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Šenica P, Žele Vengušt D, Vengušt G, Kuhar U. Genomic revelations: investigating rotavirus a presence in wild ruminants and its zoonotic potential. Front Vet Sci 2024; 11:1429654. [PMID: 39211480 PMCID: PMC11358691 DOI: 10.3389/fvets.2024.1429654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Rotaviruses A (RVA) are a major cause of acute viral gastroenteritis in humans worldwide and are responsible for about two million hospitalizations per year. They can also infect other mammals such as pigs, calves, goats, lambs, and horses, in which they are also considered a major cause of viral diarrhea. While RVA is well studied in humans and domestic animals, its occurrence in wild ruminants is not well known. The RVA genome is a double-stranded RNA consisting of 11 segments, and genotyping is based on the VP7 (G) and VP4 (P) segments. Currently, there are 42G genotypes and 58P genotypes. RVA has a high mutation rate, and some combinations of G and P genotypes can infect different animal species, leading to speculation about the potential for zoonotic transmission. Materials and methods A total of 432 fecal samples were collected from roe deer, red deer, chamois, mouflon and Alpine ibex in Slovenia between 2017 and 2021. To investigate the presence of RVA in wild ruminants, real-time RT-PCR was used. Positive samples were subjected to next generation sequencing (NGS) using RIP-seq method. Results and discussion In total, 7 samples were RVA positive. Complete genomes were determined and phylogenetically analyzed for all 7 RVAs. Four different genotype constellations were present in 7 positive RVA animals: G8-P[14]-I2- R2-C2-M2-A3-N2-T6-E2-H3, G6-P [14]-I2-R2-C2-M2-A11-N2-T6-E2-H3, G10-P [15]-I2-R2-C2-M2-A3-N2-T6-E2-H3 and G10-P [15]-I2-R2-C2-M2-A11- N2-T6-E2-H3. Genotypes G6P[14] and G10P[15] were found in both roe deer and red deer, representing the first confirmed occurrence of RVA in red deer. In addition, genotype G8P[14] was found in chamois, representing the first known case of positive RVA in this species. Some of these genotypes have also been found in humans, indicating the potential for zoonotic transmission.
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Affiliation(s)
- Petra Šenica
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Diana Žele Vengušt
- Veterinary Faculty, Institute of Pathology, Wild Animals, Fish and Bees, University of Ljubljana, Ljubljana, Slovenia
| | - Gorazd Vengušt
- Veterinary Faculty, Institute of Pathology, Wild Animals, Fish and Bees, University of Ljubljana, Ljubljana, Slovenia
| | - Urška Kuhar
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
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Epidemiology of Group A rotavirus in rodents and shrews in Bangladesh. Vet Res Commun 2023; 47:29-38. [PMID: 35380357 PMCID: PMC8980207 DOI: 10.1007/s11259-022-09923-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 03/29/2022] [Indexed: 01/27/2023]
Abstract
Rodents and shrews live in close proximity to humans and have been identified as important hosts of zoonotic pathogens. This study aimed to detect Group A rotavirus (RVA) and its potential risk factors in rodents and shrews in Bangladesh. We captured 417 small mammals from 10 districts with a high degree of contact between people and domestic animals and collected rectal swab samples between June 2011 and October 2013. We tested the swab samples for RVA RNA, targeting the NSP3 gene segment using real-time reverse transcription-polymerase chain reaction (rRT-PCR). Overall, RVA prevalence was the same (6.7%) in both rodents and shrews. We detected RVA RNA in 5.3% of Bandicota bengalensis (4/76; 95% CI: 1.4-12.9), 5.1% of B. indica (4/79; 95% CI: 1.4-12.4), 18.2% of Mus musculus (4/22; 95% CI: 5.2-40.3), 6.7% of Rattus rattus (6/90; 95% CI: 2.5-13.9), and 6.7% of Suncus murinus (10/150; 95% CI: 3.2-11.9). We found significantly more RVA in males (10.4%; OR: 3.4; P = 0.007), animals with a poor body condition score (13.9%; OR: 2.7; P = 0.05), during wet season (8.3%; OR: 4.1; P = 0.032), and in urban land gradients (10.04%; OR: 2.9; P = 0.056). These findings form a basis for understanding the prevalence of rotaviruses circulating among rodents and shrews in this region. We recommend additional molecular studies to ascertain the genotype and zoonotic potential of RVA circulating in rodents and shrews in Bangladesh.
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Liu X, Yan N, Yue H, Wang Y, Zhang B, Tang C. Detection and molecular characteristics of bovine rotavirus A in dairy calves in China. J Vet Sci 2021; 22:e69. [PMID: 34423605 PMCID: PMC8460460 DOI: 10.4142/jvs.2021.22.e69] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/11/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Abstract
Background Bovine group A rotavirus (BoRVA) is a major cause of severe gastroenteritis in newborn dairy calves. Only one study has investigated the G and P genotypes among dairy calves in a few regions of China, which were G6 and P[5]. Therefore, data on the prevalence and molecular characteristics of BoRVA in dairy calves in China remains limited. Objectives The purpose of this study was to investigate the prevalence and molecular characteristics of BoRVA in dairy calves in China. Methods 269 dairy calves diarrheic samples from 23 farms in six provinces in China were collected to detect BoRVA using reverse transcription polymerase chain reaction. Results 71% of samples were determined to be BoRVA-positive. Two G genotypes (G6, G10) and two P genotypes (P[1], P[5]) were identified, and G6P[1] BoRVA was the predominant strain. Moreover, the VP7 and VP4 gene sequences of these dairy calf BoRVA strains revealed abundant genetic diversity. Interestingly, eight out of 17 complete G6 VP7 sequences were clustered into G6 lineage VI and analysis showed the strains were closely related to Chinese yak BoRVA strains. Conclusions The results of this study show that BoRVA circulates widely among dairy calves in China, and the dominant genotype in circulation is G6P[1], first report on molecular characteristics of complete P[5] VP4 genes in chinese dairy calves. These results will help us to further understand the prevalence and genetic evolution of BoRVA among dairy calves in China and, thus, prevent the disease more effectively.
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Affiliation(s)
- Xiaoying Liu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Nan Yan
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Hua Yue
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu 610041, China
| | - Yuanwei Wang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Bin Zhang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Cheng Tang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu 610041, China.
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Tosif S, Neeland MR, Sutton P, Licciardi PV, Sarkar S, Selva KJ, Do LAH, Donato C, Quan Toh Z, Higgins R, Van de Sandt C, Lemke MM, Lee CY, Shoffner SK, Flanagan KL, Arnold KB, Mordant FL, Mulholland K, Bines J, Dohle K, Pellicci DG, Curtis N, McNab S, Steer A, Saffery R, Subbarao K, Chung AW, Kedzierska K, Burgner DP, Crawford NW. Immune responses to SARS-CoV-2 in three children of parents with symptomatic COVID-19. Nat Commun 2020; 11:5703. [PMID: 33177504 PMCID: PMC7658256 DOI: 10.1038/s41467-020-19545-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/20/2020] [Indexed: 12/27/2022] Open
Abstract
Compared to adults, children with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have predominantly mild or asymptomatic infections, but the underlying immunological differences remain unclear. Here, we describe clinical features, virology, longitudinal cellular, and cytokine immune profile, SARS-CoV-2-specific serology and salivary antibody responses in a family of two parents with PCR-confirmed symptomatic SARS-CoV-2 infection and their three children, who tested repeatedly SARS-CoV-2 PCR negative. Cellular immune profiles and cytokine responses of all children are similar to their parents at all timepoints. All family members have salivary anti-SARS-CoV-2 antibodies detected, predominantly IgA, that coincide with symptom resolution in 3 of 4 symptomatic members. Plasma from both parents and one child have IgG antibody against the S1 protein and virus-neutralizing activity detected. Using a systems serology approach, we demonstrate higher levels of SARS-CoV-2-specific antibody features of these family members compared to healthy controls. These data indicate that children can mount an immune response to SARS-CoV-2 without virological confirmation of infection, raising the possibility that immunity in children can prevent the establishment of SARS-CoV-2 infection. Relying on routine virological and serological testing may not identify exposed children, with implications for epidemiological and clinical studies across the life-span.
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Affiliation(s)
- Shidan Tosif
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia.
- Department of General Medicine, The Royal Children's Hospital, Melbourne, Victoria, Australia.
| | - Melanie R Neeland
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
| | - Philip Sutton
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
| | - Paul V Licciardi
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
| | - Sohinee Sarkar
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
| | - Kevin J Selva
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lien Anh Ha Do
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
| | - Celeste Donato
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
| | - Zheng Quan Toh
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
| | - Rachel Higgins
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
| | - Carolien Van de Sandt
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Melissa M Lemke
- Department of Biomedical Engineering, University of Michigan, MI, USA
| | - Christina Y Lee
- Department of Biomedical Engineering, University of Michigan, MI, USA
| | | | - Katie L Flanagan
- Department of Infectious Diseases, Launceston General Hospital, Launceston, Tasmania, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
- Department of Immunology and Pathology, Monash University, Commercial Road, Melbourne, Victoria, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, Victoria, Australia
| | - Kelly B Arnold
- Department of Biomedical Engineering, University of Michigan, MI, USA
| | - Francesca L Mordant
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kim Mulholland
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
- Infectious Diseases Unit, Department of General Medicine, The Royal Children's Hospital, Melbourne, Australia
| | - Julie Bines
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Gastroenterology, The Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Kate Dohle
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
| | - Daniel G Pellicci
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
- Infectious Diseases Unit, Department of General Medicine, The Royal Children's Hospital, Melbourne, Australia
| | - Sarah McNab
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
- Department of General Medicine, The Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Andrew Steer
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
- Infectious Diseases Unit, Department of General Medicine, The Royal Children's Hospital, Melbourne, Australia
| | - Richard Saffery
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, Australia
| | - Amy W Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - David P Burgner
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
- Infectious Diseases Unit, Department of General Medicine, The Royal Children's Hospital, Melbourne, Australia
| | - Nigel W Crawford
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia
- Department of General Medicine, The Royal Children's Hospital, Melbourne, Victoria, Australia
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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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Fritzen JTT, Oliveira MV, Lorenzetti E, Miyabe FM, Viziack MP, Rodrigues CA, Ayres H, Alfieri AF, Alfieri AA. Longitudinal surveillance of rotavirus A genotypes circulating in a high milk yield dairy cattle herd after the introduction of a rotavirus vaccine. Vet Microbiol 2019; 230:260-264. [PMID: 30827398 PMCID: PMC7117106 DOI: 10.1016/j.vetmic.2019.02.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 11/25/2022]
Abstract
RVA vaccination program reduces the frequency and intensity of diarrhea in dairy calves. The vaccination immune pressure can select specific genotypes in RVA field strains. RVA genotype G10P[11] in fecal samples of calves from G6P[5] vaccinated dairy cattle herds.
Worldwide, neonatal diarrhea is one of the most important health issues affecting dairy calves, and rotavirus A (RVA) is one of its primary causes. Among the measures to mitigate the risk of diarrhea outbreaks, cow vaccination stands out as one of the most important. However, the immune pressure resulting from routine vaccination may be able to select specific G and P genotypes in RVA field strains. This study aimed to determine the frequency and intensity of neonatal diarrhea and the incidence of RVA and attempted to monitor the G and P genotypes present in the RVA strains circulating in a high milk yield cattle herd vaccinated with RVA G6P[5] strain. Fecal samples (n = 1220) from 122 Holstein heifer calves between 0–30 days old that were born from RVA-vaccinated cows were collected at 10 different time points, regardless of the presence or absence of diarrhea. The presence of RVA in fecal samples was determined by the polyacrylamide gel electrophoresis (PAGE) technique and confirmed by reverse transcription polymerase chain reaction (RT-PCR). G and P amplicons from 10 RVA-positive fecal samples from calves of different ages and collections were subjected to nucleotide sequencing. The proportion of the calves and fecal samples that were positive for RVA were 62.3% (76/122) and 8.1% (99/1220), respectively. Using sequence analysis, all 10 RVA field strains presented genotype G10P[11]. The protection of G6P[5] vaccination is clear, as this genotype was not detected in this study, and it is known that vaccination against RVA reduces the incidence of diarrhea independent of genotype involved. This result demonstrates the importance of epidemiological monitoring of RVA genotypes circulating in vaccinated dairy cattle herds to the early detection of new potential pathogenic RVA strains.
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Affiliation(s)
- Juliana T T Fritzen
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, 86057-970, PO Box 10011, Londrina, Paraná, Brazil
| | - Marcos V Oliveira
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, 86057-970, PO Box 10011, Londrina, Paraná, Brazil
| | - Elis Lorenzetti
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, 86057-970, PO Box 10011, Londrina, Paraná, Brazil
| | - Flávia M Miyabe
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, 86057-970, PO Box 10011, Londrina, Paraná, Brazil
| | - Mariana P Viziack
- Department of Animal Reproduction, FMVZ/USP. 87, Prof. Dr. Orlando Marques de Paiva Ave, Cidade Universitária, 05508-270, São Paulo, São Paulo, Brazil
| | - Carlos A Rodrigues
- SAMVET, 1600, Getúlio Vargas Ave, Jardim São Paulo, 13570-390, São Carlos, São Paulo, Brazil
| | - Henderson Ayres
- MSD Animal Health, 296, Dr. Chucri Zaidan Ave, Vila Cordeiro, 50030-000, São Paulo, São Paulo, Brazil
| | - Alice F Alfieri
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, 86057-970, PO Box 10011, Londrina, Paraná, Brazil; Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, 86057-970, Londrina, Paraná, Brazil
| | - Amauri A Alfieri
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, 86057-970, PO Box 10011, Londrina, Paraná, Brazil; National Institute of Science and Technology for Dairy Production Chain (INCT - LEITE), Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, 86057-970, Londrina, Paraná, Brazil.
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Cowley D, Nirwati H, Donato CM, Bogdanovic-Sakran N, Boniface K, Kirkwood CD, Bines JE. Molecular characterisation of rotavirus strains detected during a clinical trial of the human neonatal rotavirus vaccine (RV3-BB) in Indonesia. Vaccine 2018; 36:5872-5878. [PMID: 30145099 PMCID: PMC6143382 DOI: 10.1016/j.vaccine.2018.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
Equine-like G3P[8] the major cause of gastroenteritis during RV3-BB efficacy trial. The Indonesian equine-like G3P[8] strain was genetically similar to Hungarian and Spanish strains. Equine-like G3P[8] strain is an emerging cause of gastroenteritis in Indonesia.
Background The RV3-BB human neonatal rotavirus vaccine aims to provide protection from severe rotavirus disease from birth. The aim of the current study was to characterise the rotavirus strains causing gastroenteritis during the Indonesian Phase IIb efficacy trial. Methods A randomized, double-blind placebo-controlled trial involving 1649 participants was conducted from January 2013 to July 2016 in Central Java and Yogyakarta, Indonesia. Participants received three doses of oral RV3-BB vaccine with the first dose given at 0–5 days after birth (neonatal schedule), or the first dose given at ∼8 weeks after birth (infant schedule), or placebo (placebo schedule). Stool samples from episodes of gastroenteritis were tested for rotavirus using EIA testing, positive samples were genotyped by RT-PCR. Full genome sequencing was performed on two representative rotavirus strains. Results There were 1110 episodes of acute gastroenteritis of any severity, 105 episodes were confirmed as rotavirus gastroenteritis by EIA testing. The most common genotype identified was G3P[8] (90/105), the majority (52/56) of severe (Vesikari score ≥11) rotavirus gastroenteritis episodes were due to the G3P[8] strain. Full genome analysis of two representative G3P[8] samples demonstrated the strain was an inter-genogroup reassortant, containing an equine-like G3 VP7, P[8] VP4 and a genogroup 2 backbone I2-R2-C2-M2-A2-N2-T2-E2-H2. The complete genome of the Indonesian equine-like G3P[8] strain demonstrated highest genetic identity to G3P[8] strains circulating in Hungary and Spain. Conclusions The dominant circulating strain during the Indonesian Phase IIb efficacy trial of the RV3-BB vaccine was an equine-like G3P[8] strain. The equine-like G3P[8] strain is an emerging cause of severe gastroenteritis in Indonesia and in other regions.
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Affiliation(s)
- Daniel Cowley
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Rotavirus Program, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Hera Nirwati
- Department of Microbiology, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Celeste M Donato
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Nada Bogdanovic-Sakran
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Rotavirus Program, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Karen Boniface
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Rotavirus Program, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Carl D Kirkwood
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Julie E Bines
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Rotavirus Program, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia; Department of Gastroenterology and Clinical Nutrition, Royal Children's Hospital, Parkville, Victoria, Australia.
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8
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Quaye O, Roy S, Rungsrisuriyachai K, Esona MD, Xu Z, Tam KI, Banegas DJC, Rey-Benito G, Bowen MD. Characterisation of a rare, reassortant human G10P[14] rotavirus strain detected in Honduras. Mem Inst Oswaldo Cruz 2018; 113:9-16. [PMID: 29211103 PMCID: PMC5719537 DOI: 10.1590/0074-02760170083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/24/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Although first detected in animals, the rare rotavirus strain G10P[14] has
been sporadically detected in humans in Slovenia, Thailand, United Kingdom
and Australia among other countries. Earlier studies suggest that the
strains found in humans resulted from interspecies transmission and
reassortment between human and bovine rotavirus strains. OBJECTIVES In this study, a G10P[14] rotavirus genotype detected in a human stool sample
in Honduras during the 2010-2011 rotavirus season, from an unvaccinated
30-month old boy who reported at the hospital with severe diarrhea and
vomiting, was characterised to determine the possible evolutionary origin of
the rare strain. METHODS For the sample detected as G10P[14], 10% suspension was prepared and used for
RNA extraction and sequence independent amplification. The amplicons were
sequenced by next-generation sequencing using the Illumina MiSeq 150 paired
end method. The sequence reads were analysed using CLC Genomics Workbench
6.0 and phylogenetic trees were constructed using PhyML version 3.0. FINDINGS The next generation sequencing and phylogenetic analyses of the 11-segmented
genome of the G10P[14] strain allowed classification as
G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. Six of the genes (VP1, VP2, VP3, VP6,
NSP2 and NSP4) were DS-1-like. NSP1 and NSP5 were AU-1-like and NSP3 was T6,
which suggests that multiple reassortment events occurred in the evolution
of the strain. The phylogenetic analyses and genetic distance calculations
showed that the VP7, VP4, VP6, VP1, VP3, NSP1, NSP3 and NSP4 genes clustered
predominantly with bovine strains. NSP2 and VP2 genes were most closely
related to simian and human strains, respectively, and NSP5 was most closely
related to a rhesus strain. MAIN CONCLUSIONS The genetic characterisation of the G10P[14] strain from Honduras suggests
that its genome resulted from multiple reassortment events which were
possibly mediated through interspecies transmissions.
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Affiliation(s)
- Osbourne Quaye
- Centers for Disease Control and Prevention, Gastroenteritis and Respiratory Viruses Laboratory Branch, Atlanta, Georgia, USA.,University of Ghana, Department of Biochemistry, Cell and Molecular Biology, West African Center for Cell Biology of Infectious Pathogens, Legon, Accra, Ghana
| | - Sunando Roy
- Centers for Disease Control and Prevention, Gastroenteritis and Respiratory Viruses Laboratory Branch, Atlanta, Georgia, USA
| | - Kunchala Rungsrisuriyachai
- Centers for Disease Control and Prevention, Gastroenteritis and Respiratory Viruses Laboratory Branch, Atlanta, Georgia, USA
| | - Mathew D Esona
- Centers for Disease Control and Prevention, Gastroenteritis and Respiratory Viruses Laboratory Branch, Atlanta, Georgia, USA
| | - Ziqian Xu
- China Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Ka Ian Tam
- Centers for Disease Control and Prevention, Gastroenteritis and Respiratory Viruses Laboratory Branch, Atlanta, Georgia, USA
| | | | | | - Michael D Bowen
- Centers for Disease Control and Prevention, Gastroenteritis and Respiratory Viruses Laboratory Branch, Atlanta, Georgia, USA
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9
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Jones FK, Ko AI, Becha C, Joshua C, Musto J, Thomas S, Ronsse A, Kirkwood CD, Sio A, Aumua A, Nilles EJ. Increased Rotavirus Prevalence in Diarrheal Outbreak Precipitated by Localized Flooding, Solomon Islands, 2014. Emerg Infect Dis 2016; 22:875-9. [PMID: 27088272 PMCID: PMC4861519 DOI: 10.3201/eid2205.151743] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Flooding on 1 of the Solomon Islands precipitated a nationwide epidemic of diarrhea that spread to regions unaffected by flooding and caused >6,000 cases and 27 deaths. Rotavirus was identified in 38% of case-patients tested in the city with the most flooding. Outbreak potential related to weather reinforces the need for global rotavirus vaccination.
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10
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Mandal P, Mullick S, Nayak MK, Mukherjee A, Ganguly N, Niyogi P, Panda S, Chawla-Sarkar M. Complete genotyping of unusual species A rotavirus G12P[11] and G10P[14] isolates and evidence of frequent in vivo reassortment among the rotaviruses detected in children with diarrhea in Kolkata, India, during 2014. Arch Virol 2016; 161:2773-85. [PMID: 27447463 DOI: 10.1007/s00705-016-2969-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/05/2016] [Indexed: 12/17/2022]
Abstract
Species A rotaviruses (RVA) are the most important cause of acute gastroenteritis in the young of humans and many animal species globally. G1P[8], G2P[4], G3P[8], G4P[8], G9P[6/8] and G12P[6/8] are the predominantly isolated genotypes throughout the world including India. Unusual genotypes from different host species such as G5, G6, G8, G10 and G11 have also been reported in humans with low frequency. In the present study, among >650 RVA positive stool samples collected from children with diarrhea in Kolkata, India, during 2014, two isolates each of the genotype G12P[11] and G10P[14] were obtained and their genomes completely sequenced. The full genotype constellations were G12-P[11]-I1-R1-C1-M2-A1-N1-T2-E1-H1 and G12-P[11]-I1-R1-C1-M1-A5-N1-T1-E1-H1 for G12P[11] viruses, suggesting several reassortments between Wa- and DS-1-like human RVA strains, including possible reassortment of a simian NSP1 gene. The G10P[14] viruses (G10-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3) were found to contain multiple genes closely related to RVAs of artiodactyl origin, highlighting the role of inter-host species transmissions of RVAs. From the G/P constellation of all RVA isolates, it could be concluded that approximately one quarter had likely arisen from reassortment events in vivo among RVAs of 'usual' genotypes.
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Affiliation(s)
- Paulami Mandal
- National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | - Satarupa Mullick
- National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | - Mukti Kant Nayak
- National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | - Anupam Mukherjee
- National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | | | | | - Samiran Panda
- National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T. Road, Scheme XM, Beliaghata, Kolkata, 700010, West Bengal, India.
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11
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Li K, Lin XD, Huang KY, Zhang B, Shi M, Guo WP, Wang MR, Wang W, Xing JG, Li MH, Hong WS, Holmes EC, Zhang YZ. Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans. Virology 2016; 494:168-77. [PMID: 27115729 PMCID: PMC7173014 DOI: 10.1016/j.virol.2016.04.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 01/08/2023]
Abstract
Rotaviruses are an important cause of severe diarrheal illness in children globally. We characterized rotaviruses sampled in humans, insectivores (shrews) and rodents from urban and rural regions of Zhejiang province, China. Phylogenetic analyses revealed seven genotypic constellations of human rotaviruses with six different combinations of G and P genotypes – G3P[8] (50.06%), G9P[8] (36.16%), G1P[8] (8.92%), G2P[4] (4.63%), G3P[3] (0.12%), and G3P[9] (0.12%). In rodents and shrews sampled from the same locality we identified a novel genotype constellation (G32-P[46]-I24-R18-C17-M17-A28-N17-T19-E24-H19), a novel P genotype (P[45]), and two different AU-1-like rotaviruses associated with a G3P[3] genotype combination. Of particular note was a novel rotavirus from a human patient that was closely related to viruses sampled from rodents in the same region, indicative of a local species jump. In sum, these data are suggestive of the cross-species transmission of rodent rotaviruses into humans and for reassortment among human and animal rotaviruses. Rotaviruses are an important cause of severe diarrheal illness. Although rotaviruses are associated with a diverse range of animals, relatively little attention has been directed toward rotaviruses in rodents. However, as rodents often live in close proximity to humans and domestic animals, rodents may play an important role in the cross-species transmission of rotaviruses among animals and perhaps directly or indirectly to humans. Our data suggest the direct spill-over of rodent rotaviruses in human populations, as well as the reassortment between human and zoonotic rotaviruses.
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Affiliation(s)
- Kun Li
- State Key Laboratory of Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China
| | - Kai-Yu Huang
- The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Bing Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Changping, Beijing, China
| | - Mang Shi
- State Key Laboratory of Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Changping, Beijing, China; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Wen-Ping Guo
- State Key Laboratory of Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China
| | - Miao-Ruo Wang
- Longquan Center for Disease Control and Prevention, Longquan, Zhejiang Province, China
| | - Wen Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China
| | - Jian-Guang Xing
- Wencheng Center for Disease Control and Prevention, Wencheng, Zhejiang Province, China
| | - Ming-Hui Li
- State Key Laboratory of Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China
| | - Wang-Sheng Hong
- Ruian Center for Disease Control and Prevention, Ruian, Zhejiang Province, China
| | - Edward C Holmes
- State Key Laboratory of Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Changping, Beijing, China; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Yong-Zhen Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China.
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12
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Full genomic characterization and phylogenetic analysis of a zoonotic human G8P[14] rotavirus strain detected in a sample from Guatemala. INFECTION GENETICS AND EVOLUTION 2015; 33:206-11. [PMID: 25952569 DOI: 10.1016/j.meegid.2015.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/01/2015] [Accepted: 05/04/2015] [Indexed: 02/02/2023]
Abstract
We report the genomic characterization of a rare human G8P[14] rotavirus strain, identified in a stool sample from Guatemala (GTM) during routine rotavirus surveillance. This strain was designated as RVA/Human-wt/GTM/2009726790/2009/G8P[14], with a genomic constellation of G8-P[14]-I2-R2-C2-M2-A13-N2-T6-E2-H3. The VP4 gene occupied lineage VII within the P[14] genotype. Phylogenetic analysis of each genome segment revealed close relatedness to several zoonotic simian, guanaco and bovine strains. Our findings suggest that strain RVA/Human-wt/GTM/2009726790/2009/G8P[14] is an example of a direct zoonotic transmission event. The results of this study reinforce the potential role of interspecies transmission and reassortment in generating novel and rare rotavirus strains which infect humans.
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13
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Full genomic characterization of a novel genotype combination, G4P[14], of a human rotavirus strain from Barbados. INFECTION GENETICS AND EVOLUTION 2014; 28:524-9. [PMID: 25251674 DOI: 10.1016/j.meegid.2014.09.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/09/2014] [Accepted: 09/15/2014] [Indexed: 11/21/2022]
Abstract
Since 2004, the Pan American Health Organization (PAHO) has carried out rotavirus surveillance in Latin America and the Caribbean. Here we report the characterization of human rotavirus with the novel G-P combination of G4P[14], detected through PAHO surveillance in Barbados. Full genome sequencing of strain RVA/Human-wt/BRB/CDC1133/2012/G4P[14] revealed that its genotype is G4-P[14]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The possession of a Genogroup 1 (Wa-like) backbone distinguishes this strain from other P[14] rotavirus strains. Phylogenetic analyses suggested that this strain was likely generated by genetic reassortment between human, porcine and possibly other animal rotavirus strains and identified 7 lineages within the P[14] genotype. The results of this study reinforce the potential role of interspecies transmission in generating human rotavirus diversity through reassortment. Continued surveillance is important to determine if rotavirus vaccines will protect against strains that express the P[14] rotavirus genotype.
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14
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Review of global rotavirus strain prevalence data from six years post vaccine licensure surveillance: is there evidence of strain selection from vaccine pressure? INFECTION GENETICS AND EVOLUTION 2014; 28:446-61. [PMID: 25224179 DOI: 10.1016/j.meegid.2014.08.017] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 11/23/2022]
Abstract
Comprehensive reviews of pre licensure rotavirus strain prevalence data indicated the global importance of six rotavirus genotypes, G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]. Since 2006, two vaccines, the monovalent Rotarix (RV1) and the pentavalent RotaTeq (RV5) have been available in over 100 countries worldwide. Of these, 60 countries have already introduced either RV1 or RV5 in their national immunization programs. Post licensure vaccine effectiveness is closely monitored worldwide. This review aimed at describing the global changes in rotavirus strain prevalence over time. The genotype distribution of the nearly 47,000 strains that were characterized during 2007-2012 showed similar picture to that seen in the preceding period. An intriguing finding was the transient predominance of heterotypic strains, mainly in countries using RV1. Unusual and novel antigen combinations continue to emerge, including some causing local outbreaks, even in vaccinated populations. In addition, vaccine strains have been found in both vaccinated infants and their contacts and there is evidence for genetic interaction between vaccine and wild-type strains. In conclusion, the post-vaccine introduction strain prevalence data do not show any consistent pattern indicative of selection pressure resulting from vaccine use, although the increased detection rate of heterotypic G2P[4] strains in some countries following RV1 vaccination is unusual and this issue requires further monitoring.
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15
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My PVT, Rabaa MA, Donato C, Cowley D, Phat VV, Dung TTN, Anh PH, Vinh H, Bryant JE, Kellam P, Thwaites G, Woolhouse MEJ, Kirkwood CD, Baker S. Novel porcine-like human G26P[19] rotavirus identified in hospitalized paediatric diarrhoea patients in Ho Chi Minh City, Vietnam. J Gen Virol 2014; 95:2727-2733. [PMID: 25121549 PMCID: PMC4233630 DOI: 10.1099/vir.0.068403-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
During a hospital-based diarrhoeal disease study conducted in Ho Chi Minh City, Vietnam from 2009 to 2010, we identified four symptomatic children infected with G26P[19] rotavirus (RV) – an atypical variant that has not previously been reported in human gastroenteritis. To determine the genetic structure and investigate the origin of this G26P[19] strain, the whole genome of a representative example was characterized, revealing a novel genome constellation: G26–P[19]–I5–R1–C1–M1–A8–N1–T1–E1–H1. The genome segments were most closely related to porcine (VP7, VP4, VP6 and NSP1) and Wa-like porcine RVs (VP1–3 and NSP2–5). We proposed that this G26P[19] strain was the product of zoonotic transmission coupled with one or more reassortment events occurring in human and/or animal reservoirs. The identification of such strains has potential implications for vaccine efficacy in south-east Asia, and outlines the utility of whole-genome sequencing for studying RV diversity and zoonotic potential during disease surveillance.
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Affiliation(s)
- Phan Vu Tra My
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Maia A Rabaa
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Celeste Donato
- La Trobe University, Melbourne, Australia.,Murdoch Childrens Research Institute, Melbourne, Australia
| | - Daniel Cowley
- Murdoch Childrens Research Institute, Melbourne, Australia
| | - Voong Vinh Phat
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Thi Ngoc Dung
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Hong Anh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ha Vinh
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Juliet E Bryant
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Paul Kellam
- Division of Infection and Immunity, University College London, London, United Kingdom.,The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Guy Thwaites
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Mark E J Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Carl D Kirkwood
- La Trobe University, Melbourne, Australia.,Murdoch Childrens Research Institute, Melbourne, Australia
| | - Stephen Baker
- The London School of Hygiene and Tropical Medicine, London, UK.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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16
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Donato CM, Cowley D, Snelling TL, Akopov A, Kirkness EF, Kirkwood CD. Characterization of a G1P[8] rotavirus causing an outbreak of gastroenteritis in the Northern Territory, Australia, in the vaccine era. Emerg Microbes Infect 2014; 3:e47. [PMID: 26038746 PMCID: PMC4126178 DOI: 10.1038/emi.2014.47] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/01/2014] [Accepted: 05/05/2014] [Indexed: 02/01/2023]
Abstract
In 2010, a large outbreak of rotavirus gastroenteritis occurred in the Alice Springs region of the Northern Territory, Australia. The outbreak occurred 43 months after the introduction of the G1P[8] rotavirus vaccine Rotarix®. Forty-three infants were hospitalized during the outbreak and analysis of fecal samples from each infant revealed a G1P[8] rotavirus strain. The outbreak strain was adapted to cell culture and neutralization assays were performed using VP7 and VP4 neutralizing monoclonal antibodies. The outbreak strain exhibited a distinct neutralization resistance pattern compared to the Rotarix® vaccine strain. Whole genome sequencing of the 2010 outbreak virus strain demonstrated numerous amino acid differences compared to the Rotarix® vaccine strain in the characterized neutralization epitopes of the VP7 and VP4 proteins. Phylogenetic analysis of the outbreak strain revealed a close genetic relationship to global strains, in particular RVA/Human-wt/BEL/BE0098/2009/G1P[8] and RVA/Human-wt/BEL/BE00038/2008/G1P[8] for numerous genes. The 2010 outbreak strain was likely introduced from a globally circulating population of strains rather than evolving from an endemic Australian strain. The outbreak strain possessed antigenic differences in the VP7 and VP4 proteins compared to the Rotarix® vaccine strain. The outbreak was associated with moderate vaccine coverage and possibly low vaccine take in the population.
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Affiliation(s)
- Celeste M Donato
- Murdoch Childrens Research Institute, Royal Children's Hospital , Melbourne 3052, Victoria, Australia ; La Trobe University , Bundoora 3086, Victoria, Australia
| | - Daniel Cowley
- Murdoch Childrens Research Institute, Royal Children's Hospital , Melbourne 3052, Victoria, Australia
| | - Thomas L Snelling
- Menzies School of Health Research and Charles Darwin University , Casuarina 0810, Northern Territory, Australia
| | - Asmik Akopov
- The J Craig Venter Institute , Rockville, MD 20850, USA
| | | | - Carl D Kirkwood
- Murdoch Childrens Research Institute, Royal Children's Hospital , Melbourne 3052, Victoria, Australia ; La Trobe University , Bundoora 3086, Victoria, Australia
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17
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Absence of genetic differences among G10P[11] rotaviruses associated with asymptomatic and symptomatic neonatal infections in Vellore, India. J Virol 2014; 88:9060-71. [PMID: 24899175 DOI: 10.1128/jvi.01417-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Rotaviruses (RVs) are leading causes of severe diarrhea and vomiting in infants and young children. RVs with G10P[11] genotype specificity have been associated with symptomatic and asymptomatic neonatal infections in Vellore, India. To identify possible viral genetic determinants responsible for differences in symptomology, the genome sequences of G10P[11] RVs in stool samples of 19 neonates with symptomatic infections and 20 neonates with asymptomatic infections were determined by Sanger and next-generation sequencing. The data showed that all 39 viruses had identical genotype constellations (G10-P[11]-I2-R2-C2-M2-A1-N1-T1-E2-H3), the same as those of the previously characterized symptomatic N155 Vellore isolate. The data also showed that the RNA and deduced protein sequences of all the Vellore G10P[11] viruses were nearly identical; no nucleotide or amino acid differences were found that correlated with symptomatic versus asymptomatic infection. Next-generation sequencing data revealed that some stool samples, both from neonates with symptomatic infections and from neonates with asymptomatic infections, also contained one or more positive-strand RNA viruses (Aichi virus, astrovirus, or salivirus/klassevirus) suspected of being potential causes of pediatric gastroenteritis. However, none of the positive-strand RNA viruses could be causally associated with the development of symptoms. These results indicate that the diversity of clinical symptoms in Vellore neonates does not result from genetic differences among G10P[11] RVs; instead, other undefined factors appear to influence whether neonates develop gastrointestinal disease symptoms. IMPORTANCE Rotavirus (RV) strains have been identified that preferentially replicate in neonates, in some cases, without causing gastrointestinal disease. Surveillance studies have established that G10P[11] RVs are a major cause of neonatal infection in Vellore, India, with half of infected neonates exhibiting symptoms. We used Sanger and next-generation sequencing technologies to contrast G10P[11] RVs recovered from symptomatic and asymptomatic neonates. Remarkably, the data showed that the RNA genomes of the viruses were virtually indistinguishable and lacked any differences that could explain the diversity of clinical outcomes among infected Vellore neonates. The sequencing results also indicated that some symptomatic and some asymptomatic Vellore neonates were infected with other enteric viruses (Aichi virus, astrovirus, salvirus/klassevirus); however, none could be correlated with the presence of symptoms in neonates. Together, our findings suggest that other poorly defined factors, not connected to the genetic makeup of the Vellore G10P[11] viruses, influence whether neonates develop gastrointestinal disease symptoms.
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18
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Identification of novel bovine group A rotavirus G15P[14] strain from epizootic diarrhea of adult cows by de novo sequencing using a next-generation sequencer. Vet Microbiol 2014; 171:66-73. [PMID: 24725447 PMCID: PMC7127257 DOI: 10.1016/j.vetmic.2014.03.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 12/13/2022]
Abstract
There are few reports describing diarrhea of adult cattle caused by group A rotaviruses. Here, we report the identification of a novel bovine group A rotavirus from diarrhea of adult cows. A group A rotavirus was detected from an epizootic outbreak of diarrhea in adult cows with a decrease in milk production in Japan in 2013. The comprehensive genomic analyses from fecal samples by viral metagenomics using a next-generation sequencer revealed that it had an unreported genotype combination G15P[14]. The genome constellation of this strain, namely, RVA/Cow-wt/JPN/Tottori-SG/2013/G15P[14] was G15-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3 representing VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5, respectively. Each gene segment of Tottori-SG was most closely related to Japanese bovine group A rotaviruses suggesting that Tottori-SG might have derived from multiple reassortment events from group A rotavirus strains circulating among Japanese cattle. No other diarrhea pathogen of adult cattle was detected by routine diagnosis and metagenomics. Viral metagenomics, using a next-generation sequencer, is useful to characterize group A rotaviruses from fecal samples and offers unbiased comprehensive investigations of pathogen.
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