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Maringa WM, Simwaka J, Mwangi PN, Mpabalwani EM, Mwenda JM, Mphahlele MJ, Seheri ML, Nyaga MM. Whole Genome Analysis of Human Rotaviruses Reveals Single Gene Reassortant Rotavirus Strains in Zambia. Viruses 2021; 13:1872. [PMID: 34578453 PMCID: PMC8472975 DOI: 10.3390/v13091872] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 12/28/2022] Open
Abstract
Rotarix® vaccine was implemented nationwide in Zambia in 2013. In this study, four unusual strains collected in the post-vaccine period were subjected to whole genome sequencing and analysis. The four strains possessed atypical genotype constellations, with at least one reassortant genome segment within the constellation. One of the strains (UFS-NGS-MRC-DPRU4749) was genetically and phylogenetically distinct in the VP4 and VP1 gene segments. Pairwise analyses demonstrated several amino acid disparities in the VP4 antigenic sites of this strain compared to that of Rotarix®. Although the impact of these amino acid disparities remains to be determined, this study adds to our understanding of the whole genomes of reassortant strains circulating in Zambia following Rotarix® vaccine introduction.
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Affiliation(s)
- Wairimu M. Maringa
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (W.M.M.); (P.N.M.)
| | - Julia Simwaka
- Virology Laboratory, Department of Pathology and Microbiology, University Teaching Hospital, Adult and Emergency Hospital, Lusaka 10101, Zambia;
| | - Peter N. Mwangi
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (W.M.M.); (P.N.M.)
| | - Evans M. Mpabalwani
- Department of Paediatrics and Child Health, School of Medicine, University of Zambia, Ridgeway, Lusaka RW50000, Zambia;
| | - Jason M. Mwenda
- World Health Organization, Regional Office for Africa, Brazzaville P.O. Box 06, Congo;
| | - M. Jeffrey Mphahlele
- Office of the Deputy Vice Chancellor for Research and Innovation, The North-West University, Potchefstroom 2351, South Africa;
| | - Mapaseka L. Seheri
- Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa;
| | - Martin M. Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (W.M.M.); (P.N.M.)
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Ghosh S, Navarro R, Malik YS, Willingham AL, Kobayashi N. Whole genomic analysis of a porcine G6P[13] rotavirus strain. Vet Microbiol 2015; 180:286-98. [DOI: 10.1016/j.vetmic.2015.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 09/14/2015] [Accepted: 09/20/2015] [Indexed: 01/26/2023]
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Yu X, Mishra R, Holloway G, von Itzstein M, Coulson BS, Blanchard H. Substantial Receptor-induced Structural Rearrangement of Rotavirus VP8*: Potential Implications for Cross-Species Infection. Chembiochem 2015; 16:2176-81. [PMID: 26250751 DOI: 10.1002/cbic.201500360] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 11/06/2022]
Abstract
Rotavirus-cell binding is the essential first step in rotavirus infection. This binding is a major determinant of rotavirus tropism, as host cell invasion is necessary to initiate infection. Initial rotavirus-cell interactions are mediated by carbohydrate-recognizing domain VP8* of the rotavirus capsid spike protein VP4. Here, we report the first observation of significant structural rearrangement of VP8* from human and animal rotavirus strains upon glycan receptor binding. The structural adaptability of rotavirus VP8* delivers important insights into how human and animal rotaviruses utilize the wider range of cellular glycans identified as VP8* binding partners. Furthermore, our studies on rotaviruses with atypical genetic makeup provide information expected to be critical for understanding the mechanisms of animal rotavirus gene emergence in humans and support implementation of epidemiologic surveillance of animal reservoirs as well as future vaccination schemes.
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Affiliation(s)
- Xing Yu
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, 4222, Australia.
| | - Rahul Mishra
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, 4222, Australia
| | - Gavan Holloway
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, 4222, Australia
| | - Barbara S Coulson
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Helen Blanchard
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, 4222, Australia.
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Degiuseppe JI, Parra GI, Stupka JA. Genetic diversity of G3 rotavirus strains circulating in Argentina during 1998-2012 assessed by full genome analyses. PLoS One 2014; 9:e110341. [PMID: 25337915 PMCID: PMC4206407 DOI: 10.1371/journal.pone.0110341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 09/19/2014] [Indexed: 12/28/2022] Open
Abstract
Seasonal shifts in the predominant strains and the periodic emergence of new strains are epidemiological features of human rotaviruses. After the sporadic detection in two samples in 1998, G3P[8] strains reemerged as the predominant rotavirus during 2008-2009 in Argentina. Notably, in 2011 6.3% (37/587) of samples presented the G3P[6] genotypes, which coincided with the recent detection of G3P[6] and G2P[6] strains in South America and Europe. Analyses of the 11 gene segments of four G3P[8] and two G3P[6] strains revealed that G3P[8] strains detected a decade apart (1998 and 2009) presented minor differences, while the G3P[6] strains presented a complete different genomic constellation albeit showing a similar VP7 gene. This study provides insights in the dynamics and evolution of one of the genotypes with the wider range of hosts and inter-species transmission potential.
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Affiliation(s)
- Juan Ignacio Degiuseppe
- Laboratorio de Gastroenteritis Virales, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Gabriel Ignacio Parra
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Juan Andrés Stupka
- Laboratorio de Gastroenteritis Virales, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
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Jeong S, Than VT, Lim I, Kim W. Whole-genome analysis of a rare human Korean G3P rotavirus strain suggests a complex evolutionary origin potentially involving reassortment events between feline and bovine rotaviruses. PLoS One 2014; 9:e97127. [PMID: 24818762 PMCID: PMC4018271 DOI: 10.1371/journal.pone.0097127] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/14/2014] [Indexed: 11/18/2022] Open
Abstract
A rare human rotavirus, G3P[9] strain RVA/Human-tc/KOR/CAU12-2-51/2013/G3P[9], was isolated from the stool of a 9-year-old female hospitalized with acute watery diarrhea in August 2012 in South Korea using a cell culture system, and its genome was analyzed. The complete genomic constellation of the CAU12-2-51 strain revealed a novel genotype constellation for human rotavirus, G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3. Phylogenetic analysis revealed that the CAU12-2-51 strain originated from feline- and bovine-like reassortment strains. The genes encoding VP4, VP7, NSP1, NSP3, NSP4, and NSP5 were related to human/feline-like and feline rotavirus strains, whereas the remaining five genes encoding VP1, VP2, VP3, VP6, and NSP2 were related to the human/bovine-like and bovine rotavirus strains. This novel strain was identified for the first time, providing evidence of feline/bovine-to-human transmission of rotavirus. The data presented herein provide information regarding rotavirus diversity and evolution.
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Affiliation(s)
- Sunyoung Jeong
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Van Thai Than
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Inseok Lim
- Department of Pediatrics, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- * E-mail:
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Ghosh S, Taniguchi K, Aida S, Ganesh B, Kobayashi N. Whole genomic analyses of equine group A rotaviruses from Japan: evidence for bovine-to-equine interspecies transmission and reassortment events. Vet Microbiol 2013; 166:474-85. [PMID: 23938116 DOI: 10.1016/j.vetmic.2013.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/15/2013] [Accepted: 07/19/2013] [Indexed: 11/15/2022]
Abstract
Equine group A rotaviruses (RVA) are a major cause of severe diarrhea in foals. The whole genomes of only six common and three unusual equine RVA strains have been analyzed so far. To date, there are no reports on whole genomic analyses of equine RVAs from Asian countries. We report here the whole genomic analyses of three common (strains RVA/Horse-tc/JPN/BI/1981/G3P[12], RVA/Horse-tc/JPN/HH-22/1989/G3P[12] and RVA/Horse-tc/JPN/CH-3/1987/G14P[12]) and an unusual (RVA/Horse-tc/JPN/OH-4/1982/G6P[5]) equine RVA strains isolated from diarrheic foals in Japan. Strains BI, HH-22 and CH-3 shared a largely conserved genotype constellation (G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2-H7) with each other and with those of common equine RVAs from other continents. Phylogenetically, most of the genes of BI, HH-22 and CH-3 were closely related to those of other common equine RVAs. On the other hand, the NSP2 genes of BI and CH-3 formed a distinct lineage, and were distantly related to the other, major equine RVA cluster within the NSP2-N2 genotype. The NSP4 gene of HH-22 appeared to originate from possible reassortment events involving common equine RVAs and co-circulating bovine or bovine-like equine RVAs, revealing the presence of a bovine RVA-like NSP4 gene on a typical equine RVA genetic backbone. All the 11 gene segments of the unusual equine RVA strain OH-4 were found to be more closely related to those of bovine and bovine-like human RVAs than to those of other RVAs, providing the first conclusive evidence for artiodactyl(likely bovine)-to-equine interspecies transmission events. Taken together, these observations provided important insights into the genetic diversity of equine RVAs.
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Affiliation(s)
- Souvik Ghosh
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan.
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Ghosh S, Urushibara N, Chawla-Sarkar M, Krishnan T, Kobayashi N. Whole genomic analyses of asymptomatic human G1P[6], G2P[6] and G3P[6] rotavirus strains reveal intergenogroup reassortment events and genome segments of artiodactyl origin. INFECTION GENETICS AND EVOLUTION 2013; 16:165-73. [DOI: 10.1016/j.meegid.2012.12.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/17/2012] [Accepted: 12/18/2012] [Indexed: 10/27/2022]
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Wang YH, Pang BB, Zhou X, Ghosh S, Tang WF, Peng JS, Hu Q, Zhou DJ, Kobayashi N. Complex evolutionary patterns of two rare human G3P[9] rotavirus strains possessing a feline/canine-like H6 genotype on an AU-1-like genotype constellation. INFECTION GENETICS AND EVOLUTION 2013; 16:103-12. [PMID: 23403096 DOI: 10.1016/j.meegid.2013.01.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/24/2013] [Accepted: 01/30/2013] [Indexed: 10/27/2022]
Abstract
The group A rotavirus (RVA) G3P[9] is a rare VP7-VP4 genotype combination, detected occasionally in humans and cats. Other than the prototype G3P[9] strain, RVA/Human- tc/JPN/AU-l/1982/G3P3[9], the whole genomes of only two human G3P[9] RVA strains and two feline G3P[9] RVA strains have been analyzed so far, revealing complex evolutionary patterns, distinct from that of AU-1. We report here the whole genomic analyses of two human G3P[9] RVA strains, RVA/Human-tc/CHN/L621/2006/G3P[9] and RVA/Human-wt/CHN/E2451/2011/G3P[9], detected in patients with diarrhea in China. Strains L621 and E2451 possessed a H6 NSP5 genotype on an AU-1-like genotype constellation, not reported previously. However, not all the genes of L621 and E2451 were closely related to those of AU-1, or to each other, revealing different evolutionary patterns among the AU-1-like RVAs. The VP7, VP4, VP6 and NSP4 genes of E2451 and L621 were found to cluster together with human G3P[9] RVA strains believed to be of possible feline/canine origin, and feline or raccoon dog RVA strains. The VP1, VP3, NSP2 and NSP5 genes of E2451 and L621 formed distinct clusters in genotypes typically found in feline/canine RVA strains or RVA strains from other host species which are believed to be of feline/canine RVA origin. The VP2 genes of E2451 and L621, and NSP3 gene of L621 clustered among RVA strains from different host species which are believed to have a complete or partial feline/canine RVA origin. The NSP1 genes of E2451 and L621, and NSP3 gene of E2451 clustered with AU-1 and several other strains possessing a complete or partial feline RVA strain BA222-05-like genotype constellation. Taken together, these observations suggest that nearly all the eleven gene segments of G3P[9] RVA strains L621 and E2451 might have originated from feline/canine RVAs, and that reassortments may have occurred among these feline/canine RVA strains, before being transmitted to humans.
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Affiliation(s)
- Yuan-Hong Wang
- Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei Province, China.
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Ghosh S, Urushibara N, Kawaguchiya M, Shintani T, Kobayashi N. The origin of two rare human P[10] rotavirus strains. INFECTION GENETICS AND EVOLUTION 2013. [DOI: 10.1016/j.meegid.2012.10.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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