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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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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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3
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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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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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5
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Manjate F, João ED, Mwangi P, Chirinda P, Mogotsi M, Messa A, Garrine M, Vubil D, Nobela N, Nhampossa T, Acácio S, Tate JE, Parashar U, Weldegebriel G, Mwenda JM, Alonso PL, Cunha C, Nyaga M, Mandomando I. Genomic characterization of the rotavirus G3P[8] strain in vaccinated children, reveals possible reassortment events between human and animal strains in Manhiça District, Mozambique. Front Microbiol 2023; 14:1193094. [PMID: 37342557 PMCID: PMC10277737 DOI: 10.3389/fmicb.2023.1193094] [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: 03/24/2023] [Accepted: 04/20/2023] [Indexed: 06/23/2023] Open
Abstract
Mozambique introduced the rotavirus vaccine (Rotarix®; GlaxoSmithKline Biologicals, Rixensart, Belgium) in 2015, and since then, the Centro de Investigação em Saúde de Manhiça has been monitoring its impact on rotavirus-associated diarrhea and the trend of circulating strains, where G3P[8] was reported as the predominant strain after the vaccine introduction. Genotype G3 is among the most commonly detected Rotavirus strains in humans and animals, and herein, we report on the whole genome constellation of G3P[8] detected in two children (aged 18 months old) hospitalized with moderate-to-severe diarrhea at the Manhiça District Hospital. The two strains had a typical Wa-like genome constellation (I1-R1-C1-M1-A1-N1-T1-E1-H1) and shared 100% nucleotide (nt) and amino acid (aa) identities in 10 gene segments, except for VP6. Phylogenetic analysis demonstrated that genome segments encoding VP7, VP6, VP1, NSP3, and NSP4 of the two strains clustered most closely with porcine, bovine, and equine strains with identities ranging from 86.9-99.9% nt and 97.2-100% aa. Moreover, they consistently formed distinct clusters with some G1P[8], G3P[8], G9P[8], G12P[6], and G12P[8] strains circulating from 2012 to 2019 in Africa (Mozambique, Kenya, Rwanda, and Malawi) and Asia (Japan, China, and India) in genome segments encoding six proteins (VP2, VP3, NSP1-NSP2, NSP5/6). The identification of segments exhibiting the closest relationships with animal strains shows significant diversity of rotavirus and suggests the possible occurrence of reassortment events between human and animal strains. This demonstrates the importance of applying next-generation sequencing to monitor and understand the evolutionary changes of strains and evaluate the impact of vaccines on strain diversity.
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Affiliation(s)
- Filomena Manjate
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Eva D. João
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Peter Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Percina Chirinda
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Milton Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Augusto Messa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Marcelino Garrine
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Delfino Vubil
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Nélio Nobela
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Tacilta Nhampossa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde, Ministério da Saúde, Marracuene, Mozambique
| | - Sozinho Acácio
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde, Ministério da Saúde, Marracuene, Mozambique
| | - Jacqueline E. Tate
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, United States
| | - Umesh Parashar
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, United States
| | - Goitom Weldegebriel
- African Rotavirus Surveillance Network, Immunization, Vaccines, and Development Program, Regional Office for Africa, World Health Organization, Brazzaville, Democratic Republic of Congo
| | - Jason M. Mwenda
- African Rotavirus Surveillance Network, Immunization, Vaccines, and Development Program, Regional Office for Africa, World Health Organization, Brazzaville, Democratic Republic of Congo
| | - Pedro L. Alonso
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Celso Cunha
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Martin Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Inácio Mandomando
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde, Ministério da Saúde, Marracuene, Mozambique
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
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Kunić V, Mikuletič T, Kogoj R, Koritnik T, Steyer A, Šoprek S, Tešović G, Konjik V, Roksandić Križan I, Prišlin M, Jemeršić L, Brnić D. Interspecies transmission of porcine-originated G4P[6] rotavirus A between pigs and humans: a synchronized spatiotemporal approach. Front Microbiol 2023; 14:1194764. [PMID: 37283926 PMCID: PMC10239803 DOI: 10.3389/fmicb.2023.1194764] [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: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 06/08/2023] Open
Abstract
As a leading viral cause of acute gastroenteritis in both humans and pigs, rotavirus A (RVA) poses a potential public health concern. Although zoonotic spillover of porcine RVA strains to humans is sporadic, it has been detected worldwide. The origin of chimeric human-animal strains of RVA is closely linked to the crucial role of mixed genotypes in driving reassortment and homologous recombination, which play a major role in shaping the genetic diversity of RVA. To better understand how genetically intertwined porcine and zoonotic human-derived G4P[6] RVA strains are, the present study employed a spatiotemporal approach to whole-genome characterization of RVA strains collected during three consecutive RVA seasons in Croatia (2018-2021). Notably, sampled children under 2 years of age and weanling piglets with diarrhea were included in the study. In addition to samples tested by real-time RT-PCR, genotyping of VP7 and VP4 gene segments was conducted. The unusual genotype combinations detected in the initial screening, including three human and three porcine G4P[6] strains, were subjected to next-generation sequencing, followed by phylogenetic analysis of all gene segments, and intragenic recombination analysis. Results showed a porcine or porcine-like origin for each of the eleven gene segments in all six RVA strains. The G4P[6] RVA strains detected in children most likely resulted from porcine-to-human interspecies transmission. Furthermore, the genetic diversity of Croatian porcine and porcine-like human G4P[6] strains was propelled by reassortment events between porcine and porcine-like human G4P[6] RVA strains, along with homologous intragenotype and intergenotype recombinations in VP4, NSP1, and NSP3 segments. Described concurrent spatiotemporal approach in investigating autochthonous human and animal RVA strains is essential in drawing relevant conclusions about their phylogeographical relationship. Therefore, continuous surveillance of RVA, following the One Health principles, may provide relevant data for assessing the impact on the protectiveness of currently available vaccines.
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Affiliation(s)
- Valentina Kunić
- Virology Department, Croatian Veterinary Institute, Zagreb, Croatia
| | - Tina Mikuletič
- School of Medicine, Institute for Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Rok Kogoj
- School of Medicine, Institute for Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Tom Koritnik
- Public Health Microbiology Department, National Laboratory of Health, Environment, and Food, Ljubljana, Slovenia
| | - Andrej Steyer
- Public Health Microbiology Department, National Laboratory of Health, Environment, and Food, Ljubljana, Slovenia
| | - Silvija Šoprek
- Department for Pediatric Infectious Diseases, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Zagreb, Croatia
| | - Goran Tešović
- Department for Pediatric Infectious Diseases, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Zagreb, Croatia
- School of Medicine, University of Zagreb, Zagreb, Croatia
| | | | | | - Marina Prišlin
- Virology Department, Croatian Veterinary Institute, Zagreb, Croatia
| | - Lorena Jemeršić
- Virology Department, Croatian Veterinary Institute, Zagreb, Croatia
| | - Dragan Brnić
- Virology Department, Croatian Veterinary Institute, Zagreb, Croatia
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Genomic Constellation of Human Rotavirus G8 Strains in Brazil over a 13-Year Period: Detection of the Novel Bovine-like G8P[8] Strains with the DS-1-like Backbone. Viruses 2023; 15:v15030664. [PMID: 36992373 PMCID: PMC10056101 DOI: 10.3390/v15030664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Rotavirus (RVA) G8 is frequently detected in animals, but only occasionally in humans. G8 strains, however, are frequently documented in nations in Africa. Recently, an increase in G8 detection was observed outside Africa. The aims of the study were to monitor G8 infections in the Brazilian human population between 2007 and 2020, undertake the full-genotype characterization of the four G8P[4], six G8P[6] and two G8P[8] RVA strains and conduct phylogenetic analysis in order to understand their genetic diversity and evolution. A total of 12,978 specimens were screened for RVA using ELISA, PAGE, RT-PCR and Sanger sequencing. G8 genotype represented 0.6% (15/2434) of the entirely RVA-positive samples. G8P[4] comprised 33.3% (5/15), G8P[6] 46.7% (7/15) and G8P[8] 20% (3/15). All G8 strains showed a short RNA pattern. All twelve selected G8 strains displayed a DS-1-like genetic backbone. The whole-genotype analysis on a DS-1-like backbone identified four different genotype-linage constellations. According to VP7 analysis, the Brazilian G8P[8] strains with the DS-1-like backbone strains were derived from cattle and clustered with newly DS-1-like G1/G3/G9/G8P[8] strains and G2P[4] strains. Brazilian IAL-R193/2017/G8P[8] belonged to a VP1/R2.XI lineage and were grouped with bovine-like G8P[8] strains with the DS-1-like backbone strains detected in Asia. Otherwise, the Brazilian IAL-R558/2017/G8P[8] possess a “Distinct” VP1/R2 lineage never previously described and grouped apart from any of the DS-1-like reference strains. Collectively, our findings suggest that the Brazilian bovine-like G8P[8] strains with the DS-1-like backbone strains are continuously evolving and likely reassorting with local RVA strains rather than directly relating to imports from Asia. The Brazilian G8P[6]-DS-1-like strains have been reassorted with nearby co-circulating American strains of the same DS-1 genotype constellation. However, phylogenetic analyses revealed that these strains have some genetic origin from Africa. Finally, rather than being African-born, Brazilian G8P[4]-DS-1-like strains were likely imported from Europe. None of the Brazilian G8 strains examined here exhibited signs of recent zoonotic reassortment. G8 strains continued to be found in Brazil according to their intermittent and localized pattern, thus, does not suggest that a potential emergence is taking place in the country. Our research demonstrates the diversity of G8 RVA strains in Brazil and adds to the understanding of G8P[4]/P[6]/P[8] RVA genetic diversity and evolution on a global scale.
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8
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Prevalence and genomic characterization of rotavirus group A genotypes in piglets from in southern highlands and eastern Tanzania. Heliyon 2022; 8:e11750. [DOI: 10.1016/j.heliyon.2022.e11750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/27/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
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9
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Zhang L, Jiang Z, Zhou Z, Sun J, Yan S, Gao W, Shao Y, Bai Y, Wu Y, Yan Z, Sheng S, Lai A, Su S. A TaqMan Probe-Based Multiplex Real-Time PCR for Simultaneous Detection of Porcine Epidemic Diarrhea Virus Subtypes G1 and G2, and Porcine Rotavirus Groups A and C. Viruses 2022; 14:v14081819. [PMID: 36016441 PMCID: PMC9413770 DOI: 10.3390/v14081819] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/14/2022] [Accepted: 08/14/2022] [Indexed: 12/14/2022] Open
Abstract
Porcine viral diarrhea diseases affect the swine industry, resulting in significant economic losses. Porcine epidemic diarrhea virus (PEDV) genotypes G1 and G2, and groups A and C of the porcine rotavirus, are major etiological agents of severe gastroenteritis and profuse diarrhea, particularly among piglets, with mortality rates of up to 100%. Based on the high prevalence rate and frequent co-infection of PEDV, RVA, and RVC, close monitoring is necessary to avoid greater economic losses. We have developed a multiplex TaqMan probe-based real-time PCR for the rapid simultaneous detection and differentiation of PEDV subtypes G1 and G2, RVA, and RVC. This test is highly sensitive, as the detection limits were 20 and 100 copies/μL for the G1 and G2 subtypes of PEDV, respectively, and 50 copies/μL for RVA and RVC, respectively. Eighty-eight swine clinical samples were used to evaluate this new test. The results were 100% in concordance with the standard methods. Since reassortment between porcine and human rotaviruses has been reported, this multiplex test not only provides a basis for the management of swine diarrheal viruses, but also has the potential to impact public health as well.
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Affiliation(s)
- Letian Zhang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiwen Jiang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zitong Zhou
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiumeng Sun
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Shiyu Yan
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenting Gao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuekun Shao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuhe Bai
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yifan Wu
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zefei Yan
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Shouzhi Sheng
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Alexander Lai
- School of Science, Technology, Engineering, and Mathematics, Kentucky State University, Frankfort, KY 40601, USA
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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10
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Wandera EA, Hatazawa R, Tsutsui N, Kurokawa N, Kathiiko C, Mumo M, Waithira E, Wachira M, Mwaura B, Nyangao J, Khamadi SA, Njau J, Fukuda S, Murata T, Taniguchi K, Ichinose Y, Kaneko S, Komoto S. Genomic characterization of an African G4P[6] human rotavirus strain identified in a diarrheic child in Kenya: Evidence for porcine-to-human interspecies transmission and reassortment. INFECTION GENETICS AND EVOLUTION 2021; 96:105133. [PMID: 34767977 DOI: 10.1016/j.meegid.2021.105133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 01/04/2023]
Abstract
Human rotavirus strains having the unconventional G4P[6] genotype have been sporadically identified in diarrheic patients in different parts of the world. However, the whole genome of only one human G4P[6] strain from Africa (central Africa) has been sequenced and analyzed, and thus the exact origin and evolutionary pattern of African G4P[6] strains remain to be elucidated. In this study, we characterized the full genome of an African G4P[6] strain (RVA/Human-wt/KEN/KCH148/2019/G4P[6]) identified in a stool specimen from a diarrheic child in Kenya. Full genome analysis of strain KCH148 revealed a unique Wa-like genogroup constellation: G4-P[6]-I1-R1-C1-M1-A1-N1-T7-E1-H1. NSP3 genotype T7 is commonly found in porcine rotavirus strains. Furthermore, phylogenetic analysis showed that 10 of the 11 genes of strain KCH148 (VP7, VP4, VP6, VP1-VP3, NSP1, and NSP3-NSP5) appeared to be of porcine origin, the remaining NSP2 gene appearing to be of human origin. Therefore, strain KCH148 was found to have a porcine rotavirus backbone and thus is likely to be of porcine origin. Furthermore, strain KCH148 is assumed to have been derived through interspecies transmission and reassortment events involving porcine and human rotavirus strains. To our knowledge, this is the first report on full genome-based characterization of a human G4P[6] strain from east Africa. Our observations demonstrated the diversity of human G4P[6] strains in Africa, and provide important insights into the origin and evolutionary pattern of zoonotic G4P[6] strains on the African continent.
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Affiliation(s)
- Ernest Apondi Wandera
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Naohisa Tsutsui
- Department of Project Planning and Management, Mitsubishi Tanabe Pharma Corporation, Chuo-ku, Tokyo 103-8405, Japan
| | - Natsuki Kurokawa
- Department of Project Planning and Management, Mitsubishi Tanabe Pharma Corporation, Chuo-ku, Tokyo 103-8405, Japan
| | - Cyrus Kathiiko
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Maurine Mumo
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Eunice Waithira
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Mary Wachira
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Boniface Mwaura
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - James Nyangao
- Center for Virus Research, KEMRI, Nairobi 54840-00200, Kenya
| | | | - Joseph Njau
- Department of Pediatrics, Kiambu County Referral Hospital, Kiambu 39-00900, Kenya
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Yoshio Ichinose
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Satoshi Kaneko
- Kenya Research Station, Institute of Tropical Medicine (NEKKEN), Kenya Medical Research Institute (KEMRI)/Nagasaki University, Nairobi 19993-00202, Kenya
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan.
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11
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Saied AA, Metwally AA, Mohamed HMA, Haridy MAM. The contribution of bovines to human health against viral infections. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:46999-47023. [PMID: 34272669 PMCID: PMC8284698 DOI: 10.1007/s11356-021-14941-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/12/2021] [Indexed: 04/12/2023]
Abstract
In the last 40 years, novel viruses have evolved at a much faster pace than other pathogens. Viral diseases pose a significant threat to public health around the world. Bovines have a longstanding history of significant contributions to human nutrition, agricultural, industrial purposes, medical research, drug and vaccine development, and livelihood. The life cycle, genomic structures, viral proteins, and pathophysiology of bovine viruses studied in vitro paved the way for understanding the human counterparts. Calf model has been used for testing vaccines against RSV, papillomavirus vaccines and anti-HCV agents were principally developed after using the BPV and BVDV model, respectively. Some bovine viruses-based vaccines (BPIV-3 and bovine rotaviruses) were successfully developed, clinically tried, and commercially produced. Cows, immunized with HIV envelope glycoprotein, produced effective broadly neutralizing antibodies in their serum and colostrum against HIV. Here, we have summarized a few examples of human viral infections for which the use of bovines has contributed to the acquisition of new knowledge to improve human health against viral infections covering the convergence between some human and bovine viruses and using bovines as disease models. Additionally, the production of vaccines and drugs, bovine-based products were covered, and the precautions in dealing with bovines and bovine-based materials.
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Affiliation(s)
- AbdulRahman A Saied
- Department of Food Establishments Licensing (Aswan Branch), National Food Safety Authority (NFSA), Aswan, 81511, Egypt.
- Touristic Activities and Interior Offices Sector (Aswan Office), Ministry of Tourism and Antiquities, Aswan, 81511, Egypt.
| | - Asmaa A Metwally
- Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Aswan University, Aswan, 81511, Egypt
| | - Hams M A Mohamed
- Department of Microbiology, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt
| | - Mohie A M Haridy
- Department of Pathology and Clinical Pathology, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt.
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12
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Bandeira RDS, Souto LCDS, de Souza LC, Linhares AC, Mascarenhas JDP. Detection of a novel species A, DS-1-like, G4P[6] rotavirus strain from a Brazilian child with gastroenteritis. J Med Virol 2021; 94:610-615. [PMID: 34427937 DOI: 10.1002/jmv.27283] [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: 05/26/2021] [Revised: 08/11/2021] [Accepted: 08/18/2021] [Indexed: 11/06/2022]
Abstract
Rotaviruses belonging to species A (RVA) remain among the most common causes of severe gastroenteritis in children aged <5 years, leading to substantial morbidity and mortality worldwide. Genome reassortment events between two human strains or human and animal strains represent one of the mechanisms which appear to generate the broad genetic variability of circulating. According to a nucleotide, sequence-based classification system, RVA strains are currently classified into three genotype constellations including Wa-like (genogroup I), DS-1-like (genogroup II), and AU-like (genogroup III). The present study reports the detection of an unusual RVA G4P[6] strain (coded as strain HSE005), which might have originated from a natural reassortment event between human and animal RVA strains. Molecular characterization of this isolate showed that it belonged to genogroup II, genotype G4P[6]. In addition, two genes (VP3 and NSP4) of this strain denoted evidence of reassortment events involving strains of distinct zoonotic evolutionary origins. Therefore, we propose that a new G4P[6] strain was identified, highlighting a possible first zoonotic transmission including a reassortment event that involved the VP3 gene.
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Affiliation(s)
- Renato da Silva Bandeira
- Brazilian Ministry of Health, Health Surveillance Secretariat, Evandro Chagas Institute, Postgraduate program in virology, Virology Section, Levilândia, Ananindeua-Pará, Brazil
| | - Lizandra Caroline Dos Santos Souto
- Brazilian Ministry of Health, Health Surveillance Secretariat, Evandro Chagas Institute, Scholarship of Graduating Scientific Program, Virology Section, Levilândia, Ananindeua-Pará, Brazil
| | - Layse Costa de Souza
- Brazilian Ministry of Health, Health Surveillance Secretariat, Evandro Chagas Institute, Scholarship of Graduating Scientific Program, Virology Section, Levilândia, Ananindeua-Pará, Brazil
| | - Alexandre C Linhares
- Brazilian Ministry of Health, Health Surveillance Secretariat, Evandro Chagas Institute, Virology section, Levilândia, Ananindeua-Pará, Brazil
| | - Joana D'Arc Pereira Mascarenhas
- Brazilian Ministry of Health, Health Surveillance Secretariat, Evandro Chagas Institute, Virology section, Levilândia, Ananindeua-Pará, Brazil
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13
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Tacharoenmuang R, Guntapong R, Upachai S, Singchai P, Fukuda S, Ide T, Hatazawa R, Sutthiwarakom K, Kongjorn S, Onvimala N, Luechakham T, Ruchusatsawast K, Kawamura Y, Sriwanthana B, Motomura K, Tatsumi M, Takeda N, Yoshikawa T, Murata T, Uppapong B, Taniguchi K, Komoto S. Full genome-based characterization of G4P[6] rotavirus strains from diarrheic patients in Thailand: Evidence for independent porcine-to-human interspecies transmission events. Virus Genes 2021; 57:338-357. [PMID: 34106412 DOI: 10.1007/s11262-021-01851-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/17/2021] [Indexed: 12/18/2022]
Abstract
The exact evolutionary patterns of human G4P[6] rotavirus strains remain to be elucidated. Such strains possess unique and strain-specific genotype constellations, raising the question of whether G4P[6] strains are primarily transmitted via independent interspecies transmission or human-to-human transmission after interspecies transmission. Two G4P[6] rotavirus strains were identified in fecal specimens from hospitalized patients with severe diarrhea in Thailand, namely, DU2014-259 (RVA/Human-wt/THA/DU2014-259/2014/G4P[6]) and PK2015-1-0001 (RVA/Human-wt/THA/PK2015-1-0001/2015/G4P[6]). Here, we analyzed the full genomes of the two human G4P[6] strains, which provided the opportunity to study and confirm their evolutionary origin. On whole genome analysis, both strains exhibited a unique Wa-like genotype constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The NSP1 genotype A8 is commonly found in porcine rotavirus strains. Furthermore, on phylogenetic analysis, each of the 11 genes of strains DU2014-259 and PK2015-1-0001 appeared to be of porcine origin. On the other hand, the two study strains consistently formed distinct clusters for nine of the 11 gene segments (VP4, VP6, VP1-VP3, and NSP2-NSP5), strongly indicating the occurrence of independent porcine-to-human interspecies transmission events. Our observations provide important insights into the origin of zoonotic G4P[6] strains, and into the dynamic interaction between porcine and human rotavirus strains.
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Affiliation(s)
- Ratana Tacharoenmuang
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Ratigorn Guntapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Sompong Upachai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Phakapun Singchai
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Saori Fukuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Riona Hatazawa
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Karun Sutthiwarakom
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Santip Kongjorn
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Napa Onvimala
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Tipsuda Luechakham
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | | | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Busarawan Sriwanthana
- Medical Sciences Technical Office, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Kazushi Motomura
- Thailand-Japan Research Collaboration Center on Emerging and Re-Emerging Infections, Nonthaburi, 11000, Thailand
- Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Masashi Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-Emerging Infections, Nonthaburi, 11000, Thailand
| | - Naokazu Takeda
- Thailand-Japan Research Collaboration Center on Emerging and Re-Emerging Infections, Nonthaburi, 11000, Thailand
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Ballang Uppapong
- National Institute of Health, Department of Medical Sciences, Nonthaburi, 11000, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan.
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14
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Boene SS, João ED, Strydom A, Munlela B, Chissaque A, Bauhofer AFL, Nabetse E, Latifo D, Cala A, Mapaco L, Chilaúle J, O'Neill HG, de Deus N. Prevalence and genome characterization of porcine rotavirus A in southern Mozambique. INFECTION GENETICS AND EVOLUTION 2020; 87:104637. [PMID: 33232806 DOI: 10.1016/j.meegid.2020.104637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/29/2020] [Accepted: 11/18/2020] [Indexed: 10/22/2022]
Abstract
Rotavirus A (RVA) is an important pathogen causing gastroenteritis in many species, including humans and pigs. The objective of this study was to determine the prevalence of RVA in pigs from smallholdings and commercial farms in southern Mozambique and characterize the complete genomes of selected strains. RVA was detected at a rate of 11.8% (n = 288), of which 7.6% was detected at commercial farms and 4.2% at smallholdings. The whole genomes of eight rotavirus strains were determined using an Illumina MiSeq platform. Seven displayed a G9P[13] and one a G4P[6] genotype combination, all with a typical porcine backbone (I1/5-R1-C1-M1-A1/8-N1-T1/7-E1-H1). Phylogenetic analysis indicated that the seven G9P[13] strains were in fact one strain that circulated on a commercial pig farm. The genome segments of this strain clustered with diverse segments of human and porcine RVA strains from various Asian countries. Analysis of the G4P[6] strain revealed four distinct genome segments (VP2, VP4, VP6 and VP7) and five genome segments closely related to South African porcine rotavirus strains (NSP1, NSP3, NSP4, NSP5 and VP1). These results suggest that both the G4P[6] and the G9P[13] strains possibly emerged through multiple reassortment events. The presence of these strains on the commercial farms and smallholdings calls for a more in-depth surveillance of rotavirus in Mozambique.
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Affiliation(s)
- Simone S Boene
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique.
| | - Eva D João
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Amy Strydom
- Department of Microbial, Biochemical and Food Biotechnology, University of Free State, Bloemfontein, South Africa.
| | - Benilde Munlela
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Assucênio Chissaque
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Adilson Fernando Loforte Bauhofer
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Elvino Nabetse
- Departamento de Pecuária, Ministério de Agricultura e Desenvolvimento Rural, Maputo, Mozambique
| | - Dalilo Latifo
- Departamento de Pecuária, Ministério de Agricultura e Desenvolvimento Rural, Maputo, Mozambique
| | - Aida Cala
- Direcção de Ciências Animais, Agrarian Investigation Institute of Mozambique (DCA-IIAM), Maputo, Mozambique
| | - Lourenço Mapaco
- Direcção de Ciências Animais, Agrarian Investigation Institute of Mozambique (DCA-IIAM), Maputo, Mozambique
| | | | - Hester G O'Neill
- Department of Microbial, Biochemical and Food Biotechnology, University of Free State, Bloemfontein, South Africa.
| | - Nilsa de Deus
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Departamento de Ciências Biológicas, Universidade Eduardo Mondlane, Maputo, Mozambique
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15
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Flores PS, Costa FB, Amorim AR, Mendes GS, Rojas M, Santos N. Rotavirus A, C, and H in Brazilian pigs: potential for zoonotic transmission of RVA. J Vet Diagn Invest 2020; 33:129-135. [PMID: 33090086 DOI: 10.1177/1040638720967673] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rotaviruses (RVs) have been identified as one of the main infectious causes of diarrhea in young pigs. We determined the prevalence of rotavirus A (RVA), C (RVC), and H (RVH) in pigs on a Brazilian farm. Samples were screened by reverse-transcription (RT)-PCR, and samples positive for RVA were genotyped by PCR amplification and sequencing analysis. Of the 329 fecal samples analyzed, 102 (30.9%) were positive for RV, 25 (7.6%) contained RVA only, 32 (9.7%) contained RVC only, and 31 (9.4%) contained RVH only. Co-circulation, the presence of ≥ 2 RVs in a sample, was detected in 14 (4.2%) samples. Of the 15 animals with diarrhea, 6 (40%) were positive for RV, and of the 314 asymptomatic animals, 96 (30.6%) were positive for RV; there was no statistically significant difference between the 2 groups (p = 0.441). Genotyping of RVA strains showed co-circulation of genotypes G1, G3, G9-P[8]-I1, and I2-E1. Phylogenetic analysis showed that some of the RVA genotypes found in pigs had high percentages of identity when compared with reference strains from humans, which suggests interspecies transmission. Because RVs may be zoonotic, excretion of RVs into the environment can result in transmission to agricultural workers causing interspecies infections and allowing the emergence of new reassorted viruses.
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Affiliation(s)
- Patrícia S Flores
- Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio B Costa
- Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ariane R Amorim
- Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriella S Mendes
- Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Miguel Rojas
- Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Laboratorio de Microbiologia y Parasitologia, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima, Peru.,Current address: Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Norma Santos
- Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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16
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Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia. Pathogens 2020; 9:pathogens9080663. [PMID: 32824526 PMCID: PMC7460411 DOI: 10.3390/pathogens9080663] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 11/25/2022] Open
Abstract
A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 is often observed in porcine strains. Phylogenetic analyses showed that VP6, VP7, NSP2, NSP4, and NSP5 genes were closely related to cognate gene sequences of porcine strains (e.g., RVA/Pig-wt/CHN/DZ-2/2013/G5P[X] for VP7) from the NCBI database, while VP1, VP3, VP4, and NSP3 were closely related to porcine-like human strains (e.g., RVA/Human-wt/CHN/E931/2008/G4P[6] for VP1, and VP3). On the other hand, the origin of the VP2 was not clear from our analyses, as it was not only close to both porcine (e.g., RVA/Pig-tc/CHN/SWU-1C/2018/G9P[13]) and porcine-like human strains (e.g., RVA/Human-wt/LKA/R1207/2009/G4P[6]) but also to three human strains (e.g., RVA/Human-wt/USA/1476/1974/G1P[8]). The VP7 gene was located in lineage II that comprised only porcine strains, which suggests the occurrence of independent porcine-to-human reassortment events. The study strain may have collectively been derived through interspecies transmission, or through reassortment event(s) involving strains of porcine and porcine-like human origin. The results of this study underline the importance of whole-genome characterisation of rotavirus strains and provide insights into interspecies transmissions from porcine to humans.
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Malakalinga JJ, Misinzo G, Msalya GM, Kazwala RR. Rotavirus Burden, Genetic Diversity and Impact of Vaccine in Children under Five in Tanzania. Pathogens 2019; 8:pathogens8040210. [PMID: 31671824 PMCID: PMC6963457 DOI: 10.3390/pathogens8040210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/27/2019] [Accepted: 10/07/2019] [Indexed: 01/17/2023] Open
Abstract
In Tanzania, rotavirus infections are responsible for 72% of diarrhea deaths in children under five. The Rotarix vaccine was introduced in early 2013 to mitigate rotavirus infections. Understanding the disease burden and virus genotype trends over time is important for assessing the impact of rotavirus vaccine in Tanzania. When assessing the data for this review, we found that deaths of children under five declined after vaccine introduction, from 8171/11,391 (72% of diarrhea deaths) in 2008 to 2552/7087 (36% of diarrhea deaths) in 2013. Prior to vaccination, the prevalence of rotavirus infections in children under five was 18.1–43.4%, 9.8–51%, and 29–41% in Dar es Salaam, Mwanza and Tanga, respectively, and after the introduction of vaccines, these percentages declined to 17.4–23.5%, 16–19%, and 10–29%, respectively. Rotaviruses in Tanzania are highly diverse, and include genotypes of animal origin in children under five. Of the genotypes, 10%, 28%, and 7% of the strains are untypable in Dar es Salaam, Tanga, and Zanzibar, respectively. Mixed rotavirus genotype infection accounts for 31%, 29%, and 12% of genotypes in Mwanza, Tanga and Zanzibar, respectively. The vaccine effectiveness ranges between 53% and 75% in Mwanza, Manyara and Zanzibar. Rotavirus vaccination has successfully reduced the rotavirus burden in Tanzania; however, further studies are needed to better understand the relationship between the wildtype strain and the vaccine strain as well as the zoonotic potential of rotavirus in the post-vaccine era.
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Affiliation(s)
- Joseph J Malakalinga
- Food and Microbiology Laboratory, Tanzania Bureau of Standards, Ubungo Area, Morogoro Road/Sam Nujoma Road, P.O. Box 9524, Dar es Salaam, Tanzania.
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Africa Centre of Excellence for Infectious Diseases of Humans and Animals in Eastern and Southern Africa (ACE), Sokoine University of Agriculture (SUA), P.O. Box 3297, Chuo Kikuu, SUA, Morogoro, Tanzania.
| | - Gerald Misinzo
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Africa Centre of Excellence for Infectious Diseases of Humans and Animals in Eastern and Southern Africa (ACE), Sokoine University of Agriculture (SUA), P.O. Box 3297, Chuo Kikuu, SUA, Morogoro, Tanzania.
| | - George M Msalya
- Department of Animal, Aquaculture and Range Sciences, College of Agriculture, Sokoine University of Agriculture, P.O. Box 3004, Morogoro, Tanzania.
| | - Rudovick R Kazwala
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3021, Morogoro, Tanzania.
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de Barros BDCV, Chagas EN, Bezerra LW, Ribeiro LG, Duarte Júnior JWB, Pereira D, da Penha Junior ET, Silva JR, Bezerra DAM, Bandeira RS, Pinheiro HHC, Guerra SDFDS, Guimarães RJDPSE, Mascarenhas JDP. Rotavirus A in wild and domestic animals from areas with environmental degradation in the Brazilian Amazon. PLoS One 2018; 13:e0209005. [PMID: 30562373 PMCID: PMC6298726 DOI: 10.1371/journal.pone.0209005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
Acute gastroenteritis is one of the main causes of mortality in humans and young animals. Domestic and mainly wild animals such as bats, small rodents and birds are highly diversified animals in relation to their habitats and ecological niches and are widely distributed geographically in environments of forest fragmentation in some areas of the Amazon, being considered important sources for viruses that affect humans and other animals. Due to the anthropical activities, these animals changed their natural habitat and adapted to urbanized environments, thus representing risks to human and animal health. Although the knowledge of the global diversity of enteric viruses is scarce, there are reports demonstrating the detection of rotavirus in domestic animals and animals of productive systems, such as bovines and pigs. The present study investigated the prevalence of Rotavirus A in 648 fecal samples of different animal species from the northeastern mesoregion of the state of Pará, Brazil, which is characterized as an urbanized area with forest fragments. The fecal specimens were collected from October 2014 to April 2016 and subjected to a Qualitative Real-Time Polymerase Chain Reaction (RT-qPCR), using the NSP3 gene as a target. It was observed that 27.5% (178/648) of the samples presented positive results for RVA, with 178 samples distributed in birds (23.6%), canines (21.35%), chiropterans (17.98%), bovines (14.6%), horses (8.43%), small rodents (6.74%), pigs (3.93%) and felines (3.37%), demonstrating the circulation of RVA in domestic animals and suggesting that such proximity could cause transmissions between different species and the occurrence of rearrangements in the genome of RVA as already described in the literature, associated to the traces of environmental degradation in the studied areas.
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Affiliation(s)
| | | | | | | | | | - Diego Pereira
- Amazon Metropolitan University Center, Belém, Pará, Brazil
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Establishment of porcine enterocyte/myofibroblast co-cultures for the growth of porcine rota- and coronaviruses. Sci Rep 2018; 8:15195. [PMID: 30315177 PMCID: PMC6185943 DOI: 10.1038/s41598-018-33305-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/26/2018] [Indexed: 12/15/2022] Open
Abstract
A stable culture of primary porcine enterocytes is necessary to study porcine enteric virus replication characteristics. Because the direct cultivation of primary porcine enterocytes is difficult, alternatives have to be considered. As subepithelial myofibroblasts secrete extracellular matrix and growth factors contributing to the attachment, proliferation and differentiation of epithelial cells, co-cultures of primary porcine enterocytes (ileocytes and colonocytes) with myofibroblasts were developed and evaluated for their susceptibility to enteric viruses. First, it was demonstrated that the co-cultured ileocytes and colonocytes were susceptible to an archival rotavirus strain RVA/pig-tc/BEL/RV277/1977/G1P[7] and different other rotavirus genotypes (fecal samples containing G5P[7], G5P[13], G9P[23], G4P[6]). Next, the TGEV Purdue strain infected both ileocytes and colonocytes whereas the Miller strain only infected ileocytes. Last, the PEDV CV777 Vero adapted and non-adapted (fecal suspension) strains could infect co-cultured ileocytes but not colonocytes. The infectivity of the CV777 Vero adapted strain was higher when the cells were cultured without fetal bovine serum and the CV777 fecal suspension only infected the ileocytes cultured without fetal bovine serum. In conclusion, a novel co-culture of porcine enterocytes with myofibroblasts was established, which can be used for the investigation of the replication of enteric viruses.
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Nyaga MM, Tan Y, Seheri ML, Halpin RA, Akopov A, Stucker KM, Fedorova NB, Shrivastava S, Duncan Steele A, Mwenda JM, Pickett BE, Das SR, Jeffrey Mphahlele M. Whole-genome sequencing and analyses identify high genetic heterogeneity, diversity and endemicity of rotavirus genotype P[6] strains circulating in Africa. INFECTION GENETICS AND EVOLUTION 2018; 63:79-88. [PMID: 29782933 DOI: 10.1016/j.meegid.2018.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 10/16/2022]
Abstract
Rotavirus A (RVA) exhibits a wide genotype diversity globally. Little is known about the genetic composition of genotype P[6] from Africa. This study investigated possible evolutionary mechanisms leading to genetic diversity of genotype P[6] VP4 sequences. Phylogenetic analyses on 167 P[6] VP4 full-length sequences were conducted, which included six porcine-origin sequences. Of the 167 sequences, 57 were newly acquired through whole genome sequencing as part of this study. The other 110 sequences were all publicly-available global P[6] VP4 full-length sequences downloaded from GenBank. The strength of association between the phenotypic features and the phylogeny was also determined. A number of reassortment and mixed infections of RVA genotype P[6] strains were observed in this study. Phylogenetic analyses demostrated the extensive genetic diversity that exists among human P[6] strains, porcine-like strains, their concomitant clades/subclades and estimated that P[6] VP4 gene has a higher substitution rate with the mean of 1.05E-3 substitutions/site/year. Further, the phylogenetic analyses indicated that genotype P[6] strains were endemic in Africa, characterised by an extensive genetic diversity and long-time local evolution of the viruses. This was also supported by phylogeographic clustering and G-genotype clustering of the P[6] strains when Bayesian Tip-association Significance testing (BaTS) was applied, clearly supporting that the viruses evolved locally in Africa instead of spatial mixing among different regions. Overall, the results demonstrated that multiple mechanisms such as reassortment events, various mutations and possibly interspecies transmission account for the enormous diversity of genotype P[6] strains in Africa. These findings highlight the need for continued global surveillance of rotavirus diversity.
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Affiliation(s)
- Martin M Nyaga
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa; Next Generation Sequencing Unit, Department of Medical Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Yi Tan
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mapaseka L Seheri
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Rebecca A Halpin
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD, USA
| | - Asmik Akopov
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD, USA
| | - Karla M Stucker
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD, USA
| | - Nadia B Fedorova
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD, USA
| | | | - A Duncan Steele
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa; Enteric and Diarrhoeal Diseases Programme, Global Health Program, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Jason M Mwenda
- World Health Organization, Regional Office for Africa, Brazzaville, People's Republic of Congo
| | - Brett E Pickett
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD, USA
| | - Suman R Das
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Jeffrey Mphahlele
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa.
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Detection of noroviruses in free-ranging jaguars (Panthera onca) in the Pantanal, Mato Grosso, Brazil. Arch Virol 2018. [PMID: 29516245 DOI: 10.1007/s00705-018-3789-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Nine free-ranging jaguars (Panthera onca) were captured, and rectal swabs were collected in the Pantanal of Cáceres, Mato Grosso, Brazil. Reverse transcription polymerase chain reaction specific for noroviruses was performed. Six jaguars (66.6%) tested positive for norovirus genotype GII.11.
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Vlasova AN, Amimo JO, Saif LJ. Porcine Rotaviruses: Epidemiology, Immune Responses and Control Strategies. Viruses 2017; 9:v9030048. [PMID: 28335454 PMCID: PMC5371803 DOI: 10.3390/v9030048] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 12/13/2022] Open
Abstract
Rotaviruses (RVs) are a major cause of acute viral gastroenteritis in young animals and children worldwide. Immunocompetent adults of different species become resistant to clinical disease due to post-infection immunity, immune system maturation and gut physiological changes. Of the 9 RV genogroups (A–I), RV A, B, and C (RVA, RVB, and RVC, respectively) are associated with diarrhea in piglets. Although discovered decades ago, porcine genogroup E RVs (RVE) are uncommon and their pathogenesis is not studied well. The presence of porcine RV H (RVH), a newly defined distinct genogroup, was recently confirmed in diarrheic pigs in Japan, Brazil, and the US. The complex epidemiology, pathogenicity and high genetic diversity of porcine RVAs are widely recognized and well-studied. More recent data show a significant genetic diversity based on the VP7 gene analysis of RVB and C strains in pigs. In this review, we will summarize previous and recent research to provide insights on historic and current prevalence and genetic diversity of porcine RVs in different geographic regions and production systems. We will also provide a brief overview of immune responses to porcine RVs, available control strategies and zoonotic potential of different RV genotypes. An improved understanding of the above parameters may lead to the development of more optimal strategies to manage RV diarrheal disease in swine and humans.
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Affiliation(s)
- Anastasia N Vlasova
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691, USA.
| | - Joshua O Amimo
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi 30197, Kenya.
- Bioscience of Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi 30709, Kenya.
| | - Linda J Saif
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691, USA.
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Dynamics of Virus Distribution in a Defined Swine Production Network Using Enteric Viruses as Molecular Markers. Appl Environ Microbiol 2017; 83:AEM.03187-16. [PMID: 27940545 DOI: 10.1128/aem.03187-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/01/2016] [Indexed: 11/20/2022] Open
Abstract
Modern swine production systems represent complex and dynamic networks involving numerous stakeholders. For instance, livestock transporters carry live animals between fattening sites, abattoirs, and other premises on a daily basis. This interconnected system may increase the risk of microbial spread within and between networks, although little information is available in that regard. In the present study, a swine network composed of 10 finishing farms, one abattoir, and three types of stakeholders (veterinarians, livestock transporters, and nutritional technicians) in Quebec, Canada, was selected to investigate specific vectors and reservoirs of enteric viruses. Environmental samples were collected from the premises over a 12-month period. Samples were screened using targeted reverse transcription-PCR and sequencing of two selected viral markers, group A rotaviruses (RVA) and porcine astroviruses (PoAstV), both prevalent and genetically heterogeneous swine enteric viruses. The results revealed frequent contamination of farm sites (21.4 to 100%), livestock transporter vehicles (30.6 to 68.8%) and, most importantly, the abattoir yard (46.7 to 94.1%), depending on the sample types. Although high levels of strain diversity for both viruses were found, identical PoAstV and RVA strains were detected in specific samples from farms, the abattoir yard, and the livestock transporter vehicle, suggesting interconnections between these premises and transporters. Overall, the results from this study underscore the potential role of abattoirs and livestock transport as a reservoir and transmission route for enteric viruses within and between animal production networks, respectively. IMPORTANCE Using rotaviruses and astroviruses as markers of enteric contamination in a swine network has revealed the potential role of abattoirs and livestock transporters as a reservoir and vectors of enteric pathogens. The results from this study highlight the importance of tightening biosecurity measures. For instance, implementing sanitary vacancy between animal batches and emphasizing washing, disinfection, and drying procedures on farms and for transportation vehicles, as well as giving limited access and circulation of vehicles throughout the production premises, are some examples of measures that should be applied properly. The results also emphasize the need to closely monitor the dynamics of enteric contamination in the swine industry in order to better understand and potentially prevent the spread of infectious diseases. This is especially relevant when a virulent and economically damaging agent is involved, as seen with the recent introduction of the porcine epidemic diarrhea virus in the country.
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Heylen E, Zeller M, Ciarlet M, Lawrence J, Steele D, Van Ranst M, Matthijnssens J. Human P[6] Rotaviruses From Sub-Saharan Africa and Southeast Asia Are Closely Related to Those of Human P[4] and P[8] Rotaviruses Circulating Worldwide. J Infect Dis 2016; 214:1039-49. [PMID: 27471320 DOI: 10.1093/infdis/jiw247] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/06/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND P[6] rotaviruses have been circulating with a high prevalence in African and, to a more limited extent, Asian countries, but they have not been highly prevalent in other parts of the world. METHODS To investigate the genomic relationship between African and Asian human P[6] rotaviruses and P[4] and P[8] rotaviruses circulating worldwide, we sequenced 39 P[6] strains, collected in Ghana, Mali, Kenya and Bangladesh, providing the largest data set of P[6] rotavirus genomes isolated in low-income countries or anywhere else in the world that has been published thus far. RESULTS Overall, the data indicate that the genetic backbone of human P[6] strains from the low-income countries are similar to those of P[4] or P[8] strains circulating worldwide. CONCLUSIONS The observation that gene segment 4 is the main differentiator between human P[6] and non-P[6] strains suggests that the VP4 spike protein is most likely one of the main reasons preventing the rapid spread of P[6] strains to the rest of the world despite multiple introductions. These observations reinforce previous findings about the receptor specificity of P[6] rotavirus strains.
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Affiliation(s)
- Elisabeth Heylen
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Rega Institute for Medical Research, Belgium
| | - Mark Zeller
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Rega Institute for Medical Research, Belgium
| | - Max Ciarlet
- Vaccines-Clinical Research Department, Merck, Kenilworth, New Jersey
| | - Jody Lawrence
- Vaccines-Clinical Research Department, Merck, Kenilworth, New Jersey
| | - Duncan Steele
- Vaccines and Immunization, PATH, Seattle, Washington
| | - Marc Van Ranst
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Rega Institute for Medical Research, Belgium
| | - Jelle Matthijnssens
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Rega Institute for Medical Research, Belgium
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Malik YS, Kumar N, Sharma K, Saurabh S, Dhama K, Prasad M, Ghosh S, Bányai K, Kobayashi N, Singh RK. Multispecies reassortant bovine rotavirus strain carries a novel simian G3-like VP7 genotype. INFECTION GENETICS AND EVOLUTION 2016; 41:63-72. [PMID: 27033751 DOI: 10.1016/j.meegid.2016.03.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 02/06/2023]
Abstract
Rotavirus-A (RVAs), are the major cause of severe gastroenteritis in the young of mammals and birds. RVA strains possessing G6, G8, and G10 genotypes in combination with P[1] or P[11] have been commonly detected in cattle. During a routine surveillance for enteric viruses in a bovine population on North-Western temperate Himalayan region of India, an uncommon bovine RVA strain, designated as RVA/Cow-wt/IND/M1/09/2009 was detected in a diarrhoeic crossbred calf. The examination of nearly complete genome sequence of this RVA strain revealed an unusual G-P combination (G3P[11]) on a typical bovine RVA genotype backbone (I2-R2-C2-M2-A11-N2-T6-E2-H3). The VP7 gene of M1/09 isolate displayed a maximum nucleotide sequence identity of 73.8% with simian strain (RVA/Simian-tc/USA/RRV/1975/G3P[3]). The VP4 and NSP5 genes clustered with an Indian pig strain, RVA/Pig-wt/IND/AM-P66/2012/G10P[11] (99.6%), and a caprine strain, RVA/Goat-tc/BGD/GO34/1999/G6P[1] (98.9%) from Bangladesh, respectively, whilst the, VP6, NSP1, NSP3 and NSP4 genes were identical or nearly identical to Indian bovine strains (RVA/Cow-wt/IND/B-72/2008/G10P[X], RVA/Cow-wt/IND/B85/2010/GXP[X], and RVA/Cow-wt/IND/C91/2011/G6P[X]). The remaining four genes (VP1, VP2, VP3 and NSP2) were more closely related to RVA/Human-wt/ITA/PAI11/1996/G2P[4] (93.5%), RVA/Sheep-wt/CHN/LLR/1985/G10P[15] (88.8%), RVA/Human-tc/SWE/1076/1983/G2P2A[6] (93.2%) and RVA/Human-wt/AUS/CK20003/2000/G2P[4] (91.2%), respectively. Altogether, these findings are suggestive of multiple independent interspecies transmission and reassortment events between co-circulating bovine, porcine, ovine and human rotaviruses. The complete genome sequence information is necessary to establish the evolutionary relationship, interspecies transmission and ecological features of animal RVAs from different geographical regions.
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Affiliation(s)
- Yashpal Singh Malik
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India.
| | - Naveen Kumar
- National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India.
| | - Kuldeep Sharma
- National Institute of Research in Tribal Health, Jabalpur -482 003, Madhya Pradesh, India.
| | - Sharad Saurabh
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India.
| | - Kuldeep Dhama
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India.
| | - Minakshi Prasad
- Department of Animal Biotechnology, LUVAS, Hisar 125 001, Haryana, India.
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, P. O. Box 334, Basseterre, Saint Kitts, West Indies.
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt 21, Budapest 1143, Hungary.
| | | | - Raj Kumar Singh
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India.
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Chandler-Bostock R, Hancox LR, Payne H, Iturriza-Gomara M, Daly JM, Mellits KH. Diversity of group A rotavirus on a UK pig farm. Vet Microbiol 2015; 180:205-11. [PMID: 26432051 PMCID: PMC4627360 DOI: 10.1016/j.vetmic.2015.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/27/2015] [Accepted: 09/15/2015] [Indexed: 11/15/2022]
Abstract
Group A rotaviruses (GARV) are a significant cause of enteritis in young pigs. The aim of this study was to extend our understanding of the molecular epidemiology of porcine GARV in the UK by investigating the genetic diversity of GARV on a conventional farrow-to-finish farm. Faecal samples were obtained from six batches of pigs in 2009 and 8 batches in 2010, when the pigs were 2, 3 (time point omitted in 2009), 4, 5, 6 and 8 weeks of age. Presence of rotavirus was detected by reverse transcriptase-polymerase chain reaction (RT-PCR) in 89% and 80% of samples from 2009 and 2010, respectively. A combination of multiplex PCRs and sequencing identified four VP7 genotypes (G2, G3, G4 and G5) and three VP4 genotypes (P[6], P[7] and P[32]) present in almost every combination over the 2 years. The predominant genotype combination was G5P[32] in 2009 and G4P[32] in 2010. Conservation among the P[32] sequences between 2009 and 2010 suggests that reassortment may have led to the different genotype combinations. There were significant changes in the predominant VP7 genotype prior to weaning at 4 weeks, and post weaning when pigs were moved to a different building. Phylogenetic analysis indicated that introduction of new viruses onto the farm was limited. Taken together, these findings suggest that genetically diverse GARV strains persist within the farm environment.
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Affiliation(s)
- Rebecca Chandler-Bostock
- School of Biosciences, Division of Food Science, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Laura R Hancox
- School of Biosciences, Division of Food Science, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Helen Payne
- School of Biosciences, Division of Food Science, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | | | - Janet M Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Kenneth H Mellits
- School of Biosciences, Division of Food Science, University of Nottingham, Sutton Bonington LE12 5RD, UK.
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Ianiro G, Delogu R, Fiore L, Ruggeri FM. Genomic characterization of uncommon human G3P[6] rotavirus strains causing diarrhea in children in Italy in 2009. INFECTION GENETICS AND EVOLUTION 2015; 33:143-9. [DOI: 10.1016/j.meegid.2015.04.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/31/2015] [Accepted: 04/23/2015] [Indexed: 10/23/2022]
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Lavazza A, Tittarelli C, Cerioli M. The use of convalescent sera in immune-electron microscopy to detect non-suspected/new viral agents. Viruses 2015; 7:2683-703. [PMID: 26008707 PMCID: PMC4452926 DOI: 10.3390/v7052683] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/21/2015] [Indexed: 11/26/2022] Open
Abstract
Negative staining electron microscopy methods can be employed for the diagnosis of viral particles in animal samples. In fact, negative staining electron microscopy methods are used to identify viruses, especially in minor species and wild animals, when no other methods are available and in cases of rare, emerging or re-emerging infections. In particular, immune-electron-microscopy with convalescent sera is employed to detect etiological agents when there are undiagnosed clinical outbreaks, when alternative diagnostic methods fail due to the lack of immunological reagents and primers, and when there is no indicative clinical suspect. An overview of immune-electron-microscopy with convalescent sera’s use in the diagnosis of new and unsuspected viruses in animals of domestic and wild species is provided through the descriptions of the following four diagnostic veterinary cases: (I) enteric viruses of pigs: Porcine Rotavirus, Porcine Epidemic Diarrhea Virus, Porcine Circovirus and Porcine Torovirus; (II) Rotavirus and astrovirus in young turkeys with enteritis; (III) Parvovirus-like particles in pheasants; and (IV) Lagoviruses: Rabbit Hemorrhagic Disease Virus and European Brown Hare Syndrome Virus.
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Affiliation(s)
- Antonio Lavazza
- Electron Microscopy Laboratory, Virology Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell' Emilia Romagna "Bruno Ubertini" (IZSLER), Via Bianchi 7/9, 25124 Brescia, Italy.
| | - Cristiana Tittarelli
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Sezione di Genova Piazza Borgo Pila 39, 16129 Genova, Italy.
| | - Monica Cerioli
- Epidemiological Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Via Bianchi 7/9, 25124 Brescia, Italy.
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Nyaga MM, Jere KC, Esona MD, Seheri ML, Stucker KM, Halpin RA, Akopov A, Stockwell TB, Peenze I, Diop A, Ndiaye K, Boula A, Maphalala G, Berejena C, Mwenda JM, Steele AD, Wentworth DE, Mphahlele MJ. Whole genome detection of rotavirus mixed infections in human, porcine and bovine samples co-infected with various rotavirus strains collected from sub-Saharan Africa. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 31:321-34. [PMID: 25701122 PMCID: PMC4361293 DOI: 10.1016/j.meegid.2015.02.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/27/2015] [Accepted: 02/10/2015] [Indexed: 01/13/2023]
Abstract
Group A rotaviruses (RVA) are among the main global causes of severe diarrhea in children under the age of 5years. Strain diversity, mixed infections and untypeable RVA strains are frequently reported in Africa. We analysed rotavirus-positive human stool samples (n=13) obtained from hospitalised children under the age of 5years who presented with acute gastroenteritis at sentinel hospital sites in six African countries, as well as bovine and porcine stool samples (n=1 each), to gain insights into rotavirus diversity and evolution. Polyacrylamide gel electrophoresis (PAGE) analysis and genotyping with G-(VP7) and P-specific (VP4) typing primers suggested that 13 of the 15 samples contained more than 11 segments and/or mixed G/P genotypes. Full-length amplicons for each segment were generated using RVA-specific primers and sequenced using the Ion Torrent and/or Illumina MiSeq next-generation sequencing platforms. Sequencing detected at least one segment in each sample for which duplicate sequences, often having distinct genotypes, existed. This supported and extended the PAGE and RT-PCR genotyping findings that suggested these samples were collected from individuals that had mixed rotavirus infections. The study reports the first porcine (MRC-DPRU1567) and bovine (MRC-DPRU3010) mixed infections. We also report a unique genome segment 9 (VP7), whose G9 genotype belongs to lineage VI and clusters with porcine reference strains. Previously, African G9 strains have all been in lineage III. Furthermore, additional RVA segments isolated from humans have a clear evolutionary relationship with porcine, bovine and ovine rotavirus sequences, indicating relatively recent interspecies transmission and reassortment. Thus, multiple RVA strains from sub-Saharan Africa are infecting mammalian hosts with unpredictable variations in their gene segment combinations. Whole-genome sequence analyses of mixed RVA strains underscore the considerable diversity of rotavirus sequences and genome segment combinations that result from a complex evolutionary history involving multiple host species.
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Affiliation(s)
- Martin M Nyaga
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa.
| | - Khuzwayo C Jere
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa; Institute of Infection and Global Health, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, United Kingdom.
| | - Mathew D Esona
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa; Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, CDC, Atlanta, GA, USA.
| | - Mapaseka L Seheri
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa.
| | | | | | | | | | - Ina Peenze
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa.
| | - Amadou Diop
- Albert Royer National Paediatric Hospital Laboratory, Dakar, Senegal.
| | - Kader Ndiaye
- Unite de Virologie Medicale Institut Pasteur, Dakar, Senegal.
| | - Angeline Boula
- Mother and Child Center, Chantal Biya Foundation, Yaoundé, Cameroon.
| | - Gugu Maphalala
- The National Clinical Laboratory Service, Mbabane, Swaziland.
| | - Chipo Berejena
- University of Zimbabwe, Department of Medical Microbiology, Virology Section, Harare, Zimbabwe.
| | - Jason M Mwenda
- World Health Organization, Regional Office for Africa, Brazzaville, People's Republic of Congo.
| | - A Duncan Steele
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa; Enteric and Diarrhoeal Diseases Programme, Global Health Program, Bill and Melinda Gates Foundation, Seattle, WA, USA.
| | | | - M Jeffrey Mphahlele
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa.
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Mullick S, Mandal P, Nayak MK, Ghosh S, De P, Rajendran K, Bhattacharya MK, Mitra U, Ramamurthy T, Kobayashi N, Chawla-Sarkar M. Hospital based surveillance and genetic characterization of rotavirus strains in children (<5 years) with acute gastroenteritis in Kolkata, India, revealed resurgence of G9 and G2 genotypes during 2011-2013. Vaccine 2015; 32 Suppl 1:A20-8. [PMID: 25091674 DOI: 10.1016/j.vaccine.2014.03.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION India accounts for an estimated 457,000-884,000 hospitalizations and 2 million outpatient visits for diarrhea. In spite of the huge burden of rotavirus (RV) disease, RV vaccines have not been introduced in national immunization programme of India. Therefore, continuous surveillance for prevalence and monitoring of the circulating genotypes is needed to assess the disease burden prior to introduction of vaccines in this region. METHODS During January 2011 through December 2013, 830 and 1000 stool samples were collected from hospitalized and out-patient department (OPD) patients, respectively, in two hospitals in Kolkata, Eastern India. After primary screening, the G-P typing was done by multiplex semi-nested PCR using type specific primers followed by sequencing. Phylogenetic analysis for the VP7 gene of 25 representative strains was done. RESULTS Among hospitalized and OPD patients, 53.4% and 47.5% cases were positive for rotaviruses, respectively. Unlike previous studies where G1 was predominant, in hospitalized cases G9 rotavirus strains were most prevalent (40%), followed by G2 (39.6%) whereas G1 and G12 occurred at 16.4% and 5.6% frequency. In OPD cases, the most prevalent strain was G2 (40.3%), followed by G1, G9 and G12 at 25.5%, 22.8%, 9.3%, respectively. Phylogenetically the G1, G2 and G9 strains from Kolkata did not cluster with corresponding genotypes of Rotarix, RotaTeq and Rotavac (116E) vaccine strains. CONCLUSION The study highlights the high prevalence of RV in children with gastroenteritis in Kolkata. The circulating genotypes have changed over the time with predominance of G9 and G2 strains during 2011-2013. The current G2, G9 and G1 Kolkata strains shared low amino acid homologies with current vaccine strains. Although there is substantial evidence for cross protection of vaccines against a variety of strains, still the strain variation should be monitored post vaccine introduction to determine if it has any impact on vaccine effectiveness.
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Affiliation(s)
- Satarupa Mullick
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Paulami Mandal
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Mukti Kant Nayak
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Souvik Ghosh
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Papiya De
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - K Rajendran
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Utpala Mitra
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
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Silva FDF, Espinoza LRL, Tonietti PO, Barbosa BRP, Gregori F. Whole-genomic analysis of 12 porcine group A rotaviruses isolated from symptomatic piglets in Brazil during the years of 2012-2013. INFECTION GENETICS AND EVOLUTION 2015; 32:239-54. [PMID: 25796358 DOI: 10.1016/j.meegid.2015.03.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 11/18/2022]
Abstract
Group A rotaviruses (RVAs) are leading causes of viral diarrhea in children and in the young of many animal species, particularly swine. In the current study, porcine RVAs were found in fecal specimens from symptomatic piglets on 4 farms in Brazil during the years of 2012-2013. Using RT-PCR, Sanger nucleotide sequencing, and phylogenetic analyses, the whole genomes of 12 Brazilian porcine RVA strains were analyzed. Specifically, the full-length open reading frame (ORF) sequences were determined for the NSP2-, NSP3-, and VP6-coding genes, and partial ORF sequences were determined for the VP1-, VP2-, VP3-, VP4-, VP7-, NSP1-, NSP4-, and NSP5/6-coding genes. The results indicate that all 12 strains had an overall porcine-RVA-like backbone with most segments being designated as genotype 1, with the exception of the VP6- and NSP1-coding genes, which were genotypes I5 and A8, respectively. These results add to our growing understanding of porcine RVA genetic diversity and will provide a platform for monitoring the role of animals as genetic reservoirs of emerging human RVAs strains.
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Affiliation(s)
- Fernanda D F Silva
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, 05508-270 São Paulo, SP, Brazil.
| | - Luis R L Espinoza
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, 05508-270 São Paulo, SP, Brazil.
| | - Paloma O Tonietti
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, 05508-270 São Paulo, SP, Brazil.
| | - Bruna R P Barbosa
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, 05508-270 São Paulo, SP, Brazil.
| | - Fabio Gregori
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Professor Dr. Orlando Marques de Paiva, 87, 05508-270 São Paulo, SP, Brazil.
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Amimo J, Junga J, Ogara W, Vlasova A, Njahira M, Maina S, Okoth E, Bishop R, Saif L, Djikeng A. Detection and genetic characterization of porcine group A rotaviruses in asymptomatic pigs in smallholder farms in East Africa: Predominance of P[8] genotype resembling human strains. Vet Microbiol 2015; 175:195-210. [DOI: 10.1016/j.vetmic.2014.11.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 11/03/2014] [Accepted: 11/16/2014] [Indexed: 10/24/2022]
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Quiroz-Santiago C, Vázquez-Salinas C, Natividad-Bonifacio I, Barrón-Romero BL, Quiñones-Ramírez EI. Rotavirus G2P[4] detection in fresh vegetables and oysters in Mexico City. J Food Prot 2014; 77:1953-9. [PMID: 25364930 DOI: 10.4315/0362-028x.jfp-13-426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Rotaviruses are the principal cause of dehydration caused by diarrhea in children younger than 2 years of age. Although these viral infections have mainly been associated with ingestion of fecally contaminated food and water, few studies have addressed the presence of the virus in food that is consumed raw or slightly cooked. In this work, 30 oyster samples and 33 vegetable samples were examined for the presence of rotavirus genotypes to evaluate their potential to produce gastrointestinal infections. The rotaviruses were identified by reverse transcriptase PCR amplification of the VP7 gene. G and P genotyping was also performed by reverse transcriptase PCR, with a detection sensitivity of up to 15 PFU/ml. Rotaviruses were found in 17 (26.9%) of 63 samples (10 oysters and 7 vegetables). The G2 genotype was found in 11 (64.7%) of 17 of the rotavirus strains, and 16 (94.1%) of 17 had the P[4] genotype. The combined genotypes found most frequently were G2P[4] (10 [58.82%] of 17), GNTP[4] (6 [35.29%] of 17), and G2P[NT] (1 [5.8%] of 17).
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Affiliation(s)
- Carolina Quiroz-Santiago
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico D.F., Mexico
| | - Carlos Vázquez-Salinas
- Departamento de Biotecnología, Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana-Iztapalapa, 09340 Mexico D.F., Mexico
| | - Ivan Natividad-Bonifacio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico D.F., Mexico
| | - Blanca Lilia Barrón-Romero
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico D.F., Mexico
| | - Elsa Irma Quiñones-Ramírez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico D.F., Mexico.
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Mitake H, Ito N, Okadera K, Okada K, Nakagawa K, Tanaka T, Katsuragi K, Kasahara K, Nihongi T, Tsunemitsu H, Sugiyama M. Detection of avian-like rotavirus A VP4 from a calf in Japan. J Vet Med Sci 2014; 77:221-4. [PMID: 25311984 PMCID: PMC4363026 DOI: 10.1292/jvms.14-0379] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A total of 568 normal feces from calves on a beef farm in Fukui Prefecture, Japan, in 2011–2012 were examined by RT-semi-nested PCR for rotavirus A (RVA) VP4 genes. Through partial sequencing and BLAST analyses of 84 VP4-positive specimens, we identified an avian-like RVA strain, N2342, which shares highest nucleotide identity (80.0%) with known avian-like bovine strain 993/83, in one specimen. Phylogenetic analysis also revealed a close genetic relationship between N2342 and avian RVAs, suggesting bird-to-cattle transmission. We observed frequent contact of wild birds with calves in the farm, suggesting that these birds were the source of the virus.
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Affiliation(s)
- Hiromichi Mitake
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
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Theuns S, Desmarets LM, Heylen E, Zeller M, Dedeurwaerder A, Roukaerts ID, Van Ranst M, Matthijnssens J, Nauwynck HJ. Porcine group a rotaviruses with heterogeneous VP7 and VP4 genotype combinations can be found together with enteric bacteria on Belgian swine farms. Vet Microbiol 2014; 172:23-34. [DOI: 10.1016/j.vetmic.2014.04.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 03/25/2014] [Accepted: 04/01/2014] [Indexed: 10/25/2022]
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Park JG, Kim DS, Matthijnssens J, Kwon HJ, Zeller M, Alfajaro MM, Son KY, Hosmillo M, Ryu EH, Kim JY, Lee JH, Park SJ, Kang MI, Kwon J, Choi JS, Cho KO. Comparison of pathogenicities and nucleotide changes between porcine and bovine reassortant rotavirus strains possessing the same genotype constellation in piglets and calves. Vet Microbiol 2014; 172:51-62. [DOI: 10.1016/j.vetmic.2014.04.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 04/11/2014] [Accepted: 04/15/2014] [Indexed: 11/26/2022]
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Chandler-Bostock R, Hancox LR, Nawaz S, Watts O, Iturriza-Gomara M, Mellits KH, Mellits KM. Genetic diversity of porcine group A rotavirus strains in the UK. Vet Microbiol 2014; 173:27-37. [PMID: 25123085 PMCID: PMC4158422 DOI: 10.1016/j.vetmic.2014.06.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 12/28/2022]
Abstract
This is the first study of rotavirus genotypes circulating in UK pigs. Rotavirus transmission between pigs and humans is not thought to be common in the UK. Human rotavirus genotype P[8] found in a UK pig. The uncommon rotavirus genotype P[32] is widespread in UK pig herds.
Rotavirus is endemic in pig farms where it causes a loss in production. This study is the first to characterise porcine rotavirus circulating in UK pigs. Samples from diarrheic pigs with rotavirus enteritis obtained between 2010 and 2012 were genotyped in order to determine the diversity of group A rotavirus (GARV) in UK pigs. A wide range of rotavirus genotypes were identified in UK pigs: six G types (VP7); G2, G3, G4, G5, G9 and G11 and six P types (VP4); P[6], P[7], P[8], P[13], P[23], and P[32]. With the exception of a single P[8] isolate, there was less than 95% nucleotide identity between sequences from this study and any available rotavirus sequences. The G9 and P[6] genotypes are capable of infecting both humans and pigs, but showed no species cross-over within the UK as they were shown to be genetically distinct, which suggested zoonotic transmission is rare within the UK. We identified the P[8] genotype in one isolate, this genotype is almost exclusively found in humans. The P[8] was linked to a human Irish rotavirus isolate in the same year. The discovery of human genotype P[8] rotavirus in a UK pig confirms this common human genotype can infect pigs and also highlights the necessity of surveillance of porcine rotavirus genotypes to safeguard human as well as porcine health.
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Affiliation(s)
- Rebecca Chandler-Bostock
- University of Nottingham, School of Biosciences, Division of Food Science, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Laura R Hancox
- University of Nottingham, School of Biosciences, Division of Food Science, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Sameena Nawaz
- Virus Reference Department, Public Health England, London, NW9 5HT, UK
| | - Oliver Watts
- University of Nottingham, School of Biosciences, Division of Food Science, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | | | | | - Kenneth M Mellits
- University of Nottingham, School of Biosciences, Division of Food Science, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
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Heylen E, Batoko Likele B, Zeller M, Stevens S, De Coster S, Conceição-Neto N, Van Geet C, Jacobs J, Ngbonda D, Van Ranst M, Matthijnssens J. Rotavirus surveillance in Kisangani, the Democratic Republic of the Congo, reveals a high number of unusual genotypes and gene segments of animal origin in non-vaccinated symptomatic children. PLoS One 2014; 9:e100953. [PMID: 24968018 PMCID: PMC4072759 DOI: 10.1371/journal.pone.0100953] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/27/2014] [Indexed: 12/26/2022] Open
Abstract
Group A rotavirus (RVA) infections form a major public health problem, especially in low-income countries like the Democratic Republic of the Congo (COD). However, limited data on RVA diversity is available from sub-Saharan Africa in general and the COD in particular. Therefore, the first aim of this study was to determine the genetic diversity of 99 RVAs detected during 2007–2010 in Kisangani, COD. The predominant G-type was G1 (39%) and the most predominant P-type was P[6] (53%). A total of eight different G/P-combinations were found: G1P[8] (28%), G8P[6] (26%), G2P[4] (14%), G12P[6] (13%), G1P[6] (11%), G9P[8] (4%), G4P[6] (2%) and G8P[4] (1%). The second aim of this study was to gain insight into the diversity of P[6] RVA strains in the COD. Therefore, we selected five P[6] RVA strains in combination with the G1, G4, G8 (2x) or G12 genotype for complete genome analysis. Complete genome analysis showed that the genetic background of the G1P[6] and G12P[6] strains was entirely composed of genotype 1 (Wa-like), while the segments of the two G8P[6] strains were identified as genotype 2 (DS-1-like). Interestingly, all four strains possessed a NSP4 gene of animal origin. The analyzed G4P[6] RVA strain was found to possess the unusual G4-P[6]-I1-R1-C1-M1-A1-N1-T7-E1-H1 constellation. Although the majority of its genes (if not all), were presumably of porcine origin, this strain was able to cause gastro-enteritis in humans. The high prevalence of unusual RVA strains in the COD highlights the need for continued surveillance of RVA diversity in the COD. These results also underline the importance of complete genetic characterization of RVA strains and indicate that reassortments and interspecies transmission among human and animal RVAs strains occur regularly. Based on these data, RVA vaccines will be challenged with a wide variety of different RVA strain types in the COD.
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Affiliation(s)
- Elisabeth Heylen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Bibi Batoko Likele
- Department of pediatrics, University Hospital Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Mark Zeller
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Stijn Stevens
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Sarah De Coster
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Nádia Conceição-Neto
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Christel Van Geet
- Department of pediatrics, University Hospital Leuven, Leuven, Belgium
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium
| | - Dauly Ngbonda
- Department of pediatrics, University Hospital Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
- * E-mail:
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Group A rotaviruses in children with gastroenteritis in a Canadian pediatric hospital: The prevaccine era. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2014; 24:e1-6. [PMID: 24421793 DOI: 10.1155/2013/982385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND A publicly funded, group A rotavirus (RVA) vaccination program was implemented in Quebec in November 2011. OBJECTIVES To evaluate trends in RVA infections and describe circulating genotypes before the implementation of a publicly funded vaccination program. METHODS The Montreal Children's Hospital (Montreal, Quebec) virology laboratory database was reviewed for RVA ELISA performed between July 2006 and June 2011. A five-week moving average was used to follow the proportion of positive RVA ELISA test results. A season was defined as starting with the first two and ending with the final two consecutive weeks in which the percentage of specimens testing positive for RVA was ≥10%. Duplicate tests were excluded. A random sample of 39 RVA-positive fecal samples from the final season (2010/2011) was genetically characterized: VP4, VP6, VP7 and NSP4 gene segments were genotyped using sequence analysis. RESULTS Of the 3403 nonduplicate tests, 433 were RVA positive: 15.1% (2006/2007) to 9.3% (2010/2011) of the samples were positive during the study period, with a proportionally larger decrease in the percentage of positive tests compared with the decrease in the number of tests performed. The most common RVA strain types detected were G9P[8]I1 (n=19) and G1P[8]I1 (n=14), followed by G2P[4]I2 (n=4), G3P[6]I1 (n=1) and G4P[8]I2 (n=1). Mixed RVA infection was observed in two samples. CONCLUSION Before the implementation of the vaccination program, the proportion of positive RVA tests had already begun to steadily decline. The present study was the first to report the genetic makeup of human RVA collected from a Canadian hospital based on the genotyping of four gene segments. The present study provided a baseline with which to monitor the impact of the universal vaccination program.
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Lachapelle V, Sohal JS, Lambert MC, Brassard J, Fravalo P, Letellier A, L’Homme Y. Genetic diversity of group A rotavirus in swine in Canada. Arch Virol 2014; 159:1771-9. [DOI: 10.1007/s00705-013-1951-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 11/13/2013] [Indexed: 12/31/2022]
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Theamboonlers A, Maiklang O, Thongmee T, Chieochansin T, Vuthitanachot V, Poovorawan Y. Complete genotype constellation of human rotavirus group A circulating in Thailand, 2008–2011. INFECTION GENETICS AND EVOLUTION 2014; 21:295-302. [DOI: 10.1016/j.meegid.2013.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 01/26/2023]
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Okadera K, Abe M, Ito N, Morikawa S, Yamasaki A, Masatani T, Nakagawa K, Yamaoka S, Sugiyama M. Evidence of natural transmission of group A rotavirus between domestic pigs and wild boars (Sus scrofa) in Japan. INFECTION GENETICS AND EVOLUTION 2013; 20:54-60. [DOI: 10.1016/j.meegid.2013.07.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 07/29/2013] [Accepted: 07/30/2013] [Indexed: 02/07/2023]
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Luchs A, Timenetsky MDCST. G8P[6] rotaviruses isolated from Amerindian children in Mato Grosso do Sul, Brazil, during 2009: close relationship of the G and P genes with those of bovine and bat strains. J Gen Virol 2013; 95:627-641. [PMID: 24259191 DOI: 10.1099/vir.0.058099-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
During the 2009 national group A rotavirus (RVA) surveillance, five unusual strains of the human G8P[6] genotype were detected in Brazilian indian children with acute gastroenteritis. The aim of this study was to carry out sequence analysis of the two outer capsid proteins (VP4 and VP7) and the inner capsid protein (VP6) of the G8P[6] strains detected in order to provide further information on the genetic relationship between human and animal RVA. A total of 68 stool samples, collected in Mato Grosso do Sul during 2009, were tested for RVA using ELISA, following by reverse transcriptase-PCR and sequencing. RVA infection was detected in 7.3% of samples (5/68). The IAL-RN376 G8 sequence shares a clade with bovine and human strains, displaying highest nucleotide identity to African human strains DRC86 and DRC88, followed by African bovine strain NGRBg8. IAL-RN376 and IAL-RN377 P[6] sequences showed highest identity to human strain R330 from Ireland, and a close genetic relationship to African fruit bat RVA strain KE4852/07. Strains IAL-RN376 and IAL-RN377 display genogroup I VP6 specificity and the I2 genotype, and share high nucleotide identities with human strains B1711, 272-BF and 06-242, and moderate identities with bovine (RUBV81, 86 and KJ9-1) and porcine (HP140) strains. This study suggested that a reassortment between bovine and bat RVA strains could have occurred in animal host(s) preceding the transmission to humans. In the indigenous population, zoonotic transmission is probably fairly frequent as the inhabitants live in close contact with animals under conditions of poor hygiene.
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Affiliation(s)
- Adriana Luchs
- Enteric Disease Laboratory, Adolfo Lutz Institute, São Paulo, Brazil
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Oh HK, Hong SH, Ahn BY, Min HK. Phylogenetic Analysis of the Rotavirus Genotypes Originated from Children < 5 Years of Age in 16 Cities in South Korea, between 2000 and 2004. Osong Public Health Res Perspect 2013; 3:36-42. [PMID: 24159485 PMCID: PMC3738675 DOI: 10.1016/j.phrp.2012.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/15/2012] [Accepted: 01/20/2012] [Indexed: 11/16/2022] Open
Abstract
Objectives The purpose of this study was to examine the diversity of the G and P types of human rotavirus strains isolated in South Korea during 2000 to 2004. Methods We selected 38 Group A rotavirus isolates among 652 fecal samples, which were collected from infants and children < 5 years of age with acute gastroenteritis or diarrhea admitted in 8 hospitals representative of five provinces of South Korea between 2000 and 2004. Rotavirus P- and G-genotypes were determined by nucleotide sequencing and phylogenetic analysis was performed. Results One G1P[4] consisted G1-Id-P[4]-V; one G1P[6] consisted G1-Id-P[6]-Ia; nine G1P[8] consisted G1-Ib-P[8]-Ia (n=3), G1-Ic-P[8]-Ia (n=1), and G1-Id-P[8]-Ia (n=5); 13 G2P[4] consisted G2-V-P[4]-V; two G3P[4] consisted G3-IIId-P[4]-V; five G3P[8] consisted G3-IIId-P[8]-Ia; four G4P[6] consisted G4-Ie-P[6]-Ia; two G4P[8] consisted G4-Ie-P[8]-II; one G9P[6] consisted G9-III-P[6]-Ia. Conclusions A considerable amount of rotavirus genotypic diversity was detected in South Korea from 2000 to 2004. These findings are important to develop the effective vaccines and to undertake epidemiologic studies.
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Affiliation(s)
- Ho-Kyung Oh
- National Center for Lot Release, National Institute of Food & Drug Safety Evaluation, Korea Food & Drug Administration, Osong, Korea. ; School of Life Sciences and Biotechnology, Korea University, Seoul, Korea
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da Silva Soares L, de Fátima Dos Santos Guerra S, do Socorro Lima de Oliveira A, da Silva Dos Santos F, de Fátima Costa de Menezes EM, Mascarenhas JDP, Linhares AC. Diversity of rotavirus strains circulating in Northern Brazil after introduction of a rotavirus vaccine: high prevalence of G3P[6] genotype. J Med Virol 2013; 86:1065-72. [PMID: 24136444 DOI: 10.1002/jmv.23797] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2013] [Indexed: 12/29/2022]
Abstract
Rotavirus A (RVA) is the most common cause of severe acute gastroenteritis in infants and young children worldwide, causing 453,000 deaths annually. In Brazil, the most frequent genotype identified was G1 during almost three decades in the pre-vaccination period; however, after anti-rotavirus vaccine introduction, there was a predominance of G2 genotype. The aim of this study was to determine the G and P genotypes of rotaviruses isolated from children under 5 years of age with acute gastroenteritis in the Northern region of Brazil, and discuss the emergence of G3P[6] genotype. A total of 783 stool specimens were obtained between January 2011 and March 2012. RVA antigen was detected in 33% (272/783) of samples using a commercial enzyme-linked immunosorbent assay and type-specificity was determined by reverse-transcription polymerase chain reaction. The most common binary combination was G2P[4], representing 41% of cases, followed by G3P[6] (15%), G1P[8] (8%), G3P[8] (4%), G9P[8] (3%), and G12P[6] (2%). G3P[6] strains were analyzed further and phylogenetic analysis of VP7 gene showed that G3 strains clustered into lineage I and showed a high degree of amino acid identity with vaccine strain RV3 (95.1-95.6%). For VP4 sequences, G3P[6] clustered into lineage Ia. It was demonstrated by the first time the emergence of unusual genotype G3P[6] in the Amazon region of Brazil. This genotype shares neither VP7 nor VP4 specificity with the used vaccine and may represent a challenge to vaccination strategies. A continuous monitoring of circulating strains is therefore needed during the post-vaccine era in Brazil.
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Affiliation(s)
- Luana da Silva Soares
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Brazil
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Park JG, Kim HJ, Matthijnssens J, Alfajaro MM, Kim DS, Son KY, Kwon HJ, Hosmillo M, Ryu EH, Kim JY, Cena RB, Lee JH, Kang MI, Park SI, Cho KO. Different virulence of porcine and porcine-like bovine rotavirus strains with genetically nearly identical genomes in piglets and calves. Vet Res 2013; 44:88. [PMID: 24083947 PMCID: PMC3851489 DOI: 10.1186/1297-9716-44-88] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 09/05/2013] [Indexed: 12/27/2022] Open
Abstract
Direct interspecies transmissions of group A rotaviruses (RVA) have been reported under natural conditions. However, the pathogenicity of RVA has never been directly compared in homologous and heterologous hosts. The bovine RVA/Cow-tc/KOR/K5/2004/G5P[7] strain, which was shown to possess a typical porcine-like genotype constellation similar to that of the G5P[7] prototype RVA/Pig-tc/USA/OSU/1977/G5P9[7] strain, was examined for its pathogenicity and compared with the porcine G5P[7] RVA/Pig-tc/KOR/K71/2006/G5P[7] strain possessing the same genotype constellation. The bovine K5 strain induced diarrhea and histopathological changes in the small intestine of piglets and calves, whereas the porcine K71 strain caused diarrhea and histopathological changes in the small intestine of piglets, but not in calves. Furthermore, the bovine K5 strain showed extra-intestinal tropisms in both piglets and calves, whereas the porcine K71 strain had extra-intestinal tropisms in piglets, but not in calves. Therefore, we performed comparative genomic analysis of the K71 and K5 RVA strains to determine whether specific mutations could be associated with these distinct clinical and pathological phenotypes. Full-length sequencing analyses for the 11 genomic segments for K71 and K5 revealed that these strains were genetically nearly identical to each other. Two nucleotide mutations were found in the 5′ untranslated region (UTR) of NSP5 and the 3′ UTR of NSP3, and eight amino acid mutations in VP1-VP4 and NSP2. Some of these mutations may be critical molecular determinants for RVA virulence and/or pathogenicity.
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Affiliation(s)
- Jun-Gyu Park
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju 500-757, Republic of Korea.
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Dong HJ, Qian Y, Huang T, Zhu RN, Zhao LQ, Zhang Y, Li RC, Li YP. Identification of circulating porcine-human reassortant G4P[6] rotavirus from children with acute diarrhea in China by whole genome analyses. INFECTION GENETICS AND EVOLUTION 2013; 20:155-62. [PMID: 24012957 DOI: 10.1016/j.meegid.2013.08.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/25/2013] [Accepted: 08/26/2013] [Indexed: 02/02/2023]
Abstract
P[6] group A rotavirus (RVA) strains identified in four stool specimens collected from children with acute diarrhea in Guangxi Province, southern China in 2010, with unknown G type were further analyzed by full genomic analysis. It was revealed by whole genome sequencing that 11 genomic cognate gene segments of these P[6] RVA strains shared almost 100% nucleotide identities and all exhibited an identical G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1 genotype constellation. Phylogenetic analyses of VP7, VP1-VP4, NSP1, NSP2, NSP4 and NSP5 genes revealed that these Guangxi G4P[6] RVA strains were closely related to porcine and porcine-like human RVAs, while VP6 and NSP3 were closely related to those of common human RVAs. Interestingly, the four infants from whom these specimens were collected had come from different villages and/or towns. They had not contacted with each other and had had acute diarrhea before admitted into the same hospital. The genomic analyses and the clinical data revealed that these four Guangxi G4P[6] RVA strains from China were reassortants possessing VP6 and NSP3 gene segments of human origin yet all other nine gene segments of porcine origin. It is the first report on porcine-human reassortant G4P[6] RVA with identical genome configuration circulating in children.
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Affiliation(s)
- Hui-Jin Dong
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing 100020, China
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Badaracco A, Garaicoechea L, Matthijnssens J, Louge Uriarte E, Odeón A, Bilbao G, Fernandez F, Parra G, Parreño V. Phylogenetic analyses of typical bovine rotavirus genotypes G6, G10, P[5] and P[11] circulating in Argentinean beef and dairy herds. INFECTION GENETICS AND EVOLUTION 2013; 18:18-30. [DOI: 10.1016/j.meegid.2013.04.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 10/26/2022]
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Komoto S, Maeno Y, Tomita M, Matsuoka T, Ohfu M, Yodoshi T, Akeda H, Taniguchi K. Whole genomic analysis of a porcine-like human G5P[6] rotavirus strain isolated from a child with diarrhoea and encephalopathy in Japan. J Gen Virol 2013; 94:1568-1575. [PMID: 23515025 DOI: 10.1099/vir.0.051011-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024] Open
Abstract
An unusual rotavirus strain, Ryukyu-1120, with G5P[6] genotypes (RVA/Human-wt/JPN/Ryukyu-1120/2011/G5P[6]) was identified in a stool specimen from a hospitalized child aged 4 years who showed diarrhoea and encephalopathy. In this study, we sequenced and characterized the complete genome of strain Ryukyu-1120. On whole genomic analysis, this strain was found to have a unique genotype constellation: G5-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1. The VP6 and NSP1 genotypes I5 and A8 are those commonly found in porcine strains. Furthermore, phylogenetic analysis indicated that each of the 11 genes of strain Ryukyu-1120 appeared to be of porcine origin. Thus, strain Ryukyu-1120 was found to have a porcine rotavirus genetic backbone and is likely to be of porcine origin. To our knowledge, this is the first report of whole-genome-based characterization of the emerging G5P[6] strains in Asian countries. Our observations will provide important insights into the origin of G5P[6] strains and the dynamic interactions between human and porcine rotavirus strains.
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Affiliation(s)
- Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Yoshimasa Maeno
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Mayuko Tomita
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Tsuyoshi Matsuoka
- Division of Pediatric Neurology and General, Okinawa Prefectural Nanbu Medical Center and Children's Medical Center, Haebaru-cho, Okinawa 901-1193, Japan
| | - Masaharu Ohfu
- Division of Pediatric Neurology and General, Okinawa Prefectural Nanbu Medical Center and Children's Medical Center, Haebaru-cho, Okinawa 901-1193, Japan
| | - Toshifumi Yodoshi
- Division of Pediatric Neurology and General, Okinawa Prefectural Nanbu Medical Center and Children's Medical Center, Haebaru-cho, Okinawa 901-1193, Japan
| | - Hideki Akeda
- Division of Pediatric Neurology and General, Okinawa Prefectural Nanbu Medical Center and Children's Medical Center, Haebaru-cho, Okinawa 901-1193, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
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Papp H, Borzák R, Farkas S, Kisfali P, Lengyel G, Molnár P, Melegh B, Matthijnssens J, Jakab F, Martella V, Bányai K. Zoonotic transmission of reassortant porcine G4P[6] rotaviruses in Hungarian pediatric patients identified sporadically over a 15 year period. INFECTION GENETICS AND EVOLUTION 2013; 19:71-80. [PMID: 23792183 DOI: 10.1016/j.meegid.2013.06.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/08/2013] [Accepted: 06/10/2013] [Indexed: 12/24/2022]
Abstract
Genotype G4P[6] Rotavirus A (RVA) strains collected from children admitted to hospital with gastroenteritis over a 15 year period in the pre rotavirus vaccine era in Hungary were characterized in this study. Whole genome sequencing and phylogenetic analysis was performed on eight G4P[6] RVA strains. All these RVA strains shared a fairly conservative genomic configuration (G4-P[6]-I1/I5-R1-C1-M1-A1/A8-N1-T1/T7-E1-H1) and showed striking similarities to porcine and porcine-derived human RVA strains collected worldwide, although genetic relatedness to some common human RVA strains was also seen. The resolution of phylogenetic relationship between porcine and human RVA genes was occasionally low, making the evaluation of host species origin of individual genes sometimes difficult. Yet the whole genome constellations and overall phylogenetic analyses indicated that these eight Hungarian G4P[6] RVA strains may have originated by independent zoonotic transmission, probably from pigs. Future surveillance studies of human and animal RVA should go parallel to enable the distinction between direct interspecies transmission events and those that are coupled with reassortment of cognate genes.
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Affiliation(s)
- Hajnalka Papp
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
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