,000 person-years in the pre-vaccine (2007-2011) and post-vaccine (2012-September 2014) eras, respectively. IS incidence did not increase following RV vaccine introduction in Japan. The efficacy and safety of RV vaccination were both documented in Japan. To reduce the risk of IS following RV vaccination, it is important that children receive a first dose of RV vaccine at age <15 weeks, preferably at age 2 months. Some strains that have emerged since RV vaccine introduction, such as DS-1-like G1P[8], eG3, and G8P[8], have spread nationwide. These three emerging genotypes did not affect the severity of the RV infection. Continuous city-level surveillance, using analysis of all 11 RV genome segments, is necessary to elucidate the genetic characteristics of prevalent RV strains. These efforts would also clarify the influence of vaccination on genetic changes of RV strains and the emergence of new genotypes.
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Affiliation(s)
- Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan.
| | - Yusuke Akane
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
| | - Saho Honjo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sunagawa City Hospital, Sunagawa, 073-0196, Japan
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
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15
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Kim KG, Kee HY, Park HJ, Chung JK, Kim TS, Kim MJ. The Long-Term Impact of Rotavirus Vaccines in Korea, 2008-2020; Emergence of G8P[8] Strain. Vaccines (Basel) 2021; 9:406. [PMID: 33923945 PMCID: PMC8073504 DOI: 10.3390/vaccines9040406] [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: 03/30/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/19/2022] Open
Abstract
This study evaluated the long-term impact of rotavirus vaccination on prevalence, seasonality, and genotype distribution in Gwangju, Korea for 13 seasons. Rotavirus was identified using ELISA and then sequenced for G and P genotypes by Reverse Transcription Polymerase Chain Reactions for diarrhoeagenic patient specimens from local hospitals between January 2008 and August2020. Of 26,902 fecal samples, 2919 samples (10.9%) were ELISA positive. The prevalence declined from 16.3% in pre-vaccine era to 5.4% in post-vaccine era. In the pre-vaccine period, G1P[8] was the most common genotype, followed by G2P[4], G3P[8], and G9P[8], etc. In the transitional period, the proportion of G2P[4] became the dominant genotype and G1P[8] was still commonly identified. In contrast, the novel genotype G8P[8] was predominant in the post-vaccine period. Meanwhile, G2P[4] and G8P[8] were major genotypes in both Rotarix and RotaTeq groups. The substantial decline of G1P[8] prevalence, reemergence of G1P[8], G3P[8], and G2P[4] rotavirus strains, and surge of the rare G8P[8] after vaccine introduction were interesting points to note. The continuous surveillance on the genotypes of RV will be needed to understand rotavirus epidemiology and their evolutionary patterns, as caution is required when interpreting temporal changes in RV genotype dynamic.
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Affiliation(s)
| | | | | | | | | | - Min Ji Kim
- Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (K.g.K.); (H.-y.K.); (H.j.P.); (J.K.C.); (T.s.K.)
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16
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Pasittungkul S, Lestari FB, Puenpa J, Chuchaona W, Posuwan N, Chansaenroj J, Mauleekoonphairoj J, Sudhinaraset N, Wanlapakorn N, Poovorawan Y. High prevalence of circulating DS-1-like human rotavirus A and genotype diversity in children with acute gastroenteritis in Thailand from 2016 to 2019. PeerJ 2021; 9:e10954. [PMID: 33680579 PMCID: PMC7919534 DOI: 10.7717/peerj.10954] [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: 10/08/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
Background Human rotavirus A (RVA) infection is the primary cause of acute gastroenteritis (AGE) in infants and young children worldwide, especially in children under 5 years of age and is a major public health problem causing severe diarrhea in children in Thailand. This study aimed to investigate the prevalence, genotype diversity, and molecular characterization of rotavirus infection circulating in children under 15 years of age diagnosed with AGE in Thailand from January 2016 to December 2019. Methods A total of 2,001 stool samples were collected from children with gastroenteritis (neonates to children <15 years of age) and tested for RVA by real-time polymerase chain reaction (RT-PCR). Amplified products were sequenced and submitted to an online genotyping tool for analysis. Results Overall, 301 (15.0%) stool samples were positive for RVA. RVA occurred most frequently among children aged 0-24 months. The seasonal incidence of rotavirus infection occurred typically in Thailand during the winter months (December-March). The G3P[8] genotype was identified as the most prevalent genotype (33.2%, 100/301), followed by G8P[8] (10.6%, 32/301), G9P[8] (6.3%, 19/301), G2P[4] (6.0%, 18/301), and G1P[6] (5.3%, 16/301). Uncommon G and P combinations such as G9P[4], G2P[8], G3P[4] and G3P[9] were also detected at low frequencies. In terms of genetic backbone, the unusual DS-1-like G3P[8] was the most frequently detected (28.2%, 85/301), and the phylogenetic analysis demonstrated high nucleotide identity with unusual DS-1-like G3P[8] detected in Thailand and several countries. Conclusions A genetic association between RVA isolates from Thailand and other countries ought to be investigated given the local and global dissemination of rotavirus as it is crucial for controlling viral gastroenteritis, and implications for the national vaccination programs.
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Affiliation(s)
- Siripat Pasittungkul
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Fajar Budi Lestari
- Department of Bioresources Technology and Veterinary, Vocational College, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Faculty of Graduate School, Chulalongkorn University, Inter-Department of Biomedical Sciences, Bangkok, Bangkok, Thailand
| | - Jiratchaya Puenpa
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Watchaporn Chuchaona
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Nawarat Posuwan
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Jira Chansaenroj
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - John Mauleekoonphairoj
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Natthinee Sudhinaraset
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
| | - Nasamon Wanlapakorn
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand.,Faculty of Medicine, Chulalongkorn University, Division of Academic Affairs, Bangkok, Bangkok, Thailand
| | - Yong Poovorawan
- Faculty of Medicine, Chulalongkorn University, Center of Excellence in Clinical Virology, Bangkok, Bangkok, Thailand
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17
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Akane Y, Tsugawa T, Fujii Y, Honjo S, Kondo K, Nakata S, Fujibayashi S, Ohara T, Mori T, Higashidate Y, Nagai K, Kikuchi M, Sato T, Kato S, Tahara Y, Kubo N, Katayama K, Kimura H, Tsutsumi H, Kawasaki Y. Molecular and clinical characterization of the equine-like G3 rotavirus that caused the first outbreak in Japan, 2016. J Gen Virol 2021; 102. [PMID: 33587029 DOI: 10.1099/jgv.0.001548] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Since 2013, equine-like G3 rotavirus (eG3) strains have been detected throughout the world, including in Japan, and the strains were found to be dominant in some countries. In 2016, the first eG3 outbreak in Japan occurred in Tomakomai, Hokkaido prefecture, and the strains became dominant in other Hokkaido areas the following year. There were no significant differences in the clinical characteristics of eG3 and non-eG3 rotavirus infections. The eG3 strains detected in Hokkaido across 2 years from 2016 to 2017 had DS-1-like constellations (i.e. G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2), and the genes were highly conserved (97.5-100 %). One strain, designated as To16-12 was selected as the representative strain for these strains, and all 11 genes of this strain (To16-12) exhibited the closest identity to one foreign eG3 strain (STM050) seen in Indonesia in 2015 and two eG3 strains (IS1090 and MI1125) in another Japanese prefecture in 2016, suggesting that this strain might be introduced into Japan from Indonesia. Sequence analyses of VP7 genes from animal and human G3 strains found worldwide did not identify any with close identity (>92 %) to eG3 strains, including equine RV Erv105. Analysis of another ten genes indicated that the eG3 strain had low similarity to G2P[4] strains, which are considered traditional DS-1-like strains, but high similarity to DS-1-like G1P[8] strains, which first appeared in Asia in 2012. These data suggest that eG3 strains were recently generated in Asia as mono-reassortant strain between DS-1-like G1P[8] strains and unspecified animal G3 strains. Our results indicate that rotavirus surveillance in the postvaccine era requires whole-genome analyses.
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Affiliation(s)
- Yusuke Akane
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Saho Honjo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sunagawa City Hospital, Sunagawa, Japan
| | - Shuji Nakata
- Department of Pediatrics, Nakata Pediatric Clinic, Sapporo, Japan
| | | | - Toshio Ohara
- Department of Pediatrics, Tomakomai City Hospital, Tomakomai, Japan
| | - Toshihiko Mori
- Department of Pediatrics, NTT East Sapporo Hospital, Sapporo, Japan
| | - Yoshihito Higashidate
- Department of Pediatrics, Japan Community Health Care Organization (JCHO) Sapporo Hokushin Hospital, Sapporo, Japan
| | - Kazushige Nagai
- Department of Pediatrics, Takikawa Municipal Hospital, Takikawa, Japan
| | | | - Toshiya Sato
- Department of Pediatrics, Iwamizawa Municipal General Hospital, Iwamizawa, Japan
| | - Shinsuke Kato
- Department of Pediatrics, Rumoi City Hospital, Rumoi, Japan
| | - Yasuo Tahara
- Department of Pediatrics, Steel Memorial Muroran Hospital, Muroran, Japan
| | - Noriaki Kubo
- Department of Pediatrics, Japanese Red Cross Urakawa Hospital, Urakawa, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Graduate School of Health Science, Gunma Paz University, Gunma, Japan.,Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroyuki Tsutsumi
- Present address: Midorinosato, Saiseikai Otaru Hospital, Otaru, Japan.,Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
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Hoa-Tran TN, Nakagomi T, Vu HM, Nguyen TTT, Takemura T, Hasebe F, Dao ATH, Anh PHQ, Nguyen AT, Dang AD, Nakagomi O. Detection of three independently-generated DS-1-like G9P[8] reassortant rotavirus A strains during the G9P[8] dominance in Vietnam, 2016–2018. INFECTION GENETICS AND EVOLUTION 2020; 80:104194. [DOI: 10.1016/j.meegid.2020.104194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/26/2019] [Accepted: 01/09/2020] [Indexed: 10/25/2022]
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Ono M, Tsugawa T, Nakata S, Kondo K, Tatsumi M, Tsutsumi H, Kawasaki Y. Rotavirus genotype and Vesikari score of outpatients in Japan in the vaccine era. Pediatr Int 2020; 62:569-575. [PMID: 31957129 DOI: 10.1111/ped.14150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/10/2019] [Accepted: 01/15/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Group A rotaviruses (RVs) are a major cause of severe gastroenteritis among infants and young children. In Japan, RV vaccines were introduced in 2011, leading to a reduction in severe gastroenteritis cases. Studies are required to assess the effectiveness of the vaccines and their effect on the prevalence of RV genotypes. METHODS Fecal samples were collected from outpatients with RV gastroenteritis in a pediatric clinic in Sapporo, Japan, from 2010 to 2016. GPI genotypes were determined using reverse-transcription polymerase chain reaction. Clinical information and immunization records were obtained from outpatients after 2013. GPI genotypes and clinical features were compared between patients with and without a RV vaccine history. RESULTS In total, 270 cases were genotyped. G1P[8]I1 (Wa-like G1P[8]) strains were dominant from 2010 to 2012. G1P[8]I2 (DS-1-like G1P[8]) strains appeared in 2012 and dominated in 2013 to 2015. G2P[4]I2 and G9P[8]I1 strains increased every 3 years (G2P[4]I2: 2011 and 2014, G9P[8]I1: 2010, 2013 and 2016). After the 2013 season, 137 cases were collected, 24 of which were vaccinated. Cases requiring drip infusion were fewer in the vaccination group than in the non-vaccination group (16.7% vs 52.2%). No patients required hospitalization in the vaccination group compared with 10.6% in the non-vaccination group. A severe Vesikari score was less common in the vaccination group than in the non-vaccination group (33.3% vs 78.8%). There was no significant difference in the GPI genotype distribution between the two groups. CONCLUSION Rotaviruses vaccine effectiveness, regardless of GPI genotype, was confirmed in terms of alleviation of disease severity.
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Affiliation(s)
- Mayumi Ono
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Pediatrics, Sunagawa City Hospital, Sunagawa, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | | | - Kenji Kondo
- Department of Pediatrics, Sunagawa City Hospital, Sunagawa, Japan
| | | | - Hiroyuki Tsutsumi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
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20
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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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Distribution of rotavirus genotypes in Japan from 2015 to 2018: Diversity in genotypes before and after introduction of rotavirus vaccines. Vaccine 2020; 38:3980-3986. [PMID: 32307276 DOI: 10.1016/j.vaccine.2020.03.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/18/2020] [Accepted: 03/05/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Diversity in group A rotavirus (RVA) strains after introduction of RV-vaccines remains an emerging concern worldwide. In this study, we investigated the prevalence and distribution of RVA genotypes in Japanese children with acute gastroenteritis (AGE) from 2015 to 2018. In addition, a comparison of the genotypes in pre-vaccination (2006-2012) and post-vaccination (2012-2018) periods was conducted to understand the impact of these vaccines on genotype distribution. METHODS Fecal samples were collected regularly from outpatient clinics in six localities: Hokkaido, Tokyo, Shizuoka, Osaka, Kyoto, and Saga. RVA were screened and genotyped by RT-PCR and sequence-based genotyping. RESULTS During the period 2015-2018, RVA was detected in 307 (19.7%) samples out of 1557 specimens: 29.9% (95% CI: 25.8% to 34.3%), 17.9% (95% CI: 14.7% to 21.5%), and 13% (95% CI: 10.3% to 16.0%) were detected RVA-positive in 2015-2016, 2016-2017 and 2017-2018, respectively. The average detection of RVA in pre-vaccination (2006-2012) and post-vaccination (2012-2018) era remained almost similar (18%-20%). The G2P[4]I2 (52.1%, 95% CI: 43.5%-60.6%) remained the most common genotype in 2015-2016, whereas G8P[8]I2 (55.9%, 95% CI: 45.2%-66.2%) dominated in 2016-2017. In 2017-2018, G9P[8]I2 (42.0%, 95% CI: 30.5%-53.9%) prevailed, followed by G9P[8]I1 (23.0%, 95% CI: 14.0%-34.2%). The detection rate of some common genotypes of pre-vaccination era like G1P[8] and G3P[8] has been reduced after introduction of RV-vaccine, whereas genotypes that were sporadic before the introduction of vaccines like G2P[4], G2P[8], G9P[8] and G8P[8] were emerged/reemerged in post-vaccination period. CONCLUSIONS Our study presented the diversity in circulating RVA genotypes in Japan before and after introduction of RV-vaccines. Sudden emergence of DS-1-like (I2) unusual strains in post-vaccination era remains alarming. Continuous monitoring of RVA genotypes is therefore indispensable to refine future vaccine strategy.
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Clinical Characteristics of Rotavirus-Induced Gastroenteritis in Infants. SERBIAN JOURNAL OF EXPERIMENTAL AND CLINICAL RESEARCH 2020. [DOI: 10.2478/sjecr-2020-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Rotavirus is the most common cause of acute infectious diarrhea in infants and young children up to the age of five. The disease is characterized by profuse watery diarrhea, vomiting and fever. The major complications of rotavirus gastroenteritis (RVGE) are dehydration, middle ear inflammation and upper respiratory tract infection. The basis of treatment is compensation for fluid loss and administration of probiotics. The aim of this study was to analyze the clinical characteristics of rotavirus gastroenteritis in infants. The study was conducted by the type of retrospective-prospective clinical study on infants with rotavirus gastroenteritis diagnosed on the basis of a positive Rotalex test (Orion Diagnostica Finland) and exclusion of other etiological factors at the University Children's Clinic in Belgrade, from April 2005 to December 2010. In addition to the detailed medical history and clinical examination, relevant laboratory analyzes were performed in all patients. Descriptive and analytical statistical methods were applied in the study. Among the descriptive methods, we used grouping, tabulation, graphing, calculating measures of central tendency, calculating measures of variability and calculating relative numbers. Of the analytical statistical methods, distribution normality testing, χ2 test, Mann-Whitney U test and T test were used. Statistical significance will be taken to mean p < 0.05. The average infant mortality was 6.7 ± 3.7 months. All respondents were divided into two groups according to the age. The first group consisted of infants aged 0 to 5 months (46%), the second group consisted of infants aged 6 to 12 months (54%). The incidence of aqueous diarrhea (100%), vomiting (84%) and fever (74%) in infants suffering from rotavirus gastroenteritis was analyzed. The significance of the age on the symptomatology of rotavirus gastroenteritis as well as on the importance of using probiotics has been demonstrated.
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Moutelíková R, Sauer P, Dvořáková Heroldová M, Holá V, Prodělalová J. Emergence of Rare Bovine-Human Reassortant DS-1-Like Rotavirus A Strains with G8P[8] Genotype in Human Patients in the Czech Republic. Viruses 2019; 11:v11111015. [PMID: 31683946 PMCID: PMC6893433 DOI: 10.3390/v11111015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/28/2019] [Accepted: 10/30/2019] [Indexed: 01/09/2023] Open
Abstract
Group A Rotaviruses (RVA) are the leading cause of acute gastroenteritis in children and a major cause of childhood mortality in low-income countries. RVAs are mostly host-specific, but interspecies transmission and reassortment between human and animal RVAs significantly contribute to their genetic diversity. We investigated the VP7 and VP4 genotypes of RVA isolated from 225 stool specimens collected from Czech patients with gastroenteritis during 2016–2019. The most abundant genotypes were G1P[8] (42.7%), G3P[8] (11.1%), G9P[8] (9.8%), G2P[4] (4.4%), G4P[8] (1.3%), G12P[8] (1.3%), and, surprisingly, G8P[8] (9.3%). Sequence analysis of G8P[8] strains revealed the highest nucleotide similarity of all Czech G8 sequences to the G8P[8] rotavirus strains that were isolated in Vietnam in 2014/2015. The whole-genome backbone of the Czech G8 strains was determined with the use of next-generation sequencing as DS-1-like. Phylogenetic analysis of all segments clustered the Czech isolates with RVA strains that were formerly described in Southeast Asia, which had emerged following genetic reassortment between bovine and human RVAs. This is the first time that bovine–human DS-1-like G8P[8] strains were detected at a high rate in human patients in Central Europe. Whether the emergence of this unusual genotype reflects the establishment of a new RVA strain in the population requires the continuous monitoring of rotavirus epidemiology.
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Affiliation(s)
| | - Pavel Sauer
- Institute of Microbiology, University Hospital Olomouc and Faculty of Medicine, Palacký University, 77900 Olomouc, Czech Republic.
| | - Monika Dvořáková Heroldová
- Microbiology Institute of Faculty of Medicine, Masaryk University Brno and University Hospital of St. Anne, 65691 Brno, Czech Republic.
| | - Veronika Holá
- Microbiology Institute of Faculty of Medicine, Masaryk University Brno and University Hospital of St. Anne, 65691 Brno, Czech Republic.
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Fujii Y, Oda M, Somura Y, Shinkai T. Molecular Characteristics of Novel Mono-Reassortant G9P[8] Rotavirus A Strains Possessing the NSP4 Gene of the E2 Genotype Detected in Tokyo, Japan. Jpn J Infect Dis 2019; 73:26-35. [PMID: 31564695 DOI: 10.7883/yoken.jjid.2019.211] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Rotavirus A (RVA) has been detected in patients with gastroenteritis even after vaccine introduction in Japan. To investigate circulating RVA strains, RVA-positive stool specimens obtained in Tokyo in 2017 and 2018 were analyzed using next-generation sequencing. A total of 50 and 21 RVA samples were obtained in 2017 and 2018, respectively. In 2017, G2P[4] (40.0%) was the most prevalent strain, followed by G3P[8] (DS-1-like) (28.0%), G8P[8] (10.0%), G3P[8] (Wa-like) (8.0%), G9P[8]-E1 (8.0%), and mixed infection (6.0%). In 2018, G3P[8] (DS-1-like) (28.6%) and G9P[8]-E2 (28.6%) were the most prevalent strains, followed by G9P[8]-E1 (19.0%), G2P[4] (9.5%), G8P[8] (9.5%), and mixed infection (4.8%). Six G9P[8]-E2 strains detected in 2018 showed an atypical genotype constellation (G9P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1), which had not been reported previously. Phylogenetic analyses suggested that the RVA virus was generated by inter-genogroup reassortment between commonly circulating G9P[8] and G2P[4] strains in Japan. The G9P[8] strain seemed to be reassorted with only the NSP4 gene of the E2 genotype of the G2P[4] strain. Since this newly-emerged G9P[8]-E2 virus was detected in different locations in Tokyo, the virus appears to have already begun to spread to a wider area.
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Affiliation(s)
- Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases
| | - Mayuko Oda
- Division of Virology, Department of Microbiology, Tokyo Metropolitan Institute of Public Health
| | - Yoshiko Somura
- Division of Virology, Department of Microbiology, Tokyo Metropolitan Institute of Public Health
| | - Takayuki Shinkai
- Division of Virology, Department of Microbiology, Tokyo Metropolitan Institute of Public Health
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Roczo-Farkas S, Cowley D, Bines JE. Australian Rotavirus Surveillance Program: Annual Report, 2017. Commun Dis Intell (2018) 2019. [DOI: 10.33321/cdi.2019.43.28] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This report, from the Australian Rotavirus Surveillance Program and collaborating laboratories Australia-wide, describes the rotavirus genotypes identified in children and adults with acute gastroenteritis during the period 1 January to 31 December 2017. During this period, 2,285 faecal specimens were referred for rotavirus G and P genotype analysis, including 1,103 samples that were confirmed as rotavirus positive. Of these, 1,014/1,103 were wildtype rotavirus strains and 89/1,103 were identified as rotavirus vaccine-like. Genotype analysis of the 1,014 wildtype rotavirus samples from both children and adults demonstrated that G2P[4] was the dominant genotype nationally, identified in 39% of samples, followed by equine-like G3P[8] and G8P[8] (25% and 16% respectively). Multiple outbreaks were recorded across Australia, including G2P[4] (Northern Territory, Western Australia, and South Australia), equine-like G3P[8] (New South Wales), and G8P[8] (New South Wales and Victoria). This year also marks the change in the Australian National Immunisation Program to the use of Rotarix exclusively, on 1 July 2017.
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Affiliation(s)
- Susie Roczo-Farkas
- Enteric Diseases Group, Murdoch Children’s Research Institute, Flemington Road, Parkville, Victoria, 3052
| | - Daniel Cowley
- Enteric Diseases Group, Murdoch Children’s Research Institute, Flemington Road, Parkville, Victoria, 3052
| | - Julie E Bines
- Enteric Diseases Group, Murdoch Children’s Research Institute, Flemington Road, Parkville, Victoria, 3052; Department of Paediatrics, University of Melbourne, Flemington Road, Parkville, Victoria, 3052; Department of Gastroenterology and Clinical Nutrition, Flemington Road, Parkville, Victoria, 3052
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Zeng Y, Li T, Zhao B, Lai F, Tang X, Qiao Y, Chen W, Yu F, Zhang S, Wang Y, Ge S, Xu H, Xia N. Molecular epidemiology of group A rotavirus in outpatient diarrhea infants and children in Chongqing, China, 2011-2015. J Med Virol 2019; 91:1788-1796. [PMID: 31241179 DOI: 10.1002/jmv.25530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022]
Abstract
Human group A rotavirus (RVA) is the leading cause of acute viral gastroenteritis in children under 5 years old worldwide. The aim of this study was to investigate the genotype distribution of RVA in the Midwest of China. Sentinel-based surveillance of acute diarrhea was conducted at Children's Hospital of Chongqing Medical University from 2011 to 2015. RVA was tested by using enzyme-linked immunosorbent assays. The partial VP4 genes and VP7 genes of rotavirus were amplified and sequenced, and genotyping and phylogenetic analyses were performed. Among the 2236 stool specimens collected from children with acute gastroenteritis, 681 (30.46%) were positive for RVA. The majority of children (89.28%) who tested positive for RVA were children aged ≤2 years. The seasonal peak of RVA was in the winter. As for genotype, four strain combinations, G9P[8], G3P[8], G1P[8], and G2P[4] contributed to 75.62% (515/681) of the RVA-associated diarrhea cases. After a marked increase in G9P[8] (30.77%) in 2013, G9P[8] became the predominant genotype in 2014 and 2015, whilst the prevalence of G1P[8] was decreased to 2.72% in 2015. Unusual G-P combinations (eg, G1P[4], G9P[4], G4P[6], G3P[4], G2P[8]) were also detected sporadically over the study period. Phylogenetic tree analysis results showed that the VP7 sequences of G9 strains were clustered into two main lineages, and 77.34% of them were clustered into lineage VI, with the highest nucleotide similarity to the strain JS12-17(China). VP4 gene sequences of P[8] strains were almost P[8]-lineage 3. Substantial temporal variation in the circulation of various genotypes of rotavirus in Chongqing was observed during 2011-2015, and highlights the need for continuous surveillance of RVA infection for better understanding and control of RVA infection.
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Affiliation(s)
- Yuanjun Zeng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen, China
| | - Tingdong Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen, China
| | - Biyan Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen, China
| | - Fangfang Lai
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Xiang Tang
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Yingqin Qiao
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Wanbin Chen
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Feng Yu
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Shiyin Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen, China
| | - Yingbin Wang
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Science, Xiamen University, Xiamen, China
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen, China
| | - Hongmei Xu
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen, China.,National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Science, Xiamen University, Xiamen, China
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Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains. PLoS One 2019; 14:e0217422. [PMID: 31150425 PMCID: PMC6544246 DOI: 10.1371/journal.pone.0217422] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022] Open
Abstract
Recent increase in the detection of unusual G1P[8], G3P[8], G8P[8], and G9P[4] Rotavirus A (RVA) strains bearing the DS-1-like constellation of the non-G, non-P genes (hereafter referred to as the genotype 2 backbone) requires better understanding of their evolutionary relationship. However, within a genotype, there is lack of a consensus lineage designation framework and a set of common sequences that can serve as references. Phylogenetic analyses were carried out on over 8,500 RVA genotype 2 genes systematically retrieved from the rotavirus database within the NCBI Virus Variation Resource. In line with previous designations, using pairwise comparison of cogent nucleotide sequences and stringent bootstrap support, reference lineages were defined. This study proposes a lineage framework and provides a dataset ranging from 34 to 145 sequences for each genotype 2 gene for orderly lineage designation of global genotype 2 genes of RVAs detected in human and animals. The framework identified five to 31 lineages depending on the gene. The least number of lineages (five to seven) were observed in genotypes A2 (NSP1), T2 (NSP3) and H2 (NSP5) which are limited to human RVA whereas the most number of lineages (31) was observed in genotype E2 (NSP4). Sharing of the same lineage constellations of the genotype 2 backbone genes between recently-emerging, unusual G1P[8], G3P[8], G8P[8] and G9P[4] reassortants and many contemporary G2P[4] strains provided strong support to the hypothesis that unusual genotype 2 strains originated primarily from reassortment events in the recent past involving contemporary G2P[4] strains as one parent and ordinary genotype 1 strains or animal RVA strains as the other. The lineage framework with selected reference sequences will help researchers to identify the lineage to which a given genotype 2 strain belongs, and trace the evolutionary history of common and unusual genotype 2 strains in circulation.
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Hoa-Tran TN, Nakagomi T, Vu HM, Kataoka C, Nguyen TTT, Dao ATH, Nguyen AT, Takemura T, Hasebe F, Dang AD, Nakagomi O. Whole genome characterization of feline-like G3P[8] reassortant rotavirus A strains bearing the DS-1-like backbone genes detected in Vietnam, 2016. INFECTION GENETICS AND EVOLUTION 2019; 73:1-6. [PMID: 30978460 DOI: 10.1016/j.meegid.2019.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/03/2019] [Accepted: 04/08/2019] [Indexed: 12/27/2022]
Abstract
While conducting rotavirus gastroenteritis surveillance in Vietnam, two G3P[8] rotavirus A specimens possessing an identical short RNA electropherotype were detected. They were RVA/Human-wt/VNM/0232/2016/G3P[8] and RVA/Human-wt/VNM/0248/2016/G3P[8], and recovered from 9 and 23 months old boys, respectively. The patients developed diarrhoea within one-week interval in March 2016 but in places >100 km apart in northern Vietnam. Whole genome sequencing of the two G3P[8] rotavirus A strains revealed that their genomic RNA sequences were identical across the 11 genome segments, suggesting that they derived from a single clone. The backbone gene constellation was I2-R2-C2-M2-A2-N2-T2-E2-H2. The backbone genes and the VP4 gene had a virtually identical nucleotide sequences with identities ranging from 99.2 to 100% to the corresponding genes of RVA/Human-wt/VNM/1149/2014/G8P[8]; the prototype of recently-emerging bovine-like G8P[8] reassortant strains in Vietnam. On the other hand, the VP7 gene was 98.8% identical with that of RVA/Human-wt/CHN/E2451/2011/G3P[9], and they were clustered together in the lineage represented by RVA/Cat-tc/JPN/FRV-1/1986/G3P[9]. The observations led us to hypothesise that one of the bovine-like G8P[8] strains bearing the DS-1-like backbone genes reassorted with a locally circulating FRV-1-like strain to gain the G3 VP7 gene and to emerge as a thus-far undescribed feline-like G3P[8] reassortant strain. The identification of feline-like G3P[8] strains bearing the DS-1-like backbone genes exemplifies the strength and necessity of the whole genome sequencing approach in monitoring, describing and understanding the evolutionary changes that are occurring in emerging strains and their interactions with co-circulating strains.
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Affiliation(s)
- Thi Nguyen Hoa-Tran
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam.
| | - Toyoko Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Hung Manh Vu
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Chikako Kataoka
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Trang Thi Thu Nguyen
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Anh Thi Hai Dao
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Anh The Nguyen
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Taichiro Takemura
- Vietnam Research Station, National Institute of Hygiene and Epideimmiology-Nagasaki University, Hanoi, Viet Nam
| | - Futoshi Hasebe
- Vietnam Research Station, Center for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Anh Duc Dang
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Osamu Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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Fujii Y, Doan YH, Wahyuni RM, Lusida MI, Utsumi T, Shoji I, Katayama K. Improvement of Rotavirus Genotyping Method by Using the Semi-Nested Multiplex-PCR With New Primer Set. Front Microbiol 2019; 10:647. [PMID: 30984154 PMCID: PMC6449864 DOI: 10.3389/fmicb.2019.00647] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/14/2019] [Indexed: 12/24/2022] Open
Abstract
Rotavirus A (RVA) is a major cause of gastroenteritis in infants and young children. After vaccine introduction, RVA surveillance has become more important for monitoring changes in genotype distribution, and the semi-nested multiplex-PCR is a popular method for RVA genotyping. In particular, the VP7 primer set reported by Gouvea and colleagues in 1990 is still widely used worldwide as the recommended WHO primer set in regional and national reference RVA surveillance laboratories. However, this primer set yielded some mistakes with recent epidemic strains. The newly emerged equine-like G3 strains were mistyped as G1, G8 strains were mistyped as G3, the G9 lineage 3 strains showed very weak band, and the G9 lineage 6 strains showed a G9-specific band and a non-specific band. Gouvea’s standard protocol has become relatively unreliable for identifying genotypes correctly. To overcome this limitation, we redesigned the primer set to include recent epidemic strains. Our new primer set enabled us to correctly identify the VP7 genotypes of representative epidemic strains by agarose gel electrophoresis (G1, G2, human typical G3, equine-like G3, G4, G8, G9, and G12). We believe that the multiplex-PCR method with our new primer set is a useful and valuable tool for surveillance of RVA epidemics.
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Affiliation(s)
- Yoshiki Fujii
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yen Hai Doan
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Rury Mega Wahyuni
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Maria Inge Lusida
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Takako Utsumi
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia.,Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ikuo Shoji
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
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30
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Kamiya H, Tacharoenmuang R, Ide T, Negoro M, Tanaka T, Asada K, Nakamura H, Sugiura K, Umemoto M, Kuroki H, Ito H, Tanaka S, Ito M, Fukuda S, Hatazawa R, Hara Y, Guntapong R, Murata T, Taniguchi K, Suga S, Nakano T, Taniguchi K, Komoto S. Characterization of an Unusual DS-1-Like G8P[8] Rotavirus Strain from Japan in 2017: Evolution of Emerging DS-1-Like G8P[8] Strains through Reassortment. Jpn J Infect Dis 2019; 72:256-260. [PMID: 30814461 DOI: 10.7883/yoken.jjid.2018.484] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The emergence of unusual DS-1-like intergenogroup reassortant rotaviruses with a bovine-like G8 genotype (DS-1-like G8P[8] strains) has been reported in several Asian countries. During the rotavirus surveillance program in Japan in 2017, a DS-1-like G8P[8] strain (RVA/Human-wt/JPN/SO1162/2017/G8P[8]) was identified in 43 rotavirus-positive stool samples. Strain SO1162 was shown to have a unique genotype constellation, including genes from both genogroup 1 and 2: G8-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis revealed that the VP1 gene of strain SO1162 appeared to have originated from DS-1-like G1P[8] strains from Thailand and Vietnam, while the remaining 10 genes were closely related to those of previously reported DS-1-like G8P[8] strains. Thus, SO1162 was suggested to be a reassortant strain that acquired the VP1 gene from Southeast Asian DS-1-like G1P[8] strains on the genetic background of co-circulating DS-1-like G8P[8] strains. Our findings provide important insights into the evolutionary dynamics of emerging DS-1-like G8P[8] strains.
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Affiliation(s)
- Hajime Kamiya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases
| | - Ratana Tacharoenmuang
- Department of Virology and Parasitology, Fujita Health University School of Medicine.,National Institute of Health, Department of Medical Sciences
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine
| | - Manami Negoro
- Institute for Clinical Research, National Mie Hospital
| | | | | | | | | | | | | | - Hiroaki Ito
- Department of Pediatrics, Kameda Medical Center
| | | | - Mitsue Ito
- Department of Pediatrics, Japanese Red Cross Ise Hospital
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine
| | - Yuya Hara
- Department of Virology and Parasitology, Fujita Health University School of Medicine
| | | | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine
| | | | | | | | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine
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31
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Lucero Y, O'Ryan M, Liparoti G, Huerta N, Mamani N, Ramani S, Lagomarcino AJ, Del Canto F, Quense J. Predominance of Rotavirus G8P[8] in a City in Chile, a Country Without Rotavirus Vaccination. J Pediatr 2019; 204:298-300.e1. [PMID: 30297290 DOI: 10.1016/j.jpeds.2018.08.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/27/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
Rotavirus G8P[8] infection has been common in Africa, but rare in the Americas. Among 23 rotavirus episodes observed during 18 months of surveillance of 100 families in Chile, 11 (48%) were identified as G8P[8]. Genotypes from these strains shared >99% identity with rotavirus sequences described in Asia, and may be misclassified as mixed G8/G12.
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Affiliation(s)
- Yalda Lucero
- Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Miguel O'Ryan
- Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Millenium Institute of Immunology and Immunotherapy, University of Chile, Santiago, Chile.
| | - Giulia Liparoti
- Department of Medicine, University of Perugia, Perugia, Italy
| | - Nicole Huerta
- Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Nora Mamani
- Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX
| | - Anne J Lagomarcino
- Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Felipe Del Canto
- Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Jorge Quense
- Geography Institute, Pontificia Universidad Católica de Chile, Santiago, Chile
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An unusual outbreak of rotavirus G8P[8] gastroenteritis in adults in an urban community, Singapore, 2016. J Clin Virol 2018; 105:57-63. [PMID: 29902679 DOI: 10.1016/j.jcv.2018.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/02/2018] [Accepted: 06/05/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND An outbreak of gastroenteritis (GE) occurred in community-dwelling adults in the Central Region of urban Singapore, in May 2016. OBJECTIVES To investigate the cause of the outbreak. STUDY DESIGN We conducted a case-cohort study on GE patients linked to the outbreak who presented to the emergency department of a tertiary-care hospital near the outbreak area, from 18 May to 11 June 2016. Stools were tested for gastrointestinal pathogens including rotavirus antigen and positive rotavirus samples were subject to genotyping. RESULTS A total of 57 adult GE patients, with a median age of 40 (range 18 to 84) years, were included. Predominant symptoms were diarrhoea (98.2%), vomiting (64.9%), and abdominal discomfort (38.6%). Age 65 years and above (Adjusted OR 21.78, 95% CI 1.49-318.84; P = 0.02) was the only predictor of admission, after adjusting for comorbidities and clinical severity. Molecular microbiological investigations confirmed that the outbreak was caused by a novel human-bovine reassortant strain of rotavirus G8P[8] with DS-1-like backbone. Exposure to the market in the outbreak area was strongly associated with rotavirus infection (OR 46.14; 95% CI 43.04-49.25, P < 0.01). No particular food item could be identified as the outbreak cause. CONCLUSIONS This is the first report of an outbreak of rotavirus G8P[8] in adults in an urban community that is not waterborne. Transmission was likely through fomites in the market and its surrounding areas, via consumption or contact with contaminated food items purchased from the market, and from person-to-person. The potential for novel G8P[8] strains to cause outbreaks cannot be overemphasized.
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Increasing predominance of G8P[8] species A rotaviruses in children admitted to hospital with acute gastroenteritis in Thailand, 2010-2013. Arch Virol 2018; 163:2165-2178. [DOI: 10.1007/s00705-018-3848-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 04/04/2018] [Indexed: 01/05/2023]
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Okitsu S, Hikita T, Thongprachum A, Khamrin P, Takanashi S, Hayakawa S, Maneekarn N, Ushijima H. Detection and molecular characterization of two rare G8P[14] and G3P[3] rotavirus strains collected from children with acute gastroenteritis in Japan. INFECTION GENETICS AND EVOLUTION 2018; 62:95-108. [PMID: 29656042 DOI: 10.1016/j.meegid.2018.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/01/2018] [Accepted: 04/07/2018] [Indexed: 12/11/2022]
Abstract
This study describes the detection and molecular characterization of two rare G8P[14] and G3P[3] rotavirus strains, which were collected from children with acute gastroenteritis in 2014 in Japan. Among 247 rotaviruses, one G8P[14] (strain 12,597) and one G3P[3] (strain 12,638) rotaviruses were detected. The genotypes of 11 gene segments of these two rotavirus strains (RVA/Human-wt/JPN/12597/2014/G8P[14] and RVA/Human-wt/JPN/12638/2014/G3P[3]) were characterized. The genotype constellation of strain 12,597 was assigned to G8-P[14]-I2-R2-C2-M2-A3-N2-T9-E2-H3, and this strain possessed a rare T9 genotype of NSP3 gene which has never been reported previously in combination with G8 genotype of VP7 gene. Molecular characterization and phylogenetic analysis suggested that the strain 12,597 had the consensus G8P[14] backbone that originated from the rotaviruses of animal origins such as cows, deer, dogs, and cats. The genotype constellation of strain 12,638 was identified as G3-P[3]-I3-R3-C3-M3-A9-N2-T3-E3-H6. The VP7 and VP4 genotypes of strain 12,638 was similar to those of the Cat97-like strains, but the VP1, VP2, and VP3 were closely related to those of the AU-1-like strain. Interestingly, the NSP1 to NSP3 genes shared highest identities with those of a bat rotavirus (RVA/Bat-wt/ZMB/LUS12-14/2012/G3P[3] strain). These findings indicated that the strain 12,638 was an intra-genotype reassortant strain among the AU-1-like strains, the Cat97-like strains and the bat strain. Interestingly, the strains 12,597 and 12,638 possessed the same N2 genotype of NSP2 gene. The results of this study support the possible roles of interspecies transmission and multiple reassortment events for generating the genetic diversity of rotavirus in human.
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Affiliation(s)
- Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan; Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | | | | | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan; Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Role of rotavirus vaccination on an emerging G8P[8] rotavirus strain causing an outbreak in central Japan. Vaccine 2017; 36:43-49. [PMID: 29183732 DOI: 10.1016/j.vaccine.2017.11.056] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/11/2017] [Accepted: 11/14/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND In this study, we examined the effectiveness of RV1 and RV5 vaccines during an outbreak of G8P[8] rotavirus group A strain (G8P[8]-RVA). These vaccines were originally designed to provide protection against severe diseases caused by common circulating strains, whereas G8P[8]-RVA remains emerging strain and partially heterotypic to the vaccines. It is imperative to investigate vaccine effectiveness (VE) against G8P[8]-RVA because this strain appears to be predominant in recent years, particularly, in post-vaccine era. METHODS RVA infection and genotypes were confirmed by polymerase chain reaction (PCR) followed by sequence-based genotyping. VE was determined during an outbreak of G8P[8]-RVA in Shizuoka Prefecture, Japan, in February-July 2017, retrospectively, by comparing vaccination status of children suffering from acute gastroenteritis (AGE) between 'PCR-positive' and 'PCR-negative' cases using conditional logistic regression adjusted for age. RESULTS Among 80 AGE children, RVA was detected in 58 (73%), of which 53 (66%) was G8P[8]-RVA. The clinical characteristics of G8P[8]-RVA and other RVA strains were identically severe. Notably, the attack rates of G8P[8]-RVA in vaccinated (61.1%) and unvaccinated (65.5%) children were almost similar. Indeed, no substantial effectiveness were found against G8P[8]-RVA (VE, 14% [95% CI: -140% to 70%]) or other RVA strains (VE, 58% [95% CI: -20% to 90%]) for mild infections. However, these vaccines remained strongly effective against moderate (VE, 75% [95% CI: 1% to 40%]) and severe (VE, 92% [95% CI: 60% to 98%]) RVA infections. The disease severity including Vesikari score, duration and frequency of diarrhea, and body temperature were significantly lower in vaccinated children. CONCLUSIONS This study demonstrates the effectiveness of current RV vaccines against moderate and severe, but not against the mild infections during an outbreak caused by unusual G8P[8]-RVA, which was virtually not targeted in the vaccines.
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