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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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Ihira M, Kawamura Y, Miura H, Hattori F, Higashimoto Y, Sugata K, Ide T, Komoto S, Taniguchi K, Yoshikawa T. Molecular characterization of rotaviruses obtained from patients with rotavirus-associated encephalitis/encephalopathy. Microbiol Immunol 2020; 64:541-555. [PMID: 32511783 DOI: 10.1111/1348-0421.12827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022]
Abstract
Group A rotavirus (RVA) rarely causes severe complications such as encephalitis/encephalopathy. However, the pathophysiology of this specific complication remains unclear. Next-generation sequence analysis was used to compare the entire genome sequences of RVAs detected in patients with encephalitis/encephalopathy and gastroenteritis. This study enrolled eight patients with RVA encephalitis/encephalopathy and 10 with RVA gastroenteritis who were treated between February 2013 and July 2014. Viral RNAs were extracted from patients' stool, and whole-genome sequencing analysis was carried out to identify the specific gene mutations in RVA obtained from patients with severe neurological complications. Among the eight encephalitis/encephalopathy cases, six strains were DS-1-like G1P[8] and the remaining two were Wa-like G1P[8] (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). Meanwhile, eight of the 10 viruses detected in rotavirus gastroenteritis patients were DS-1-like G1P[8], and the remaining two were Wa-like G1P[8]. These strains were further characterized by conducting phylogenetic analysis. No specific clustering was demonstrated in RVAs detected from encephalitis/encephalopathy patients. Although the DS-1-like G1P[8] strain was predominant in both groups, no specific molecular characteristics were detected in RVAs from patients with severe central nervous system complications.
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Affiliation(s)
- Masaru Ihira
- Faculty of Clinical Engineering, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Hiroki Miura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Fumihiko Hattori
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yuki Higashimoto
- Faculty of Medical Technology, Fujita Health University School of Medical Sciences, Toyoake, Aichi, Japan
| | - Ken Sugata
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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Morozova OV, Sashina TA, Epifanova NV, Zverev VV, Kashnikov AU, Novikova NA. Phylogenetic comparison of the VP7, VP4, VP6, and NSP4 genes of rotaviruses isolated from children in Nizhny Novgorod, Russia, 2015-2016, with cogent genes of the Rotarix and RotaTeq vaccine strains. Virus Genes 2017; 54:225-235. [PMID: 29236215 DOI: 10.1007/s11262-017-1529-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 12/07/2017] [Indexed: 02/01/2023]
Abstract
Group A rotaviruses (RVA) are one of the leading causes of gastroenteritis in young children worldwide. The introduction of universal mass vaccination around the world has contributed to a reduction in hospitalizations and outpatient visits associated with rotavirus infection. Continued surveillance of RVA strains is needed to determine long-term effects of vaccine introduction. In the present work, we carried out the analysis of the genotypic diversity of RVA strains isolated in Nizhny Novgorod (Russia) during the 2015-2016 epidemic season. Also we conducted a comparative analysis of the amino acid sequences of T-cell epitopes of wild-type and vaccine (RotaTeq and Rotarix) strains. In total, 1461 samples were examined. RVAs were detected in 30.4% of cases. Rotaviruses with genotype G9P[8] (40.5%) dominated in the 2015-16 epidemic season. Additionally, RVAs with the following genotypes were detected: G4P[8] (25.4%), G1P[8] (13%), G2P[4] (3.2%). Rotaviruses with genotypes G3P[9], G6P[9], and G1P[9] totaled 3%. The number of partially typed and untyped RVA samples was 66 (14.9%). The findings of a RVA of G6P[9] genotype in Russia were an original observation. Our analysis of VP6 and NSP4 T-cell epitopes showed highly conserved amino acid sequences. The found differences seem not to be caused by the immune pressure but were rather related to the genotypic affiliations of the proteins. Vaccination against rotavirus infection is not included in the national vaccination schedule in Russia. Monitoring of the genotypic and antigenic diversity of contemporary RVA will allow providing a comparative analysis of wild-type strains in areas with and without vaccine campaign.
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Affiliation(s)
- O V Morozova
- I. N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation. .,Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russian Federation.
| | - T A Sashina
- I. N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N V Epifanova
- I. N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - V V Zverev
- I. N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - A U Kashnikov
- I. N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N A Novikova
- I. N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation.,Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russian Federation
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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.
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Sashina TA, Morozova OV, Epifanova NV, Novikova NA. Predominance of new G9P[8] rotaviruses closely related to Turkish strains in Nizhny Novgorod (Russia). Arch Virol 2017; 162:2387-2392. [PMID: 28429133 DOI: 10.1007/s00705-017-3364-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/01/2017] [Indexed: 11/27/2022]
Abstract
Genotype G9P[8] rotaviruses are rare in the territory of Russia. They were found in Nizhny Novgorod only in 2011-2012 for the first time, when their proportion was 25.9%. During the next two seasons, G9P[8] strains were detected in only 1.8% of cases. Their proportion substantially increased again in 2014, and they became predominant in the city by 2016. Phylogenetic analysis on the basis of gene VP7 nucleotide sequences showed that this increase was accompanied by the emergence of new strains in the population. These isolates were related to Turkish strains, but not to Russian ones detected earlier.
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Affiliation(s)
- T A Sashina
- I. N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation.
| | - O V Morozova
- I. N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
- Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russian Federation
| | - N V Epifanova
- I. N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N A Novikova
- I. N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
- Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russian Federation
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Naseer O, Jarvis MC, Ciarlet M, Marthaler DG. Genotypic and epitope characteristics of group A porcine rotavirus strains circulating in Canada. Virology 2017; 507:53-63. [PMID: 28399437 DOI: 10.1016/j.virol.2017.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 02/04/2023]
Abstract
Surveillance of Rotavirus A (RVA) infections in North America swine populations are limited and not performed over a significant time period to properly assess the diversity of RVA strains in swine. The VP7 (G) and VP4 (P) genes of 32 Canadian RVA strains, circulating between 2009 and 2015 were sequenced, identifying the G3P[13], G5P[7], G9P[7], G9[13], and G9[19] genotype combinations. The Canadian RVA strains were compared to the RVA strains present in the swine ProSystems RCE rotavirus vaccine. The comparison revealed multiple amino acid differences in the G and P antigenic epitopes, regardless of the G and P genotypes but specifically in the Canadian G3, P[13] and P[19] genotypes. Our study further contributes to the characterization of RVA's evolution and disease mitigation among swine, which may optimize target vaccine design, thereby minimizing RVA disease in this economically important animal population.
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Affiliation(s)
- Omer Naseer
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Matthew C Jarvis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Max Ciarlet
- Vaccines Clinical Research and Development, GlaxoSmithKline Vaccines, Cambridge, MA, United States
| | - Douglas G Marthaler
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States.
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