1
|
Gutierrez MB, Arantes I, Bello G, Berto LH, Dutra LH, Kato RB, Fumian TM. Emergence and dissemination of equine-like G3P[8] rotavirus A in Brazil between 2015 and 2021. Microbiol Spectr 2024; 12:e0370923. [PMID: 38451227 PMCID: PMC10986506 DOI: 10.1128/spectrum.03709-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/22/2024] [Indexed: 03/08/2024] Open
Abstract
Rotavirus A (RVA) is a major cause of acute gastroenteritis globally that is classically genotyped by its two immunodominant outer capsid proteins, VP7 (G-) and VP4 (P-). Recent evidence suggests that the reassortant equine-like G3P[8] strain played a substantial role in RVA transmission in Brazil since 2015. To understand its global emergence and dissemination in Brazilian territory, stool samples collected from 11 Brazilian states (n = 919) were genotyped by RT-qPCR and proceeded to sequence the VP7 gene (n = 102, 79 being newly generated) of the G3P[8] samples with pronounced viral loads. Our phylogenetic genotyping showed that G3P[8] became the dominant strain in Brazil between 2017 and 2020, with equine-like variants representing 75%-100% of VP7 samples in this period. A Bayesian discrete phylogeographic analysis strongly suggests that the equine-like G3P[8] strain originated in Asia during the early 2010s and subsequently spread to Europe, the Caribbean, and South America. Multiple introductions were detected in Brazil between 2014 and 2017, resulting in five national clusters. The reconstruction of the effective population size of the largest Brazilian cluster showed an expansion until 2017, followed by a plateau phase until 2019 and subsequent contraction. Our study also supports that most mutations fixed during equine-like G3P[8] evolution were synonymous, suggesting that adaptive evolution was not an important driving force during viral dissemination in humans, potentially increasing its susceptibility to acquired immunity. This research emphasizes the need for comprehensive rotavirus genomic surveillance that allows close monitoring of its ever-shifting composition and informs more effective public health policies.IMPORTANCEOur original article demonstrated the origin and spread in a short time of equine-like G3P[8] in Brazil and the world. Due to its segmented genome, it allows numerous mechanisms including genetic drift and reassortment contribute substantially to the genetic diversity of rotavirus. Although the effectiveness and increasing implementation of vaccination have not been questioned, a matter of concern is its impact on the emergence of escape mutants or even the spread of unusual strains of zoonotic transmission that could drive epidemic patterns worldwide. This research emphasizes the need for comprehensive rotavirus genomic surveillance, which could facilitate the formulation of public policies aimed at preventing and mitigating its transmission.
Collapse
Affiliation(s)
| | - Ighor Arantes
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Lúcia Helena Berto
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Leonardo Hermes Dutra
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Rodrigo Bentes Kato
- Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Tulio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| |
Collapse
|
2
|
Carossino M, Vissani MA, Barrandeguy ME, Balasuriya UBR, Parreño V. Equine Rotavirus A under the One Health Lens: Potential Impacts on Public Health. Viruses 2024; 16:130. [PMID: 38257830 PMCID: PMC10819593 DOI: 10.3390/v16010130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/29/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Group A rotaviruses are a well-known cause of viral gastroenteritis in infants and children, as well as in many mammalian species and birds, affecting them at a young age. This group of viruses has a double-stranded, segmented RNA genome with high genetic diversity linked to point mutations, recombination, and, importantly, reassortment. While initial molecular investigations undertaken in the 1900s suggested host range restriction among group A rotaviruses based on the fact that different gene segments were distributed among different animal species, recent molecular surveillance and genome constellation genotyping studies conducted by the Rotavirus Classification Working Group (RCWG) have shown that animal rotaviruses serve as a source of diversification of human rotavirus A, highlighting their zoonotic potential. Rotaviruses occurring in various animal species have been linked with contributing genetic material to human rotaviruses, including horses, with the most recent identification of equine-like G3 rotavirus A infecting children. The goal of this article is to review relevant information related to rotavirus structure/genomic organization, epidemiology (with a focus on human and equine rotavirus A), evolution, inter-species transmission, and the potential zoonotic role of equine and other animal rotaviruses. Diagnostics, surveillance and the current status of human and livestock vaccines against RVA are also reviewed.
Collapse
Affiliation(s)
- Mariano Carossino
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Maria Aldana Vissani
- Escuela de Veterinaria, Facultad de Ciencias Agrarias y Veterinarias, Universidad del Salvador, Pilar, Buenos Aires B1630AHU, Argentina; (M.A.V.); (M.E.B.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Maria E. Barrandeguy
- Escuela de Veterinaria, Facultad de Ciencias Agrarias y Veterinarias, Universidad del Salvador, Pilar, Buenos Aires B1630AHU, Argentina; (M.A.V.); (M.E.B.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
| | - Udeni B. R. Balasuriya
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Viviana Parreño
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Mhango C, Banda A, Chinyama E, Mandolo JJ, Kumwenda O, Malamba-Banda C, Barnes KG, Kumwenda B, Jambo KC, Donato CM, Esona MD, Mwangi PN, Steele AD, Iturriza-Gomara M, Cunliffe NA, Ndze VN, Kamng’ona AW, Dennis FE, Nyaga MM, Chaguza C, Jere KC. Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi. Virus Evol 2023; 9:vead030. [PMID: 37305707 PMCID: PMC10256189 DOI: 10.1093/ve/vead030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/12/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
G3 rotaviruses rank among the most common rotavirus strains worldwide in humans and animals. However, despite a robust long-term rotavirus surveillance system from 1997 at Queen Elizabeth Central Hospital in Blantyre, Malawi, these strains were only detected from 1997 to 1999 and then disappeared and re-emerged in 2017, 5 years after the introduction of the Rotarix rotavirus vaccine. Here, we analysed representative twenty-seven whole genome sequences (G3P[4], n = 20; G3P[6], n = 1; and G3P[8], n = 6) randomly selected each month between November 2017 and August 2019 to understand how G3 strains re-emerged in Malawi. We found four genotype constellations that were associated with the emergent G3 strains and co-circulated in Malawi post-Rotarix vaccine introduction: G3P[4] and G3P[6] strains with the DS-1-like genetic backbone genes (G3-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2), G3P[8] strains with the Wa-like genetic backbone genes (G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1), and reassortant G3P[4] strains consisting of the DS-1-like genetic backbone genes and a Wa-like NSP2 (N1) gene (G3-P[4]-I2-R2-C2-M2-A2-N1-T2-E2-H2). Time-resolved phylogenetic trees demonstrated that the most recent common ancestor for each ribonucleic acid (RNA) segment of the emergent G3 strains was between 1996 and 2012, possibly through introductions from outside the country due to the limited genetic similarity with G3 strains which circulated before their disappearance in the late 1990s. Further genomic analysis revealed that the reassortant DS-1-like G3P[4] strains acquired a Wa-like NSP2 genome segment (N1 genotype) through intergenogroup reassortment; an artiodactyl-like VP3 through intergenogroup interspecies reassortment; and VP6, NSP1, and NSP4 segments through intragenogroup reassortment likely before importation into Malawi. Additionally, the emergent G3 strains contain amino acid substitutions within the antigenic regions of the VP4 proteins which could potentially impact the binding of rotavirus vaccine-induced antibodies. Altogether, our findings show that multiple strains with either Wa-like or DS-1-like genotype constellations have driven the re-emergence of G3 strains. The findings also highlight the role of human mobility and genome reassortment events in the cross-border dissemination and evolution of rotavirus strains in Malawi necessitating the need for long-term genomic surveillance of rotavirus in high disease-burden settings to inform disease prevention and control.
Collapse
Affiliation(s)
| | - Akuzike Banda
- Department of Computer Science, Faculty of Science, University of Malawi, Zomba 305205, Malawi
| | - End Chinyama
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Jonathan J Mandolo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Orpha Kumwenda
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Chikondi Malamba-Banda
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK
- Department of Biological Sciences, Academy of Medical Sciences, Malawi University of Science and Technology, Thyolo 310105, Malawi
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Kayla G Barnes
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Benjamin Kumwenda
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Kondwani C Jambo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Celeste M Donato
- Enteric Diseases Group, Murdoch Children’s Research Institute, 50 Flemington Road, Parkville, Melbourne 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Peter N Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of Free State, Bloemfontein 9300, South Africa
| | - A Duncan Steele
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa
| | - Miren Iturriza-Gomara
- Centre for Vaccine Innovation and Access, Program for Appropriate Technology in Health (PATH), Geneva 1218, Switzerland
| | - Nigel A Cunliffe
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool L69 7BE, UK
| | - Valentine N Ndze
- Faculty of Health Sciences, University of Buea, PO Box 63, Buea, Cameroon
| | | | - Francis E Dennis
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, P. O. Box LG 581, Legon, Ghana
| | | | | | | |
Collapse
|
5
|
Zhao Q, Liu L, Huang T, Tian Y, Guo X, Liu C, Huang B, Chen Q. Complete genomic analysis of rabbit rotavirus G3P[22] in China. Arch Virol 2023; 168:129. [PMID: 37004683 DOI: 10.1007/s00705-023-05740-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/20/2023] [Indexed: 04/04/2023]
Abstract
A rabbit rotavirus Z3171 isolate from diarrheic rabbits was identified and sequenced. The genotype constellation of Z3171 is G3-P[22]-I2-R3-C3-M3-A9-N2-T1-E3-H3, which is different from the constellation observed in previously characterized LRV strains. However, the genome of Z3171 differed substantially from those of the rabbit rotavirus strains N5 and Rab1404 in terms of both gene content and gene sequence. Our study suggests that either a reassortment event occurred between human and rabbit rotavirus strains or there are undetected genotypes circulating in the rabbit population. This is the first report of detection of a G3P[22] RVA strain in rabbits in China.
Collapse
Affiliation(s)
- Qiaoya Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, 210095, Nanjing, Jiangsu Province, China
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China
| | - Liping Liu
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China
| | - Tao Huang
- College of Veterinary Medicine, Southwest University, 402460, Chongqing, China
| | - Ye Tian
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China
| | - Xiaozhen Guo
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China
| | - Cunxia Liu
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China
| | - Bing Huang
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China.
| | - Qiusheng Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, 210095, Nanjing, Jiangsu Province, China.
| |
Collapse
|
6
|
Yandle Z, Gonzalez G, Carr M, Matthijnssens J, De Gascun C. A viral metagenomic protocol for nanopore sequencing of group A rotavirus. J Virol Methods 2023; 312:114664. [PMID: 36494024 DOI: 10.1016/j.jviromet.2022.114664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
AIM Development of an unbiased methodology using Oxford Nanopore Technology (ONT) sequencing to obtain whole-genome sequences (WGS) of Rotavirus A (RVA) from clinical samples. METHODS 157 RVA qRT-PCR positive faecal samples were enriched by virus-like particle (VLP) purification and host nuclease digestion to enhance the detection of viral nucleic acids and cDNA generated as per the NetoVIR protocol. ONT sequencing was then performed using the ONT Native Barcoding kit (SQK-LSK-109) on the GridION platform. Data was basecalled, demultiplexed and assembled into near complete RVA genomes. The accuracy and quality of the obtained sequences was assessed by comparing to Sanger sequencing and RVA reference genomes. RESULTS The developed protocol generated 146 near-complete RVA WGS out of the 157 RVA-positive clinical samples. The quality of the assembled genomes was assessed by comparison against publicly-available sequences with results showing 98.76 % ± 0.03 % similarity and > 90 % genome coverage. A concordance assessment was performed comparing the identity of partial RVA VP7 and VP4 segments obtained by Sanger sequencing (n = 51) against corresponding nanopore sequences which demonstrated an overall identity of 100.0 % ± 0.02 %. CONCLUSIONS The nanopore protocol generated both high quality and accurate RVA WGS extracted from faecal samples. This protocol can be extended to other viral agents in other sample types.
Collapse
Affiliation(s)
- Zoe Yandle
- UCD National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland.
| | - Gabriel Gonzalez
- UCD National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan; Japan Initiative for World-leading Vaccine Research and Development Centers, Hokkaido University, Institute for Vaccine Research and Development, Hokkaido, Japan
| | - Michael Carr
- UCD National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium
| | - Cillian De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| |
Collapse
|
7
|
Kachooei A, Tava Koli A, Minaeian S, Hosseini M, Jalilvand S, Latifi T, Arashkia A, Ataei-Pirkooh A, Shoja Z. Molecular characterization of rotavirus infections in children less than 5 years of age with acute gastroenteritis in Tehran, Iran, 2021-2022: Emergence of uncommon G9P[4] and G9P[8] rotavirus strains. J Med Virol 2023; 95:e28529. [PMID: 36698258 DOI: 10.1002/jmv.28529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023]
Abstract
The present study was conducted to monitor the genotypes of circulating species A rotavirus (RVA) in Iran and investigate genetic linkages between specific RVA VP7, VP4, VP6, and NSP4 segments. For this purpose, 48 RVA strains were detected during the 2021-2022 seasons. The two combinations of G9P[4] and G9P[8] RVA strains were predominant. However, several other combinations of RVA also were detected. Based on the distribution of I and E genotypes (46 strains) with respect to G and P, the most common strains were G9P[4]-I2-E2 (19.5%), G9P[4]-I2-E1 (6.5%), G9P[4]-I1-E1 (4.3%), G9P[8]-I1-E1 (19.5%), and G9P[8]-I2-E2 (10.9%), which were followed by several other combinations of G and P RVA strains with different pattern of I-E genotypes and also emerging, rare and uncommon strains. The present study described the continued circulation of G9 strains with the emergence of uncommon G9P[4] and G9P[8] reassortants with three and two different I-E genotypes, respectively, which have not been reported previously in Iran. Our findings indicated that these uncommon strains exhibited a unique genotype pattern comprising a mixture of genogroup 1 and 2 genes and suggest the need for further analysis of rare, uncommon, and emerging strains of RVA at all 11 gene segments to determine intergenogroup and intragenotype reassortments.
Collapse
Affiliation(s)
- Atefeh Kachooei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Ahmad Tava Koli
- Rsearch Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Minaeian
- Antimicrobial Resistance Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Mahdieh Hosseini
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Tayebeh Latifi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Arash Arashkia
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran.,Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Angila Ataei-Pirkooh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran.,Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
8
|
Díaz Alarcón RG, Liotta DJ, Miño S. Zoonotic RVA: State of the Art and Distribution in the Animal World. Viruses 2022; 14:v14112554. [PMID: 36423163 PMCID: PMC9694813 DOI: 10.3390/v14112554] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
Rotavirus species A (RVA) is a pathogen mainly affecting children under five years old and young animals. The infection produces acute diarrhea in its hosts and, in intensively reared livestock animals, can cause severe economic losses. In this study, we analyzed all RVA genomic constellations described in animal hosts. This review included animal RVA strains in humans. We compiled detection methods, hosts, genotypes and complete genomes. RVA was described in 86 animal species, with 52% (45/86) described by serology, microscopy or the hybridization method; however, strain sequences were not described. All of these reports were carried out between 1980 and 1990. In 48% (41/86) of them, 9251 strain sequences were reported, with 28% being porcine, 27% bovine, 12% equine and 33% from several other animal species. Genomic constellations were performed in 80% (32/40) of hosts. Typical constellation patterns were observed in groups such as birds, domestic animals and artiodactyls. The analysis of the constellations showed RVA's capacity to infect a broad range of species, because there are RVA genotypes (even entire constellations) from animal species which were described in other studies. This suggests that this virus could generate highly virulent variants through gene reassortments and that these strains could be transmitted to humans as a zoonotic disease, making future surveillance necessary for the prevention of future outbreaks.
Collapse
Affiliation(s)
- Ricardo Gabriel Díaz Alarcón
- Laboratory of Applied Molecular Biology (LaBiMAp), Faculty of Exacts, Chemical and Natural Sciences, National University of Misiones (UNaM), Posadas 3300, Misiones, Argentina
| | - Domingo Javier Liotta
- Laboratory of Applied Molecular Biology (LaBiMAp), Faculty of Exacts, Chemical and Natural Sciences, National University of Misiones (UNaM), Posadas 3300, Misiones, Argentina
- National Institute of Tropical Medicine (INMeT)—ANLIS “Dr. Carlos Malbrán”, Puerto Iguazú 3370, Misiones, Argentina
| | - Samuel Miño
- Laboratory of Applied Molecular Biology (LaBiMAp), Faculty of Exacts, Chemical and Natural Sciences, National University of Misiones (UNaM), Posadas 3300, Misiones, Argentina
- National Institute of Agricultural Technology (INTA), EEA Cerro Azul, National Route 14, Km 836, Cerro Azul 3313, Misiones, Argentina
- Correspondence: ; Tel.: +54-376-449-4740 (ext. 120)
| |
Collapse
|
9
|
El-Gayar MH, Saleh SE, Mohamed AF, Aboulwafa MM, Hassouna NA, Allayeh AK. Isolation, Propagation and Genotyping of Human Rotaviruses Circulating among Children with Gastroenteritis in Two Egyptian University Hospitals. BIOLOGY 2022; 11:biology11101413. [PMID: 36290316 PMCID: PMC9598786 DOI: 10.3390/biology11101413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/24/2022] [Accepted: 09/25/2022] [Indexed: 11/19/2022]
Abstract
Simple Summary Group A rotaviruses are the most common cause of acute gastroenteritis affecting Egyptian children under the age of five, with symptoms ranging from asymptomatic infection to severe dehydration or death. In the present work, diarrheal samples from Egyptian children admitted to gastrointestinal pediatric wards of two main governmental hospitals were collected and molecularly analyzed for Group A rotavirus. Our findings revealed that rotaviruses accounted for more than one-sixth of all cases under study, peaking in the winter. G1P[8] was the most prevalent rotavirus genotype in this study. The two cell lines used in our work coherently isolated and propagated rotavirus strains. Continuous rotavirus detection and genome sequencing of the successfully isolated strains will be recommended in the future in order to support the control of such viruses, and tackle the problem in Egypt. Abstract The most prevalent cause of infectious neonatal diarrhea is Group A rotavirus (RVA). Unfortunately, there is a dearth of data on the incidence of rotavirus-associated infections among Egyptian children. The present study aimed to isolate, propagate, and genotype human rotaviruses circulating among Egyptian children with acute gastroenteritis admitted to two main university pediatric hospitals, Abo El-Reesh and El-Demerdash, over two consecutive winters, 2018–2020. Diarrheal samples (n = 230) were screened for Group A rotavirus RNA using RT-PCR assay. In positive samples (n = 34), multiplex semi-nested PCR was utilized to determine G and P genotypes. Thirty-four (14.8%) of the collected samples tested positive. The genotype distribution revealed that G1P[8] was the predominant rotavirus genotype throughout the current study. All rotavirus-positive fecal samples were passaged twice on human colorectal adenocarcinoma cell line (Caco-2) and rhesus monkey kidney epithelial cell line (MA104). Both cell lines could successfully isolate 14.7% (n = 5 out of 34) of the identified strains; however, Caco-2 cell line was shown to be more efficient than MA104 in promoting the propagation of human rotaviruses identified in Egyptian children’s feces.
Collapse
Affiliation(s)
- Mona H. El-Gayar
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Cairo 11566, Egypt
| | - Sarra E. Saleh
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Cairo 11566, Egypt
| | - Aly F. Mohamed
- The International Center for Training & Advanced Researches (ICTAR–Egypt1), Cairo 12622, Egypt
| | - Mohammad M. Aboulwafa
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Cairo 11566, Egypt
- Faculty of Pharmacy, King Salman International University, Ras-Sudr 46612, Egypt
- Correspondence: or ; Tel.: +20-1002350371
| | - Nadia A. Hassouna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Cairo 11566, Egypt
| | - Abdou Kamal Allayeh
- Virology Laboratory, Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Center, Giza 12622, Egypt
| |
Collapse
|
10
|
Li Y, Wang F, Kan R, Cao H, Tang C, Yue H, Zhang B. Genetic and immunological characterization of G9 group A porcine rotaviruses in China. Zoonoses Public Health 2022; 69:694-703. [PMID: 35608375 DOI: 10.1111/zph.12958] [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: 02/22/2022] [Revised: 04/18/2022] [Accepted: 04/29/2022] [Indexed: 11/28/2022]
Abstract
G9 group A rotaviruses (RVAs) are considered emerging pathogens in pigs and humans, and pigs are considered a potential host reservoir for human G9 RVAs. In this study, RVAs of two genotypes, G9P[23] and G9P[13], were successfully isolated and the genomic sequences were obtained, the genome constellation is G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1 and G9-P[13]-I5-R1-C1-M1-A8-N1-T7-E1-H1 respectively. One strain which amplified from clinic faecal sample had an unique genome constellation G9-P[23]-I1-R1-C1-M1-A8-N1-T1-E1-H1. All the genomic segments of three porcine G9 RVAs were closely related to those of porcine and/or porcine-like human RVAs, demonstrating that the three viruses were porcine-human reassortant strains. To study the immunogenicity of the porcine G9 RVAs, 6-week-old female BALB/c mice were immunized with inactivated vaccines derived from porcine RVAs and then mated. The highest titres of neutralizing antibodies against G9P[23] and G9P[13] porcine RVAs (1,291 ± 35.22 and 1:232 ± 39.28 respectively) were produced in mice 7 days after the second immunization. Suckling mice born to the vaccinated dams were protected by maternal antibodies against challenge with homologous strains. Overall, our data demonstrate the occurrence of porcine-human reassortants of G9 RVAs, and extend our understanding of the immunogenicity of porcine G9 rotaviruses. They also provide a basis for the development of a porcine G9 RVA vaccine.
Collapse
Affiliation(s)
- Yu Li
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Fengxuan Wang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Key laboratory of Ministry of Education and Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
| | - Ruici Kan
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Hui Cao
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Cheng Tang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Key laboratory of Ministry of Education and Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
| | - Hua Yue
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Key laboratory of Ministry of Education and Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
- Sichuan Veterinary Medicine and Drug Innovation Group of China Agricultural Research System, China, Chengdu
| | - Bin Zhang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Key laboratory of Ministry of Education and Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
- Sichuan Veterinary Medicine and Drug Innovation Group of China Agricultural Research System, China, Chengdu
| |
Collapse
|
11
|
Mao T, Wang M, Wang J, Ma Y, Liu X, Wang M, Sun X, Li L, Li H, Zhang Q, Li D, Duan Z. Phylogenetic analysis of the viral proteins VP4/VP7 of circulating human rotavirus strains in China from 2016 to 2019 and comparison of their antigenic epitopes with those of vaccine strains. Front Cell Infect Microbiol 2022; 12:927490. [PMID: 36004332 PMCID: PMC9393338 DOI: 10.3389/fcimb.2022.927490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022] Open
Abstract
Group A rotaviruses (RVAs) are the most common etiological agents of severe acute diarrhea among children under 5 years old worldwide. At present, two live-attenuated RVA vaccines, LLR (G10P[15]) and RotaTeq (G1–G4, G6 P[8], P[5]), have been introduced to mainland China. Although RVA vaccines can provide homotypic and partially heterotypic protection against several strains, it is necessary to explore the genetic and antigenic variations between circulating RVAs and vaccine strains. In this study, we sequenced viral protein VP7 and VP4 outer capsid proteins of 50 RVA strains circulating in China from 2016 to 2019. The VP7 and VP4 sequences of almost all strains showed high homology to those of previously reported human strains and vaccine strains of the same genotype. However, in the presumed antigenic epitopes of the VP7 and VP4, multiple amino acid variations were found, regardless of the G and P genotypes of these strains. Moreover, all circulating G3 RVA strains in China potentially possess an extra N-linked glycosylation site compared with the G3 strain of RotaTeq. The potential N-linked glycosylation site at residues 69–71 was found in all G9 strains in China but not in the G9 strain of the Rotavac or Rotasill vaccine. These variations in antigenic sites might result in the selection of strains that escape the RVA neutralizing-antibody pressure imposed by vaccines. Furthermore, the G4 and P[6] genotypes in this study showed high homology to those of porcine strains, indicating the transmission of G4 and P[6] genotypes from pigs to humans in China. More genetic surveillance with antigenic evaluation in prevalent RVAs is necessary for developing and implementing rotavirus vaccines in China.
Collapse
Affiliation(s)
- Tongyao Mao
- Key Laboratory for Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, National Health Commission of the People’s Republic of China, Beijing, China
| | - Mengxuan Wang
- Key Laboratory for Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, National Health Commission of the People’s Republic of China, Beijing, China
| | - Jindong Wang
- Department of Medical Microbiology, Weifang Medical University, Weifang, China
| | - Yalin Ma
- Key Laboratory for Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, National Health Commission of the People’s Republic of China, Beijing, China
- School of Public Health, Gansu University of Chinese Medicine, Lanzhou, China
| | - Xiafei Liu
- Key Laboratory for Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, National Health Commission of the People’s Republic of China, Beijing, China
| | - Mingwen Wang
- Key Laboratory for Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, National Health Commission of the People’s Republic of China, Beijing, China
| | - Xiaoman Sun
- Key Laboratory for Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, National Health Commission of the People’s Republic of China, Beijing, China
| | - Lili Li
- Key Laboratory for Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, National Health Commission of the People’s Republic of China, Beijing, China
| | - Huiying Li
- Key Laboratory for Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, National Health Commission of the People’s Republic of China, Beijing, China
| | - Qing Zhang
- Key Laboratory for Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, National Health Commission of the People’s Republic of China, Beijing, China
| | - Dandi Li
- Key Laboratory for Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, National Health Commission of the People’s Republic of China, Beijing, China
- *Correspondence: Dandi Li, ; Zhaojun Duan,
| | - Zhaojun Duan
- Key Laboratory for Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, National Health Commission of the People’s Republic of China, Beijing, China
- *Correspondence: Dandi Li, ; Zhaojun Duan,
| |
Collapse
|
12
|
Mozgovoj M, Miño S, Barbieri E, Tort F, Victoria-Montero M, Frydman C, Cap M, Baron P, Colina R, Matthijnssens J, Parreño V. GII.4 human norovirus and G8P[1] bovine-like rotavirus in oysters (Crassostrea gigas) from Argentina. Int J Food Microbiol 2022; 365:109553. [DOI: 10.1016/j.ijfoodmicro.2022.109553] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 12/30/2022]
|
13
|
Duarte Júnior JWB, Chagas EHN, Serra ACS, Souto LCDS, da Penha Júnior ET, Bandeira RDS, e Guimarães RJDPS, Oliveira HGDS, Sousa TKS, Lopes CTDA, Domingues SFS, Pinheiro HHC, Malik YS, Salvarani FM, Mascarenhas JDP. Ocurrence of rotavirus and picobirnavirus in wild and exotic avian from amazon forest. PLoS Negl Trop Dis 2021; 15:e0008792. [PMID: 34506499 PMCID: PMC8432778 DOI: 10.1371/journal.pntd.0008792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 08/11/2021] [Indexed: 12/25/2022] Open
Abstract
The present study reports the occurrence of rotavirus A (RVA), rotavirus D (RVD), rotavirus F (RVF), rotavirus G (RVG), and picobirnavirus (PBV) in fecal specimens of wild (n = 22), and exotic birds (n = 1) from different cities of Pará state. These animals were hospitalized at Veterinary Hospital of the Federal University of Pará, Brazil, in a period from January 2018 to June 2019. The animals exhibited different clinical signs, such as diarrhea, malnutrition, dehydration, and fractures. The results showed 39.1% (9/23) of positivity for RVA by RT-qPCR. Among these, one sample (1/9) for the NSP3 gene of T2 genotype was characterized. About 88.9% (8/9) for the VP7 gene belonging to G1, G3 equine like and G6 genotypes, and 55.5% (5/9) for the VP4 gene of P[2] genotype were obtained. In the current study, approximately 4.5% of the samples (1/23) revealed coinfection for the RVA, RVD and RVF groups. Furthermore, picobirnavirus (PBV) was detected in one of the 23 samples tested, and was classified in the Genogroup I. The findings represent the first report of RVA, RVD, RVF, RVG, and PBV genotypes in wild birds in Brazil, and due to wide distribution it can implies potential impacts of RVs, and PBVs on avian health, and other animals contributing to construction of new knowledge, and care perspectives.
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Tsugawa T, Fujii Y, Akane Y, Honjo S, Kondo K, Nihira H, Kimura H, Kawasaki Y. Molecular characterization of the first human G15 rotavirus strain of zoonotic origin from the bovine species. J Gen Virol 2021; 102. [PMID: 33847554 DOI: 10.1099/jgv.0.001581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Group A rotaviruses (RVAs) infect a wide variety of mammalian and avian species. Animals act as a potential reservoir to RVA human infections by direct virion transmission or by contributing genes to reassortants. Here, we report the molecular characterization of a rare human RVA strain Ni17-46 with a genotype G15P[14], isolated in Japan in 2017 during rotavirus surveillance in a paediatric outpatient clinic. The genome constellation of this strain was G15-P[14]-I2-R2-C2-M2-A13-N2-T9-E2-H3. This is the first report of an RVA with G15 genotype in humans, and sequencing and phylogenetic analysis results suggest that human infection with this strain has zoonotic origin from the bovine species. Given the fact that this strain was isolated from a patient with gastroenteritis and dehydration symptoms, we must take into account the virulence of this strain in humans.
Collapse
Affiliation(s)
- Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Yoshiki Fujii
- Department of Virology Ⅱ, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Yusuke Akane
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Saho Honjo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sunagawa City Hospital, Sunagawa, Hokkaido, Japan
| | | | - Hirokazu Kimura
- Graduate School of Health Science, Gunma Paz University, Takasaki, Gunma, Japan
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| |
Collapse
|
16
|
Silva Serra AC, Júnior EC, Cruz JF, Lobo PS, Júnior ET, Bandeira RS, Bezerra DA, Mascarenhas JD, Santos Guerra SF, Soares LS. Molecular analysis of G3P[6] rotavirus in the Amazon region of Brazil: evidence of reassortment with equine-like strains. Future Microbiol 2021; 16:847-862. [PMID: 34318682 DOI: 10.2217/fmb-2020-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To perform a molecular analysis of rotavirus A (RVA) G3P[6] strains detected in 2012 and 2017 in the Amazon region of Brazil. Materials & methods: Eighteen RVA G3P[6] strains were collected from children aged under 10 years hospitalized with acute gastroenteritis, and partial sequencing of each segment genome was performed using Sanger sequencing. Results: Phylogenetic analysis showed that all G3P[6] strains had a DS-1-like genotype constellation. Two strains had the highest nucleotide identities with equine-like G3P[6]/G3P[8] genotypes. Several amino acid alterations in VP4 and VP7 neutralizing epitopes of equine-like RVA G3P[6] strains were observed in comparison with vaccine strains. Conclusion: These findings suggest that equine-like RVA G3P[6] strains have been circulating in the Amazon region of Brazil as a result of direct importation, and support natural RVA evolutionary mechanisms.
Collapse
Affiliation(s)
- Ana C Silva Serra
- Program in Virology, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Edivaldo Cs Júnior
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Jonas F Cruz
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Patrícia S Lobo
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Edvaldo Tp Júnior
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Renato S Bandeira
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Delana Am Bezerra
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Joana Dp Mascarenhas
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Sylvia F Santos Guerra
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| | - Luana S Soares
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, BR 316, Ananindeua, Pará, 67030-000, Brazil
| |
Collapse
|
17
|
Hoxie I, Dennehy JJ. Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns. Viruses 2021; 13:v13081460. [PMID: 34452326 PMCID: PMC8402926 DOI: 10.3390/v13081460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.
Collapse
Affiliation(s)
- Irene Hoxie
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
- Correspondence:
| | - John J. Dennehy
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
| |
Collapse
|
18
|
Wa-1 Equine-Like G3P[8] Rotavirus from a Child with Diarrhea in Colombia. Viruses 2021; 13:v13061075. [PMID: 34199978 PMCID: PMC8226935 DOI: 10.3390/v13061075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
Rotavirus A (RVA) has been considered the main cause of diarrheal disease in children under five years in emergency services in both developed and developing countries. RVA belongs to the Reoviridae family, which comprises 11 segments of double-stranded RNA (dsRNA) as a genomic constellation that encodes for six structural and five to six nonstructural proteins. RVA has been classified in a binary system with Gx[Px] based on the spike protein (VP4) and the major outer capsid glycoprotein (VP7), respectively. The emerging equine-like G3P[8] DS-1-like strains reported worldwide in humans have arisen an important concern. Here, we carry out the complete genome characterization of a previously reported G3P[8] strain in order to recognize the genetic diversity of RVA circulating among infants in Colombia. A near-full genome phylogenetic analysis was done, confirming the presence of the novel equine-like G3P[8] with a Wa-like backbone for the first time in Colombia. This study demonstrated the importance of surveillance of emerging viruses in the Colombian population; furthermore, additional studies must focus on the understanding of the spread and transmission dynamic of this important RVA strain in different areas of the country.
Collapse
|
19
|
Sadiq A, Bostan N. Comparative Analysis of G1P[8] Rotaviruses Identified Prior to Vaccine Implementation in Pakistan With Rotarix™ and RotaTeq™ Vaccine Strains. Front Immunol 2020; 11:562282. [PMID: 33133073 PMCID: PMC7562811 DOI: 10.3389/fimmu.2020.562282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/21/2020] [Indexed: 01/05/2023] Open
Abstract
Group A rotavirus (RVA) is the leading cause of severe childhood diarrhea globally, even with all effective interventions, particularly in developing countries. Among the diverse genotypes of RVA, G1P[8] is a common genotype that has continued to pervade around the world, including Pakistan. Two universally accepted rotavirus vaccines-Rotarix™ and RotaTeq™ contain the genotype G1P[8]. The current work was aimed at identifying differences between antigenic epitopes of Pakistan’s G1P[8] strains and those of the two licensed vaccines. We sequenced 6 G1P[8] rotavirus strains previously reported in Rawalpindi, Islamabad, Pakistan in 2015 and 2016 for their outer capsid genes (VP7 and VP4). Phylogenetic analysis was then conducted in order to classify their specific lineages and to detect their association with strains isolated throughout world. Compared with the Rotarix™ and RotaTeq™ vaccine strains (G1-lineage II, P[8]-lineage III), our study G1-lineage I, P[8]-lineage IV strains showed 3 and 5 variations in the VP7 epitopes, respectively, and 13 and 11 variations in the VP4 epitopes, respectively. The G1 lineage II strains showed no single amino acid change compared to Rotarix™ (lineage II), but exhibited changes at 2 positions compared to RotaTeq™ (lineage III). So, this has been proposed that these G1 strains exist in our natural setting, or that they may have been introduced in Pakistan from other countries of the world. The distinct P[8]-lineage IV (OP354-like) strains showed twelve and thirteen amino acid variations, with Rotarix™ and RotaTeq™ (lineages II and III) strains, respectively. Such findings have shown that the VP4-P[8] component of the G1P[8] strains circulating in Pakistan differs considerably from that of the vaccine viruses compared to that of the VP7-G1. To monitor the long-term effects of vaccines on the emergence of G1P[8] strains with different lineages, routine and successful monitoring of these strains will be crucial.
Collapse
Affiliation(s)
- Asma Sadiq
- Department of Biosciences, COMSATS University (CUI), Islamabad, Pakistan
| | - Nazish Bostan
- Department of Biosciences, COMSATS University (CUI), Islamabad, Pakistan
| |
Collapse
|
20
|
Zhou X, Wang YH, Pang BB, Chen N, Kobayashi N. Surveillance of Human Rotavirus in Wuhan, China (2011-2019): Predominance of G9P[8] and Emergence of G12. Pathogens 2020; 9:pathogens9100810. [PMID: 33023203 PMCID: PMC7600066 DOI: 10.3390/pathogens9100810] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children worldwide. To learn the shift of genotypes and genetic characteristics of Rotavirus A (RVA) causing diarrhea in children and adults, a hospital-based surveillance of rotavirus was conducted in Wuhan, China from June 2011 through May 2019, and representative virus strains were phylogenetically analyzed. Among a total of 6733 stool specimens collected from both children and adults with acute gastroenteritis, RVA was detected in 25.5% (1125/4409) and 12.3% (285/2324) of specimens, respectively. G9P[8] was the most common genotype (74.5%), followed by G1P[8] (8.7%), G2P[4] (8.4%), and G3P[8] (7.3%), with G9P[8] increasing rapidly during the study period. The predominant genotype shifted from G1P[8] to G9P[8] in 2012-2013 epidemic season. G12P[6] strain RVA/Human-wt/CHN/Z2761/2019/G12P[6] was detected in April 2019 and assigned to G12-P[6]-I1-R1-C1-M1-A1-N1-T2-E1-H1 genotypes. Phylogenetic analysis revealed that VP7, VP4, VP6, VP3, NSP1, NSP2, and NSP5 genes of Z2761 clustered closely with those of Korean G12P[6] strain CAU_214, showing high nucleotide identities (98.0-98.8%). The NSP3 gene of Z2761 was closely related to those of G2P[4] and G12P[6] rotaviruses in Asia. All the eleven gene segments of Z2761 kept distance from those of cocirculating G9P[8], G1P[8], and G3P[8] strains detected in Wuhan during this study period. This is the first identification of G12 rotavirus in China. It is deduced that Z2761 is a reassortant having DS-1-like NSP3 gene in the background of G12P[6] rotavirus genetically close to CAU_214.
Collapse
Affiliation(s)
- Xuan Zhou
- Division of Microbiology, Wuhan Centers for Disease Control and Prevention, Wuhan 430024, China; (X.Z.); (B.-B.P.)
| | - Yuan-Hong Wang
- Division of Microbiology, Wuhan Centers for Disease Control and Prevention, Wuhan 430024, China; (X.Z.); (B.-B.P.)
- Correspondence: ; Tel.: + 86-27-85801763
| | - Bei-Bei Pang
- Division of Microbiology, Wuhan Centers for Disease Control and Prevention, Wuhan 430024, China; (X.Z.); (B.-B.P.)
| | - Nan Chen
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China;
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan;
| |
Collapse
|
21
|
Kuang X, Gong X, Zhang X, Pan H, Teng Z. Genetic diversity of group A rotavirus in acute gastroenteritis outpatients in Shanghai from 2017 to 2018. BMC Infect Dis 2020; 20:596. [PMID: 32787859 PMCID: PMC7425067 DOI: 10.1186/s12879-020-05279-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/20/2020] [Indexed: 12/20/2022] Open
Abstract
Background Group A Rotavirus (RVA), despite being an important pathogen in hospitalized children, is less studied in pediatric outpatients, and even rarely investigated in adults. This study aims to understand the genetic diversity of RVA in outpatients across all age groups in Shanghai, and thus providing a molecular basis for vaccine implementation and evaluation. Methods Stool samples were first screened by Real-time Reverse Transcription Polymerase Chain Reaction (rRT-PCR). RVA genotyping was performed through the amplification of partial VP7 and VP4 gene. Strains of interest were further sequenced and analyzed using MEGA 6.0. Results Four thousand nine hundred one samples were collected, from which 7.61% (373 cases) were screened positive for RVA. RVA prevalence was higher in children (9.30%) than in adults (7.21%) (χ2 = 4.72, P < 0.05). 9.38% RVA positive cases had taken antibiotics before hospital visit while 49.60% had been prescribed antibiotics afterwards. RVA displayed a strong seasonality in both adults and children with a shared commonality in genotype repertoire, where G9P[8] was the most prevalent strain (67.96%) followed by G3P[8] (15.49%) and G1P[8] (12.32%). Meanwhile the first local case of fecal shedding of the G10P[15] vaccine strain was also discovered. Conclusions While the prevalence of rotavirus is highest during cold seasons, it is revealed for the first time that G9P[8] is the predominant genotype in both adults and pediatric outpatients. Clinically, higher occurrence of nausea or vomiting was observed in RVA positive cases. Antibiotic overuse was implicated in both non-clinical and clinical settings. The finding emphasizes the importance of RVA genotyping in surveillance as it provides the basis for new vaccine application as well as a baseline for future vaccine efficacy evaluation.
Collapse
Affiliation(s)
- Xiaozhou Kuang
- Shanghai Municipal Center for Disease Control and Prevention, 1380 Zhongshan Road (west), Shanghai, 200336, China
| | - Xiaohuan Gong
- Shanghai Municipal Center for Disease Control and Prevention, 1380 Zhongshan Road (west), Shanghai, 200336, China
| | - Xi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, 1380 Zhongshan Road (west), Shanghai, 200336, China
| | - Hao Pan
- Shanghai Municipal Center for Disease Control and Prevention, 1380 Zhongshan Road (west), Shanghai, 200336, China.
| | - Zheng Teng
- Shanghai Institutes of Preventive Medicine, 1380 Zhongshan Road (west), Shanghai, 200336, China.
| |
Collapse
|
22
|
Castells M, Caffarena RD, Casaux ML, Schild C, Miño S, Castells F, Castells D, Victoria M, Riet-Correa F, Giannitti F, Parreño V, Colina R. Phylogenetic Analyses of Rotavirus A from Cattle in Uruguay Reveal the Circulation of Common and Uncommon Genotypes and Suggest Interspecies Transmission. Pathogens 2020; 9:pathogens9070570. [PMID: 32674420 PMCID: PMC7400708 DOI: 10.3390/pathogens9070570] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/20/2020] [Accepted: 06/30/2020] [Indexed: 12/21/2022] Open
Abstract
Uruguay is one of the main exporters of beef and dairy products, and cattle production is one of the main economic sectors in this country. Rotavirus A (RVA) is the main pathogen associated with neonatal calf diarrhea (NCD), a syndrome that leads to significant economic losses to the livestock industry. The aims of this study are to determine the frequency of RVA infections, and to analyze the genetic diversity of RVA strains in calves in Uruguay. A total of 833 samples from dairy and beef calves were analyzed through RT-qPCR and sequencing. RVA was detected in 57.0% of the samples. The frequency of detection was significantly higher in dairy (59.5%) than beef (28.4%) calves (p < 0.001), while it did not differ significantly among calves born in herds that were vaccinated (64.0%) or not vaccinated (66.7%) against NCD. The frequency of RVA detection and the viral load were significantly higher in samples from diarrheic (72.1%, 7.99 log10 genome copies/mL of feces) than non-diarrheic (59.9%, 7.35 log10 genome copies/mL of feces) calves (p < 0.005 and p = 0.007, respectively). The observed G-types (VP7) were G6 (77.6%), G10 (20.7%), and G24 (1.7%), while the P-types were P[5] (28.4%), P[11] (70.7%), and P[33] (0.9%). The G-type and P-type combinations were G6P[11] (40.4%), G6P[5] (38.6%), G10P[11] (19.3%), and the uncommon genotype G24P[33] (1.8%). VP6 and NSP1-5 genotyping were performed to better characterize some strains. The phylogenetic analyses suggested interspecies transmission, including transmission between animals and humans.
Collapse
Affiliation(s)
- Matías Castells
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Centro Universitario de Salto, Universidad de la República, Rivera 1350, Salto 50000, Uruguay;
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Estación Experimental la Estanzuela, Ruta 50 km 11, Colonia 70000, Uruguay; (R.D.C.); (M.L.C.); (C.S.); (F.R.-C.); (F.G.)
- Correspondence: (M.C.); (R.C.); Tel.: +598-4734-2924 (M.C. & R.C.)
| | - Rubén Darío Caffarena
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Estación Experimental la Estanzuela, Ruta 50 km 11, Colonia 70000, Uruguay; (R.D.C.); (M.L.C.); (C.S.); (F.R.-C.); (F.G.)
- Facultad de Veterinaria, Universidad de la República, Alberto Lasplaces 1620, Montevideo 11600, Uruguay
| | - María Laura Casaux
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Estación Experimental la Estanzuela, Ruta 50 km 11, Colonia 70000, Uruguay; (R.D.C.); (M.L.C.); (C.S.); (F.R.-C.); (F.G.)
| | - Carlos Schild
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Estación Experimental la Estanzuela, Ruta 50 km 11, Colonia 70000, Uruguay; (R.D.C.); (M.L.C.); (C.S.); (F.R.-C.); (F.G.)
| | - Samuel Miño
- Sección de Virus Gastroentéricos, Instituto de Virología, CICVyA, INTA Castelar, Buenos Aires 1686, Argentina; (S.M.); (V.P.)
| | - Felipe Castells
- Doctor en Veterinaria en Ejercicio Libre, Asociado al Laboratorio de Virología Molecular, CENUR Litoral Norte, Centro Universitario de Salto, Universidad de la República, Rivera 1350, Salto 50000, Uruguay;
| | - Daniel Castells
- Centro de Investigación y Experimentación Dr. Alejandro Gallinal, Secretariado Uruguayo de la Lana, Ruta 7 km 140, Cerro Colorado, Florida 94000, Uruguay;
| | - Matías Victoria
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Centro Universitario de Salto, Universidad de la República, Rivera 1350, Salto 50000, Uruguay;
| | - Franklin Riet-Correa
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Estación Experimental la Estanzuela, Ruta 50 km 11, Colonia 70000, Uruguay; (R.D.C.); (M.L.C.); (C.S.); (F.R.-C.); (F.G.)
| | - Federico Giannitti
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Estación Experimental la Estanzuela, Ruta 50 km 11, Colonia 70000, Uruguay; (R.D.C.); (M.L.C.); (C.S.); (F.R.-C.); (F.G.)
| | - Viviana Parreño
- Sección de Virus Gastroentéricos, Instituto de Virología, CICVyA, INTA Castelar, Buenos Aires 1686, Argentina; (S.M.); (V.P.)
| | - Rodney Colina
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Centro Universitario de Salto, Universidad de la República, Rivera 1350, Salto 50000, Uruguay;
- Correspondence: (M.C.); (R.C.); Tel.: +598-4734-2924 (M.C. & R.C.)
| |
Collapse
|
23
|
Ono M, Tsugawa T, Nakata S, Kondo K, Tatsumi M, Tsutsumi H, Kawasaki Y. Rotavirus genotype and Vesikari score of outpatients in Japan in the vaccine era. Pediatr Int 2020; 62:569-575. [PMID: 31957129 DOI: 10.1111/ped.14150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/10/2019] [Accepted: 01/15/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Group A rotaviruses (RVs) are a major cause of severe gastroenteritis among infants and young children. In Japan, RV vaccines were introduced in 2011, leading to a reduction in severe gastroenteritis cases. Studies are required to assess the effectiveness of the vaccines and their effect on the prevalence of RV genotypes. METHODS Fecal samples were collected from outpatients with RV gastroenteritis in a pediatric clinic in Sapporo, Japan, from 2010 to 2016. GPI genotypes were determined using reverse-transcription polymerase chain reaction. Clinical information and immunization records were obtained from outpatients after 2013. GPI genotypes and clinical features were compared between patients with and without a RV vaccine history. RESULTS In total, 270 cases were genotyped. G1P[8]I1 (Wa-like G1P[8]) strains were dominant from 2010 to 2012. G1P[8]I2 (DS-1-like G1P[8]) strains appeared in 2012 and dominated in 2013 to 2015. G2P[4]I2 and G9P[8]I1 strains increased every 3 years (G2P[4]I2: 2011 and 2014, G9P[8]I1: 2010, 2013 and 2016). After the 2013 season, 137 cases were collected, 24 of which were vaccinated. Cases requiring drip infusion were fewer in the vaccination group than in the non-vaccination group (16.7% vs 52.2%). No patients required hospitalization in the vaccination group compared with 10.6% in the non-vaccination group. A severe Vesikari score was less common in the vaccination group than in the non-vaccination group (33.3% vs 78.8%). There was no significant difference in the GPI genotype distribution between the two groups. CONCLUSION Rotaviruses vaccine effectiveness, regardless of GPI genotype, was confirmed in terms of alleviation of disease severity.
Collapse
Affiliation(s)
- Mayumi Ono
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Pediatrics, Sunagawa City Hospital, Sunagawa, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | | | - Kenji Kondo
- Department of Pediatrics, Sunagawa City Hospital, Sunagawa, Japan
| | | | - Hiroyuki Tsutsumi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| |
Collapse
|
24
|
Ranshing SS, Cherian SS, Agarwal MS, Jagtap AS, Patil CM, Gopalkrishna V. Full genome based sequence and structural characterization of an unusual group A rotavirus G12P[11] isolated from neonates in Pune, western India. Vaccine 2020; 38:2275-2291. [DOI: 10.1016/j.vaccine.2020.01.081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 11/27/2022]
|
25
|
Characterization of rotavirus possessing a DS-1-like VP3 gene from pigs in Brazil: Evidence for zooanthroponotic transmission. INFECTION GENETICS AND EVOLUTION 2019; 79:104151. [PMID: 31870971 DOI: 10.1016/j.meegid.2019.104151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/26/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022]
Abstract
Porcine group A rotavirus (RVA) strains SUI15A and SUI24A are suggested to have VP3 genes of human origin possessing DS-1-like backbone. The aim of the present study was to analyse the genome of two strains (SUI15A and SUI24A) and understand the evolution of a rare human-like M2 genotype in pigs. On partial genomic analysis, strains SUI24A (G3-P[13]-I5-R1-C1-M2-A8-N1-T7-E1-H1) and SUI15A (G3-P[x]-Ix-R1-C1-M2-Ax-Nx-T7-E1-H1) were found to have VP3 gene RVA different from those of typical porcine RVA strains described in Brazil and worldwide. This genotypic constellation was a novel constellation that has not been reported previously in both humans and pigs. Furthermore, on phylogenetic analysis, VP3 gene of strains appeared to be of human origin. Therefore, suggested to have evidence for human-to-porcine zooanthroponotic transmission.
Collapse
|
26
|
Dual Recognition of Sialic Acid and αGal Epitopes by the VP8* Domains of the Bovine Rotavirus G6P[5] WC3 and of Its Mono-reassortant G4P[5] RotaTeq Vaccine Strains. J Virol 2019; 93:JVI.00941-19. [PMID: 31243129 PMCID: PMC6714814 DOI: 10.1128/jvi.00941-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 01/02/2023] Open
Abstract
Group A rotaviruses initiate infection through the binding of the VP8* domain of the VP4 protein to sialic acids (SAs) or histo-blood group antigens (HBGAs). Although the bovine G6P[5] WC3 strain is an important animal pathogen and is used as the backbone in the bovine-human reassortant RotaTeq vaccine, the receptor(s) for their P[5] VP8* domain has remained elusive. Using a variety of approaches, we demonstrated that the WC3 and bovine-human mono-reassortant G4P[5] vaccine strains recognize both α2,6-linked SA and αGal HBGA as ligands. Neither ligand is expressed on human small intestinal epithelial cells, explaining the absence of natural human infection by P[5]-bearing strains. However, we observed that the P[5]-bearing WC3 and G4P[5] RotaTeq vaccine strains could still infect human intestinal epithelial cells. Thus, the four P[5] RotaTeq vaccine strains potentially binding to additional alternative receptors may be efficient and effective in providing protection against severe rotavirus disease in human. Group A rotaviruses, an important cause of severe diarrhea in children and young animals, initiate infection via interactions of the VP8* domain of the VP4 spike protein with cell surface sialic acids (SAs) or histo-blood group antigens (HBGAs). Although the bovine G6P[5] WC3 strain is an important animal pathogen and is also used in the bovine-human reassortant RotaTeq vaccine, the receptor(s) for the VP8* domain of WC3 and its reassortant strains have not yet been identified. In the present study, HBGA- and saliva-binding assays showed that both G6P[5] WC3 and mono-reassortant G4P[5] strains recognized the αGal HBGA. The infectivity of both P[5]-bearing strains was significantly reduced in αGal-free MA-104 cells by pretreatment with a broadly specific neuraminidase or by coincubation with the α2,6-linked SA-specific Sambucus nigra lectin, but not by the α2,3-linked specific sialidase or by Maackia amurensis lectin. Free NeuAc and the αGal trisaccharide also prevented the infectivity of both strains. This indicated that both P[5]-bearing strains utilize α2,6-linked SA as a ligand on MA104 cells. However, the two strains replicated in differentiated bovine small intestinal enteroids and in their human counterparts that lack α2,6-linked SA or αGal HBGA, suggesting that additional or alternative receptors such as integrins, hsp70, and tight-junction proteins bound directly to the VP5* domain can be used by the P[5]-bearing strains to initiate the infection of human cells. In addition, these data also suggested that P[5]-bearing strains have potential for cross-species transmission. IMPORTANCE Group A rotaviruses initiate infection through the binding of the VP8* domain of the VP4 protein to sialic acids (SAs) or histo-blood group antigens (HBGAs). Although the bovine G6P[5] WC3 strain is an important animal pathogen and is used as the backbone in the bovine-human reassortant RotaTeq vaccine, the receptor(s) for their P[5] VP8* domain has remained elusive. Using a variety of approaches, we demonstrated that the WC3 and bovine-human mono-reassortant G4P[5] vaccine strains recognize both α2,6-linked SA and αGal HBGA as ligands. Neither ligand is expressed on human small intestinal epithelial cells, explaining the absence of natural human infection by P[5]-bearing strains. However, we observed that the P[5]-bearing WC3 and G4P[5] RotaTeq vaccine strains could still infect human intestinal epithelial cells. Thus, the four P[5] RotaTeq vaccine strains potentially binding to additional alternative receptors may be efficient and effective in providing protection against severe rotavirus disease in human.
Collapse
|
27
|
Oem JK, Lee SY, Kim YS, Na EJ, Choi KS. Genetic characteristics and analysis of a novel rotavirus G3P[22] identified in diarrheic feces of Korean rabbit. INFECTION GENETICS AND EVOLUTION 2019; 73:368-377. [PMID: 31173932 PMCID: PMC7106088 DOI: 10.1016/j.meegid.2019.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 01/22/2023]
Abstract
Group A rotaviruses (RVAs) are important gastroenteric pathogens that infect humans and animals. This study aimed to analyze the complete genome sequence, i.e., 11 genome segments of the lapine rotavirus (LRV) identified in the intestine of a dead rabbit in the Republic of Korea (ROK) and to describe the genetic relationships between this lapine isolate [RVA/Rabbit-wt/KOR/Rab1404/2014/G3P[22] (Rab1404)] and other lapine isolates/strains. Rab1404 possessed the following genotype constellation: G3-P[22]-I2-R3-C3-M3-A9-N2-T3-E3-H3. The P[22] genotype was found to originate from rabbits and was for the first time identified in the ROK. Phylogenetic analysis showed that Rab1404 possessed VP1-3 and VP7 genes, which were closely related to those of the bat strain LZHP2; NSP1-4 genes, which were closely related to those of the simian strain RRV; and VP4, VP6, and NSP5 genes, which were closely related to the genes obtained from other rabbits. Interestingly, a close relationship between Rab1404 and simian RVA strain RVA/Simian-tc/USA/RRV/1975/G3P[3] for 8 gene segments was observed. RRV is believed to be a reassortant between bovine-like RVA strain and canine/feline RVA strains. Rab1404 and canine/feline RVAs shared the genes encoding VP1, VP3, VP7, NSP3, and NSP4. Additionally, the genome segments VP6 (I2), NSP1 (N2), and NSP5 (H3) of Rab1404 were closely related to those of bovine RVAs. This is the first report describing the complete genome sequence of an LRV detected in the ROK. These results indicate that Rab1404 could be a result of interspecies transmission, possibly through multiple reassortment events in the strains of various animal species and the subsequent transmission of the virus to a rabbit. Additional studies are required to determine the evolutionary source and to identify possible reservoirs of RVAs in nature. This is the first report to describe the complete genome sequence of a rabbit rotavirus (Rab1404) detected in the ROK. The 11 genome segments of Rab1404 were determined; G3-P[22]-I2-R3-C3-M3-A9-N2-T3-E3-H3. G3P[22] identified in this study is found to originate from rabbit and may have more species specificity. Rab1404 could be a result of multiple reassortment events from strains originating from various animal species and transmitted to the rabbit.
Collapse
Affiliation(s)
- Jae-Ku Oem
- College of Veterinary Medicine, Chonbuk National University, Iksan 54596, Republic of Korea
| | - Soo-Young Lee
- College of Veterinary Medicine, Chonbuk National University, Iksan 54596, Republic of Korea
| | - Young-Sik Kim
- College of Veterinary Medicine, Chonbuk National University, Iksan 54596, Republic of Korea
| | - Eun-Jee Na
- College of Veterinary Medicine, Chonbuk National University, Iksan 54596, Republic of Korea
| | - Kyoung-Seong Choi
- College of Ecology and Environmental Science, Kyungpook National University, Sangju 37224, Republic of Korea.
| |
Collapse
|
28
|
Emergence of G12P[6] rotavirus strains among hospitalised children with acute gastroenteritis in Belém, Northern Brazil, following introduction of a rotavirus vaccine. Arch Virol 2019; 164:2107-2117. [PMID: 31144039 DOI: 10.1007/s00705-019-04295-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 04/29/2019] [Indexed: 10/26/2022]
Abstract
Species A rotavirus still remains a major cause of acute gastroenteritis in infants and young children. Globally, six genotypes (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]) account for >90% of circulating strains; however, genotype G12 in combination with P[6] or P[9] has been detected at increasing rates. We sought to broaden our knowledge about the rotavirus strains circulating during the early post-vaccine-introduction period. Stool samples were obtained from children hospitalised for acute gastroenteritis in Belém, Northern Brazil, from May 2008 to May 2011 and examined by reverse transcription polymerase chain reaction and nucleotide sequencing. A total of 122 out of the original 1076 rotavirus strains were judged to be non-typeable in the first analysis and were therefore re-examined. G2P[4] was the most prevalent genotype (58.0%), followed by G1P[8] (16.9%), and G12P[6] (7.5%). G12P[6] strains were identified at similar rates during the first (2.5%) and second (3.9%) years, and the rate jumped to 15.6% in the third year. Analysis of VP7 sequences of the G12P[6] strains showed that they belonged to lineage III. In addition, co-circulating G12P[6] strains displaying long and short RNA patterns were found to belong to the Wa-like and DS-1-like constellation, respectively. Additional unusual circulating strains G12P[9] and G3P[9] were also identified. This hospital-based study showed a high prevalence of G12P[6] strains in the third year of surveillance. Our results highlight the need for continuous longitudinal monitoring of circulating rotavirus strains after introduction of rotavirus vaccines in Brazil and elsewhere.
Collapse
|
29
|
Tamim S, Matthijnssens J, Heylen E, Zeller M, Van Ranst M, Salman M, Hasan F. Evidence of zoonotic transmission of VP6 and NSP4 genes into human species A rotaviruses isolated in Pakistan in 2010. Arch Virol 2019; 164:1781-1791. [PMID: 31079214 DOI: 10.1007/s00705-019-04271-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/30/2019] [Indexed: 10/26/2022]
Abstract
Introduction of animal group A rotavirus (RVA) gene segments into the human RVA population is a major factor shaping the genetic landscape of human RVA strains. The VP6 and NSP4 genes of 74 G/P-genotyped RVA isolates collected in Rawalpindi during 2010 were analyzed, revealing the presence of VP6 genotypes I1 (60.8%) and I2 (39.2%) and NSP4 genotypes E1 (60.8%), E2 (28.3%) and E-untypable (10.8%) among the circulating human RVA strains. The typical human RVA combinations I1E1 and I2E2 were found in 59.4% and 24.3% of the cases, respectively, whereas 5.4% of the RVA strains were reassortants, i.e., either I1E2 or I2E1. The phylogeny of the NSP4 gene showed that one G2P[4] and two G1P[6] RVA strains clustered with porcine E1 RVA strains or RVA strains that were considered to be (partially) of porcine origin. In addition, the NSP4 gene segment of the unusual human G6P[1] RVA strains clustered closely with bovine E2 RVA strains, further strengthening the hypothesis of an interspecies transmission event. The study further demonstrates the role of genomic re-assortment and the involvement of interspecies transmission in the evolution of human RVA strains. The VP6 and NSP4 nucleotide sequences analyzed in the study received the GenBank accession numbers KC846908- KC846971 and KC846972-KC847037, respectively.
Collapse
Affiliation(s)
- Sana Tamim
- Public Health Laboratories Division, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan.
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Rega Institute, Herestraat 49 box 1040, 3000, Leuven, Belgium
| | - Elisabeth Heylen
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium
| | - Muhammad Salman
- Public Health Laboratories Division, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan
| | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| |
Collapse
|
30
|
Kozyra I, Kozyra J, Dors A, Rzeżutka A. Molecular chracterisation of porcine group A rotaviruses: Studies on the age-related occurrence and spatial distribution of circulating virus genotypes in Poland. Vet Microbiol 2019; 232:105-113. [PMID: 31030833 DOI: 10.1016/j.vetmic.2019.03.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 01/17/2023]
Abstract
Rotaviruses of group A (RVAs) commonly occur in farm animals. In pigs, they cause acute gastrointestinal disease which is considered as significant factor of economic losses in pig farming. The aim of the study was an assessment of the prevalence of rotavirus (RV) infections in farmed pigs in Poland, genotype identification of the virus strains in conjunction with their age-related occurrence and regional (province) distribution pattern in pig herds. In total, 920 pig faecal samples were collected from pigs between the ages of one week and two years old from 131 farms. RVAs were detected using ELISA and molecular methods followed by a sequence-based identification of G (VP7) and P (VP4) virus genotypes. RV antigen was found in 377 (41%) of pig faecal samples. The correlation between pig age and frequency of RV infections was shown. In the Polish pig population, 145 RVA strains representing 33 GP genotypes were identified. Subsequent molecular analysis revealed an age-dependent and regional diversity in distribution of genotypes and virus strains. Besides typical pig RVA strains, novel strains such as G5P [34], G9P[34], and human G1P[8] were identified in this animal host. Findings from this study showed a change over time in the genotype occurrence of circulating pig RVAs in Poland. The high genetic variability of RV strains and acquisition of new virus genotypes have led to the emergence of novel, genetically distinct RVAs. The changes in the genotype occurrence of RVA strains in pigs indicate the need for their continuous epidemiological surveillance.
Collapse
Affiliation(s)
- Iwona Kozyra
- Department of Food and Environmental Virology, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Puławy, Poland
| | - Jerzy Kozyra
- Department of Bioeconomy and Systems Analysis, Institute of Soil Science and Plant Cultivation, ul. Czartoryskich 8, 24-100, Puławy, Poland
| | - Arkadiusz Dors
- Department of Swine Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Puławy, Poland
| | - Artur Rzeżutka
- Department of Food and Environmental Virology, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Puławy, Poland.
| |
Collapse
|
31
|
Santos F, Sousa Junior E, Guerra S, Lobo P, Penha Junior E, Lima A, Vinente C, Chagas E, Justino M, Linhares A, Matthijnssens J, Soares L, Mascarenhas J. G1P[8] Rotavirus in children with severe diarrhea in the post-vaccine introduction era in Brazil: Evidence of reassortments and structural modifications of the antigenic VP7 and VP4 regions. INFECTION GENETICS AND EVOLUTION 2019; 69:255-266. [DOI: 10.1016/j.meegid.2019.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/06/2019] [Accepted: 02/11/2019] [Indexed: 12/17/2022]
|
32
|
Tarek F, Hassou N, Benchekroun MN, Boughribil S, Hafid J, Ennaji MM. Impact of rotavirus and hepatitis A virus by worldwide climatic changes during the period between 2000 and 2013. Bioinformation 2019; 15:194-200. [PMID: 31354195 PMCID: PMC6637397 DOI: 10.6026/97320630015194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/10/2018] [Accepted: 11/12/2018] [Indexed: 11/23/2022] Open
Abstract
Enteric viruses are present in the environment as a result of the discharge of poorly or untreated wastewater. The spread of enteric viruses in the environment depend to human activities like stools of infected individuals ejected in the external environment can be transmitted by water sources and back to susceptible individuals for other cycles of illness. Among the enteric viruses Rotaviruses (RV) and Hepatitis A viruses (HAV) is the most detected in wastewater causing gastroenteritis and acute hepatitis. Therefore, it is of interest to climate change, mainly temperature and carbon Dioxide (CO2) variations, on Rotavirus and Hepatitis A as a model of enteric viruses present in the aquatic environment using computational modelling tools. The results of genetic ratio showed a negative correlation between the epidemiological data and the mutation rate. However, the correlation was positive between the temperature, CO2 increase, and the rate of mutation. The positive correlation is explained by the adaptation of the viruses to the climatic changes, the RNA polymerase of the RV induces errors to adapt to the environmental conditions. The simultaneous increase in number of infections and temperature in 2010 has been demonstrated in previous studies deducing that viral pathogenicity increase with temperature increase.
Collapse
Affiliation(s)
- Fatima Tarek
- Team of Virology and Oncology, Laboratory of Virology, Microbiology, Quality and Biotechnology/Ecotoxicology and Biodiversity, Faculty of Sciences and Techniques Mohammedia, University Hassan II of Casablanca
| | - Najwa Hassou
- Team of Virology and Oncology, Laboratory of Virology, Microbiology, Quality and Biotechnology/Ecotoxicology and Biodiversity, Faculty of Sciences and Techniques Mohammedia, University Hassan II of Casablanca
| | - Mohammed Nabil Benchekroun
- Team of Biotechnology an Environment Laboratory of Virology, Microbiology, Quality and Biotechnology/ Eco toxicology and Biodiversity, Faculty of Sciences and techniques Mohammedia,University Hassan II of Casablanca
| | - Said Boughribil
- Team of Eco toxicology and Biodiversity, Laboratory of Virology, Microbiology, Quality and Biotechnology/Ecotoxicology and Biodiversity, Faculty of Sciences and techniques Mohammedia, University Hassan II of Casablanca
| | - Jamal Hafid
- Team of Immuno parasitology, Laboratory food, Environment and Health FST Gueliz, University Cadi Ayyad Marrakech
| | - My Mustapha Ennaji
- Team of Virology and Oncology, Laboratory of Virology, Microbiology, Quality and Biotechnology/Ecotoxicology and Biodiversity, Faculty of Sciences and Techniques Mohammedia, University Hassan II of Casablanca
| |
Collapse
|
33
|
Development of a live attenuated trivalent porcine rotavirus A vaccine against disease caused by recent strains most prevalent in South Korea. Vet Res 2019; 50:2. [PMID: 30616694 PMCID: PMC6323864 DOI: 10.1186/s13567-018-0619-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/13/2018] [Indexed: 12/20/2022] Open
Abstract
Porcine rotaviruses cause severe economic losses in the Korean swine industry due to G- and P-genotype mismatches between the predominant field and vaccine strains. Here, we developed a live attenuated trivalent porcine group A rotavirus vaccine using 80 cell culture passages of the representative Korean predominant strains G8P[7] 174-1, G9P[23] PRG942, and G5P[7] K71. Vaccination with the trivalent vaccine or its individual components induced no diarrhea during the first 2 weeks post-vaccination, i.e., the vaccines were attenuated. Challenge of trivalent-vaccinated or component-vaccinated piglets with homologous virulent strain(s) did not induce diarrhea for 2 weeks post-challenge. Immunization with the trivalent vaccine or its individual components also alleviated the histopathological lesions in the small intestines caused by challenge with the corresponding original virulent strain(s). Fecal secretory IgAs specific for each of vaccine strains were detected starting at 14 days post-vaccination (dpv), and IgA levels gradually increased up to 28 dpv. Oral immunization with the trivalent vaccine or its individual components induced high levels of serum virus-neutralizing antibody by 7 dpv. No diarrhea was observed in any experimental piglets during five consecutive passages of each vaccine strain. Our data indicated that the live attenuated trivalent vaccine was safe and effective at protecting piglets from diarrhea induced by challenge exposure of homologous virulent strains. This trivalent vaccine will potentially contribute toward controlling porcine rotavirus disease in South Korea and other countries where rotavirus infections with similar G and P genotypes are problematic.
Collapse
|
34
|
Gómez MM, Silva MFMD, Volotão EM, Fialho AM, Mazzoco CS, Rocha MS, Leite JPG. G26P[19] rotavirus A strain causing acute gastroenteritis in the American continent. Mem Inst Oswaldo Cruz 2018. [PMCID: PMC6254902 DOI: 10.1590/0074-02760180344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In Brazil, the rotavirus A genotype G26 was first identified in suckling piglets, while the P[19] genotype has not been identified in any animal species so far. This report details the genetic characterisation of a G26P[19] RVA strain detected from an eight year-old child, vaccinated with Rotarix®, hospitalised with acute diarrhoeal disease in Rio de Janeiro in 2015. Most likely, the genome constellation (I5-R1-C1-M1-A8-N1-T1-E1-H1) observed in the G26P[19] Brazilian strain was a result of interspecies transmission events between humans and pigs. In addition, a rearrangement in the NSP5 gene was observed downstream of the 3’ non-coding region.
Collapse
|
35
|
Increasing predominance of G8P[8] species A rotaviruses in children admitted to hospital with acute gastroenteritis in Thailand, 2010-2013. Arch Virol 2018; 163:2165-2178. [DOI: 10.1007/s00705-018-3848-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 04/04/2018] [Indexed: 01/05/2023]
|
36
|
Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events. Sci Rep 2018; 8:6011. [PMID: 29662148 PMCID: PMC5902508 DOI: 10.1038/s41598-018-24511-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/05/2018] [Indexed: 01/02/2023] Open
Abstract
After the introduction of two global rotavirus vaccines, RotaTeq in 2007 and Rotarix in 2008 in South Korea, G1[P8] rotavirus was the major rotavirus genotype in the country until 2012. However, in this study, an emergence of G2P[4] as the dominant genotype during the 2013 to 2015 season has been reported. Genetic analysis revealed that these viruses had typical DS-1-like genotype constellation and showed evidence of re-assortment in one or more genome segments, including the incorporation of NSP4 genes from strains B-47/2008 from a cow and R4/Haryana/2007 from a buffalo in India, and the VP1 and VP3 genes from strain GO34/1999 from a goat in Bangladesh. Compared to the G2 RotaTeq vaccine strain, 17–24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.
Collapse
|
37
|
Azaran A, Makvandi M, Teimoori A, Ebrahimi S, Heydari F, Nikfar R. Distribution of Rotavirus Genotypes Ccirculating
in Ahvaz, Iran in 2016. IRANIAN BIOMEDICAL JOURNAL 2018; 22:107-16. [PMID: 28915725 PMCID: PMC5786656 DOI: 10.22034/ibj.22.2.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 05/06/2017] [Accepted: 05/08/2017] [Indexed: 02/06/2023]
Abstract
Background Group A rotavirus (RVA) mainly causes acute gastroenteritis, exclusively in young children in developing countries. The prevalence and determination of the molecular epidemiology of rotavirus genotypes will determine the dominant rotavirus genotypes in the region and provide a strategy for the development of appropriate vaccines. Methods A total of 100 fecal samples were collected from children below five years with acute gastroenteritis who referred to Aboozar Children’s Hospital of Ahvaz city during October 2015 to March 2016. All samples were screened by latex agglutination for the presence of rotavirus antigen. Rotavirus-positive samples were further analyzed by the semi-multiplex RT-PCR, and the sequencing was performed for G/P genotyping. Results Findings showed that 32% of the specimens were RVA-positive. Among the 32 VP7 genotyped strains, the predominant G genotype was G9 (37.5%), followed by G2 (21.9%), G1 (12.5%), G12 (9.4%), G4 (9.4%), G2G9 (6.3%), and G3 (3.1%). Among the 31 VP4 genotyped strains, P[8] genotype was the dominant (62.5%), followed by P[4] (31.3%) and P[4] P[8] (3.1%). The genotypes for G and P were identified for 31 rotaviruses (96.87%), but only one strain, G9, remained non-typeable for the P genotype. The most prevalent G/P combination was G9P[8] (28.5%), followed by G2P[4] (18.8%), G1P[8] (9.4%), G12P[8] (9.4%), G4P[8] (9.4%), G2G9P[4] (6.3%), G9P[4] P[8] (3.1%), G3P[8] (3.1%), G9P[4] (3.1%), G2P[8] (3.1%), and G9P[non-typeable] (3.1%). Conclusion A novel rotavirus strain, G12, was detected, for the first time, in patients from the southwest of Iran. Comprehensive investigations are required to evaluate the emergence of this strain.
Collapse
Affiliation(s)
- Azarakhsh Azaran
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Manoochehr Makvandi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Teimoori
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeedeh Ebrahimi
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farzad Heydari
- Cukurova University, Medicine Faculty, Medical Microbiology Department, Adana, Turkey
| | - Roya Nikfar
- Department of Infectious Diseases, Aboozar Children’s Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| |
Collapse
|
38
|
Faecal shedding of rotavirus vaccine in Chinese children after vaccination with Lanzhou lamb rotavirus vaccine. Sci Rep 2018; 8:1001. [PMID: 29343800 PMCID: PMC5772666 DOI: 10.1038/s41598-018-19469-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 01/02/2018] [Indexed: 12/15/2022] Open
Abstract
Lanzhou lamb rotavirus vaccine (LLR) is an oral live attenuated vaccine first licensed in China in 2000. To date, > 60 million doses of LLR have been distributed to children. However, very little is known about faecal shedding of LLR in children. Therefore, faecal samples (n = 1,184) were collected from 114 children for 15 days post-vaccination in September–November 2011/2012. Faecal shedding and viral loads were determined by an enzyme immunoassay kit (EIA) and real-time RT-PCR. The complete genome was sequenced and the vaccine strain was isolated by culture in MA104 cells. Approximately 14.0% (16/114) of children had rotavirus-positive samples by EIA for at least 1 day post-vaccination. Viral loads in EIA-positive samples ranged from < 1.0 × 103 to 1.9 × 108 copies/g. Faecal shedding occurred as early as post-vaccination day 2 and as late as post-vaccination day 13 and peaked on post-vaccination day 5–10. One LLR strain was isolated by culture in MA104 cells. Sequence analysis showed 99% identity with LLR prototype strain. Faecal shedding of LLR in stool is common within 15 days of LLR vaccination, indicating vaccine strains can replicate in human enteric tissues.
Collapse
|
39
|
Molecular characterization of a human G20P[28] rotavirus a strain with multiple genes related to bat rotaviruses. INFECTION GENETICS AND EVOLUTION 2017; 57:166-170. [PMID: 29187315 DOI: 10.1016/j.meegid.2017.11.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/20/2017] [Accepted: 11/25/2017] [Indexed: 12/14/2022]
Abstract
Group A rotaviruses are the major cause of severe gastroenteritis in the young of mammals and birds. This report describes characterization of an unusual G20P[28] rotavirus strain detected in a 24month old child from Suriname. Genomic sequence analyses revealed that the genotype constellation of the Suriname strain RVA/Human-wt/SUR/2014735512/2013/G20P[28] was G20-P[28]-I13-R13-C13-M12-A23-N13-T15-E20-H15. Genes VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5 were recently assigned novel genotypes by the Rotavirus Classification Working Group (RCWG). Three of the 11 gene segments (VP7, VP4, VP6) were similar to cognate gene sequences of bat-like human rotavirus strain Ecu534 from Ecuador and the VP7, NSP3 and NSP5 gene segments of strain RVA/Human-wt/SUR/2014735512/2013/G20P[28] were found to be closely related to gene sequences of bat rotavirus strain 3081/BRA detected in Brazil. Although distantly related, the VP1 gene of the study strain and bat strain BatLi09 detected in Cameroon in 2014 are monophyletic. The NSP1 gene was found to be most closely related to human strain QUI-35-F5 from Brazil. These findings suggest that strain RVA/Human-wt/SUR/2014735512/2013/G20P[28] represents a zoonotic infection from a bat host.
Collapse
|
40
|
Xie X, Bil J, Shantz E, Hammermueller J, Nagy E, Turner PV. Prevalence of lapine rotavirus, astrovirus, and hepatitis E virus in Canadian domestic rabbit populations. Vet Microbiol 2017; 208:146-149. [DOI: 10.1016/j.vetmic.2017.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/10/2017] [Accepted: 07/14/2017] [Indexed: 01/15/2023]
|
41
|
Almeida TNV, de Sousa TT, da Silva RA, Fiaccadori FS, Souza M, Badr KR, de Paula Cardoso DDD. Phylogenetic analysis of G1P[8] and G12P[8] rotavirus A samples obtained in the pre- and post-vaccine periods, and molecular modeling of VP4 and VP7 proteins. Acta Trop 2017; 173:153-159. [PMID: 28606817 DOI: 10.1016/j.actatropica.2017.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/31/2017] [Accepted: 06/07/2017] [Indexed: 11/24/2022]
Abstract
Reduction in morbimortality rates for acute gastroenteritis (AGE) by Rotavirus A (RVA) has been observed after the introduction of vaccines, however the agent continues to circulate. The present study described the genomic characterization of the 11 dsRNA segments of two RVA samples G1P[8] obtained in the pre- and post-vaccination periods and one of G12P[8] sample (post-vaccine), compared to Rotarix™ vaccine. Analysis by molecular sequencing of the samples showed that the three samples belonged to genogroup I. In addition, the analysis of VP7 gene revealed that the samples G1 (pre-vaccine), G1 (post-vaccine) and G12 were characterized as lineages II, I and III, respectively. Regarding to VP4 and NSP4 gene it was observed that all samples belonged to lineage III, whereas for VP6 gene, the sample of the pre- and post-vaccine belonged to the lineage IV and I, respectively. Considering the VP7 gene, it was observed high nucleotide and amino acid identity for the two G1 samples when compared to Rotarix™ vaccine and lesser identity for the G12 sample. In relation to antigenic epitope of VP7 greater modifications were observed for the G12 sample in the 7-2 epitope that was confirmed by molecular modeling. On the other hand, for VP4, some changes in the 8-1 and 8-3 antigenic epitopes was observed for the three samples. This data could be interpreted as a low selective pressure exerted by vaccination in relation to G1P[8] samples and lesser protection in relation to G12P[8]. Thus, the continuous monitoring of RVA circulating samples remains important.
Collapse
|
42
|
Esona MD, Roy S, Rungsrisuriyachai K, Sanchez J, Vasquez L, Gomez V, Rios LA, Bowen MD, Vazquez M. Characterization of a triple-recombinant, reassortant rotavirus strain from the Dominican Republic. J Gen Virol 2017; 98:134-142. [PMID: 27983480 DOI: 10.1099/jgv.0.000688] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We report the genome of a novel human triple-recombinant G4P[6-8_R] mono-reassortant strain identified in a stool sample from the Dominican Republic during routine facility-based rotavirus strain surveillance. The strain was designated as RVA/Human-wt/DOM/2013840364/2013/G4P[6-8_R], with a genomic constellation of G4-P[6-8_R]-I1-R1-C1-M1-(A1-A8_R)-N1-(T1-T7_R)-E1-H1. Recombinant gene segments NSP1 and NSP3 were generated as a result of recombination between genogroup 1 rotavirus A1 human strain and a genotype A8 porcine strain and between genogroup 1 rotavirus T1 human strain and a genotype T7 bovine strain, respectively. Analyses of the RNA secondary structures of gene segment VP4, NSP1 and NSP3 showed that all the recombinant regions appear to start in a loop (single-stranded) region and terminate in a stem (double-stranded) structure. Also, the VP7 gene occupied lineage VII within the G4 genotypes consisting of mostly porcine or porcine-like G4 strains, suggesting the occurrence of reassortment. The remaining gene segments clustered phylogenetically with genogroup 1 strains. This exchange of whole or partial genetic materials between rotaviruses by recombination and reassortment contributes directly to their diversification, adaptation and evolution.
Collapse
Affiliation(s)
- Mathew D Esona
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sunando Roy
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Jacqueline Sanchez
- Hospital Infantil Dr Robert Reid Cabral, Santo Domingo, Dominican Republic
| | - Lina Vasquez
- Hospital Infantil Dr Robert Reid Cabral, Santo Domingo, Dominican Republic
| | - Virgen Gomez
- Hospital Infantil Dr Robert Reid Cabral, Santo Domingo, Dominican Republic
| | | | - Michael D Bowen
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | |
Collapse
|
43
|
Bezerra DAM, Guerra SFS, Serra ACS, Fecury PCMS, Bandeira RS, Penha ET, Lobo PS, Sousa EC, Linhares AC, Soares LS, Mascarenhas JDP. Analysis of a genotype G3P[9] rotavirus a strain that shows evidence of multiple reassortment events between animal and human rotaviruses. J Med Virol 2016; 89:974-981. [PMID: 27862014 DOI: 10.1002/jmv.24733] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/09/2016] [Accepted: 11/09/2016] [Indexed: 11/07/2022]
Abstract
The species A rotaviruses (RVA) are important gastroenteric pathogens that infect humans and animals. RVA genotype G3P[9] has been described in human-animal reassortment events, and the complexity of its hosts motivates the genetic investigation of this strain. Therefore, the aim of this study is to analyse a G3P[9] sample that was detected in a child with acute gastroenteritis. The 1A3739 sample featured the constellation G3P[9]-I18-R3-C3-Mx-A19-N3-T3-E3-H6. The sequence for VP3 gene was not obtained. The phylogeny showed a closer relationship among genes VP7, VP1, NSP3, NSP4, and NSP5 with genes of animal origin, such as chiropter, alpaca, equine, and simian. In addition, the genes VP6 and NSP1 belong to the new genotypes I18 and A19, respectively. The emergence of strains such as these can interfere with the effectiveness of the RVA vaccine, and continuous monitoring is therefore important. Additional studies are needed to determine the evolutionary source and to identify a possible reservoir of RVA in nature.
Collapse
Affiliation(s)
- Delana A M Bezerra
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Sylvia F S Guerra
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | - Ana C S Serra
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | | | - Renato S Bandeira
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Edvaldo T Penha
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | - Patrícia S Lobo
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Edivaldo C Sousa
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Alexandre C Linhares
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | - Luana S Soares
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | - Joana D P Mascarenhas
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| |
Collapse
|
44
|
Yodmeeklin A, Khamrin P, Chuchaona W, Kumthip K, Kongkaew A, Vachirachewin R, Okitsu S, Ushijima H, Maneekarn N. Analysis of complete genome sequences of G9P[19] rotavirus strains from human and piglet with diarrhea provides evidence for whole-genome interspecies transmission of nonreassorted porcine rotavirus. INFECTION GENETICS AND EVOLUTION 2016; 47:99-108. [PMID: 27894992 DOI: 10.1016/j.meegid.2016.11.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 11/22/2016] [Accepted: 11/22/2016] [Indexed: 12/22/2022]
Abstract
Whole genomes of G9P[19] human (RVA/Human-wt/THA/CMH-S070-13/2013/G9P[19]) and porcine (RVA/Pig-wt/THA/CMP-015-12/2012/G9P[19]) rotaviruses concurrently detected in the same geographical area in northern Thailand were sequenced and analyzed for their genetic relationships using bioinformatic tools. The complete genome sequence of human rotavirus RVA/Human-wt/THA/CMH-S070-13/2013/G9P[19] was most closely related to those of porcine rotavirus RVA/Pig-wt/THA/CMP-015-12/2012/G9P[19] and to those of porcine-like human and porcine rotaviruses reference strains than to those of human rotavirus reference strains. The genotype constellation of G9P[19] detected in human and piglet were identical and displayed as the G9-P[19]-I5-R1-C1-M1-A8-N1-T1-E1-H1 genotypes with the nucleotide sequence identities of VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4, and NSP5 at 99.0%, 99.5%, 93.2%, 97.7%, 97.7%, 85.6%, 89.5%, 93.2%, 92.9%, 94.0%, and 98.1%, respectively. The findings indicate that human rotavirus strain RVA/Human-wt/THA/CMH-S070-13/2013/G9P[19] containing the genome segments of porcine genetic backbone is most likely a human rotavirus of porcine origin. Our data provide an evidence of interspecies transmission and whole-genome transmission of nonreassorted G9P[19] porcine RVA to human occurring in nature in northern Thailand.
Collapse
Affiliation(s)
- Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Watchaporn Chuchaona
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Aphisek Kongkaew
- Animal House Unit, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Ratchaya Vachirachewin
- Department of Food Animal Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan; Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan; Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
| |
Collapse
|
45
|
Pradhan GN, Walimbe AM, Chitambar SD. Molecular characterization of emerging G9P[4] rotavirus strains possessing a rare E6 NSP4 or T1 NSP3 genotype on a genogroup-2 backbone using a refined classification framework. J Gen Virol 2016; 97:3139-3153. [PMID: 27902372 DOI: 10.1099/jgv.0.000650] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rotavirus infections associated with unusual strains are an emerging concern in rotavirus vaccination programmes. Recently, an increase in circulation of unusual G9P[4] strains was reported from different regions of India, placing this genotype in third position, after G1P[8] and G2P[4], of the most common rotavirus strains. The aim of the present study was to analyse the complete genomic constellation of three G9P[4] strains (RV09, RV10 and RV11), determine their genetic relatedness to other genogroup-2 strains and understand the evolution of a rare E6 and other NSP4 genotypes. All strains revealed the presence of a genogroup-2 backbone, with RV09 constituting the NSP3 T1 genotype and RV10 and RV11 bearing the NSP4 E6 genotype. A refined criterion adopted to classify the nine internal gene segments of G2P[4] and non-G2P[4] strains with the genogroup-2 backbone into lineages and sub-lineages indicated divergence of >8 % (except NSP1: >5.5 %) for lineages and >3 % for sub-lineages. The VP1 and/or VP3 genes of study strains showed close relationships with animal-like human rotaviruses. The estimated evolutionary rate for the NSP4 E6 genotype was marginally higher (3.78×10-3 substitutions per site per year) than that of genotypes E1 (2.6×10-3 substitutions per site per year) and E2 (3.06×10-3 substitutions per site per year), suggesting a step towards adaptation of E6 on a genogroup-2 backbone. The time and origin of the most recent common ancestor of E6 genotype were estimated to be 1981 and South Asia, respectively. Full-genome and evolutionary analyses performed in this study for G9P[4] strains will help better understand the extent of gene reassortment and origin in unusual rotavirus strains that may remain viable and cause infections in humans.
Collapse
Affiliation(s)
- Gauri N Pradhan
- Enteric Viruses Group, National Institute of Virology, Pune, India
| | - Atul M Walimbe
- Bioinformatics Group, National Institute of Virology, Pune, India
| | | |
Collapse
|
46
|
Guerra SFS, Soares LS, Lobo PS, Penha Júnior ET, Sousa Júnior EC, Bezerra DAM, Vaz LR, Linhares AC, Mascarenhas JDP. Detection of a novel equine-like G3 rotavirus associated with acute gastroenteritis in Brazil. J Gen Virol 2016; 97:3131-3138. [PMID: 27902376 DOI: 10.1099/jgv.0.000626] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genotype G3P[8] of rotavirus A (RVA) is detected worldwide, usually associated with Wa-like constellation and exhibiting a long RNA migration pattern. More recently, a novel inter-genogroup, G3P[8] reassortant variant with a short electropherotype, has emerged in Asia, Oceania and Europe, denoting an overall potential of unusual rotavirus strains. During a RVA surveillance in Brazil, G3P[8] strains were found displaying a short electropherotype pattern, which had not been detected before in this region. This study aims to characterize the complete genome of 10 G3P[8] strains detected in the northern region of Brazil. All G3P[8] samples were subjected to partial sequencing, and the whole-genome phylogenetic analysis demonstrated that all strains possessed I2-R2-C2-M2-A2-N1-T2-E2-H2 genotype background, representing reassortants with an equine-like G3 VP7 and amino acid changes in VP4 and VP7 antigenic regions as compared to vaccine strains. Phylogenetic analysis demonstrated high nucleotide identity in almost all RNA segments of G3P[8] DS-1 samples detected in Asia, Oceania and Europe as well as G3P[4] strains in Japan. This study reports a novel, equine-like G3P[8] strain circulating in Brazil and isolated from children hospitalized for severe gastroenteritis, and highlights the complex dynamics of RVA molecular epidemiology. Our findings point to a novel RVA strain emerging in this region, and studies should be done to detect whether this may represent a challenge to current vaccine strategies.
Collapse
Affiliation(s)
| | - Luana Silva Soares
- Evandro Chagas Institute, Health Surveillance Secretariat, Belém, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Whole genome sequencing of a rare rotavirus from archived stool sample demonstrates independent zoonotic origin of human G8P[14] strains in Hungary. Virus Res 2016; 227:96-103. [PMID: 27671785 DOI: 10.1016/j.virusres.2016.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 09/19/2016] [Accepted: 09/22/2016] [Indexed: 11/21/2022]
Abstract
Genotype P[14] rotaviruses in humans are thought to be zoonotic strains originating from bovine or ovine host species. Over the past 30 years only few genotype P[14] strains were identified in Hungary totaling<0.1% of all human rotaviruses whose genotype had been determined. In this study we report the genome sequence and phylogenetic analysis of a human genotype G8P[14] strain, RVA/Human-wt/HUN/182-02/2001/G8P[14]. The whole genome constellation (G8-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3) of this strain was shared with another Hungarian zoonotic G8P[14] strain, RVA/Human-wt/HUN/BP1062/2004/G8P[14], although phylogenetic analyses revealed the two rotaviruses likely had different progenitors. Overall, our findings indicate that human G8P[14] rotavirus detected in Hungary in the past originated from independent zoonotic events. Further studies are needed to assess the public health risk associated with infections by various animal rotavirus strains.
Collapse
|
48
|
Asano KM, Gregori F, Hora AS, Scheffer KC, Fahl WO, Iamamoto K, Mori E, Silva FDF, Taniwaki SA, Brandão PE. Group A rotavirus in Brazilian bats: description of novel T15 and H15 genotypes. Arch Virol 2016; 161:3225-30. [PMID: 27518402 DOI: 10.1007/s00705-016-3010-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/03/2016] [Indexed: 12/19/2022]
Abstract
This study aimed to survey for group A rotaviruses (RVA) in bats from Brazil and to perform phylogenetic inferences for VP4, VP7, NSP3, NSP4 and NSP5 genes. RVA was found in 9.18 % (28/305) of tested samples. The partial genotype constellation of a Molossus molossus RVA strain was G3-P[3]-Ix-Rx-Cx-Mx-Ax-Nx-T3-E3-H6, and that of a Glossophaga soricina RVA strain was G20-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-T15-Ex-H15. These findings demonstrate an important role of bats in RVA epidemiology and provide evidence of participation of bat RVA strains in interspecies transmission and reassortment events.
Collapse
Affiliation(s)
- Karen Miyuki Asano
- Instituto Pasteur of São Paulo, Av. Paulista, 393, São Paulo, SP, 01311-000, Brazil.
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Orlando Marques de Paiva, 87, Cidade Universitária, São Paulo, SP, 05508-270, Brazil.
| | - Fabio Gregori
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Orlando Marques de Paiva, 87, Cidade Universitária, São Paulo, SP, 05508-270, Brazil
| | - Aline Santana Hora
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Orlando Marques de Paiva, 87, Cidade Universitária, São Paulo, SP, 05508-270, Brazil
| | | | | | - Keila Iamamoto
- Instituto Pasteur of São Paulo, Av. Paulista, 393, São Paulo, SP, 01311-000, Brazil
| | - Enio Mori
- Instituto Pasteur of São Paulo, Av. Paulista, 393, São Paulo, SP, 01311-000, Brazil
| | - Fernanda Dornelas Florentino Silva
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Orlando Marques de Paiva, 87, Cidade Universitária, São Paulo, SP, 05508-270, Brazil
| | - Sueli Akemi Taniwaki
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Orlando Marques de Paiva, 87, Cidade Universitária, São Paulo, SP, 05508-270, Brazil
| | - Paulo Eduardo Brandão
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Orlando Marques de Paiva, 87, Cidade Universitária, São Paulo, SP, 05508-270, Brazil
| |
Collapse
|
49
|
Dulgheroff ACB, Silva GAVD, Naveca FG, Oliveira AGD, Domingues ALDS. Diversity of group A rotavirus genes detected in the Triângulo Mineiro region, Minas Gerais, Brazil. Braz J Microbiol 2016; 47:731-40. [PMID: 27266629 PMCID: PMC4927641 DOI: 10.1016/j.bjm.2016.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 12/08/2015] [Indexed: 12/15/2022] Open
Abstract
Group A rotaviruses are the main causative agent of infantile gastroenteritis. The segmented nature of the viral genome allows reassortment of genome segments, which can generate genetic variants. In this study, we characterized the diversity of the VP7, VP4 (VP8*), VP6, NSP4, and NSP5 genes of the rotaviruses that circulated from 2005 to 2011 in the Triângulo Mineiro (TM) region of Brazil. Samples with genotypes G2 (sublineages IVa-1 and IVa-3), G1 (sublineage I-A), G9 (lineage III), G12 (lineages II and III), G8 (lineage II), G3 (lineage III), P[4] (sublineages IVa and IVb), P[8] (sublineages P[8]-3.6, P[8]-3.3, and P[8]-3.1), I2 (lineage VII), E2 (lineages VI, XII, and X), and H2 (lineage III) were identified. The associations found in the samples were G1, G9, or G12 with P[8]-I1-E1-H1; G2 or G8 with P[4]-I2-E2-H2; G12 with I3-E3-H6; and G3 with P[4]-I2-E3-H3 (previously unreported combination). Reassortment events in G2P[4] strains and an apparent pattern of temporal segregation within the lineages were observed. Five TM samples contained genes that exhibited high nucleotide and amino acid identities with strains of animal origin. The present study includes a period of pre- and post-introduction of rotavirus vaccination in all Brazilian territories, thereby serving as a basis for monitoring changes in the genetic constitution of rotaviruses. The results also contribute to the understanding of the diversity and evolution of rotaviruses in a global context.
Collapse
Affiliation(s)
- Ana Carolina Bernardes Dulgheroff
- Laboratory of Microbiology, Institute of Biological and Natural Science, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil; Health Technical School, Health Science Center, Federal University of Paraíba, João Pessoa, Paraíba, Brazil.
| | - George Allan Villarouco da Silva
- Laboratory of Infectious Disease Ecology in the Amazon, Leonidas e Maria Deane Institute, Oswaldo Cruz Foundation, Manaus, Amazonas, Brazil
| | - Felipe Gomes Naveca
- Laboratory of Infectious Disease Ecology in the Amazon, Leonidas e Maria Deane Institute, Oswaldo Cruz Foundation, Manaus, Amazonas, Brazil
| | - Adriana Gonçalves de Oliveira
- Laboratory of Microbiology, Institute of Biological and Natural Science, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - André Luiz da Silva Domingues
- Laboratory of Microbiology, Institute of Biological and Natural Science, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| |
Collapse
|
50
|
Gautam R, Mijatovic-Rustempasic S, Esona MD, Tam KI, Quaye O, Bowen MD. One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples. PeerJ 2016; 4:e1560. [PMID: 26839745 PMCID: PMC4734446 DOI: 10.7717/peerj.1560] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/12/2015] [Indexed: 12/28/2022] Open
Abstract
Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8-100% sensitivity, 99.7-100% specificity, 85-95% efficiency and a limit of detection of 4-60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81-92% efficiency and limit of detection of 150-600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98.8-100% sensitivity, 100% specificity, 86-89% efficiency and a limit of detection of 12-400 copies per singleplex reactions. The VP4 qRT-PCRs exhibited 82-90% efficiency and limit of detection of 120-4000 copies in multiplex reaction. Discussion. The one-step multiplex qRT-PCR assay will facilitate high-throughput rotavirus genotype characterization for monitoring circulating rotavirus wild-type strains causing rotavirus infections, determining the frequency of Rotarix® and RotaTeq® vaccine strains and vaccine-derived reassortants associated with AGE, and help to identify novel rotavirus strains derived by reassortment between vaccine and wild-type strains.
Collapse
Affiliation(s)
- Rashi Gautam
- Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention , Atlanta, Georgia , United States of America
| | - Slavica Mijatovic-Rustempasic
- Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention , Atlanta, Georgia , United States of America
| | - Mathew D Esona
- Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention , Atlanta, Georgia , United States of America
| | - Ka Ian Tam
- Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention , Atlanta, Georgia , United States of America
| | - Osbourne Quaye
- Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention , Atlanta, Georgia , United States of America
| | - Michael D Bowen
- Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention , Atlanta, Georgia , United States of America
| |
Collapse
|