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Munlela B, João ED, Donato CM, Strydom A, Boene SS, Chissaque A, Bauhofer AFL, Langa J, Cassocera M, Cossa-Moiane I, Chilaúle JJ, O’Neill HG, de Deus N. Whole Genome Characterization and Evolutionary Analysis of G1P[8] Rotavirus A Strains during the Pre- and Post-Vaccine Periods in Mozambique (2012-2017). Pathogens 2020; 9:pathogens9121026. [PMID: 33291333 PMCID: PMC7762294 DOI: 10.3390/pathogens9121026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022] Open
Abstract
Mozambique introduced the Rotarix® vaccine (GSK Biologicals, Rixensart, Belgium) into the National Immunization Program in September 2015. Although G1P[8] was one of the most prevalent genotypes between 2012 and 2017 in Mozambique, no complete genomes had been sequenced to date. Here we report whole genome sequence analysis for 36 G1P[8] strains using an Illumina MiSeq platform. All strains exhibited a Wa-like genetic backbone (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). Phylogenetic analysis showed that most of the Mozambican strains clustered closely together in a conserved clade for the entire genome. No distinct clustering for pre- and post-vaccine strains were observed. These findings may suggest no selective pressure by the introduction of the Rotarix® vaccine in 2015. Two strains (HJM1646 and HGM0544) showed varied clustering for the entire genome, suggesting reassortment, whereas a further strain obtained from a rural area (MAN0033) clustered separately for all gene segments. Bayesian analysis for the VP7 and VP4 encoding gene segments supported the phylogenetic analysis and indicated a possible introduction from India around 2011.7 and 2013.0 for the main Mozambican clade. Continued monitoring of rotavirus strains in the post-vaccine period is required to fully understand the impact of vaccine introduction on the diversity and evolution of rotavirus strains.
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Affiliation(s)
- Benilde Munlela
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo 3453, Mozambique
- Correspondence: or (B.M.); (E.D.J.); Tel.: +258-848814087 (B.M.); +258-827479229 (E.D.J.)
| | - Eva D. João
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
- Correspondence: or (B.M.); (E.D.J.); Tel.: +258-848814087 (B.M.); +258-827479229 (E.D.J.)
| | - 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 3010, Australia
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Amy Strydom
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, 205 Nelson Mandela Avenue, Bloemfontein 9301, South Africa; (A.S.); (H.G.O.)
| | - Simone S. Boene
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo 3453, Mozambique
| | - Assucênio Chissaque
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Adilson F. L. Bauhofer
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Jerónimo Langa
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
| | - Marta Cassocera
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Idalécia Cossa-Moiane
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Institute of Tropical Medicine (ITM), Kronenburgstraat 43, 2000 Antwerp, Belgium
| | - Jorfélia J. Chilaúle
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
| | - Hester G. O’Neill
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, 205 Nelson Mandela Avenue, Bloemfontein 9301, South Africa; (A.S.); (H.G.O.)
| | - Nilsa de Deus
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Departamento de Ciências Biológicas, Universidade Eduardo Mondlane, Maputo 3453, Mozambique
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Wang Y, Liu Y, Wang M, Yu L, Ma C, Li X, Guo T, Bao H, Kou K, Chen Y, Gong H, Zhou X. Establishment of a cell-based quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay for detection of multivalent rotavirus vaccine. J Med Virol 2020; 92:3157-3164. [PMID: 32492198 DOI: 10.1002/jmv.26128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 11/10/2022]
Abstract
Because of deficiencies of traditional potency tests in rotavirus detection, a one-step TaqMan probe-based quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay combined with cell-based method was established to determine the infectious potency of the target virus in multivalent live rotavirus vaccines in vitro. Series dilutions of rotavirus samples were inoculated into Vero cells and cultured for 24 hours. The cells were lysed and the potency was detected by RT-qPCR. The reference standards with a known titer (lgCCID50 /mL) were assayed in parallel, and the potencies of each sample were determined using parallel line method. The specificity, precision and accuracy of the assay were evaluated, respectively. The results showed that messenger RNA produced during rotavirus replication was the primary template of RT-qPCR and the primers and probes were specific to each strain. The coefficient of variation of different wells and different working days did not exceed 6% and the results of the assay were proved to be concordant with those of cell culture infective dose 50% with a relative deviation less than 5%. This assay is a more rapid, cost-effective and high-throughput way for detecting multivalent rotavirus vaccine, and will be a valuable tool in the quality control and stability monitoring of live multivalent rotavirus vaccine.
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Affiliation(s)
- Yunjin Wang
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Yueyue Liu
- Division of Enteric Virus Vaccine, National Institutes for Food and Drug Control, Beijing, China
| | - Mingqiang Wang
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Li Yu
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Chao Ma
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Xiongxiong Li
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Tai Guo
- Division of Enteric Virus Vaccine, National Institutes for Food and Drug Control, Beijing, China
| | - Hong Bao
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Kuiying Kou
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Yueru Chen
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Hanbo Gong
- Faculty of Science, University of Alberta, Alberta, Canada
| | - Xu Zhou
- General Manager's Office, Shanghai Institute of Biological Products Co, Ltd, Shanghai, China
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Whole genome and in-silico analyses of G1P[8] rotavirus strains from pre- and post-vaccination periods in Rwanda. Sci Rep 2020; 10:13460. [PMID: 32778711 PMCID: PMC7417577 DOI: 10.1038/s41598-020-69973-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/17/2020] [Indexed: 11/09/2022] Open
Abstract
Rwanda was the first low-income African country to introduce RotaTeq vaccine into its Expanded Programme on Immunization in May 2012. To gain insights into the overall genetic make-up and evolution of Rwandan G1P[8] strains pre- and post-vaccine introduction, rotavirus positive fecal samples collected between 2011 and 2016 from children under the age of 5 years as part of ongoing surveillance were genotyped with conventional RT-PCR based methods and whole genome sequenced using the Illumina MiSeq platform. From a pool of samples sequenced (n = 158), 36 were identified as G1P[8] strains (10 pre-vaccine and 26 post-vaccine), of which 35 exhibited a typical Wa-like genome constellation. However, one post vaccine strain, RVA/Human-wt/RWA/UFS-NGS:MRC-DPRU442/2012/G1P[8], exhibited a RotaTeq vaccine strain constellation of G1-P[8]-I2-R2-C2-M2-A3-N2-T6-E2-H3, with most of the gene segments having a close relationship with a vaccine derived reassortant strain, previously reported in USA in 2010 and Australia in 2012. The study strains segregated into two lineages, each containing a paraphyletic pre- and post-vaccine introduction sub-lineages. In addition, the study strains demonstrated close relationship amongst each other when compared with globally selected group A rotavirus (RVA) G1P[8] reference strains. For VP7 neutralization epitopes, amino acid substitutions observed at positions T91A/V, S195D and M217T in relation to the RotaTeq vaccine were radical in nature and resulted in a change in polarity from a polar to non-polar molecule, while for the VP4, amino acid differences at position D195G was radical in nature and resulted in a change in polarity from a polar to non-polar molecule. The polarity change at position T91A/V of the neutralizing antigens might play a role in generating vaccine-escape mutants, while substitutions at positions S195D and M217T may be due to natural fluctuation of the RVA. Surveillance of RVA at whole genome level will enhance further assessment of vaccine impact on circulating strains, the frequency of reassortment events under natural conditions and epidemiological fitness generated by such events.
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Uncovering the First Atypical DS-1-like G1P[8] Rotavirus Strains That Circulated during Pre-Rotavirus Vaccine Introduction Era in South Africa. Pathogens 2020; 9:pathogens9050391. [PMID: 32443835 PMCID: PMC7281366 DOI: 10.3390/pathogens9050391] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/06/2020] [Accepted: 05/18/2020] [Indexed: 11/21/2022] Open
Abstract
Emergence of DS-1-like G1P[8] group A rotavirus (RVA) strains during post-rotavirus vaccination period has recently been reported in several countries. This study demonstrates, for the first time, rare atypical DS-1-like G1P[8] RVA strains that circulated in 2008 during pre-vaccine era in South Africa. Rotavirus positive samples were subjected to whole-genome sequencing. Two G1P[8] strains (RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1971/2008/G1P[8] and RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1973/2008/G1P[8]) possessed a DS-1-like genome constellation background (I2-R2-C2-M2-A2-N2-T2-E2-H2). The outer VP4 and VP7 capsid genes of the two South African G1P[8] strains had the highest nucleotide (amino acid) nt (aa) identities of 99.6–99.9% (99.1–100%) with the VP4 and the VP7 genes of a locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU1039/2008/G1P[8]. All the internal backbone genes (VP1–VP3, VP6, and NSP1-NSP5) had the highest nt (aa) identities with cognate internal genes of another locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU2344/2008/G2P[6]. The two study strains emerged through reassortment mechanism involving locally circulating South African strains, as they were distinctly unrelated to other reported atypical G1P[8] strains. The identification of these G1P[8] double-gene reassortants during the pre-vaccination period strongly supports natural RVA evolutionary mechanisms of the RVA genome. There is a need to maintain long-term whole-genome surveillance to monitor such atypical strains.
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Tatte VS, Maran D, Walimbe AM, Gopalkrishna V. Rotavirus G9P[4], G9P[6] and G1P[6] strains isolated from children with acute gastroenteritis in Pune, western India, 2013-2015: evidence for recombination in genes encoding VP3, VP4 and NSP1. J Gen Virol 2019; 100:1605-1630. [PMID: 31553304 DOI: 10.1099/jgv.0.001323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species A rotaviruses (RVAs) are genetically diverse pathogens. These are the most evolutionarily adaptable organisms, with a multitude of mechanisms for evolutionary change. To date, full-genome classification has been proved to be an excellent tool for studying the evolution of unusual rotavirus strains. As limited data are available from Pune (Maharashtra), western India, the current study was undertaken with the aim of understanding the genetic diversity in three (G1P[6], G9P[4] and G9P[4]) unusual RVA strains circulating in Pune, India during 2013-2015. Full-genome analysis of these strains classified them as G1-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, G9-P[4]-I2-R2-C2-[M1-M2_R]-[A1-A2_R]-N2-T2-E6-H2 and G9-[P4-P6_R]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Sequencing and phylogenetic analysis of the structural and non-structural genes of these unusual RVA strains showed nucleotide/amino acid identities of 82.3-98.5 %/77.3-99.8 % and 86.6-97.6 %/89.6-97.8 % between the strains of the study. Evidence of recombination events was found within the genes encoding VP3, VP4 and NSP1, which showed a combination of genetic information for genogroup 1 [M1/P[6]/A1] and genogroup 2 [M2/P[4]/A2] strains. This study will facilitate future investigations into the molecular pathogenesis of such RVAs as the exchange of whole or partial genetic material between rotaviruses through recombination contributes directly to their diversification, adaptation and evolution.
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Affiliation(s)
- Vaishali S Tatte
- Enteric Viruses Group, National Institute of Virology, Pune, India
| | - Deepthy Maran
- Enteric Viruses Group, National Institute of Virology, Pune, India
| | - Atul M Walimbe
- Bioinformatics Group, National Institute of Virology, Pune, India
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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]
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Xu C, Fu J, Ai J, Zhang J, Liu C, Huo X, Bao C, Zhu Y. Phylogenetic analysis of human G9P[8] rotavirus strains circulating in Jiangsu, China between 2010 and 2016. J Med Virol 2018; 90:1461-1470. [PMID: 29719060 DOI: 10.1002/jmv.25214] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 04/30/2018] [Indexed: 12/27/2022]
Abstract
Rotavirus A (RVA) is the leading cause of acute viral gastroenteritis in children under 5 years of age worldwide. G9P[8] is a common RVA genotype that has been persistently prevalent in Jiangsu, China. To determine the genetic diversity of G9P[8] RVAs, 7 representative G9P[8] strains collected from Suzhou Children's Hospital between 2010 and 2016 (named JS2010-JS2016) were analyzed through whole-genome sequencing. All evaluated strains showed the Wa-like constellation G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Furthermore, phylogenetic analysis revealed that the VP7 genes of all strains clustered into lineage G9-III and G9-VI. With the exception of strain JS2012 (P[8]-4), the VP4 sequences of all strains belonged to the P[8]-3 lineage. Sequencing further revealed that amino acid substitutions were present in the antigenic regions of the VP7 and VP4 genes of all strains. Moreover, there were multiple substitutions in antigenic sites I and II of the nonstructural protein 4 (NSP4) genes, whereas the other NSP genes were relatively conserved. In conclusion, our phylogenetic analysis of these 7 G9P[8] strains suggests that RVA varied across regions and time. Therefore, our findings suggest that continued surveillance is necessary to explore the molecular evolutionary characteristics of RVA for better prevention and treatment of acute viral gastroenteritis.
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Affiliation(s)
- Cheng Xu
- Laboratory Medicine Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianguang Fu
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jing Ai
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jun Zhang
- Department of Acute Infectious Disease Control and Prevention, Suzhou Center for Disease Control and Prevention, Suzhou, China
| | - Cheng Liu
- Department of Acute Infectious Disease Control and Prevention, Suzhou Center for Disease Control and Prevention, Suzhou, China
| | - Xiang Huo
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Changjun Bao
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yefei Zhu
- Laboratory Medicine Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Pradhan GN, Chitambar SD. Genetic analysis of rotavirus G2P[4] strains in Pune, Western India: circulation of a novel reassortant bearing E6 NSP4 genotype. Arch Virol 2018; 163:1391-1394. [PMID: 29411134 DOI: 10.1007/s00705-018-3710-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/01/2017] [Indexed: 11/29/2022]
Abstract
In India, G2P[4] strains are known to be the second most predominant group A rotaviruses causing acute gastroenteritis among children. This study was performed to determine the diversity within VP7(G), VP4(P), VP6(I) and NSP4(E) genes of 16 G2P[4] rotavirus strains detected in children hospitalized for acute gastroenteritis in Pune, Western India during 2009-2013. Fourteen strains showed G2-P[4]-I2-E2 and two strains showed G2-P[4]-I2-E6 genotype constellation. Phylogenetic analysis showed their clustering into G2-IV-a3, P[4]-5bi/ii, I2-3ii and E2-4i/ii or E6 genotypes/lineages. These data reveal inter- and/or intra-genotypic variations in a genogroup-2 constellation of G2P[4] rotavirus strains circulating in Pune, Western India, providing evidence of a novel G2P[4] reassortant bearing a rare NSP4 genotype, E6 during 2009-2013.
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Affiliation(s)
- Gauri N Pradhan
- National Institute of Virology, 20/A, Dr. Ambedkar Road. Post Box No. 11, Pune, 411001, India
| | - Shobha D Chitambar
- National Institute of Virology, 20/A, Dr. Ambedkar Road. Post Box No. 11, Pune, 411001, India.
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Pradhan GN, Chitambar SD. Full genomic analysis of G1P[8] rotavirus strains recovered from rotavirus vaccinated and non-vaccinated children hospitalized for acute gastroenteritis in Pune, western India. J Med Virol 2018; 90:772-778. [DOI: 10.1002/jmv.25007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/19/2017] [Accepted: 11/23/2017] [Indexed: 01/22/2023]
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10
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Donovan SM. Human Milk Oligosaccharides: Potent Weapons in the Battle against Rotavirus Infection. J Nutr 2017; 147:1605-1606. [PMID: 28724660 PMCID: PMC6584111 DOI: 10.3945/jn.117.255836] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sharon M Donovan
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL
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11
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Tatte VS, Chaphekar D, Gopalkrishna V. Full genome analysis of rotavirus G9P[8] strains identified in acute gastroenteritis cases reveals genetic diversity: Pune, western India. J Med Virol 2017; 89:1354-1363. [DOI: 10.1002/jmv.24799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/29/2017] [Indexed: 12/24/2022]
Affiliation(s)
| | - Deepa Chaphekar
- Enteric Viruses Group; National Institute of Virology; Pune India
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12
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Molecular Analysis of VP7 Gene of Rotavirus G1 Strains Isolated from North India. Curr Microbiol 2016; 73:781-789. [DOI: 10.1007/s00284-016-1129-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/20/2016] [Indexed: 10/21/2022]
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13
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Silva FDF, Gregori F, McDonald SM. Distinguishing the genotype 1 genes and proteins of human Wa-like rotaviruses vs. porcine rotaviruses. INFECTION GENETICS AND EVOLUTION 2016; 43:6-14. [PMID: 27180895 DOI: 10.1016/j.meegid.2016.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 11/16/2022]
Abstract
Group A rotaviruses (RVAs) are 11-segmented, double-stranded RNA viruses and important causes of gastroenteritis in the young of many animal species. Previous studies have suggested that human Wa-like RVAs share a close evolutionary relationship with porcine RVAs. Specifically, the VP1-VP3 and NSP2-5/6 genes of these viruses are usually classified as genotype 1 with >81% nucleotide sequence identity. Yet, it remains unknown whether the genotype 1 genes and proteins of human Wa-like strains are distinguishable from those of porcine strains. To investigate this, we performed comprehensive bioinformatic analyses using all known genotype 1 gene sequences. The RVAs analyzed represent wildtype strains isolated from humans or pigs at various geographical locations during the years of 2004-2013, including 11 newly-sequenced porcine RVAs from Brazil. We also analyzed archival strains that were isolated during the years of 1977-1992 as well as atypical strains involved in inter-species transmission between humans and pigs. We found that, in general, the genotype 1 genes of typical modern human Wa-like RVAs clustered together in phylogenetic trees and were separate from those of typical modern porcine RVAs. The only exception was for the NSP5/6 gene, which showed no host-specific phylogenetic clustering. Using amino acid sequence alignments, we identified 34 positions that differentiated the VP1-VP3, NSP2, and NSP3 genotype 1 proteins of typical modern human Wa-like RVAs versus typical modern porcine RVAs and documented how these positions vary in the archival/unusual isolates. No host-specific amino acid positions were identified for NSP4, NSP5, or NSP6. Altogether, the results of this study support the notion that human Wa-like RVAs and porcine RVAs are evolutionarily related, but indicate that some of their genotype 1 genes and proteins have diverged over time possibly as a reflection of sequestered replication and protein co-adaptation in their respective hosts.
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Affiliation(s)
- Fernanda D F Silva
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Brazil
| | - F Gregori
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Brazil
| | - Sarah M McDonald
- Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA; Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA.
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Kulkarni R, Arora R, Arora R, Chitambar SD. Sequence analysis of VP7 and VP4 genes of G1P[8] rotaviruses circulating among diarrhoeic children in Pune, India: a comparison with Rotarix and RotaTeq vaccine strains. Vaccine 2015; 32 Suppl 1:A75-83. [PMID: 25091685 DOI: 10.1016/j.vaccine.2014.03.080] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND The G1P[8] rotaviruses are a common cause of rotavirus diarrhoea among children in India. Two rotavirus vaccines licensed in India, Rotarix and RotaTeq, contain strains with G1 and P[8] genotypes. A comparative analysis of these genotypes in the live rotavirus vaccines with circulating rotavirus strains is essential for assessment of rotavirus diversity. METHODS G1P[8] strains detected during rotavirus surveillance among diarrhoeic children hospitalized in Pune in 1992-1993 and 2006-2008, were included in the study. Amplification, sequencing and phylogenetic analysis of the VP7 and VP4 genes were carried out for identification of the G1 and P[8] lineages, respectively. Antigenic epitopes of VP7 and VP4 encoded proteins were compared to determine the differences between the G1P[8] strains from Pune and the vaccine strains. RESULTS G1-Lineage 1, P[8]-Lineage 3 strains were predominant in Pune during 1992-1993 and 2006-2008. Strains of G1-Lineage 2, P[8]-Lineage 3 and G1-Lineage 1, P[8]-Lineage 4 were detected at low levels during 2006-2008. The G1-Lineage 1, P[8]-Lineage 3 strains showed up to eight amino acid changes, each in the VP7 and VP4 epitopes, with respect to the Rotarix vaccine strain (G1-Lineage 2, P[8]-Lineage 1) and the G1 (Lineage-3) and P[8] (Lineage 2) components of the RotaTeq vaccine. The G1-Lineage 2 strains were closer to both vaccine strains with no or only two amino acid substitutions in the VP7 epitopes. The divergent P[8]-Lineage 4 (OP354-like) strains showed fourteen and fifteen amino acid differences, with Rotarix and RotaTeq vaccine strains, respectively, in the VP4 epitopes. CONCLUSION The differences between the G1P[8] strains in Pune and the G1 and P[8] components of the vaccine strains need to be described for appropriate evaluation of vaccine shedding. Continuous monitoring of the G1P[8] subgenotypic lineages would be necessary to study any long term impact of vaccine use on G1P[8] strain evolution.
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Affiliation(s)
- Ruta Kulkarni
- Enteric Viruses Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune-411001, India
| | - Ritu Arora
- Enteric Viruses Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune-411001, India
| | - Rashmi Arora
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, Ansari Nagar, New Delhi-110029, India
| | - Shobha D Chitambar
- Enteric Viruses Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune-411001, India.
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da Silva MFM, Rose TL, Gómez MM, Carvalho-Costa FA, Fialho AM, de Assis RMS, de Andrade JDSR, Volotão EDM, Leite JPG. G1P[8] species A rotavirus over 27 years--pre- and post-vaccination eras--in Brazil: full genomic constellation analysis and no evidence for selection pressure by Rotarix® vaccine. INFECTION GENETICS AND EVOLUTION 2015; 30:206-218. [PMID: 25562122 DOI: 10.1016/j.meegid.2014.12.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/28/2014] [Accepted: 12/24/2014] [Indexed: 12/26/2022]
Abstract
Epidemiological data on species A rotavirus (RVA) infections have demonstrated the genetic diversity of strains circulating worldwide. Many G and P genotype combinations have been described over the years, varying regionally and temporally, especially in developing countries. However, the most common G and P genotype combinations identified in RVA human strains worldwide are G1P[8], G2P[4], G3P[8], G4P[8] and G9P[8]. RVA genotype G1P[8] strains are responsible for more than 50% of child infections worldwide and component of the two vaccines (Rotarix® [RV1] and RotaTeq® [RV5]) licensed globally. For a better understanding of the evolutionary mechanisms of this genotype in Brazil, phylogenetic analyses based on the 11 RVA genome segments (genomic constellation) from 90 G1P[8] RVA strains collected in two eras - (i) pre-vaccination with RV1 (1996-February 2006); (ii) post-vaccination (March 2006-2013) - in different Brazilian states were performed. The results showed the Wa-like genomic constellation of the Brazilian G1P[8] strains with a I1-R1-C1-M1-A1-N1-T1-E1-H1 specificity, except for two strains (rj14055-07 and ba19030-10) that belong to a I1-R1-C1-M1-A1-N1-T3-E1-H1 genomic constellation, evidencing the occurrence of reassortment (Wa-like×AU-1-like) of the NSP3 gene. Reassortment events were also demonstrated between Brazilian G1P[8] strains and the RV1 vaccine strain in some genes in vaccinated and unvaccinated children. VP7 and VP8* antigenic site analysis showed that the amino acid substitutions observed in samples collected after the introduction of RV1 in Brazil were already detected in samples collected in the 1980s and 1990s, suggesting that mass Brazilian RV1 vaccination had no impact on the diversity observed inside antigenic sites for these two proteins.
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Affiliation(s)
- Marcelle Figueira Marques da Silva
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.
| | - Tatiana Lundgren Rose
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Mariela Martínez Gómez
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Filipe Anibal Carvalho-Costa
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Alexandre Madi Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Rosane Maria Santos de Assis
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | | | - Eduardo de Mello Volotão
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
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Magagula NB, Esona MD, Nyaga MM, Stucker KM, Halpin RA, Stockwell TB, Seheri ML, Steele AD, Wentworth DE, Mphahlele MJ. Whole genome analyses of G1P[8] rotavirus strains from vaccinated and non-vaccinated South African children presenting with diarrhea. J Med Virol 2014; 87:79-101. [PMID: 24841697 DOI: 10.1002/jmv.23971] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2014] [Indexed: 12/18/2022]
Abstract
Group A rotaviruses (RVAs) are the leading cause of severe gastroenteritis and eventually death among infants and young children worldwide, and disease prevention and management through vaccination is a public health priority. In August 2009, Rotarix™ was introduced in the South African Expanded Programme on Immunisation. As a result, substantial reductions in RVA disease burden have been reported among children younger than 5 years old. Rotavirus strain surveillance post-vaccination is crucial to, inter alia, monitor and study the evolution of vaccine escape strains. Here, full-genome sequence data for the 11 gene segments from 11 South African G1P[8] rotavirus strains were generated, including 5 strains collected from non-vaccinated children during the 2004-2009 rotavirus seasons and 6 strains collected from vaccinated children during the 2010 rotavirus season. These data were analyzed to gain insights into the overall genetic makeup and evolution of South African G1P[8] rotavirus strains and to compare their genetic backbones with those of common human Wa-like RVAs from other countries, as well as with the Rotarix™ and RotaTeq™ G1P[8] vaccine components. All 11 South African G1P[8] strains revealed a complete Wa-like genotype constellation of G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. On the basis of sequence similarities, the South African G1P[8] strains (with the exception of strain RVA/Human-wt/ZAF/1262/2004/G1P[8]) were closely related to each other (96-100% identity in all gene segments). Comparison to the Rotarix™ and RotaTeq™ G1P[8] vaccine components revealed a moderate nucleotide identity of 89-96% and 93-95%, respectively. The results indicated that none of the gene segments of these 11 South African G1P[8] strains were vaccine-derived. This study illustrates that large-scale next generation sequencing will provide crucial information on the influence of the vaccination program on evolution of rotavirus strains. This is the first report to describe full genomic analyses of G1P[8] RVA strains collected from both non-vaccinated and vaccinated children in South Africa.
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Affiliation(s)
- Nonkululeko B Magagula
- Medical Research Council/Diarrhoeal Pathogens Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa
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Moyo SJ, Blomberg B, Hanevik K, Kommedal O, Vainio K, Maselle SY, Langeland N. Genetic diversity of circulating rotavirus strains in Tanzania prior to the introduction of vaccination. PLoS One 2014; 9:e97562. [PMID: 24844631 PMCID: PMC4028215 DOI: 10.1371/journal.pone.0097562] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 04/21/2014] [Indexed: 12/25/2022] Open
Abstract
Background Tanzania currently rolls out vaccination against rotavirus-diarrhea, a major cause of child illness and death. As the vaccine covers a limited number of rotavirus variants, this study describes the molecular epidemiology of rotavirus among children under two years in Dar es Salaam, Tanzania, prior to implementation of vaccination. Methods Stool specimens, demographic and clinical information, were collected from 690 children admitted to hospital due to diarrhea (cases) and 545 children without diarrhea (controls) during one year. Controls were inpatient or children attending child health clinics. Rotavirus antigen was detected using ELISA and positive samples were typed by multiplex semi-nested PCR and sequencing. Results The prevalence of rotavirus was higher in cases (32.5%) than in controls (7.7%, P<0.001). The most common G genotypes were G1 followed by G8, G12, and G4 in cases and G1, G12 and G8 in controls. The Tanzanian G1 variants displayed 94% similarity with the Rotarix vaccine G1 variant. The commonest P genotypes were P[8], P[4] and P[6], and the commonest G/P combination G1 P[8] (n = 123), G8 P[4] and G12 P[6]. Overall, rotavirus prevalence was higher in cool (23.9%) than hot months (17.1%) of the year (P = 0.012). We also observed significant seasonal variation of G genotypes. Rotavirus was most frequently found in the age group of four to six months. The prevalence of rotavirus in cases was lower in stunted children (28.9%) than in non-stunted children (40.1%, P = 0.003) and lower in HIV-infected (15.4%, 4/26) than in HIV-uninfected children (55.3%, 42/76, P<0.001). Conclusion This pre-vaccination study shows predominance of genotype G1 in Tanzania, which is phylogenetically distantly related to the vaccine strains. We confirm the emergence of genotype G8 and G12. Rotavirus infection and circulating genotypes showed seasonal variation. This study also suggests that rotavirus may not be an opportunistic pathogen in children infected with HIV.
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Affiliation(s)
- Sabrina J. Moyo
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- * E-mail:
| | - Bjørn Blomberg
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Centre for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Centre for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Oyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Kirsti Vainio
- Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway
| | - Samuel Y. Maselle
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Theamboonlers A, Maiklang O, Thongmee T, Chieochansin T, Vuthitanachot V, Poovorawan Y. Complete genotype constellation of human rotavirus group A circulating in Thailand, 2008–2011. INFECTION GENETICS AND EVOLUTION 2014; 21:295-302. [DOI: 10.1016/j.meegid.2013.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 01/26/2023]
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19
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Evidence of VP7 and VP4 intra-lineage diversification in G4P[8] Italian human rotaviruses. Virus Genes 2013; 48:361-5. [DOI: 10.1007/s11262-013-1026-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/11/2013] [Indexed: 10/25/2022]
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20
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Iftikhar T, Butt A, Nawaz K, Sarwar Y, Ali A, Mustafa T, Haque A. Genotyping of rotaviruses detected in children admitted to hospital from Faisalabad Region, Pakistan. J Med Virol 2012; 84:2003-7. [DOI: 10.1002/jmv.23402] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Full genomic analysis of rabbit rotavirus G3P[14] strain N5 in China: Identification of a novel VP6 genotype. INFECTION GENETICS AND EVOLUTION 2012; 12:1567-76. [DOI: 10.1016/j.meegid.2012.06.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 06/11/2012] [Accepted: 06/18/2012] [Indexed: 11/20/2022]
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22
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Maranhão AG, Vianez-Júnior JLS, Benati FJ, Bisch PM, Santos N. Polymorphism of rotavirus genotype G1 in Brazil: In silico analysis of variant strains circulating in Rio de Janeiro from 1996 to 2004. INFECTION GENETICS AND EVOLUTION 2012; 12:1397-404. [DOI: 10.1016/j.meegid.2012.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 04/20/2012] [Accepted: 04/21/2012] [Indexed: 01/20/2023]
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Cho MK, Jheong WH, Lee SG, Park CJ, Jung KH, Paik SY. Full genomic analysis of a human rotavirus G1P[8] strain isolated in South Korea. J Med Virol 2012; 85:157-70. [PMID: 23023979 DOI: 10.1002/jmv.23366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2012] [Indexed: 11/07/2022]
Abstract
A rotavirus G1P[8] strain C1-81 was isolated from a 5-month-old female infant admitted to hospital with fever and severe diarrhea in Incheon, South Korea. To investigate its full genomic relatedness and its group, the full genome of strain C1-81 was determined. Based on a full genome classification system, C1-81 was shown to possess the typical Wa-like genotype constellation: G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. On the basis of sequence similarities, the strain was shown to be the closest related strain to contemporary human rotavirus strains with recent strains isolated in Asia. This C1-81 strain showed the highest degree of nucleic acid similarity (98.8% and 97%) to G1 B4633-03 and P[8] (Thai-1604 and Dhaka8-02), respectively. This is the first report that group A rotavirus was analyzed with G1P[8] in South Korea. The study of the complete genome of the virus will help understanding of the evolution of rotavirus.
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Affiliation(s)
- Min-Kyu Cho
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Nordgren J, Bonkoungou IJO, Nitiema LW, Sharma S, Ouermi D, Simpore J, Barro N, Svensson L. Rotavirus in diarrheal children in rural Burkina Faso: high prevalence of genotype G6P[6]. INFECTION GENETICS AND EVOLUTION 2012; 12:1892-8. [PMID: 22964045 DOI: 10.1016/j.meegid.2012.08.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 08/09/2012] [Accepted: 08/14/2012] [Indexed: 10/27/2022]
Abstract
Group A rotavirus (RVA) is the most common cause of severe gastroenteritis in young children globally, and responsible for a significant number of deaths in African countries. While vaccines are available, trials have shown a lesser efficacy in Africa. One of the reasons could be the prevalence and/or emergence of unusual or novel RVA strains, as many strains detected in African countries remain uncharacterized. In this study, we characterized RVA positive specimens from two remote rural areas in Burkina Faso, West Africa. In total 56 RVA positive specimens were subgrouped by their VP6 gene, and G-and P typed by PCR and/or sequencing of the VP7 and VP4 genes, respectively. Notably, we found a high prevalence of the unusual G6P[6]SGI strains (23%). It was the second most common constellation after G9P[8]SGII (32%); and followed by G1P[8]SGII (20%) and G2P[4]SGI (9%). We also detected a G8P[6]SGI strain, for the first time in Burkina Faso. The intra-genetic diversity was high for the VP4 gene with two subclusters within the P[8] genotype and three subclusters within the P[6] genotype which were each associated with a specific G-type, thereby suggesting a genetic linkage. The G6P[6]SGI and other SGI RVA strains infected younger children as compared to SGII strains (p<0.05). To conclude, in this study we observed the emergence of unusual RVA strains and high genetic diversity of RVA in remote rural areas of Burkina Faso. The results highlight the complexity of RVA epidemiology which may have implication for the introduction of rotavirus vaccines currently being evaluated in many African countries.
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Affiliation(s)
- Johan Nordgren
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, SE-58185 Linköping, Sweden.
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Shintani T, Ghosh S, Wang YH, Zhou X, Zhou DJ, Kobayashi N. Whole genomic analysis of human G1P[8] rotavirus strains from different age groups in China. Viruses 2012; 4:1289-304. [PMID: 23012626 PMCID: PMC3446763 DOI: 10.3390/v4081289] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 08/13/2012] [Accepted: 08/15/2012] [Indexed: 11/16/2022] Open
Abstract
G1P[8] rotaviruses are an important cause of diarrhea in humans in China. To date, there are no reports on the whole genomic analysis of the Chinese G1P[8] rotaviruses. To determine the origin and overall genetic makeup of the recent Chinese G1P[8] strains, the whole genomes of three strains, RVA/Human-wt/CHN/E1911/2009/G1P[8], RVA/Human-tc/CHN/R588/2005/G1P[8] and RVA/Human-tc/CHN/Y128/2004/G1P[8], detected in an infant, a child and an adult, respectively, were analyzed. Strains E1911, R588 and Y128 exhibited a typical Wa-like genotype constellation. Except for the NSP3 gene of E1911, the whole genomes of strains E1911, R588 and Y128 were found to be more closely related to those of the recent Wa-like common human strains from different countries than those of the prototype G1P[8] strain, or other old strains. On the other hand, the NSP3 gene of E1911 was genetically distinct from those of Y128, R588, or other Wa-like common human strains, and appeared to share a common origin with those of the porcine-like human G9 strains, providing evidence for intergenotype reassortment events. Comparisons of the amino acid residues defining the VP7 and VP4 antigenic domains revealed several mismatches between these Chinese G1P[8] strains and the G1 and P[8] strains contained in the currently licensed rotavirus vaccines Rotarix(TM )and RotaTeq(TM).
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Affiliation(s)
- Tsuzumi Shintani
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan; (T.S.); (N.K.)
| | - Souvik Ghosh
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan; (T.S.); (N.K.)
- Author to whom correspondence should be addressed; ; Tel.: +81-11-611-2111 ext. 2733; Fax: +81-11-612-1660
| | - Yuan-Hong Wang
- Wuhan Centers for Disease Prevention and Control, Wuhan 430015, China; (Y.-H.W.); (X.Z.); (D.-J.Z.)
| | - Xuan Zhou
- Wuhan Centers for Disease Prevention and Control, Wuhan 430015, China; (Y.-H.W.); (X.Z.); (D.-J.Z.)
| | - Dun-Jin Zhou
- Wuhan Centers for Disease Prevention and Control, Wuhan 430015, China; (Y.-H.W.); (X.Z.); (D.-J.Z.)
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan; (T.S.); (N.K.)
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Matthijnssens J, Van Ranst M. Genotype constellation and evolution of group A rotaviruses infecting humans. Curr Opin Virol 2012; 2:426-33. [PMID: 22683209 DOI: 10.1016/j.coviro.2012.04.007] [Citation(s) in RCA: 235] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 03/01/2012] [Accepted: 04/19/2012] [Indexed: 12/12/2022]
Abstract
Numerous rotavirus group A (RVA) strains with distinct G-genotype and P-genotype combinations have been described infecting humans worldwide. However, the increasing amount of complete RVA genome data which have become available, suggest that only RVA strains with 2 discrete genotype constellations have been successful in sustaining infection of humans worldwide over longer periods of time. Those genotype constellations have been designated I1-R1-C1-M1-A1-N1-T1-E1-H1 and I2-R2-C2-M2-A2-N2-T2-E2-H2 and are also known as Wa-like and DS-1-like, respectively. RVAs of other genotype constellations which were able to spread to a limited extent in the human population are AU-1-related RVA strains (I3-R3-C3-M3-A3/A12-N3-T3-E3-H3/H6) in combination with G3P[9] or G12P[9], and neonatal G10P[11] RVA strains in India (bovine×human Wa-like reassortants). On the basis of the analysis of complete genomes, it is suggested that the overall genetic diversity of epidemiologically widespread human RVA strains is more limited than generally assumed. This conclusion has consequences for how we look at host range restriction and the criteria according to which the effectiveness of RVA universal mass vaccination programs is assessed.
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Affiliation(s)
- Jelle Matthijnssens
- Laboratory of Clinical & Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium.
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Ghosh S, Kobayashi N. Whole-genomic analysis of rotavirus strains: current status and future prospects. Future Microbiol 2011; 6:1049-65. [DOI: 10.2217/fmb.11.90] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Studies on genetic diversity of rotaviruses have been primarily based on the genes encoding the antigenically significant VP7 and VP4 proteins. Since the rotavirus genome has 11 segments of RNA that are vulnerable to reassortment events, analyses of the VP7 and VP4 genes may not be sufficient to obtain conclusive data on the overall genetic diversity, or true origin of strains. In the last few years following the advent of the whole-genome-based genotype classification system, the whole genomes of at least 167 human group A rotavirus strains have been analyzed, providing a plethora of new and important information on the complex origin of strains, inter- and intra-genogroup reassortment events, animal–human reassortment events, zoonosis, and genetic linkages involving different group A rotavirus gene segments. In addition, the whole genomes of a limited number of human group B, C and novel group rotavirus strains have been analyzed. This article briefly reviews the available data on whole-genomic analysis of human rotavirus strains. The significance and future prospects of whole-genome-based studies are also discussed.
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Affiliation(s)
- Souvik Ghosh
- Department of Hygiene, Sapporo Medical University School of Medicine, S 1, W 17, Chuo-Ku, Sapporo, Hokkaido 060-8556, Japan
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Ghosh S, Paul SK, Yamamoto D, Nagashima S, Kobayashi N. Full genomic analyses of human rotavirus strains possessing the rare P[8]b VP4 subtype. INFECTION GENETICS AND EVOLUTION 2011; 11:1481-6. [DOI: 10.1016/j.meegid.2011.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 05/16/2011] [Accepted: 05/18/2011] [Indexed: 11/30/2022]
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McDonald SM, Davis K, McAllen JK, Spiro DJ, Patton JT. Intra-genotypic diversity of archival G4P[8] human rotaviruses from Washington, DC. INFECTION GENETICS AND EVOLUTION 2011; 11:1586-94. [PMID: 21712102 DOI: 10.1016/j.meegid.2011.05.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 05/24/2011] [Accepted: 05/26/2011] [Indexed: 12/12/2022]
Abstract
Group A human rotaviruses (RVs) remain the most frequently detected viral agents associated with acute gastroenteritis in infants and young children. Despite their medical importance, relatively few complete genome sequences have been determined for commonly circulating G/P-type strains (i.e., G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8]). In the current study, we sequenced the genomes of 11 G4P[8] isolates from stool specimens that were collected in Washington, DC during the years of 1974-1991. We found that the VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6-encoding genes of all 11 G4P[8] RVs have the genotypes of G4-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. By constructing phylogenetic trees for each gene, extensive intra-genotypic diversity was revealed among the G4P[8] RVs, and new sub-genotype gene alleles were identified. Several of these alleles are nearly identical to those of G3P[8] isolates previously sequenced from this same Washington, DC collection, strongly suggesting that the RVs underwent gene reassortment. On the other hand, we observed that some G4P[8] RVs exhibit completely different allele-based genome constellations, despite being collected during the same epidemic season; there was no evidence of gene reassortment between these strains. This observation extends our previous findings and supports the notion that stable, genetically-distinct clades of human RVs with the same G/P-type can co-circulate in a community. Interestingly, the sub-genotype gene alleles found in some of the DC RVs share a close evolutionary relationship with genes of more contemporary human strains. Thus, archival human RVs sequenced in this study might represent evolutionary precursors to modern-day strains.
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Affiliation(s)
- Sarah M McDonald
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Matthijnssens J, Ciarlet M, McDonald SM, Attoui H, Bányai K, Brister JR, Buesa J, Esona MD, Estes MK, Gentsch JR, Iturriza-Gómara M, Johne R, Kirkwood CD, Martella V, Mertens PPC, Nakagomi O, Parreño V, Rahman M, Ruggeri FM, Saif LJ, Santos N, Steyer A, Taniguchi K, Patton JT, Desselberger U, Van Ranst M. Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch Virol 2011; 156:1397-413. [PMID: 21597953 DOI: 10.1007/s00705-011-1006-z] [Citation(s) in RCA: 740] [Impact Index Per Article: 56.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 04/19/2011] [Indexed: 12/31/2022]
Abstract
In April 2008, a nucleotide-sequence-based, complete genome classification system was developed for group A rotaviruses (RVs). This system assigns a specific genotype to each of the 11 genome segments of a particular RV strain according to established nucleotide percent cutoff values. Using this approach, the genome of individual RV strains are given the complete descriptor of Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx. The Rotavirus Classification Working Group (RCWG) was formed by scientists in the field to maintain, evaluate and develop the RV genotype classification system, in particular to aid in the designation of new genotypes. Since its conception, the group has ratified 51 new genotypes: as of April 2011, new genotypes for VP7 (G20-G27), VP4 (P[28]-P[35]), VP6 (I12-I16), VP1 (R5-R9), VP2 (C6-C9), VP3 (M7-M8), NSP1 (A15-A16), NSP2 (N6-N9), NSP3 (T8-T12), NSP4 (E12-E14) and NSP5/6 (H7-H11) have been defined for RV strains recovered from humans, cows, pigs, horses, mice, South American camelids (guanaco), chickens, turkeys, pheasants, bats and a sugar glider. With increasing numbers of complete RV genome sequences becoming available, a standardized RV strain nomenclature system is needed, and the RCWG proposes that individual RV strains are named as follows: RV group/species of origin/country of identification/common name/year of identification/G- and P-type. In collaboration with the National Center for Biotechnology Information (NCBI), the RCWG is also working on developing a RV-specific resource for the deposition of nucleotide sequences. This resource will provide useful information regarding RV strains, including, but not limited to, the individual gene genotypes and epidemiological and clinical information. Together, the proposed nomenclature system and the NCBI RV resource will offer highly useful tools for investigators to search for, retrieve, and analyze the ever-growing volume of RV genomic data.
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Affiliation(s)
- Jelle Matthijnssens
- Laboratory of Clinical & Epidemiological Virology, Department of Microbiology & Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium.
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