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Ghonaim AH, Yi G, Lei M, Xie D, Ma H, Yang Z, Usama U, Wu H, Jiang Y, Li W, He Q. Isolation, characterization and whole-genome analysis of G9 group a rotaviruses in China: Evidence for possible Porcine-Human interspecies transmission. Virology 2024; 597:110129. [PMID: 38908046 DOI: 10.1016/j.virol.2024.110129] [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: 03/18/2024] [Revised: 05/22/2024] [Accepted: 06/02/2024] [Indexed: 06/24/2024]
Abstract
Group A rotaviruses (RVAs) are major causes of severe gastroenteritis in infants and young animals. To enhance our understanding of the relationship between human and animals RVAs, complete genome data are necessary. We screened 92 intestinal and stool samples from diarrheic piglets by RT‒PCR targeting the VP6 gene, revealing a prevalence of 10.9%. RVA was confirmed in two out of 5 calf samples. We successfully isolated two porcine samples using MA104 cell line. The full-length genetic constellation of the two isolates were determined to be G9-P[23]-I5-R1-C1-M1-A8-N1-T7-E1-H1, with close similarity to human Wa-like and porcine strains. Sequence analysis revealed the majority of genes were closely related to porcine and human RVAs. Phylogenetic analysis revealed that these isolates might have their ancestral origin from pigs, although some of their gene segments were related to human strains. This study reveals evidence of reassortment and possible interspecies transmission between pigs and humans in China.
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Affiliation(s)
- Ahmed H Ghonaim
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China; Desert Research Centre, Cairo, Egypt
| | - GuangYuan Yi
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China
| | - Mingkai Lei
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China
| | - Dongqi Xie
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China
| | - Hailong Ma
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Zhengxin Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China
| | - Usama Usama
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China
| | - Hao Wu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China
| | - Yunbo Jiang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China
| | - Wentao Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China; The Animal Disease Diagnostic Centre of Huazhong Agricultural University, Wuhan, 430070, China.
| | - Qigai He
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China; The Animal Disease Diagnostic Centre of Huazhong Agricultural University, Wuhan, 430070, China
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Jalilvand S, Latifi T, Kachooei A, Mirhoseinian M, Hoseini-Fakhr SS, Behnezhad F, Roohvand F, Shoja Z. Circulating rotavirus strains in children with acute gastroenteritis in Iran, 1986 to 2023 and their genetic/antigenic divergence compared to approved vaccines strains (Rotarix, RotaTeq, ROTAVAC, ROTASIIL) before mass vaccination: Clues for vaccination policy makers. Virus Res 2024; 346:199411. [PMID: 38823689 PMCID: PMC11190746 DOI: 10.1016/j.virusres.2024.199411] [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: 03/13/2024] [Revised: 05/18/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
In the present study, first, rotaviruses that caused acute gastroenteritis in children under five years of age during the time before the vaccine was introduced in Iran (1986 to 2023) are reviewed. Subsequently, the antigenic epitopes of the VP7 and VP4/VP8 proteins in circulating rotavirus strains in Iran and that of the vaccine strains were compared and their genetic differences in histo-blood group antigens (HBGAs) and the potential impact on rotavirus infection susceptibility and vaccine efficacy were discussed. Overall data indicate that rotavirus was estimated in about 38.1 % of samples tested. The most common genotypes or combinations were G1 and P[8], or G1P[8]. From 2015 to 2023, there was a decline in the prevalence of G1P[8], with intermittent peaks of genotypes G3P[8] and G9P[8]. The analyses suggested that the monovalent Rotarix vaccine or monovalent vaccines containing the G1P[8] component might be proper in areas with a similar rotavirus genotype pattern and genetic background as the Iranian population where the G1P[8] strain is the most predominant and has the ability to bind to HBGA secretors. While the same concept can be applied to RotaTeq and RotasIIL vaccines, their complex vaccine technology, which involves reassortment, makes them less of a priority. The ROTASIIL vaccine, despite not having the VP4 arm (P[5]) as a suitable protection option, has previously shown the ability to neutralize not only G9-lineage I strains but also other G9-lineages at high titers. Thus, vaccination with the ROTASIIL vaccine may be more effective in Iran compared to RotaTeq. However, considering the rotavirus genotypic pattern, ROTAVAC might not be a good choice for Iran. Overall, the findings of this study provide valuable insights into the prevalence of rotavirus strains and the potential effectiveness of different vaccines in the Iranian and similar populations.
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Affiliation(s)
- Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Tayebeh Latifi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Atefeh Kachooei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahtab Mirhoseinian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Farzane Behnezhad
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farzin Roohvand
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Zabihollah Shoja
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran; Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.
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Uprety T, Soni S, Sreenivasan C, Hause BM, Naveed A, Ni S, Graves AJ, Morrow JK, Meade N, Mellits KH, Adam E, Kennedy MA, Wang D, Li F. Genetic and antigenic characterization of two diarrhoeicdominant rotavirus A genotypes G3P[12] and G14P[12] circulating in the global equine population. J Gen Virol 2024; 105:002016. [PMID: 39163114 PMCID: PMC11335307 DOI: 10.1099/jgv.0.002016] [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: 05/31/2024] [Accepted: 07/30/2024] [Indexed: 08/21/2024] Open
Abstract
Equine rotavirus species A (ERVA) G3P[12] and G14P[12] are two dominant genotypes that cause foal diarrhoea with a significant economic impact on the global equine industry. ERVA can also serve as a source of novel (equine-like) rotavirus species A (RVA) reassortants with zoonotic potential as those identified previously in 2013-2019 when equine G3-like RVA was responsible for worldwide outbreaks of severe gastroenteritis and hospitalizations in children. One hurdle to ERVA research is that the standard cell culture system optimized for human rotavirus replication is not efficient for isolating ERVA. Here, using an engineered cell line defective in antiviral innate immunity, we showed that both equine G3P[12] and G14P[12] strains can be rapidly isolated from diarrhoeic foals. The genome sequence analysis revealed that both G3P[12] and G14P[12] strains share the identical genotypic constellation except for VP7 and VP6 segments in which G3P[12] possessed VP7 of genotype G3 and VP6 of genotype I6 and G14P[12] had the combination of VP7 of genotype G14 and VP6 of genotype I2. Further characterization demonstrated that two ERVA genotypes have a limited cross-neutralization. The lack of an in vitro broad cross-protection between both genotypes supported the increased recent diarrhoea outbreaks due to equine G14P[12] in foals born to dams immunized with the inactivated monovalent equine G3P[12] vaccine. Finally, using the structural modelling approach, we provided the genetic basis of the antigenic divergence between ERVA G3P[12] and G14P[12] strains. The results of this study will provide a framework for further investigation of infection biology, pathogenesis and cross-protection of equine rotaviruses.
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Affiliation(s)
- Tirth Uprety
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Shalini Soni
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Chithra Sreenivasan
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Ben M. Hause
- Department of Veterinary and Biomedical Sciences, Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, South Dakota, 57007, USA
| | - Ahsan Naveed
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Shuisong Ni
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Amy J. Graves
- Equine Diagnostic Solutions, LLC, 1501 Bull Lea Rd, Suite 104, Lexington, Kentucky 40511, USA
| | - Jennifer K. Morrow
- Equine Diagnostic Solutions, LLC, 1501 Bull Lea Rd, Suite 104, Lexington, Kentucky 40511, USA
| | - Nathan Meade
- Division of Microbiology, Brewing, and Biotechnology, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Kenneth H. Mellits
- Division of Microbiology, Brewing, and Biotechnology, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Emma Adam
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Michael A. Kennedy
- Department of Veterinary and Biomedical Sciences, Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, South Dakota, 57007, USA
| | - Dan Wang
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Feng Li
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky 40546, USA
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Kachooei A, Mirhoseinian M, Jalilvand S, Latifi T, Feizi M, Shahosseini Z, Arashkia A, Marashi SM, Shoja Z. Molecular characterization of human astrovirus infection in children under 5 years of age with acute gastroenteritis in Tehran, Iran, 2021-2022: co-infection with rotavirus. Virus Genes 2024; 60:357-369. [PMID: 38744749 DOI: 10.1007/s11262-024-02075-6] [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: 10/31/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024]
Abstract
Human astroviruses (HAstVs) are considered important causative pathogens of acute gastroenteritis (AGE) in children under 5 years of age worldwide, along with group A rotavirus (RVA), norovirus (NoV), and enteric adenovirus (EAdV). The present study was aimed to both detect HAstV and its co-infections and investigate genetic analysis of circulating HAstV and co-infected virus in hospitalized children under 5 years of age with AGE in Iran. Accordingly, a sum of 200 stool specimens were screened by PCR for HAstV during 2021-2022. The HAstV was found in 0.5% of 200 specimens (n = 1) while was co-infected with RVA. The genetic and phylogenetic analysis indicated HAstV1 genotype, which clustered with viruses from lineage 1b, which has not been previously reported in Iran. The detected RVA strain belonged to G1 lineage II/P[8]-lineage III, which has been reported previously in Iran as the most common strain. The further genetic analysis of RVA VP6 and NSP4 demonstrated an atypical genotype pattern G1P[8]-I1-E2, as a mono-reassortant of a Wa-like genogroup, which appeared to be reassorted with the NSP4 gene of E2 genotype of the G2P[4] DS-1 genogroup. Although the clinical outcomes of the AGE-causing viruses co-infection is not yet entirely clear, it seems that future studies will be helpful to merge clinical and epidemiological data of co-infecting viruses for a more accurate medical and clinical relevance in symptomatic children.
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Affiliation(s)
- Atefeh Kachooei
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahtab Mirhoseinian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Tayebeh Latifi
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Mahsa Feizi
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Arash Arashkia
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Sayed Mahdi Marashi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran.
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.
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Barua SR, Das T, Rakib TM, Nath BK, Gupta SD, Sarker S, Chowdhury S, Raidal SR, Das S. Complete genome constellation of a dominant Bovine rotavirus genotype circulating in Bangladesh reveals NSP4 intragenic recombination with human strains. Virology 2024; 598:110195. [PMID: 39089050 DOI: 10.1016/j.virol.2024.110195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/22/2024] [Accepted: 07/28/2024] [Indexed: 08/03/2024]
Abstract
Rotavirus A is a leading cause of non-bacterial gastroenteritis in humans and domesticated animals. Despite the vast diversity of bovine Rotavirus A strains documented in South Asian countries, there are very few whole genomes available for phylogenetic study. A cross-sectional study identified a high prevalence of the G6P[11] genotype of bovine Rotavirus A circulating in the commercial cattle population in Bangladesh. Next-generation sequencing and downstream phylogenetic analysis unveiled all 11 complete gene segments of this strain (BD_ROTA_CVASU), classifying it under the genomic constellation G6P[11]-I2-R2-C2-M2-A13-N2-T6-E2-H3, which belongs to a classical DS-1-like genomic backbone. We found strong evidence of intragenic recombination between human and bovine strains in the Non-structural protein 4 (NSP4) gene, which encodes a multifunctional enterotoxin. Our analyses highlight frequent zoonotic transmissions of rotaviruses in diverse human-animal interfaces, which might have contributed to the evolution and pathogenesis of this dominant genotype circulating in the commercial cattle population in Bangladesh.
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Affiliation(s)
- Shama Ranjan Barua
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University, Chattogram, 4225, Bangladesh; Department of Livestock Services, Ministry of Fisheries and Livestock, Bangladesh
| | - Tridip Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW-2678, Australia; Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW-2678, Australia; Training Hub Promoting Regional Industry and Innovation in Virology and Epidemiology, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW-2678, Australia
| | - Tofazzal Md Rakib
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University, Chattogram, 4225, Bangladesh
| | - Babu Kanti Nath
- Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW-2678, Australia
| | - Suman Das Gupta
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW-2678, Australia; Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW-2678, Australia
| | - Subir Sarker
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD-4814, Australia
| | - Sharmin Chowdhury
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University, Chattogram, 4225, Bangladesh
| | - Shane R Raidal
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW-2678, Australia; Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW-2678, Australia; Training Hub Promoting Regional Industry and Innovation in Virology and Epidemiology, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW-2678, Australia
| | - Shubhagata Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW-2678, Australia; Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW-2678, Australia; Training Hub Promoting Regional Industry and Innovation in Virology and Epidemiology, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW-2678, Australia.
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Munlela B, João ED, Strydom A, Bauhofer AFL, Chissaque A, Chilaúle JJ, Maurício IL, Donato CM, O’Neill HG, de Deus N. Whole-Genome Characterization of Rotavirus G9P[6] and G9P[4] Strains That Emerged after Rotavirus Vaccine Introduction in Mozambique. Viruses 2024; 16:1140. [PMID: 39066302 PMCID: PMC11281483 DOI: 10.3390/v16071140] [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: 05/15/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Mozambique introduced the Rotarix® vaccine into the National Immunization Program in September 2015. Following vaccine introduction, rotavirus A (RVA) genotypes, G9P[4] and G9P[6], were detected for the first time since rotavirus surveillance programs were implemented in the country. To understand the emergence of these strains, the whole genomes of 47 ELISA RVA positive strains detected between 2015 and 2018 were characterized using an Illumina MiSeq-based sequencing pipeline. Of the 29 G9 strains characterized, 14 exhibited a typical Wa-like genome constellation and 15 a DS-1-like genome constellation. Mostly, the G9P[4] and G9P[6] strains clustered consistently for most of the genome segments, except the G- and P-genotypes. For the G9 genotype, the strains formed three different conserved clades, separated by the P type (P[4], P[6] and P[8]), suggesting different origins for this genotype. Analysis of the VP6-encoding gene revealed that seven G9P[6] strains clustered close to antelope and bovine strains. A rare E6 NSP4 genotype was detected for strain RVA/Human-wt/MOZ/HCN1595/2017/G9P[4] and a genetically distinct lineage IV or OP354-like P[8] was identified for RVA/Human-wt/MOZ/HGJM0644/2015/G9P[8] strain. These results highlight the need for genomic surveillance of RVA strains detected in Mozambique and the importance of following a One Health approach to identify and characterize potential zoonotic strains causing acute gastroenteritis in Mozambican children.
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Affiliation(s)
- Benilde Munlela
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Eva D. João
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
| | - Amy Strydom
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Avenue, Bloemfontein 9301, South Africa; (A.S.); (H.G.O.)
| | - Adilson Fernando Loforte Bauhofer
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Assucênio Chissaque
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Jorfélia J. Chilaúle
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
| | - Isabel L. Maurício
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal;
| | - Celeste M. Donato
- The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3000, Australia;
| | - Hester G. O’Neill
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Avenue, Bloemfontein 9301, South Africa; (A.S.); (H.G.O.)
| | - Nilsa de Deus
- Instituto Nacional de Saúde (INS), Parcela 3943, Vila de Marracuene, Maputo 0205-02, Mozambique; (E.D.J.); (A.F.L.B.); (A.C.); (J.J.C.); (N.d.D.)
- Departamento de Ciências Biológicas, Universidade Eduardo Mondlane, Julius Nyerere Avenue, Maputo 3453, Mozambique
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7
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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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8
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Omatola CA, Olaniran AO. Molecular Characterization and Phylogenetic analyses of Rotaviruses Circulating in Municipal Sewage and Sewage-Polluted River Waters in Durban Area, South Africa. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09598-z. [PMID: 38914870 DOI: 10.1007/s12560-024-09598-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/17/2024] [Indexed: 06/26/2024]
Abstract
Globally, rotavirus continues to be the leading etiology of severe pediatric gastroenteritis, and transmission of the disease via environmental reservoirs has become an emerging concern in developing countries. From August to October 2021, a total of 69 samples comprising 48 of raw and treated sewage, and 21 surface waters, were collected from four Durban wastewater treatment plants (DWWTP), and effluent receiving rivers, respectively. Rotaviruses recovered and identified from the samples were subjected to sequencing, genotyping, and phylogenetic analysis. Of the 65 (94.2%) rotavirus-positive samples, 33.3% were from raw sewage, 16% from activated sludge, 15.9% from final effluents, and 29.0% were from the receiving river samples. A total of 49 G and 41 P genotypes were detected in sewage while 15 G and 22 P genotypes were detected in river samples. G1 genotype predominated in sewage (24.5%) followed by G3 (22.4%), G2 (14.3%), G4 (12.2%), G12 (10.2%), G9 (8.2%), and G8 (6.1%). Similarly, G1 predominated in river water samples (33.3%) and was followed by G2, G4 (20.0% each), G3, and G12 (13.3% each). Rotavirus VP4 genotypes P[4], P[6], and P[8] accounted for 36.6%, 29.3%, and 9.8%, respectively, in sewage. Correspondingly, 45.5%, 31.8%, and 13.6% were detected in river samples. The G and P genotypes not identified by the methods used were 2.1% versus 24.3% and 0.1% versus 9.1% for sewage and river water samples, respectively. Sequence comparison studies indicated a high level of nucleotide identity in the G1, G2, G3, G4, G8 VP7, and P[4], P[6], and P[8] VP4 gene sequences between strains from the environment and those from patients in the region. This is the first environmental-based study on the G and P genotypes diversity of rotavirus in municipal wastewater and their receiving rivers in this geographical region. The high similarity between environmental and clinical rotavirus strains suggests both local circulation of the virus and potential exposure risks. In addition, it highlights the usefulness of sewage surveillance as an additional tool for an epidemiological investigation, especially in populations that include individuals with subclinical or asymptomatic infections that are precluded in case-based studies.
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Affiliation(s)
- Cornelius Arome Omatola
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, Republic of South Africa
| | - Ademola Olufolahan Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, Republic of South Africa.
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9
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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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10
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Carter MH, Gribble J, Diller JR, Denison MR, Mirza SA, Chappell JD, Halasa NB, Ogden KM. Human Rotaviruses of Multiple Genotypes Acquire Conserved VP4 Mutations during Serial Passage. Viruses 2024; 16:978. [PMID: 38932271 PMCID: PMC11209247 DOI: 10.3390/v16060978] [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: 05/14/2024] [Revised: 06/06/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Human rotaviruses exhibit limited tropism and replicate poorly in most cell lines. Attachment protein VP4 is a key rotavirus tropism determinant. Previous studies in which human rotaviruses were adapted to cultured cells identified mutations in VP4. However, most such studies were conducted using only a single human rotavirus genotype. In the current study, we serially passaged 50 human rotavirus clinical specimens representing five of the genotypes most frequently associated with severe human disease, each in triplicate, three to five times in primary monkey kidney cells then ten times in the MA104 monkey kidney cell line. From 13 of the 50 specimens, we obtained 25 rotavirus antigen-positive lineages representing all five genotypes, which tended to replicate more efficiently in MA104 cells at late versus early passage. We used Illumina next-generation sequencing and analysis to identify variants that arose during passage. In VP4, variants encoded 28 mutations that were conserved for all P[8] rotaviruses and 12 mutations that were conserved for all five genotypes. These findings suggest there may be a conserved mechanism of human rotavirus adaptation to MA104 cells. In the future, such a conserved adaptation mechanism could be exploited to study human rotavirus biology or efficiently manufacture vaccines.
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Affiliation(s)
- Maximilian H. Carter
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jennifer Gribble
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Julia R. Diller
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mark R. Denison
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sara A. Mirza
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - James D. Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Natasha B. Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kristen M. Ogden
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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11
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Miura T, Kadoya SS, Miura Y, Takino H, Akiba M, Sano D, Masuda T. Pepper mild mottle virus intended for use as a process indicator for drinking water treatment: Present forms and quantitative relations to norovirus and rotavirus in surface water. WATER RESEARCH 2024; 257:121713. [PMID: 38733963 DOI: 10.1016/j.watres.2024.121713] [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: 11/06/2023] [Revised: 03/19/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
Pepper mild mottle virus (PMMoV) has been proposed as a potential indicator of human enteric viruses in environmental water and for viral removal during drinking water treatment. To investigate the occurrence and present forms of PMMoV and quantitative relations to norovirus GII and rotavirus A (RVA) in surface waters, 147 source water samples were collected from 21 drinking water treatment plants (DWTPs) in Japan between January 2018 and January 2021, and the concentrations of viruses in suspended and dissolved fractions were measured using real-time RT-PCR. PMMoV was detected in 81-100 % of samples in each sample month and observed concentrations ranged from 3.0 to 7.0 log10 copies/L. The concentrations of PMMoV were higher in dissolved fraction compared to suspended fractions, while different partitioning was observed for NoV GII depending on seasons. The concentrations of PMMoV were basically higher than those of norovirus GII (1.9-5.3 log10 copies/L) and RVA (1.9-6.6 log10 copies/L), while in 18 samples, RVA presented higher concentrations than PMMoV. Partial regions of VP7, VP4, and VP6 of the RVA in the 18 samples were amplified using nested PCR, and the genotypes were determined using an amplicon-based next-generation sequencing approach. We found that these source water samples included not only human RVA but also various animal RVA and high genetic diversity due to the existence of animal RVA was associated with a higher RVA concentration than PMMoV. Our findings suggest that PMMoV can be used as an indicator of norovirus GII and human RVA in drinking water sources and that the indicator performance should be evaluated by comparing to zoonotic viruses as well as human viruses.
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Affiliation(s)
- Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan.
| | - Syun-Suke Kadoya
- Department of Civil and Environmental Engineering, Tohoku University, Japan; Department of Urban Engineering, The University of Tokyo, Japan
| | - Yohei Miura
- Department of Civil and Environmental Engineering, Tohoku University, Japan
| | - Hiroyuki Takino
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Michihiro Akiba
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Japan
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12
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Zhou X, Hou X, Xiao G, Liu B, Jia H, Wei J, Mi X, Guo Q, Wei Y, Zhai SL. Emergence of a Novel G4P[6] Porcine Rotavirus with Unique Sequence Duplication in NSP5 Gene in China. Animals (Basel) 2024; 14:1790. [PMID: 38929409 PMCID: PMC11200575 DOI: 10.3390/ani14121790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Rotavirus is a major causative agent of diarrhoea in children, infants, and young animals around the world. The associated zoonotic risk necessitates the serious consideration of the complete genetic information of rotavirus. A segmented genome makes rotavirus prone to rearrangement and the formation of a new viral strain. Monitoring the molecular epidemiology of rotavirus is essential for its prevention and control. The quantitative RT-PCR targeting the NSP5 gene was used to detect rotavirus group A (RVA) in pig faecal samples, and two pairs of universal primers and protocols were used for amplifying the G and P genotype. The genotyping and phylogenetic analysis of 11 genes were performed by RT-PCR and a basic bioinformatics method. A unique G4P[6] rotavirus strain, designated S2CF (RVA/Pig-tc/CHN/S2CF/2023/G4P[6]), was identified in one faecal sample from a piglet with severe diarrhoea in Guangdong, China. Whole genome sequencing and analysis suggested that the 11 segments of the S2CF strain showed a unique Wa-like genotype constellation and a typical porcine RVA genomic configuration of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Notably, 4 of the 11 gene segments (VP4, VP6, VP2, and NSP5) clustered consistently with human-like RVAs, suggesting independent human-to-porcine interspecies transmission. Moreover, a unique 344-nt duplicated sequence was identified for the first time in the untranslated region of NSP5. This study further reveals the genetic diversity and potential inter-species transmission of porcine rotavirus.
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Affiliation(s)
- Xia Zhou
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
| | - Xueyan Hou
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Guifa Xiao
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
| | - Bo Liu
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
| | - Handuo Jia
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
| | - Jie Wei
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi 830013, China; (J.W.); (X.M.)
| | - Xiaoyun Mi
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi 830013, China; (J.W.); (X.M.)
| | - Qingyong Guo
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Yurong Wei
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi 830013, China; (J.W.); (X.M.)
| | - Shao-Lun Zhai
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
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13
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Fukuda Y, Kondo K, Nakata S, Morita Y, Adachi N, Kogawa K, Ukae S, Kudou Y, Adachi S, Yamamoto M, Fukumura S, Tsugawa T. Whole-genome analysis of human group A rotaviruses in 1980s Japan and evolutionary assessment of global Wa-like strains across half a century. J Gen Virol 2024; 105. [PMID: 38836747 DOI: 10.1099/jgv.0.001998] [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] [Indexed: 06/06/2024] Open
Abstract
Historically, the Wa-like strains of human group A rotavirus (RVA) have been major causes of gastroenteritis. However, since the 2010s, the circulation of non-Wa-like strains has been increasingly reported, indicating a shift in the molecular epidemiology of RVA. Although understanding RVA evolution requires the analysis of both current and historical strains, comprehensive pre-1980's sequencing data are scarce globally. We determined the whole-genome sequences of representative strains from six RVA gastroenteritis outbreaks observed at an infant home in Sapporo, Japan, between 1981 and 1989. These outbreaks were mainly caused by G1 or G3 Wa-like strains, resembling strains from the United States in the 1970s-1980s and from Malawi in the 1990s. Phylogenetic analysis of these infant home strains, together with Wa-like strains collected worldwide from the 1970s to 2020, revealed a notable trend: pre-2010 strains diverged into multiple lineages in many genomic segments, whereas post-2010 strains tended to converge into a single lineage. However, Bayesian skyline plot indicated near-constant effective population sizes from the 1970s to 2020, and selection pressure analysis identified positive selection only at amino acid 75 of NSP2. These results suggest that evidence supporting the influence of rotavirus vaccines, introduced globally since 2006, on Wa-like RVA molecular evolution is lacking at present, and phylogenetic analysis may simply reflect natural fluctuations in RVA molecular evolution. Evaluating the long-term impact of RV vaccines on the molecular evolution of RVA requires sustained surveillance.
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Affiliation(s)
- Yuya Fukuda
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shuji Nakata
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yasuyuki Morita
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noriaki Adachi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Keiko Kogawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Susumu Ukae
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yoshimasa Kudou
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shuhei Adachi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masaki Yamamoto
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shinobu Fukumura
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
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14
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Kawagishi T, Sánchez-Tacuba L, Feng N, Greenberg HB, Ding S. Reverse Genetics of Murine Rotavirus: A Comparative Analysis of the Wild-Type and Cell-Culture-Adapted Murine Rotavirus VP4 in Replication and Virulence in Neonatal Mice. Viruses 2024; 16:767. [PMID: 38793648 PMCID: PMC11125933 DOI: 10.3390/v16050767] [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: 04/09/2024] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Small-animal models and reverse genetics systems are powerful tools for investigating the molecular mechanisms underlying viral replication, virulence, and interaction with the host immune response in vivo. Rotavirus (RV) causes acute gastroenteritis in many young animals and infants worldwide. Murine RV replicates efficiently in the intestines of inoculated suckling pups, causing diarrhea, and spreads efficiently to uninoculated littermates. Because RVs derived from human and other non-mouse animal species do not replicate efficiently in mice, murine RVs are uniquely useful in probing the viral and host determinants of efficient replication and pathogenesis in a species-matched mouse model. Previously, we established an optimized reverse genetics protocol for RV and successfully generated a murine-like RV rD6/2-2g strain that replicates well in both cultured cell lines and in the intestines of inoculated pups. However, rD6/2-2g possesses three out of eleven gene segments derived from simian RV strains, and these three heterologous segments may attenuate viral pathogenicity in vivo. Here, we rescued the first recombinant RV with all 11 gene segments of murine RV origin. Using this virus as a genetic background, we generated a panel of recombinant murine RVs with either N-terminal VP8* or C-terminal VP5* regions chimerized between a cell-culture-adapted murine ETD strain and a non-tissue-culture-adapted murine EW strain and compared the diarrhea rate and fecal RV shedding in pups. The recombinant viruses with VP5* domains derived from the murine EW strain showed slightly more fecal shedding than those with VP5* domains from the ETD strain. The newly characterized full-genome murine RV will be a useful tool for dissecting virus-host interactions and for studying the mechanism of pathogenesis in neonatal mice.
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Affiliation(s)
- Takahiro Kawagishi
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- VA Palo Alto Health Care System, Department of Veterans Affairs, Palo Alto, CA 94304, USA
| | - Liliana Sánchez-Tacuba
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- VA Palo Alto Health Care System, Department of Veterans Affairs, Palo Alto, CA 94304, USA
| | - Ningguo Feng
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- VA Palo Alto Health Care System, Department of Veterans Affairs, Palo Alto, CA 94304, USA
| | - Harry B. Greenberg
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- VA Palo Alto Health Care System, Department of Veterans Affairs, Palo Alto, CA 94304, USA
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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15
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França Y, Medeiros RS, Viana E, de Azevedo LS, Guiducci R, da Costa AC, Luchs A. Genetic diversity and evolution of G12P[6] DS-1-like and G12P[9] AU-1-like Rotavirus strains in Brazil. Funct Integr Genomics 2024; 24:92. [PMID: 38733534 DOI: 10.1007/s10142-024-01360-9] [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: 02/29/2024] [Revised: 03/31/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
In the early 2000s, the global emergence of rotavirus (RVA) G12P[8] genotype was noted, while G12P[6] and G12P[9] combinations remained rare in humans. This study aimed to characterize and phylogenetically analyze three Brazilian G12P[9] and four G12P[6] RVA strains from 2011 to 2020, through RT-PCR and sequencing, in order to enhance our understanding of the genetic relationship between human and animal-origin RVA strains. G12P[6] strains displayed a DS-1-like backbone, showing a distinct genetic clustering. G12P[6] IAL-R52/2020, IAL-R95/2020 and IAL-R465/2019 strains clustered with 2019 Northeastern G12P[6] Brazilian strains and a 2018 Benin strain, whereas IAL-R86/2011 strain grouped with 2010 Northern G12P[6] Brazilian strains and G2P[4] strains from the United States and Belgium. These findings suggest an African genetic ancestry and reassortments with co-circulating American strains sharing the same DS-1-like constellation. No recent zoonotic reassortment was observed, and the DS-1-like constellation detected in Brazilian G12P[6] strains does not seem to be genetically linked to globally reported intergenogroup G1/G3/G9/G8P[8] DS-1-like human strains. G12P[9] strains exhibited an AU-1-like backbone with two different genotype-lineage constellations: IAL-R566/2011 and IAL-R1151/2012 belonged to a VP3/M3.V Lineage, and IAL-R870/2013 to a VP3/M3.II Lineage, suggesting two co-circulating strains in Brazil. This genetic diversity is not observed elsewhere, and the VP3/M3.II Lineage in G12P[9] strains seems to be exclusive to Brazil, indicating its evolution within the country. All three G12P[9] AU-1-like strains were closely relate to G12P[9] strains from Paraguay (2006-2007) and Brazil (2010). Phylogenetic analysis also highlighted that all South American G12P[9] AU-1-like strains had a common origin and supports the hypothesis of their importation from Asia, with no recent introduction from globally circulating G12P[9] strains or reassortments with local G12 strains P[8] or P[6]. Notably, certain genes in the Brazilian G12P[9] AU-1-like strains share ancestry with feline/canine RVAs (VP3/M3.II, NSP4/E3.IV and NSP2/N3.II), whereas NSP1/A3.VI likely originated from artiodactyls, suggesting a history of zoonotic transmission with human strains. This genomic data adds understanding to the molecular epidemiology of G12P[6] and G12P[9] RVA strains in Brazil, offering insights into their genetic diversity and evolution.
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Affiliation(s)
- Yasmin França
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Ellen Viana
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Raquel Guiducci
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Antonio Charlys da Costa
- Medical Parasitology Laboratory (LIM/46), São Paulo Tropical Medicine Institute, University of Sao Paulo, Sao Paulo, Brazil
| | - Adriana Luchs
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil.
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Wang J, Zhou J, Zhu X, Bian X, Han N, Fan B, Gu L, Cheng X, Li S, Tao R, Li J, Zhang X, Li B. Isolation and characterization of a G9P[23] porcine rotavirus strain AHFY2022 in China. Microb Pathog 2024; 190:106612. [PMID: 38467166 DOI: 10.1016/j.micpath.2024.106612] [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: 01/06/2024] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/13/2024]
Abstract
Rotavirus group A (RVA) is a main pathogen causing diarrheal diseases in humans and animals. Various genotypes are prevalent in the Chinese pig herd. The genetic diversity of RVA lead to distinctly characteristics. In the present study, a porcine RVA strain, named AHFY2022, was successfully isolated from the small intestine tissue of piglets with severe diarrhea. The AHFY2022 strain was identified by cytopathic effects (CPE) observation, indirect immunofluorescence assay (IFA), electron microscopy (EM), high-throughput sequencing, and pathogenesis to piglets. The genomic investigation using NGS data revealed that AHFY2022 exhibited the genotypes G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1, using the online platform the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) (https://www.bv-brc.org/). Moreover, experimental inoculation in 5-day-old and 27-day-old piglets demonstrated that AHFY2022 caused severe diarrhea, fecal shedding, small intestinal villi damage, and colonization in all challenged piglets. Taken together, our results detailed the virological features of the porcine rotavirus G9P[23] from China, including the whole-genome sequences, genotypes, growth kinetics in MA104 cells and the pathogenicity in suckling piglets.
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Affiliation(s)
- Jianxin Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China; College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071000, China
| | - Jinzhu Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, 225300, China
| | - Xuejiao Zhu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, 225300, China
| | - Xianyu Bian
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China
| | - Nan Han
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, 225300, China
| | - Laqiang Gu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China
| | - Xi Cheng
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China
| | - Sufen Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China
| | - Ran Tao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, 225300, China
| | - Jizong Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, 225300, China
| | - Xuehan Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China.
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China; College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071000, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, 225300, China.
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Valusenko-Mehrkens R, Schilling-Loeffler K, Johne R, Falkenhagen A. VP4 Mutation Boosts Replication of Recombinant Human/Simian Rotavirus in Cell Culture. Viruses 2024; 16:565. [PMID: 38675907 PMCID: PMC11054354 DOI: 10.3390/v16040565] [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: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Rotavirus A (RVA) is the leading cause of diarrhea requiring hospitalization in children and causes over 100,000 annual deaths in Sub-Saharan Africa. In order to generate next-generation vaccines against African RVA genotypes, a reverse genetics system based on a simian rotavirus strain was utilized here to exchange the antigenic capsid proteins VP4, VP7 and VP6 with those of African human rotavirus field strains. One VP4/VP7/VP6 (genotypes G9-P[6]-I2) triple-reassortant was successfully rescued, but it replicated poorly in the first cell culture passages. However, the viral titer was enhanced upon further passaging. Whole genome sequencing of the passaged virus revealed a single point mutation (A797G), resulting in an amino acid exchange (E263G) in VP4. After introducing this mutation into the VP4-encoding plasmid, a VP4 mono-reassortant as well as the VP4/VP7/VP6 triple-reassortant replicated to high titers already in the first cell culture passage. However, the introduction of the same mutation into the VP4 of other human RVA strains did not improve the rescue of those reassortants, indicating strain specificity. The results show that specific point mutations in VP4 can substantially improve the rescue and replication of recombinant RVA reassortants in cell culture, which may be useful for the development of novel vaccine strains.
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Affiliation(s)
| | | | | | - Alexander Falkenhagen
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (R.V.-M.); (K.S.-L.); (R.J.)
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Gutierrez MB, Arantes I, Bello G, Berto LH, Dutra LH, Kato RB, Fumian TM. Emergence and dissemination of equine-like G3P[8] rotavirus A in Brazil between 2015 and 2021. Microbiol Spectr 2024; 12:e0370923. [PMID: 38451227 PMCID: PMC10986506 DOI: 10.1128/spectrum.03709-23] [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: 10/19/2023] [Accepted: 02/22/2024] [Indexed: 03/08/2024] Open
Abstract
Rotavirus A (RVA) is a major cause of acute gastroenteritis globally that is classically genotyped by its two immunodominant outer capsid proteins, VP7 (G-) and VP4 (P-). Recent evidence suggests that the reassortant equine-like G3P[8] strain played a substantial role in RVA transmission in Brazil since 2015. To understand its global emergence and dissemination in Brazilian territory, stool samples collected from 11 Brazilian states (n = 919) were genotyped by RT-qPCR and proceeded to sequence the VP7 gene (n = 102, 79 being newly generated) of the G3P[8] samples with pronounced viral loads. Our phylogenetic genotyping showed that G3P[8] became the dominant strain in Brazil between 2017 and 2020, with equine-like variants representing 75%-100% of VP7 samples in this period. A Bayesian discrete phylogeographic analysis strongly suggests that the equine-like G3P[8] strain originated in Asia during the early 2010s and subsequently spread to Europe, the Caribbean, and South America. Multiple introductions were detected in Brazil between 2014 and 2017, resulting in five national clusters. The reconstruction of the effective population size of the largest Brazilian cluster showed an expansion until 2017, followed by a plateau phase until 2019 and subsequent contraction. Our study also supports that most mutations fixed during equine-like G3P[8] evolution were synonymous, suggesting that adaptive evolution was not an important driving force during viral dissemination in humans, potentially increasing its susceptibility to acquired immunity. This research emphasizes the need for comprehensive rotavirus genomic surveillance that allows close monitoring of its ever-shifting composition and informs more effective public health policies.IMPORTANCEOur original article demonstrated the origin and spread in a short time of equine-like G3P[8] in Brazil and the world. Due to its segmented genome, it allows numerous mechanisms including genetic drift and reassortment contribute substantially to the genetic diversity of rotavirus. Although the effectiveness and increasing implementation of vaccination have not been questioned, a matter of concern is its impact on the emergence of escape mutants or even the spread of unusual strains of zoonotic transmission that could drive epidemic patterns worldwide. This research emphasizes the need for comprehensive rotavirus genomic surveillance, which could facilitate the formulation of public policies aimed at preventing and mitigating its transmission.
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Affiliation(s)
| | - Ighor Arantes
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Lúcia Helena Berto
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Leonardo Hermes Dutra
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Rodrigo Bentes Kato
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Tulio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
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Fukuda Y, Kusuhara H, Takai-Todaka R, Haga K, Katayama K, Tsugawa T. Human transmission and outbreaks of feline-like G6 rotavirus revealed with whole-genome analysis of G6P[9] feline rotavirus. J Med Virol 2024; 96:e29565. [PMID: 38558056 DOI: 10.1002/jmv.29565] [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: 12/18/2023] [Revised: 03/01/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
Group A rotaviruses (RVAs) are generally highly species-specific; however, some strains infect across species. Feline RVAs sporadically infect humans, causing gastroenteritis. In 2012 and 2013, rectal swab samples were collected from 61 asymptomatic shelter cats at a public health center in Mie Prefecture, Japan, to investigate the presence of RVA and any association with human infections. The analysis identified G6P[9] strains in three cats and G3P[9] strains in two cats, although no feline RVA sequence data were available for the former. A whole-genome analysis of these G6P[9] strains identified the genotype constellation G6-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3. The nucleotide identity among these G6P[9] strains exceeded 99.5% across all 11 gene segments, indicating the circulation of this G6P[9] strain among cats. Notably, strain RVA/Human-wt/JPN/KF17/2010/G6P[9], previously detected in a 3-year-old child with gastroenteritis, shares high nucleotide identity (>98%) with Mie20120017f, the representative G6P[9] strain in this study, across all 11 gene segments, confirming feline RVA infection and symptomatic presentation in this child. The VP7 gene of strain Mie20120017f also shares high nucleotide identity with other sporadically reported G6 RVA strains in humans. This suggests that feline-origin G6 strains as the probable source of these sporadic G6 RVA strains causing gastroenteritis in humans globally. Moreover, a feline-like human G6P[8] strain circulating in Brazil in 2022 was identified, emphasizing the importance of ongoing surveillance to monitor potential global human outbreaks of RVA.
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Affiliation(s)
- Yuya Fukuda
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Hajime Kusuhara
- Mie Prefecture Health and Environment Research Institute, Mie, Japan
| | - Reiko Takai-Todaka
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kei Haga
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
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Snyder AJ, Agbemabiese CA, Patton JT. Production of OSU G5P[7] Porcine Rotavirus Expressing a Fluorescent Reporter via Reverse Genetics. Viruses 2024; 16:411. [PMID: 38543776 PMCID: PMC10974435 DOI: 10.3390/v16030411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 05/23/2024] Open
Abstract
Rotaviruses are a significant cause of severe, potentially life-threatening gastroenteritis in infants and the young of many economically important animals. Although vaccines against porcine rotavirus exist, both live oral and inactivated, their effectiveness in preventing gastroenteritis is less than ideal. Thus, there is a need for the development of new generations of porcine rotavirus vaccines. The Ohio State University (OSU) rotavirus strain represents a Rotavirus A species with a G5P[7] genotype, the genotype most frequently associated with rotavirus disease in piglets. Using complete genome sequences that were determined via Nanopore sequencing, we developed a robust reverse genetics system enabling the recovery of recombinant (r)OSU rotavirus. Although rOSU grew to high titers (~107 plaque-forming units/mL), its growth kinetics were modestly decreased in comparison to the laboratory-adapted OSU virus. The reverse genetics system was used to generate the rOSU rotavirus, which served as an expression vector for a foreign protein. Specifically, by engineering a fused NSP3-2A-UnaG open reading frame into the segment 7 RNA, we produced a genetically stable rOSU virus that expressed the fluorescent UnaG protein as a functional separate product. Together, these findings raise the possibility of producing improved live oral porcine rotavirus vaccines through reverse-genetics-based modification or combination porcine rotavirus vaccines that can express neutralizing antigens for other porcine enteric diseases.
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Affiliation(s)
- Anthony J. Snyder
- Department of Biology, Indiana University, 212 S. Hawthorne Drive, Simon Hall 011, Bloomington, IN 47405, USA; (A.J.S.); (C.A.A.)
| | - Chantal A. Agbemabiese
- Department of Biology, Indiana University, 212 S. Hawthorne Drive, Simon Hall 011, Bloomington, IN 47405, USA; (A.J.S.); (C.A.A.)
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra 00233, Ghana
| | - John T. Patton
- Department of Biology, Indiana University, 212 S. Hawthorne Drive, Simon Hall 011, Bloomington, IN 47405, USA; (A.J.S.); (C.A.A.)
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Shizawa S, Fukuda F, Kikkawa Y, Oi T, Takemae H, Masuda T, Ishida H, Murakami H, Sakaguchi S, Mizutani T, Nagai M, Oba M. Genomic diversity of group A rotaviruses from wild boars and domestic pigs in Japan: wide prevalence of NSP5 carrying the H2 genotype. Arch Virol 2024; 169:63. [PMID: 38451342 DOI: 10.1007/s00705-023-05954-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/24/2023] [Indexed: 03/08/2024]
Abstract
Group A rotavirus (RVA) sequences were detected in 10.8% (23/212) and 20.7% (87/421) of fecal samples collected in 2017-2022 from wild boars and domestic pigs, using next-generation sequencing. Complete genome sequence analysis of one wild boar and 13 domestic pig RVAs revealed that six of them carried the rare H2 NSP5 genotype. Out of the 39 samples for which the NSP5 genotype could be determined, 23 (59.0%) were of genotype H2. H2 porcine RVAs consist exclusively of Japanese porcine RVAs and exhibit sequence diversity in each segment, suggesting that H2 porcine RVAs may have evolved through reassortment within the Japanese pig population.
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Affiliation(s)
- Shigeki Shizawa
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
| | - Fujiko Fukuda
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa, 920-3101, Japan
| | | | - Toru Oi
- Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
| | - Hitoshi Takemae
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Tsuneyuki Masuda
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, 794-0085, Japan
| | - Hiroho Ishida
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
| | - Hironobu Murakami
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Tetsuya Mizutani
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Makoto Nagai
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Mami Oba
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan.
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
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De Grazia S, Filizzolo C, Bonura F, Pizzo M, Di Bernardo F, Collura A, Pellegrini F, Martella V, Giammanco GM. Identification of a novel intra-genotype reassortant G1P[8] rotavirus in Italy, 2021. Int J Infect Dis 2024; 140:113-118. [PMID: 38307378 DOI: 10.1016/j.ijid.2024.01.020] [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: 10/16/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/04/2024] Open
Abstract
OBJECTIVES Rotaviruses G1P[8] are epidemiologically relevant and are targeted by vaccines. The introduction of vaccines has altered rotavirus epidemiology. Hospital-based surveillance conducted in Sicily, Italy, showed a progressive decline in rotavirus prevalence since 2014, along with an increasing vaccine coverage (63.8% in 2020), and a marked decrease in circulation of G1P[8] strains. Surprisingly in 2021, G1P[8] viruses accounted for 90.5% (19/21) of rotavirus infections. This study aimed to understand if the increased activity of G1P[8]'s was related to virus-related peculiarities. DESIGN In 2021, 266 patients <15 years of age were hospitalized with acute gastroenteritis (AGE) and included in rotavirus surveillance. Viral proteins (VP7 and VP4) genotyping and sequence data were generated from all rotavirus-positive samples. The genetic makeup of G1P[8] rotaviruses was investigated by full-genome sequencing. RESULTS Peculiar G1P[8] rotaviruses, with VP7 and VP4 belonging to novel sub-lineages, circulated in 2021, accounting for 76.2% (16/21) of all rotavirus infections. On full-genome analysis, the novel G1P[8] variant displayed an intra-genotype (Wa-like) reassortant constellation, involving G12 and G1 strains, into a unique arrangement never observed before. The novel G1P[8] variant showed peculiar amino acid substitutions in 8-1 and 8-3 epitopes of the VP4 with respect to the Rotarix strain. CONCLUSIONS Prompt identification of virus variants circulating in the human population is pivotal to understanding epidemiological trends and assessing vaccine efficacy.
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Affiliation(s)
- Simona De Grazia
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", A.O.U.P "P. Giaccone", Università degli Studi di Palermo, Italy.
| | - Chiara Filizzolo
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", A.O.U.P "P. Giaccone", Università degli Studi di Palermo, Italy
| | - Floriana Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", A.O.U.P "P. Giaccone", Università degli Studi di Palermo, Italy
| | - Mariangela Pizzo
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", A.O.U.P "P. Giaccone", Università degli Studi di Palermo, Italy
| | - Francesca Di Bernardo
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e Di Cristina, ARNAS, Palermo, Italy
| | - Antonina Collura
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e Di Cristina, ARNAS, Palermo, Italy
| | | | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università di Bari, Italy
| | - Giovanni M Giammanco
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", A.O.U.P "P. Giaccone", Università degli Studi di Palermo, Italy
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23
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Hensley C, Roier S, Zhou P, Schnur S, Nyblade C, Parreno V, Frazier A, Frazier M, Kiley K, O’Brien S, Liang Y, Mayer BT, Wu R, Mahoney C, McNeal MM, Petsch B, Rauch S, Yuan L. mRNA-Based Vaccines Are Highly Immunogenic and Confer Protection in the Gnotobiotic Pig Model of Human Rotavirus Diarrhea. Vaccines (Basel) 2024; 12:260. [PMID: 38543894 PMCID: PMC10974625 DOI: 10.3390/vaccines12030260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 04/01/2024] Open
Abstract
Human rotavirus (HRV) is still a leading cause of severe dehydrating gastroenteritis globally, particularly in infants and children. Previously, we demonstrated the immunogenicity of mRNA-based HRV vaccine candidates expressing the viral spike protein VP8* in rodent models. In the present study, we assessed the immunogenicity and protective efficacy of two mRNA-based HRV trivalent vaccine candidates, encoding VP8* of the genotypes P[8], P[6], or P[4], in the gnotobiotic (Gn) pig model of Wa (G1P[8]) HRV infection and diarrhea. Vaccines either encoded VP8* alone fused to the universal T-cell epitope P2 (P2-VP8*) or expressed P2-VP8* as a fusion protein with lumazine synthase (LS-P2-VP8*) to allow the formation and secretion of protein particles that present VP8* on their surface. Gn pigs were randomly assigned into groups and immunized three times with either P2-VP8* (30 µg) or LS-P2-VP8* (30 µg or 12 µg). A trivalent alum-adjuvanted P2-VP8* protein vaccine or an LNP-formulated irrelevant mRNA vaccine served as the positive and negative control, respectively. Upon challenge with virulent Wa HRV, a significantly shortened duration and decreased severity of diarrhea and significant protection from virus shedding was induced by both mRNA vaccine candidates compared to the negative control. Both LS-P2-VP8* doses induced significantly higher VP8*-specific IgG antibody titers in the serum after immunizations than the negative as well as the protein control. The P[8] VP8*-specific IgG antibody-secreting cells in the ileum, spleen, and blood seven days post-challenge, as well as VP8*-specific IFN-γ-producing T-cell numbers increased in all three mRNA-vaccinated pig groups compared to the negative control. Overall, there was a clear tendency towards improved responses in LS-P2-VP8* compared to the P2-VP8*mRNA vaccine. The demonstrated strong humoral immune responses, priming for effector T cells, and the significant reduction of viral shedding and duration of diarrhea in Gn pigs provide a promising proof of concept and may provide guidance for the further development of mRNA-based rotavirus vaccines.
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Affiliation(s)
- Casey Hensley
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; (C.H.); (P.Z.); (S.S.); (C.N.); (V.P.); (A.F.); (M.F.); (K.K.); (S.O.); (Y.L.)
| | - Sandro Roier
- CureVac SE, 72076 Tübingen, Germany; (S.R.); (B.P.); (S.R.)
| | - Peng Zhou
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; (C.H.); (P.Z.); (S.S.); (C.N.); (V.P.); (A.F.); (M.F.); (K.K.); (S.O.); (Y.L.)
| | - Sofia Schnur
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; (C.H.); (P.Z.); (S.S.); (C.N.); (V.P.); (A.F.); (M.F.); (K.K.); (S.O.); (Y.L.)
| | - Charlotte Nyblade
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; (C.H.); (P.Z.); (S.S.); (C.N.); (V.P.); (A.F.); (M.F.); (K.K.); (S.O.); (Y.L.)
| | - Viviana Parreno
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; (C.H.); (P.Z.); (S.S.); (C.N.); (V.P.); (A.F.); (M.F.); (K.K.); (S.O.); (Y.L.)
| | - Annie Frazier
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; (C.H.); (P.Z.); (S.S.); (C.N.); (V.P.); (A.F.); (M.F.); (K.K.); (S.O.); (Y.L.)
| | - Maggie Frazier
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; (C.H.); (P.Z.); (S.S.); (C.N.); (V.P.); (A.F.); (M.F.); (K.K.); (S.O.); (Y.L.)
| | - Kelsey Kiley
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; (C.H.); (P.Z.); (S.S.); (C.N.); (V.P.); (A.F.); (M.F.); (K.K.); (S.O.); (Y.L.)
| | - Samantha O’Brien
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; (C.H.); (P.Z.); (S.S.); (C.N.); (V.P.); (A.F.); (M.F.); (K.K.); (S.O.); (Y.L.)
| | - Yu Liang
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; (C.H.); (P.Z.); (S.S.); (C.N.); (V.P.); (A.F.); (M.F.); (K.K.); (S.O.); (Y.L.)
| | - Bryan T. Mayer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; (B.T.M.); (R.W.); (C.M.)
| | - Ruizhe Wu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; (B.T.M.); (R.W.); (C.M.)
| | - Celia Mahoney
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; (B.T.M.); (R.W.); (C.M.)
| | - Monica M. McNeal
- Department of Pediatrics, University of Cincinnati College of Medicine, and Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
| | | | - Susanne Rauch
- CureVac SE, 72076 Tübingen, Germany; (S.R.); (B.P.); (S.R.)
| | - Lijuan Yuan
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; (C.H.); (P.Z.); (S.S.); (C.N.); (V.P.); (A.F.); (M.F.); (K.K.); (S.O.); (Y.L.)
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24
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Carossino M, Vissani MA, Barrandeguy ME, Balasuriya UBR, Parreño V. Equine Rotavirus A under the One Health Lens: Potential Impacts on Public Health. Viruses 2024; 16:130. [PMID: 38257830 PMCID: PMC10819593 DOI: 10.3390/v16010130] [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: 12/15/2023] [Revised: 12/29/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Group A rotaviruses are a well-known cause of viral gastroenteritis in infants and children, as well as in many mammalian species and birds, affecting them at a young age. This group of viruses has a double-stranded, segmented RNA genome with high genetic diversity linked to point mutations, recombination, and, importantly, reassortment. While initial molecular investigations undertaken in the 1900s suggested host range restriction among group A rotaviruses based on the fact that different gene segments were distributed among different animal species, recent molecular surveillance and genome constellation genotyping studies conducted by the Rotavirus Classification Working Group (RCWG) have shown that animal rotaviruses serve as a source of diversification of human rotavirus A, highlighting their zoonotic potential. Rotaviruses occurring in various animal species have been linked with contributing genetic material to human rotaviruses, including horses, with the most recent identification of equine-like G3 rotavirus A infecting children. The goal of this article is to review relevant information related to rotavirus structure/genomic organization, epidemiology (with a focus on human and equine rotavirus A), evolution, inter-species transmission, and the potential zoonotic role of equine and other animal rotaviruses. Diagnostics, surveillance and the current status of human and livestock vaccines against RVA are also reviewed.
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Affiliation(s)
- Mariano Carossino
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Maria Aldana Vissani
- Escuela de Veterinaria, Facultad de Ciencias Agrarias y Veterinarias, Universidad del Salvador, Pilar, Buenos Aires B1630AHU, Argentina; (M.A.V.); (M.E.B.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Maria E. Barrandeguy
- Escuela de Veterinaria, Facultad de Ciencias Agrarias y Veterinarias, Universidad del Salvador, Pilar, Buenos Aires B1630AHU, Argentina; (M.A.V.); (M.E.B.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
| | - Udeni B. R. Balasuriya
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Viviana Parreño
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
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25
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Sadiq A, Khan J. Rotavirus in developing countries: molecular diversity, epidemiological insights, and strategies for effective vaccination. Front Microbiol 2024; 14:1297269. [PMID: 38249482 PMCID: PMC10797100 DOI: 10.3389/fmicb.2023.1297269] [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: 09/19/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
Rotavirus (RV) causes the loss of numerous children's lives worldwide each year, and this burden is particularly heavy in low- and lower-middle-income countries where access to healthcare is limited. RV epidemiology exhibits a diverse range of genotypes, which can vary in prevalence and impact across different regions. The human genotypes that are most commonly recognized are G1P[8], G2P[4], G3P[8], G4P[8], G8P[8], G9P[8], and G12P[8]. The diversity of rotavirus genotypes presents a challenge in understanding its global distribution and developing effective vaccines. Oral, live-attenuated rotavirus vaccines have undergone evaluation in various contexts, encompassing both low-income and high-income populations, demonstrating their safety and effectiveness. Rotavirus vaccines have been introduced and implemented in over 120 countries, offering an opportunity to assess their effectiveness in diverse settings. However, these vaccines were less effective in areas with more rotavirus-related deaths and lower economic status compared to wealthier regions with fewer rotavirus-related deaths. Despite their lower efficacy, rotavirus vaccines significantly decrease the occurrence of diarrheal diseases and related mortality. They also prove to be cost-effective in regions with a high burden of such diseases. Regularly evaluating the impact, influence, and cost-effectiveness of rotavirus vaccines, especially the newly approved ones for worldwide use, is essential for deciding if these vaccines should be introduced in countries. This is especially important in places with limited resources to determine if a switch to a different vaccine is necessary. Future research in rotavirus epidemiology should focus on a comprehensive understanding of genotype diversity and its implications for vaccine effectiveness. It is crucial to monitor shifts in genotype prevalence and their association with disease severity, especially in high-risk populations. Policymakers should invest in robust surveillance systems to monitor rotavirus genotypes. This data can guide vaccine development and public health interventions. International collaboration and data sharing are vital to understand genotype diversity on a global scale and facilitate the development of more effective vaccines.
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Affiliation(s)
- Asma Sadiq
- Department of Microbiology, University of Jhang, Jhang, Pakistan
| | - Jadoon Khan
- Department of Allied and Health Sciences, IQRA University, Chak Shahzad Campus, Islamabad, Pakistan
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26
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Li Q, Wang Z, Jiang J, He B, He S, Tu C, Guo Y, Gong W. Outbreak of piglet diarrhea associated with a new reassortant porcine rotavirus B. Vet Microbiol 2024; 288:109947. [PMID: 38101077 DOI: 10.1016/j.vetmic.2023.109947] [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: 09/27/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
Rotavirus B (RVB) is a causative agent leading to acute viral gastroenteritis diarrhea in both children and young animals, and has been commonly detected in piglets. In order to determine the causative agent of diarrheal outbreak occurring in December 2022 in piglets from a pig herd in Luoyang, Henan province of China, four common viral pathogens causing piglet diarrhea-three coronaviruses and rotavirus A (RVA) were first tested and found negative, therefore metagenomic sequencing was performed to explore other potential pathogens in the diarrheal samples. Unexpectedly, the most abundant viral reads mapped to RVB, and were de novo assembled to complete 11 viral gene segments. Sequence comparisons revealed that 5 gene segments encoding VP1, VP2, VP3, NSP3 and NSP4 of RVB strain designated as HNLY-2022 are most closely related to RVB strains derived from herbivores with low nucleotide similarities of 65.7-75.3%, and the remaining segments were relatively close to porcine RVB strains with the VP4 gene segment showing very low nucleotide identity (65.0%) with reference strains, indicating HNLY-2022 is a new reassortant RVB strain. Based on the previously proposed genotype classification criterion, the genotype constellation of RVB strain HNLY-2022 is G6-P[6]-I4-R6-C6-M6-A7-N5-T7-E5-H4 with more than half of the genotypes (P[6], R6, C6, M6, T7 and E5) newly reported. Therefore, the new reassortant RVB strain is the likely causative agent for the diarrheal outbreak of piglets occurred in China and more epidemiological studies should be conducted to monitor the spread of this newly identified porcine RVB strain.
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Affiliation(s)
- Qingxian Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Zunbao Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Jianfeng Jiang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Biao He
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Sun He
- TECON Biopharmaceutical Co., Ltd., Urumqi 830000, China
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yidi Guo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Wenjie Gong
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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27
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Ferrari E, Vignola G, Bertasio C, Chiapponi C, Alborali GL, Martella V, Boniotti MB. Identification of Putative Novel Rotavirus H VP7, VP4, VP6 and NSP4 Genotypes in Pigs. Viruses 2023; 16:68. [PMID: 38257768 PMCID: PMC10819321 DOI: 10.3390/v16010068] [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: 11/23/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Rotavirus H (RVH) has been detected in humans, pigs and bats. Recently, RVH infections were reported in different porcine farms worldwide, suggesting epidemiological relevance. However, to date, the genome information of RVH strains has been limited due to the scarcity of deposited sequences. This study aimed to characterize the VP7, VP4, VP6 and NSP4 genes of RVHs from 27 symptomatic pigs, in Italy, between 2017 and 2021. RVH genes were amplified via RT-PCR using specific primers, and the amplicons were sequenced. By coupling the data generated in this study with the sequences available in the databases, we elaborated a classification scheme useful to genotype the VP7, VP4, VP6 and NSP4 genes. The nucleotide identity and phylogenetic analyses unveiled an impressive genetic heterogeneity and allowed the classification of the Italian RVH strains into 12G (VP7), 6P (VP4), 8I (VP6) and 8E (NSP4) genotypes, of which 6I, 5E and the totality of the G and P genotypes were of novel identification. Our data highlight the high genetic variability of the RVH strains circulating in pigs and underline the importance of a robust classification system to track the epidemiology of RVHs.
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Affiliation(s)
- Elena Ferrari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Via Bianchi 7/9, 25124 Brescia, Italy; (G.V.); (C.B.); (C.C.); (G.L.A.); (M.B.B.)
| | - Greta Vignola
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Via Bianchi 7/9, 25124 Brescia, Italy; (G.V.); (C.B.); (C.C.); (G.L.A.); (M.B.B.)
| | - Cristina Bertasio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Via Bianchi 7/9, 25124 Brescia, Italy; (G.V.); (C.B.); (C.C.); (G.L.A.); (M.B.B.)
| | - Chiara Chiapponi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Via Bianchi 7/9, 25124 Brescia, Italy; (G.V.); (C.B.); (C.C.); (G.L.A.); (M.B.B.)
| | - Giovanni Loris Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Via Bianchi 7/9, 25124 Brescia, Italy; (G.V.); (C.B.); (C.C.); (G.L.A.); (M.B.B.)
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy;
| | - Maria Beatrice Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, Via Bianchi 7/9, 25124 Brescia, Italy; (G.V.); (C.B.); (C.C.); (G.L.A.); (M.B.B.)
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28
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Kumar D, Anderson Reever AV, Pittman JS, Springer NL, Mallen K, Roman-Sosa G, Sangewar N, Casey-Moore MC, Bowen MD, Mwangi W, Marthaler DG. Role of Pre-Farrow Natural Planned Exposure of Gilts in Shaping the Passive Antibody Response to Rotavirus A in Piglets. Vaccines (Basel) 2023; 11:1866. [PMID: 38140269 PMCID: PMC10748143 DOI: 10.3390/vaccines11121866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/17/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Natural planned exposure (NPE) remains one of the most common methods in swine herds to boost lactogenic immunity against rotaviruses. However, the efficacy of NPE protocols in generating lactogenic immunity has not been investigated before. A longitudinal study was conducted to investigate the dynamics of genotype-specific antibody responses to different doses (3, 2 and 1) of Rotavirus A (RVA) NPE (genotypes G4, G5, P[7] and P[23]) in gilts and the transfer of lactogenic immunity to their piglets. Group 1 gilts received three doses of NPE at 5, 4 and 3 weeks pre-farrow (WPF), group 2 received two doses at 5 and 3 WPF, group 3 received one dose at 5 WPF, and group 4 received no NPE (control group). VP7 (G4 and G5) and truncated VP4* (P[7] and P[23]) antigens of RVA were expressed in mammalian and bacterial expression systems, respectively, and used to optimize indirect ELISAs to determine antibody levels against RVA in gilts and piglets. In day-0 colostrum samples, group 1 had significantly higher IgG titers compared to the control group for all four antigens, and either significantly or numerically higher IgG titers than groups 2 and 3. Group 1 also had significantly higher colostrum IgA levels than the control group for all antigens (except G4), and either significantly or numerically higher IgA levels compared to groups 2 and 3. In piglet serum, group 1 piglets had higher IgG titers for all four antigens at day 0 than the other groups. Importantly, RVA NPE stimulated antibodies in all groups regardless of the treatment doses and prevented G4, G5, P[7] and P[23] RVA fecal shedding prior to weaning in piglets in the absence of viral challenge. The G11 and P[34] RVA genotypes detected from pre-weaning piglets differed at multiple amino acid positions with parent NPE strains. In conclusion, the results of this study suggest that the group 1 NPE regimen (three doses of NPE) resulted in the highest anti-RVA antibody (IgG and IgA) levels in the colostrum/milk, and the highest IgG levels in piglet serum.
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Affiliation(s)
- Deepak Kumar
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA (N.S.); (W.M.)
| | - Amanda V. Anderson Reever
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA;
| | | | - Nora L. Springer
- Clinical Pathology, Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA;
| | - Kylynn Mallen
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA (N.S.); (W.M.)
| | - Gleyder Roman-Sosa
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany;
| | - Neha Sangewar
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA (N.S.); (W.M.)
| | - Mary C. Casey-Moore
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA 30329, USA; (M.C.C.-M.); (M.D.B.)
| | - Michael D. Bowen
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA 30329, USA; (M.C.C.-M.); (M.D.B.)
| | - Waithaka Mwangi
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA (N.S.); (W.M.)
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29
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Doan YH, Dennis FE, Takemae N, Haga K, Shimizu H, Appiah MG, Lartey BL, Damanka SA, Hayashi T, Suzuki T, Kageyama T, Armah GE, Katayama K. Emergence of Intergenogroup Reassortant G9P[4] Strains Following Rotavirus Vaccine Introduction in Ghana. Viruses 2023; 15:2453. [PMID: 38140694 PMCID: PMC10747750 DOI: 10.3390/v15122453] [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: 11/22/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023] Open
Abstract
Rotavirus (RVA) is a leading cause of childhood gastroenteritis. RVA vaccines have reduced the global disease burden; however, the emergence of intergenogroup reassortant strains is a growing concern. During surveillance in Ghana, we observed the emergence of G9P[4] RVA strains in the fourth year after RVA vaccine introduction. To investigate whether Ghanaian G9P[4] strains also exhibited the DS-1-like backbone, as seen in reassortant G1/G3/G8/G9 strains found in other countries in recent years, this study determined the whole genome sequences of fifteen G9P[4] and two G2P[4] RVA strains detected during 2015-2016. The results reveal that the Ghanaian G9P[4] strains exhibited a double-reassortant genotype, with G9-VP7 and E6-NSP4 genes on a DS-1-like backbone (G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2). Although they shared a common ancestor with G9P[4] DS-1-like strains from other countries, further intra-reassortment events were observed among the original G9P[4] and co-circulating strains in Ghana. In the post-vaccine era, there were significant changes in the distribution of RVA genotype constellations, with unique strains emerging, indicating an impact beyond natural cyclical fluctuations. However, reassortant strains may exhibit instability and have a limited duration of appearance. Current vaccines have shown efficacy against DS-1-like strains; however, ongoing surveillance in fully vaccinated children is crucial for addressing concerns about long-term effectiveness.
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Affiliation(s)
- Yen Hai Doan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.H.D.)
| | - Francis Ekow Dennis
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nobuhiro Takemae
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.H.D.)
| | - Kei Haga
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Michael Gyasi Appiah
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Belinda Larteley Lartey
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Susan Afua Damanka
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Takaya Hayashi
- Department of Molecular Virology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8549, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Pathogenesis, Infection and Host Response, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8549, Japan
| | - Tsutomu Kageyama
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.H.D.)
| | - George Enyimah Armah
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Kazuhiko Katayama
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
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Cao M, Yuan F, Zhang W, Wang X, Ma J, Ma X, Kuai W, Ma X. Genomic analysis of two rare human G3P[9] rotavirus strains in Ningxia, China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105518. [PMID: 37890809 DOI: 10.1016/j.meegid.2023.105518] [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: 09/22/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
G3P (Matthijnssens et al., 2008b [9]) is a rare combination of human rotavirus VP7/VP4 genotypes with a complex evolutionary pattern but limited related studies. Detailed genomic characterisation and genetic evolutionary analyses of G3P (Matthijnssens et al., 2008b [9]) rotaviruses have helped to enhance our understanding of rotavirus diversity. For the first time, we detected two human G3P (Matthijnssens et al., 2008b [9]) Rotavirus A (RVA) strains, RVA/Human-tc/CHN/2020999/2020/G3P (Matthijnssens et al., 2008b [9]) and RVA/Human-wt/CHN/23582009/2023/G3P (Matthijnssens et al., 2008b [9]), in diarrhoea patients from the Ningxia region of China, and carried out a whole-genome analysis of these strains. 2,020,999 and 23,582,009 have identical gene constellations: G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3, and this genotypic constellation was reported first time in China. They are closely related in 11 genome segments. The genotypes of these two strains are different from the human RVA strains L621 and E2451, which are only G3P (Matthijnssens et al., 2008b [9]) strains reported so far in China, but are identical to those of the Thai feline strain Meesuk and the Korean human strain CAU12-2-51.Phylogenetic analysis showed that the VP6, VP1-VP3, and NSP2 genes of the two strains in this study clustered with human/bovine and feline/bovine rotavirus strains to form a sublineage distinct from the common DS-1-like G2 human rotavirus. In contrast, the VP7, VP4, NSP1, and NSP3-NSP5 gene segments were closely associated with human/feline rotavirus and feline rotavirus strains. These findings suggest that the evolutionary origin of the G3P (Matthijnssens et al., 2008b [9]) human rotavirus found in Ningxia, China, is consistent with the Meesuk and CAU12-2-51 strains, may have arisen through reassortment between uncommon human/bovine, feline/bovine rotavirus strains and human/feline, feline rotaviruses. However, VP1-VP2 gene segments did not have the same lineage as strains Meesuk and CAU12-2-51, suggesting that these genes might be derived from additional reassortment event.
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Affiliation(s)
- Min Cao
- Ningxia center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Fang Yuan
- Ningxia center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Wei Zhang
- Ningxia center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Xiuqin Wang
- Ningxia center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Jiangtao Ma
- Ningxia center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Xuemin Ma
- Ningxia center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Wenhe Kuai
- Ningxia center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Xueping Ma
- Ningxia center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China.
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Morozova OV, Sashina TA, Epifanova NV, Velikzhanina EI, Novikova NA. Phylodynamic characteristics of reassortant DS-1-like G3P[8]-strains of rotavirus type A isolated in Nizhny Novgorod (Russia). Braz J Microbiol 2023; 54:2867-2877. [PMID: 37897627 PMCID: PMC10689624 DOI: 10.1007/s42770-023-01155-3] [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: 06/01/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Since 2013, there has been an increase in reports of the spread of a double intergroup reassortant strain of rotavirus type A (RVA) with the genotype G3P[8] and other genes belonging to the second genogroup I2-R2-C2-M2-A2-N2-T2-E2-H2. In our study, we provide a molecular genetic characterization of rotaviruses with genotype G3P[8]-I2 isolated in Nizhny Novgorod. In our study, we used RT-PCR, Sanger sequencing, RNA-PAGE methods. Phylogenetic and phylodynamic analysis were performed using the Bayesian approach. According to our study, there was a significant increase in the proportion of G3P[8] from 15% during the period of 2020-2021 to 53% during the period of 2021-2022 in Nizhny Novgorod, Russia. Phylogenetic analysis based on the VP4 gene revealed that DS-1-like RVAs isolated in Nizhny Novgorod belong to different clusters of the P[8]-3.1 lineage, with a level of variation ranging from 1.1% to 1.3%. Based on the VP6 gene, the equine-like RVAs identified by us carry genetic variants belonging to three distinct clusters of the lineage I2-V, with a variation level ranging from 2.0% to 4.5%. These data indicate the genotypic diversity of circulating DS-1-like G3 RVAs. Phylogenetic analysis of the VP7 gene allowed us to assign the isolates identified in our study to the G3-1 lineage. We estimated that the circulation of the most recent common ancestor of the spreading strains dates back to 2002. Additionally, we determined the typical level of mutations in the VP7 gene, which amounted to 2.14*10-3 substitutions/per site/per year.
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Affiliation(s)
- Olga V Morozova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia.
| | - T A Sashina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N V Epifanova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - E I Velikzhanina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N A Novikova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
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Mwape I, Laban NM, Chibesa K, Moono A, Silwamba S, Malisheni MM, Chisenga C, Chauwa A, Simusika P, Phiri M, Simuyandi M, Chilengi R, De Beer C, Ojok D. Characterization of Rotavirus Strains Responsible for Breakthrough Diarrheal Diseases among Zambian Children Using Whole Genome Sequencing. Vaccines (Basel) 2023; 11:1759. [PMID: 38140164 PMCID: PMC10748035 DOI: 10.3390/vaccines11121759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 12/24/2023] Open
Abstract
The occurrence of rotavirus (RV) infection among vaccinated children in high-burden settings poses a threat to further disease burden reduction. Genetically altered viruses have the potential to evade both natural infection and vaccine-induced immune responses, leading to diarrheal diseases among vaccinated children. Studies characterizing RV strains responsible for breakthrough infections in resource-limited countries where RV-associated diarrheal diseases are endemic are limited. We aimed to characterize RV strains detected in fully vaccinated children residing in Zambia using next-generation sequencing. We conducted whole genome sequencing on Illumina MiSeq. Whole genome assembly was performed using Geneious Prime 2023.1.2. A total of 76 diarrheal stool specimens were screened for RV, and 4/76 (5.2%) were RV-positive. Whole genome analysis revealed RVA/Human-wt/ZMB/CIDRZ-RV2088/2020/G1P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and RVA/Human-wt/ZMB/CIDRZ-RV2106/2020/G12P[4]-I1-R2-C2-M2-A2-N1-T2-E1-H2 strains were mono and multiple reassortant (exchanged genes in bold) respectively, whilst RVA/Human-wt/ZMB/CIDRZ-RV2150/2020/G12P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 was a typical Wa-like strain. Comparison of VP7 and VP4 antigenic epitope of breakthrough strains and Rotarix strain revealed several amino acid differences. Variations in amino acids in antigenic epitope suggested they played a role in immune evasion of neutralizing antibodies elicited by vaccination. Findings from this study have the potential to inform national RV vaccination strategies and the design of highly efficacious universal RV vaccines.
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Affiliation(s)
- Innocent Mwape
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town 8000, South Africa;
| | - Natasha Makabilo Laban
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Kennedy Chibesa
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
- Division of Medical Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein P.O. Box 339, South Africa
| | - Andrew Moono
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Suwilanji Silwamba
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | | | - Caroline Chisenga
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Adriace Chauwa
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Paul Simusika
- University Teaching Hospitals, Lusaka 10101, Zambia
- Institute of Basic and Biomedical Sciences, Levy Mwanawasa Medical University, Lusaka 10101, Zambia
| | - Mabvuto Phiri
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Michelo Simuyandi
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Roma Chilengi
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Corena De Beer
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town 8000, South Africa;
| | - David Ojok
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
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Akari Y, Hatazawa R, Kuroki H, Ito H, Negoro M, Tanaka T, Miwa H, Sugiura K, Umemoto M, Tanaka S, Ogawa M, Ito M, Fukuda S, Murata T, Taniguchi K, Suga S, Kamiya H, Nakano T, Taniguchi K, Komoto S. Full genome-based characterization of an Asian G3P[6] human rotavirus strain found in a diarrheic child in Japan: Evidence for porcine-to-human zoonotic transmission. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 115:105507. [PMID: 37757900 DOI: 10.1016/j.meegid.2023.105507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
Human rotavirus strains having the unconventional G3P[6] genotype have been sporadically detected in diarrheic patients in different parts of the world. However, the full genomes of only three human G3P[6] strains from Asian countries (China, Indonesia, and Vietnam) have been sequenced and characterized, and thus the exact origin and evolution of G3P[6] strains in Asia remain to be elucidated. Here, we sequenced and characterized the full genome of a G3P[6] strain (RVA/Human-wt/JPN/SO1199/2020/G3P[6]) found in a stool sample from a 3-month-old infant admitted with acute gastroenteritis in Japan. On full genomic analysis, strain SO1199 was revealed to have a unique Wa-like genogroup configuration: G3-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1. VP6 genotype I5 and NSP1 genotype A8 are commonly found in porcine rotavirus strains. Furthermore, phylogenetic analysis demonstrated that all 11 genes of strain SO1199 were closely related to those of porcine and/or porcine-like human rotaviruses and thus appeared to be of porcine origin. Thus, strain SO1199 was shown to possess a porcine-like genomic backbone and thus is likely to be the result of interspecies transmission of a porcine rotavirus strain. Of note is that all 11 genes of strain SO1199 were phylogenetically located in clusters, distinct from those of the previously identified porcine-like human G3P[6] strains from around the world including Asia, suggesting the occurrence of independent porcine-to-human zoonotic transmission events. To our knowledge, this is the first report on full genome-based characterization of a human G3P[6] strain that has emerged in Japan. Our findings revealed the diversity of unconventional human G3P[6] strains in Asia, and provide important insights into the origin and evolution of G3P[6] strains.
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Affiliation(s)
- Yuki Akari
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Riona Hatazawa
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Haruo Kuroki
- Sotobo Children's Clinic, Isumi, Chiba 299-4503, Japan
| | - Hiroaki Ito
- Department of Pediatrics, Kameda Medical Center, Kamogawa, Chiba 296-8602, Japan
| | - Manami Negoro
- Institute for Clinical Research, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Takaaki Tanaka
- Department of Pediatrics, Kawasaki Medical School, Okayama, Okayama 700-8505, Japan
| | - Haruna Miwa
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Katsumi Sugiura
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | | | - Shigeki Tanaka
- Department of Pediatrics, Mie Chuo Medical Center, Tsu, Mie 514-1101, Japan
| | - Masahiro Ogawa
- Department of Pediatrics, Mie Chuo Medical Center, Tsu, Mie 514-1101, Japan
| | - Mitsue Ito
- Department of Pediatrics, Japanese Red Cross Ise Hospital, Ise, Mie 516-8512, Japan
| | - Saori Fukuda
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Takayuki Murata
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan; Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Kiyosu Taniguchi
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Shigeru Suga
- Department of Pediatrics, National Mie Hospital, Tsu, Mie 514-0125, Japan
| | - Hajime Kamiya
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Takashi Nakano
- Department of Pediatrics, Kawasaki Medical School, Okayama, Okayama 700-8505, Japan
| | - Koki Taniguchi
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Satoshi Komoto
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan; Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi 470-1192, Japan; Division of One Health, Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Yufu, Oita 879-5593, Japan.
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Sawant P, Kulkarni A, Mane R, Patil R, Lavania M. Metatranscriptomic assessment of diarrhoeic faeces reveals diverse RNA viruses in rotavirus group A infected piglets and calves from India. Front Cell Infect Microbiol 2023; 13:1258660. [PMID: 37965252 PMCID: PMC10642067 DOI: 10.3389/fcimb.2023.1258660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/04/2023] [Indexed: 11/16/2023] Open
Abstract
RNA viruses are a major group contributing to emerging infectious diseases and neonatal diarrhoea, causing morbidity and mortality in humans and animals. Hence, the present study investigated the metatranscriptomic-derived faecal RNA virome in rotavirus group A (RVA)-infected diarrheic piglets and calves from India. The viral genomes retrieved belonged to Astroviridae in both species, while Reoviridae and Picornaviridae were found only in piglets. The nearly complete genomes of porcine RVA (2), astrovirus (AstV) (6), enterovirus G (EVG) (2), porcine sapelovirus (PSV) (2), Aichivirus C (1), and porcine teschovirus (PTV) (1) were identified and characterised. In the piglet, AstVs of PAstV2 (MAstV-26) and PAstV4 (MAstV-31) lineages were predominant, followed by porcine RVA, EVG, PSV, Aichivirus C, teschovirus (PTV-17) in decreasing order of sequence reads. In contrast, AstV accounted for the majority of reads in bovines and belonged to MAstV-28 and a proposed MAstV-35. Both RVA G4P[6] strains exhibited prototype Gottfried strains like a genotypic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Ten out of eleven genes were of porcine origin, while the VP7 gene clustered with G4-lineage-1, consisting of human strains, suggesting a natural porcine-human reassortant. In the recombination analysis, multiple recombination events were detected in the PAstV4 and PAstV2 genomes, pointing out that these viruses were potential recombinants. Finally, the study finds diverse RNA virome in Indian piglets and calves for the first time, which may have contributed to diarrhoea. In the future, the investigation of RNA virome in animals will help in revealing pathogen diversity in multifactorial diseases, disease outbreaks, monitoring circulating viruses, viral discovery, and evaluation of their zoonotic potential.
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Affiliation(s)
- Pradeep Sawant
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rajkumar Mane
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
| | - Renu Patil
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
| | - Mallika Lavania
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
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35
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Louge Uriarte EL, Badaracco A, Spetter MJ, Miño S, Armendano JI, Zeller M, Heylen E, Späth E, Leunda MR, Moreira AR, Matthijnssens J, Parreño V, Odeón AC. Molecular Epidemiology of Rotavirus A in Calves: Evolutionary Analysis of a Bovine G8P[11] Strain and Spatio-Temporal Dynamics of G6 Lineages in the Americas. Viruses 2023; 15:2115. [PMID: 37896894 PMCID: PMC10611311 DOI: 10.3390/v15102115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Rotavirus A (RVA) causes diarrhea in calves and frequently possesses the G6 and P[5]/P[11] genotypes, whereas G8 is less common. We aimed to compare RVA infections and G/P genotypes in beef and dairy calves from major livestock regions of Argentina, elucidate the evolutionary origin of a G8 strain and analyze the G8 lineages, infer the phylogenetic relationship of RVA field strains, and investigate the evolution and spatio-temporal dynamics of the main G6 lineages in American countries. Fecal samples (n = 422) from diarrheic (beef, 104; dairy, 137) and non-diarrheic (beef, 78; dairy, 103) calves were analyzed by ELISA and semi-nested multiplex RT-PCR. Sequencing, phylogenetic, phylodynamic, and phylogeographic analyses were performed. RVA infections were more frequent in beef (22.0%) than in dairy (14.2%) calves. Prevalent genotypes and G6 lineages were G6(IV)P[5] in beef (90.9%) and G6(III)P[11] (41.2%) or mixed genotypes (23.5%) in dairy calves. The only G8 strain was phylogenetically related to bovine and artiodactyl bovine-like strains. Re-analyses inside the G8 genotype identified G8(I) to G8(VIII) lineages. Of all G6 strains characterized, the G6(IV)P[5](I) strains from "Cuenca del Salado" (Argentina) and Uruguay clustered together. According to farm location, a clustering pattern for G6(IV)P[5] strains of beef farms was observed. Both G6 lineage strains together revealed an evolutionary rate of 1.24 × 10-3 substitutions/site/year, and the time to the most recent common ancestor was dated in 1853. The most probable ancestral locations were Argentina in 1981 for G6(III) strains and the USA in 1940 for G6(IV) strains. The highest migration rates for both G6 lineages together were from Argentina to Brazil and Uruguay. Altogether, the epidemiology, genetic diversity, and phylogeny of RVA in calves can differ according to the production system and farm location. We provide novel knowledge about the evolutionary origin of a bovine G8P[11] strain. Finally, bovine G6 strains from American countries would have originated in the USA nearly a century before its first description.
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Affiliation(s)
- Enrique L. Louge Uriarte
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Alejandra Badaracco
- Instituto Nacional de Tecnología Agropecuaria, EEA Montecarlo, Av. El Libertador Nº 2472, Montecarlo CP3384, Misiones, Argentina;
| | - Maximiliano J. Spetter
- Facultad de Ciencias Veterinarias, Departamento de Fisiopatología, Centro de Investigación Veterinaria de Tandil (CIVETAN), Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil CP7000, Buenos Aires, Argentina; (M.J.S.); (J.I.A.)
| | - Samuel Miño
- Instituto Nacional de Tecnología Agropecuaria, EEA Cerro Azul, Ruta 14, km 836, Cerro Azul CP3313, Misiones, Argentina;
| | - Joaquín I. Armendano
- Facultad de Ciencias Veterinarias, Departamento de Fisiopatología, Centro de Investigación Veterinaria de Tandil (CIVETAN), Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil CP7000, Buenos Aires, Argentina; (M.J.S.); (J.I.A.)
| | - Mark Zeller
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Elisabeth Heylen
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Ernesto Späth
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (E.S.); (A.C.O.)
| | - María Rosa Leunda
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Ana Rita Moreira
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Viviana Parreño
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Virología e Innovaciones Tecnológicas, Nicolas Repetto y de los Reseros s/n, Hurlingham CP1686, Buenos Aires, Argentina
| | - Anselmo C. Odeón
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (E.S.); (A.C.O.)
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Phan T, Hikita T, Okitsu S, Akari Y, Komoto S, Hayakawa S, Ushijima H. Whole genome sequencing and genomic characterization of a DS-1-like G2P[4] group A rotavirus in Japan. Virus Genes 2023; 59:688-692. [PMID: 37405556 DOI: 10.1007/s11262-023-02018-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/26/2023] [Indexed: 07/06/2023]
Abstract
After rotavirus was discovered in 1973, it became the leading pathogen in causing acute gastroenteritis in humans worldwide. In this study, we performed whole genome sequencing and genomic characterization of a DS-1-like G2P[4] group A rotavirus in feces of a Japanese child with acute gastroenteritis who was fully Rotarix® vaccinated. The genomic investigation determined a genomic constellation G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 of this rotavirus strain. Its antigenic epitopes of the VP7 and VP4 proteins had significant mismatches compared with the vaccine strains. Our study is the latest attempt to investigate the evolution of the VP7 and VP4 genes of emerging G2P[4] rotavirus in Japan.
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Affiliation(s)
- Tung Phan
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Shoko Okitsu
- Division of Microbiology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Yuki Akari
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Division of One Health, Research Center for Global and Local Infectious Diseases, Oita University, Yufu, Oita, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan.
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37
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Dong HJ, Liu LY, Jia LP, Zhao LQ, Jin FH, Zhou L, Qian Y. Prevalence and genomic analysis of t203-like G9 (G9-VI) rotaviruses circulating in children with gastroenteritis in Beijing, China. Arch Virol 2023; 168:257. [PMID: 37755543 PMCID: PMC10533636 DOI: 10.1007/s00705-023-05860-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/24/2023] [Indexed: 09/28/2023]
Abstract
Our previous surveillance revealed that t203-like G9 (tentatively designated subtype G9-VI) rotaviruses re-emerged in 2010 in Beijing and rapidly prevailed over the G9-III subtype (the most common G9 subtype globally) and previously predominant G genotypes over the following two years. G9-VI belongs to the VP7 evolutionary lineage VI, which includes unusual and sporadic human rotaviruses from China (t203) and Japan. To obtain insight into the epidemiology, evolution, and transmission advantages of G9-VI rotavirus, we performed follow-up surveillance (2014-2017) and whole-genome analysis of 12 representative G9 strains. The results showed that the G9 genotype was predominant (77.4%), with a marked increase in prevalence (previously 43.5%). Within the G9 genotype, subtype G9-VI accounted for the majority (98.3%) of cases. The most prevalent P-genotype was P[8] (93.7%), within which subtype P[8]b was rare (0.7%). Phylogenetically, the G9-VI subtype strains in this study clustered closely with contemporary emerging human rotaviruses from many other countries in VP7 lineage VI, indicating that this subtype is capable of spreading globally. These currently emerging G9-VI rotaviruses formed a distinct monophyletic subcluster when compared to early G9-VI rotaviruses. Furthermore, four specific amino acid substitutions and synonymous codon substitutions were observed in the VP7 genes between the current G9-VI and globally common G9-III rotaviruses. The remaining nine genes of all of the analyzed representative G9 strains, whether G9-VI or G9-III, combined with the P[8]a, P[8]b, or P[6] genotype and exhibited the same Wa-like backbone constellation.
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Affiliation(s)
- Hui-Jin Dong
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Li-Ying Liu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Li-Ping Jia
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Lin-Qing Zhao
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Feng-Hua Jin
- Department of Infectious Diseases, Affiliated Children's Hospital to Capital Institute of Pediatrics, Beijing, 100020, China
| | - Lin Zhou
- Department of Clinical Laboratory, Affiliated Children's Hospital to Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yuan Qian
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, 100020, China.
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38
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Khakha SA, Varghese T, Giri S, Durbin A, Tan GS, Kalaivanan M, Prasad JH, Kang G. Whole-genome characterization of common rotavirus strains circulating in Vellore, India from 2002 to 2017: emergence of non-classical genomic constellations. Gut Pathog 2023; 15:44. [PMID: 37730725 PMCID: PMC10510252 DOI: 10.1186/s13099-023-00569-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/27/2023] [Indexed: 09/22/2023] Open
Abstract
Rotaviruses (RVs) are the most common etiological agent of acute gastroenteritis among young children, even after vaccine introduction in low-income countries. A whole-genome classification representing the 11 RV genes, was introduced for surveillance and characterization of RVs. This study characterized the common circulating strains in Vellore, India from 2002 to 2017 to understand rotavirus strain diversity and evolution using Whole genome sequencing (WGS) carried out on Illumina MiSeq. The 89% (92% of Wa-like, 86% of DS-1-like) of strains had classical constellations, while reassortant constellations were seen in 11% (8% of Wa-like, 14% of DS-1-like) of the strains. The rare E6-NSP4 in combination with DS-1 like G1P[8] and the emergence of the OP-354 subtype of P[8] were identified. Phylogenetics of RV strains revealed multiple subtypes circulating in the past 15 years, with strong evidence of animal to human gene transmission among several strains.
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Affiliation(s)
- Shainey Alokit Khakha
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Tintu Varghese
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Sidhartha Giri
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Alan Durbin
- J. Craig Venter Institute, La Jolla, San Diego, CA, 92037, USA
| | - Gene S Tan
- J. Craig Venter Institute, La Jolla, San Diego, CA, 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, San Diego, CA, 92037, USA
| | - Maheswari Kalaivanan
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | - Gagandeep Kang
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India.
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Degiuseppe JI, Martelli A, Barrios Mathieur C, Stupka JA. Genetic diversity of rotavirus A in Argentina during 2019-2022: detection of G6 strains and insights regarding its dissemination. Arch Virol 2023; 168:251. [PMID: 37702836 DOI: 10.1007/s00705-023-05874-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023]
Abstract
One of the challenges associated with introducing a vaccine is monitoring its impact through clinical and molecular surveillance. The aims of this study were to analyze the genetic diversity of rotavirus A in Argentina between 2019 and 2022 and to assess the phylogenetic and phylodynamic features of the unusual G6 strains detected. A significant decline in the Wa-like genogroup strains was observed, and G6 strains were detected for the first time in Argentina, in association with P[8] and P[9]. Spatiotemporal analysis showed that the G6-lineage I strains detected recently in Argentina and Brazil might have emerged from European strains. This study provides recent evidence of the genetic diversity of rotaviruses in isolated cases. It is considered important to support continuous surveillance of rotavirus in the post-vaccine scenario, mainly to evaluate potential changes that may occur after the COVID-19 pandemic.
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Affiliation(s)
- Juan Ignacio Degiuseppe
- Argentine Reference Laboratory for Rotavirus and Norovirus, INEI-ANLIS "Dr. Carlos G. Malbrán", Avenida Vélez Sársfield 563, Buenos Aires, Argentina.
| | - Antonella Martelli
- Laboratory of Clinical Virology, Centro de Educación Médica e Investigaciones Clínicas "Dr. Norberto Quirno" (CEMIC), Galván 4102, Buenos Aires, Argentina
| | - Christian Barrios Mathieur
- Argentine Reference Laboratory for Rotavirus and Norovirus, INEI-ANLIS "Dr. Carlos G. Malbrán", Avenida Vélez Sársfield 563, Buenos Aires, Argentina
| | - Juan Andrés Stupka
- Argentine Reference Laboratory for Rotavirus and Norovirus, INEI-ANLIS "Dr. Carlos G. Malbrán", Avenida Vélez Sársfield 563, Buenos Aires, Argentina
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40
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Hasan MA, Suzuki M, Sakai K, Kabir MH, Miyaoka Y, Hakim H, Kadota C, Shoham D, Takehara K. Complete genome constellations of two bovine rotavirus A strains isolated in Japan reveal a unique T9 NSP3 genotype. J Vet Med Sci 2023; 85:998-1003. [PMID: 37495525 PMCID: PMC10539819 DOI: 10.1292/jvms.23-0268] [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] [Indexed: 07/28/2023] Open
Abstract
Full genome sequencing of two bovine rotavirus A (RVA) strains isolated in Japan in 2019 revealed two genotype constellations; one had a constellation of G8-P[1]-I2-R2-C2-M2-A3-N2-T9-E2-H3. Thereupon, genotype T9 carried by RVA/Bovine-tc/JPN/AH1041/2022/G8P[1], constitutes a rare NSP3 genotype, and only two unusual Japanese bovine RVA strains have thus far been reported to carry this genotype. The other RVA/Bovine-tc/JPN/AH1207/2022/G6P[5] strain possessed a constellation of G6-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3. Phylogenetic analyses indicate that the majority of gene segments were most closely related to Japanese bovine RVAs, suggesting that both strains might have derived through multiple reassortment events from RVA strains circulating within Japanese cattle. The emergence of RVA strains in Japan and their reassortment with locally circulating atypical RVAs could have implications for current vaccination strategies.
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Affiliation(s)
- Md Amirul Hasan
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kouji Sakai
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Md Humayun Kabir
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yu Miyaoka
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hakimullah Hakim
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Chisaki Kadota
- Laboratory of Animal Health, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Dany Shoham
- Bar-Ilan University, Begin-Sadat Center for Strategic Studies, Ramat Gan, Israel
| | - Kazuaki Takehara
- Laboratory of Animal Health, Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Laboratory of Animal Health, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
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41
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Zhuo R, Freedman SB, Xie J, Charlton C, Plitt S, Croxen MA, Li V, Tarr GAM, Lee B, Ali S, Chui L, Luong J, Pang X. Molecular epidemiology of rotavirus among children in Western Canada: Dynamic changes in genotype prevalence in four consecutive seasons. J Med Virol 2023; 95:e29028. [PMID: 37573569 DOI: 10.1002/jmv.29028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/19/2023] [Accepted: 07/29/2023] [Indexed: 08/15/2023]
Abstract
Rotavirus molecular surveillance remains important in the postvaccine era to monitor the changes in transmission patterns, identify vaccine-induced antigenic changes and discover potentially pathogenic vaccine-related strains. The Canadian province of Alberta introduced rotavirus vaccination into its provincial vaccination schedule in June 2015. To evaluate the impact of this program on stool rotavirus positivity rate, strain diversity, and seasonal trends, we analyzed a prospective cohort of children with acute gastroenteritis recruited between December 2014 and August 2018. We identified dynamic changes in rotavirus positivity and genotype trends during pre- and post-rotavirus vaccine introduction periods. Genotypes G9P[8], G1P[8], G2P[4], and G12P[8] predominated consecutively each season with overall lower rotavirus incidence rates in 2016 and 2017. The demographic and clinical features of rotavirus gastroenteritis were comparable among wild-type rotaviruses; however, children with G12P[8] infections were older (p < 0.001). Continued efforts to monitor changes in the molecular epidemiology of rotavirus using whole genome sequence characterization are needed to further understand the impact of the selection pressure of vaccination on rotavirus evolution.
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Affiliation(s)
- Ran Zhuo
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Stephen B Freedman
- Sections of Pediatric Emergency Medicine and Gastroenterology, Departments of Pediatrics and Emergency Medicine, Alberta Children's Hospital and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jianling Xie
- Sections of Pediatric Emergency Medicine and Gastroenterology, Departments of Pediatrics and Emergency Medicine, Alberta Children's Hospital and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Carmen Charlton
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Sabrina Plitt
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
- Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Mathew A Croxen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
- Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Vincent Li
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Gillian A M Tarr
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Bonita Lee
- Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Samina Ali
- Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Jasper Luong
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaoli Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
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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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43
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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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Carossino M, Balasuriya UBR, Thieulent CJ, Barrandeguy ME, Vissani MA, Parreño V. Quadruplex Real-Time TaqMan ® RT-qPCR Assay for Differentiation of Equine Group A and B Rotaviruses and Identification of Group A G3 and G14 Genotypes. Viruses 2023; 15:1626. [PMID: 37631969 PMCID: PMC10459720 DOI: 10.3390/v15081626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Equine rotavirus A (ERVA) is the leading cause of diarrhea in foals, with G3P[12] and G14P[12] genotypes being the most prevalent. Recently, equine G3-like RVA was recognized as an emerging infection in children, and a group B equine rotavirus (ERVB) was identified as an emergent cause of foal diarrhea in the US. Thus, there is a need to adapt molecular diagnostic tools for improved detection and surveillance to identify emerging strains, understand their molecular epidemiology, and inform future vaccine development. We developed a quadruplex TaqMan® RT-qPCR assay for differentiation of ERVA and ERVB and simultaneous G-typing of ERVA strains, evaluated its analytical and clinical performance, and compared it to (1) a previously established ERVA triplex RT-qPCR assay and (2) standard RT-PCR assay and Sanger sequencing of PCR products. This quadruplex RT-qPCR assay demonstrated high sensitivity (>90%)/specificity (100%) for every target and high overall agreement (>96%). Comparison between the triplex and quadruplex assays revealed only a slightly higher sensitivity for the ERVA NSP3 target using the triplex format (p-value 0.008) while no significant differences were detected for other targets. This quadruplex RT-qPCR assay will significantly enhance rapid surveillance of both ERVA and ERVB circulating and emerging strains with potential for interspecies transmission.
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Affiliation(s)
- Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Udeni B. R. Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Côme J. Thieulent
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Maria E. Barrandeguy
- Escuela de Veterinaria, Universidad del Salvador, Buenos Aires B1630, Argentina; (M.E.B.); (M.A.V.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
| | - Maria Aldana Vissani
- Escuela de Veterinaria, Universidad del Salvador, Buenos Aires B1630, Argentina; (M.E.B.); (M.A.V.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425, Argentina
| | - Viviana Parreño
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425, Argentina
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Gutierrez MB, de Assis RMS, de Andrade JDSR, Fialho AM, Fumian TM. Rotavirus A during the COVID-19 Pandemic in Brazil, 2020-2022: Emergence of G6P[8] Genotype. Viruses 2023; 15:1619. [PMID: 37631962 PMCID: PMC10458023 DOI: 10.3390/v15081619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 08/29/2023] Open
Abstract
Rotavirus A (RVA) remains a leading cause of acute gastroenteritis (AGE) hospitalizations in children worldwide. During the COVID-19 pandemic, a reduction in vaccination coverage in Brazil and elsewhere was observed, and some reports have demonstrated a reduction in AGE notifications during the pandemic. This study aims to investigate the diversity and prevalence of RVA genotypes in children and adults presenting with AGE symptoms in Brazil during the COVID-19 pandemic between 2020 and 2022. RVA was screened using RT-qPCR; then, G and P genotypes were characterized using one-step multiplex RT-PCR. A total of 2173 samples were investigated over the three-year period, and we detected RVA in 7.7% of samples (n = 167), being 15.5% in 2020, 0.5% in 2021, and 13.8% in 2022. Higher RVA prevalence was observed in the Northeastern region (19.3%) compared to the Southeastern (6.1%) and Southern regions (5.5%). The most affected age group was children aged between 0 and 6 months old; however, this was not statistically significant. Genotyping and phylogenetic analysis identified the emergence of G6P[8] during the period; moreover, it was detected in 10.6% of samples in 2020 and in 83.5% in 2022. In contrast, the prevalence of G3P[8], the previous dominant genotype, decreased from 72.3% in 2020 to 11.3% in 2022. We also identified unusual strains, such as G3P[9] and G9P[4], being sporadically detected during the period. This is the first report on the molecular epidemiology and surveillance of RVA during the COVID-19 pandemic period in Brazil. Our study provides evidence for the importance of maintaining high and sustainable levels of vaccine coverage to protect against RVA disease. Furthermore, it highlights the need to maintain nationwide surveillance in order to monitor future trends and changes in the epidemiology of RVA in Brazil.
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Affiliation(s)
| | | | | | | | - Tulio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (M.B.G.)
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Wang J, Pan YF, Yang LF, Yang WH, Lv K, Luo CM, Wang J, Kuang GP, Wu WC, Gou QY, Xin GY, Li B, Luo HL, Chen S, Shu YL, Guo D, Gao ZH, Liang G, Li J, Chen YQ, Holmes EC, Feng Y, Shi M. Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential. Nat Commun 2023; 14:4079. [PMID: 37429936 DOI: 10.1038/s41467-023-39835-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within individual bats, and hence the frequency of virus co-infection and spillover among them. We characterize the mammal-associated viruses in 149 individual bats sampled from Yunnan province, China, using an unbiased meta-transcriptomics approach. This reveals a high frequency of virus co-infection (simultaneous infection of bat individuals by multiple viral species) and spillover among the animals studied, which may in turn facilitate virus recombination and reassortment. Of note, we identify five viral species that are likely to be pathogenic to humans or livestock, based on phylogenetic relatedness to known pathogens or in vitro receptor binding assays. This includes a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV and SARS-CoV-2. In vitro assays indicate that this recombinant virus can utilize the human ACE2 receptor such that it is likely to be of increased emergence risk. Our study highlights the common occurrence of co-infection and spillover of bat viruses and their implications for virus emergence.
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Affiliation(s)
- Jing Wang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yuan-Fei Pan
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Fen Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Wei-Hong Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Kexin Lv
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Chu-Ming Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Juan Wang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Guo-Peng Kuang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Wei-Chen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Qin-Yu Gou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Gen-Yang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Bo Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Huan-le Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shoudeng Chen
- Molecular Imaging Center, Central Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong, China
| | - Yue-Long Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Deyin Guo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong Province, China
| | - Zi-Hou Gao
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Yun Feng
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China.
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
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Lagan P, Mooney MH, Lemon K. Genome analyses of species A rotavirus isolated from various mammalian hosts in Northern Ireland during 2013-2016. Virus Evol 2023; 9:vead039. [PMID: 37547380 PMCID: PMC10403756 DOI: 10.1093/ve/vead039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/25/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
Rotavirus group A (RVA) is the most important cause of acute diarrhoea and severe dehydration in young mammals. Infection in livestock is associated with significant mortality and economic losses and, together with wildlife reservoirs, acts as a potential source of zoonotic transmission. Therefore, molecular surveillance of circulating RVA strains in animal species is necessary to assess the risks posed to humans and their livestock. An RVA molecular epidemiological surveillance study on clinically diseased livestock species revealed high prevalence in cattle and pigs (31 per cent and 18 per cent, respectively) with significant phylogenetic diversity including a novel and divergent ovine artiodactyl DS-1-like constellation G10-P[15]-I2-R2-C2-M2-A11-N2-T6-E2-H3. An RVA gene reassortment occurred in an RVA asymptomatic pig and identified as a G5-P[13] strain, and a non-structural protein (NSP)2 gene had intergenomically reassorted with a human RVA strain (reverse zoonosis) and possessed a novel NSP4 enterotoxin E9 which may relate to the asymptomatic RVA infection. Analysis of a novel sheep G10-P[15] strain viral protein 4 gene imparts a putative homologous intergenic and interspecies recombination event, subsequently creating the new P[15] divergent lineage. While surveillance across a wider range of wildlife and exotic species identified generally negative or low prevalence, a novel RVA interspecies transmission in a non-indigenous pudu deer (zoo origin) with the constellation of G6-P[11]12-R2-C2-M2-A3-N2-T6-E2-H3 was detected at a viral load of 11.1 log10 copies/gram. The detection of novel emerging strains, interspecies reassortment, interspecies infection, and recombination of RVA circulating in animal livestock and wildlife reservoirs is of paramount importance to the RVA epidemiology and evolution for the One Health approach and post-human vaccine introduction era where highly virulent animal RVA genotypes have the potential to be zoonotically transmitted.
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Affiliation(s)
- Paula Lagan
- Virology, Veterinary Science Division, Agri-Food and Biosciences Institute, Stormont, Belfast BT4 3SD, UK
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast BT9 5DL, UK
| | - Mark H Mooney
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast BT9 5DL, UK
| | - Ken Lemon
- Virology, Veterinary Science Division, Agri-Food and Biosciences Institute, Stormont, Belfast BT4 3SD, UK
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Jampanil N, Kumthip K, Maneekarn N, Khamrin P. Genetic Diversity of Rotaviruses Circulating in Pediatric Patients and Domestic Animals in Thailand. Trop Med Infect Dis 2023; 8:347. [PMID: 37505643 PMCID: PMC10383398 DOI: 10.3390/tropicalmed8070347] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Rotavirus A is a highly contagious virus that causes acute gastroenteritis in humans and a wide variety of animals. In this review, we summarized the information on rotavirus described in the studies in the last decade (2008 to 2021) in Thailand, including the prevalence, seasonality, genetic diversity, and interspecies transmission. The overall prevalence of rotavirus infection in humans ranged from 15-33%. Rotavirus infection was detected throughout the year and most frequently in the dry and cold months, typically in March. The diversity of rotavirus genotypes varied year to year and from region to region. From 2008 to 2016, rotavirus G1P[8] was detected as the most predominant genotype in Thailand. After 2016, G1P[8] decreased significantly and other genotypes including G3P[8], G8P[8], and G9P[8] were increasingly detected from 2016 to 2020. Several uncommon rotavirus strains such as G1P[6], G4P[6], and G3P[10] have also been occasionally detected. In addition, most studies on rotavirus A infection in animals in Thailand from 2011 to 2021 reported the detection of rotavirus A in piglets and canine species. It was reported that rotavirus could cross the host species barrier between humans and animals through interspecies transmission and genetic reassortment mechanisms. The surveillance of rotavirus infection is crucial to identify the trend of rotavirus infection and the emergence of novel rotavirus genotypes in this country. The data provide information on rotavirus infection and the diversity of rotavirus genotypes circulating in the pre-vaccination period, and the data will be useful for the evaluation of the effectiveness of rotavirus vaccine implementation in Thailand.
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Affiliation(s)
- Nutthawadee Jampanil
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Emerging and Re-Emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Emerging and Re-Emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Emerging and Re-Emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai 50200, Thailand
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49
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Peng R, Li D, Wang J, Xiong G, Wang M, Liu D, Wei Y, Pang L, Sun X, Li H, Kong X, Shahar S, Duan Z. Reassortment and genomic analysis of a G9P[8]-E2 rotavirus isolated in China. Virol J 2023; 20:135. [PMID: 37349792 PMCID: PMC10286334 DOI: 10.1186/s12985-023-02064-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/07/2023] [Indexed: 06/24/2023] Open
Abstract
OBJECTIVE To isolate a prevalent G9P[8] group A rotavirus (RVA) (N4006) in China and investigate its genomic and evolutionary characteristics, with the goal of facilitating the development of a new rotavirus vaccine. METHODS The RVA G9P[8] genotype from a diarrhea sample was passaged in MA104 cells. The virus was evaluated by TEM, polyacrylamide gel electrophoresis, and indirect immunofluorescence assay. The complete genome of virus was obtained by RT-PCR and sequencing. The genomic and evolutionary characteristics of the virus were evaluated by nucleic acid sequence analysis with MEGA ver. 5.0.5 and DNASTAR software. The neutralizing epitopes of VP7 and VP4 (VP5* and VP8*) were analyzed using BioEdit ver. 7.0.9.0 and PyMOL ver. 2.5.2. RESULTS The RVA N4006 (G9P[8] genotype) was adapted in MA104 cells with a high titer (105.5 PFU/mL). Whole-genome sequence analysis showed N4006 to be a reassortant rotavirus of Wa-like G9P[8] RVA and the NSP4 gene of DS-1-like G2P[4] RVA, with the genotype constellation G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2). Phylogenetic analysis indicated that N4006 had a common ancestor with Japanese G9P[8]-E2 rotavirus. Neutralizing epitope analysis showed that VP7, VP5*, and VP8* of N4006 had low homology with vaccine viruses of the same genotype and marked differences with vaccine viruses of other genotypes. CONCLUSION The RVA G9P[8] genotype with the G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2) constellation predominates in China and may originate from reassortment between Japanese G9P[8] with Japanese DS-1-like G2P[4] rotaviruses. The antigenic variation of N4006 with the vaccine virus necessitates an evaluation of the effect of the rotavirus vaccine on G9P[8]-E2 genotype rotavirus.
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Affiliation(s)
- Rui Peng
- Department of Biosciences, Faculty of Sciences, Universiti Teknologi Malaysia, Johor Bahru, 81310 Malaysia
- NHC Key Laboratory of Medical Viruses and Viral Diseases, Institute of Viral Disease Prevention and Control, National Health Commission, Chinese Centre for Disease Control and Prevention, Beijing, 102206 China
- College of Life Science, Hengshui University, Hengshui, 053000 China
| | - Dandi Li
- NHC Key Laboratory of Medical Viruses and Viral Diseases, Institute of Viral Disease Prevention and Control, National Health Commission, Chinese Centre for Disease Control and Prevention, Beijing, 102206 China
| | - Jindong Wang
- Department of Pathogenic Biology, Weifang Medical University, Weifang, 261053 China
| | - Guangping Xiong
- College of Public Health, Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Mengxuan Wang
- NHC Key Laboratory of Medical Viruses and Viral Diseases, Institute of Viral Disease Prevention and Control, National Health Commission, Chinese Centre for Disease Control and Prevention, Beijing, 102206 China
| | - Dan Liu
- NHC Key Laboratory of Medical Viruses and Viral Diseases, Institute of Viral Disease Prevention and Control, National Health Commission, Chinese Centre for Disease Control and Prevention, Beijing, 102206 China
| | - Yuhang Wei
- College of Public Health, Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Lili Pang
- NHC Key Laboratory of Medical Viruses and Viral Diseases, Institute of Viral Disease Prevention and Control, National Health Commission, Chinese Centre for Disease Control and Prevention, Beijing, 102206 China
| | - Xiaoman Sun
- NHC Key Laboratory of Medical Viruses and Viral Diseases, Institute of Viral Disease Prevention and Control, National Health Commission, Chinese Centre for Disease Control and Prevention, Beijing, 102206 China
| | - Huiying Li
- NHC Key Laboratory of Medical Viruses and Viral Diseases, Institute of Viral Disease Prevention and Control, National Health Commission, Chinese Centre for Disease Control and Prevention, Beijing, 102206 China
| | - Xiangyu Kong
- NHC Key Laboratory of Medical Viruses and Viral Diseases, Institute of Viral Disease Prevention and Control, National Health Commission, Chinese Centre for Disease Control and Prevention, Beijing, 102206 China
| | - Saleha Shahar
- Department of Biosciences, Faculty of Sciences, Universiti Teknologi Malaysia, Johor Bahru, 81310 Malaysia
| | - Zhaojun Duan
- NHC Key Laboratory of Medical Viruses and Viral Diseases, Institute of Viral Disease Prevention and Control, National Health Commission, Chinese Centre for Disease Control and Prevention, Beijing, 102206 China
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50
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Raque M, Raev SA, Guo Y, Kick MK, Saif LJ, Vlasova AN. Host Cell Response to Rotavirus Infection with Emphasis on Virus-Glycan Interactions, Cholesterol Metabolism, and Innate Immunity. Viruses 2023; 15:1406. [PMID: 37515094 PMCID: PMC10385841 DOI: 10.3390/v15071406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Although rotavirus A (RVA) is the primary cause of acute viral gastroenteritis in children and young animals, mechanisms of its replication and pathogenesis remain poorly understood. We previously demonstrated that the neuraminidase-mediated removal of terminal sialic acids (SAs) significantly enhanced RVA-G9P[13] replication, while inhibiting RVA-G5P[7] replication. In this study, we compared the transcriptome responses of porcine ileal enteroids (PIEs) to G5P[7] vs. G9P[13] infections, with emphasis on the genes associated with immune response, cholesterol metabolism, and host cell attachment. The analysis demonstrated that G9P[13] infection led to a robust modulation of gene expression (4093 significantly modulated genes vs. 488 genes modulated by G5P[7]) and a significant modulation of glycosyltransferase-encoding genes. The two strains differentially affected signaling pathways related to immune response, with G9P[13] mostly upregulating and G5P[7] inhibiting them. Both RVAs modulated the expression of genes encoding for cholesterol transporters. G9P[13], but not G5P[7], significantly affected the ceramide synthesis pathway known to affect both cholesterol and glycan metabolism. Thus, our results highlight the unique mechanisms regulating cellular response to infection caused by emerging/re-emerging and historical RVA strains relevant to RVA-receptor interactions, metabolic pathways, and immune signaling pathways that are critical in the design of effective control strategies.
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Affiliation(s)
- Molly Raque
- Center for Food Animal Health Research Program, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Department of Animal Sciences, College of Food Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 43210, USA
| | - Sergei A Raev
- Center for Food Animal Health Research Program, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Department of Animal Sciences, College of Food Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 43210, USA
| | - Yusheng Guo
- Center for Food Animal Health Research Program, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Department of Animal Sciences, College of Food Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 43210, USA
| | - Maryssa K Kick
- Center for Food Animal Health Research Program, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Department of Animal Sciences, College of Food Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 43210, USA
| | - Linda J Saif
- Center for Food Animal Health Research Program, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Department of Animal Sciences, College of Food Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 43210, USA
| | - Anastasia N Vlasova
- Center for Food Animal Health Research Program, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Department of Animal Sciences, College of Food Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 43210, USA
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