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Morozova OV, Sashina TA, Epifanova NV, Velikzhanina EI, Novikova NA. Phylodynamic characteristics of reassortant DS-1-like G3P[8]-strains of rotavirus type A isolated in Nizhny Novgorod (Russia). Braz J Microbiol 2023; 54:2867-2877. [PMID: 37897627 PMCID: PMC10689624 DOI: 10.1007/s42770-023-01155-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Since 2013, there has been an increase in reports of the spread of a double intergroup reassortant strain of rotavirus type A (RVA) with the genotype G3P[8] and other genes belonging to the second genogroup I2-R2-C2-M2-A2-N2-T2-E2-H2. In our study, we provide a molecular genetic characterization of rotaviruses with genotype G3P[8]-I2 isolated in Nizhny Novgorod. In our study, we used RT-PCR, Sanger sequencing, RNA-PAGE methods. Phylogenetic and phylodynamic analysis were performed using the Bayesian approach. According to our study, there was a significant increase in the proportion of G3P[8] from 15% during the period of 2020-2021 to 53% during the period of 2021-2022 in Nizhny Novgorod, Russia. Phylogenetic analysis based on the VP4 gene revealed that DS-1-like RVAs isolated in Nizhny Novgorod belong to different clusters of the P[8]-3.1 lineage, with a level of variation ranging from 1.1% to 1.3%. Based on the VP6 gene, the equine-like RVAs identified by us carry genetic variants belonging to three distinct clusters of the lineage I2-V, with a variation level ranging from 2.0% to 4.5%. These data indicate the genotypic diversity of circulating DS-1-like G3 RVAs. Phylogenetic analysis of the VP7 gene allowed us to assign the isolates identified in our study to the G3-1 lineage. We estimated that the circulation of the most recent common ancestor of the spreading strains dates back to 2002. Additionally, we determined the typical level of mutations in the VP7 gene, which amounted to 2.14*10-3 substitutions/per site/per year.
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Affiliation(s)
- Olga V Morozova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia.
| | - T A Sashina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N V Epifanova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - E I Velikzhanina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N A Novikova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
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Sashina TA, Velikzhanina EI, Morozova OV, Epifanova NV, Novikova NA. Detection and full-genotype determination of rare and reassortant rotavirus A strains in Nizhny Novgorod in the European part of Russia. Arch Virol 2023; 168:215. [PMID: 37524885 DOI: 10.1007/s00705-023-05838-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/13/2023] [Indexed: 08/02/2023]
Abstract
Reassortant DS-1-like rotavirus A strains have been shown to circulate widely in many countries around the world. In Russia, the prevalence of such strains remains unclear due to the preferred use of the traditional binary classification system. In this work, we obtained partial sequence data from all 11 genome segments and determined the full-genotype constellations of rare and reassortant rotaviruses circulating in Nizhny Novgorod in 2016-2019. DS-1-like G3P[8] and G8P[8] strains were found, reflecting the global trend. Most likely, these strains were introduced into the territory of Russia from other countries but subsequently underwent further evolutionary changes locally. G3P[8], G9P[8], and G12P[8] Wa-like strains of subgenotypic lineages that are unusual for the territory of Russia were also identified. Reassortant G2P[8], G4P[4], and G9P[4] strains with one Wa-like gene (VP4 or VP7) on a DS-1-like backbone were found, and these apparently had a local origin. Feline-like G3P[9] and G6P[9] strains were found to be phylogenetically close to BA222 isolated from a cat in Italy but carried some traces of reassortment with human strains from Russia and other countries. Thus, full-genotype determination of rotavirus A strains in Nizhny Novgorod has clarified some questions related to their origin and evolution.
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Affiliation(s)
- Tatiana A Sashina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation.
| | - E I Velikzhanina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - O V Morozova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N V Epifanova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N A Novikova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
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Masson L, Barbé L, Henaff F, Ahmed T, Le Moullac-Vaidye B, Peltier C, Marchand SS, Scherdel P, Vibet MA, Ruvoën-Clouet N, Elenga N, Imbert-Marcille BM, Gras-Le Guen C, Le Pendu J. Extent of the protection afforded by histo-blood group polymorphism against rotavirus gastroenteritis in metropolitan France and French Guiana. Front Microbiol 2023; 14:1141652. [PMID: 36970669 PMCID: PMC10036354 DOI: 10.3389/fmicb.2023.1141652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
Human rotaviruses attach to histo-blood group antigens glycans and null alleles of the ABO, FUT2 and FUT3 genes seem to confer diminished risk of gastroenteritis. Yet, the true extent of this protection remains poorly quantified. Here, we conducted a prospective study to evaluate the risk of consulting at the hospital in non-vaccinated pediatric patients according to the ABO, FUT2 (secretor) and FUT3 (Lewis) polymorphisms, in Metropolitan France and French Guiana. At both locations, P genotypes were largely dominated by P [8]-3, with P [6] cases exclusively found in French Guiana. The FUT2 null (nonsecretor) and FUT3 null (Lewis negative) phenotypes conferred near full protection against severe gastroenteritis due to P [8]-3 strains (OR 0.03, 95% CI [0.00–0.21] and 0.1, 95% CI [0.01–0.43], respectively in Metropolitan France; OR 0.08, 95% CI [0.01–0.52] and 0.14, 95%CI [0.01–0.99], respectively in French Guiana). Blood group O also appeared protective in Metropolitan France (OR 0.38, 95% CI [0.23–0.62]), but not in French Guiana. The discrepancy between the two locations was explained by a recruitment at the hospital of less severe cases in French Guiana than in Metropolitan France. Considering the frequencies of the null ABO, Secretor and Lewis phenotypes, the data indicate that in a Western European population, 34% (95% CI [29%; 39%]) of infants are genetically protected against rotavirus gastroenteritis of sufficient severity to lead to hospital visit.
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Affiliation(s)
- Lydie Masson
- Department of Pediatrics, University Hospital of Nantes, Nantes, France
| | - Laure Barbé
- Nantes Université, Inserm, CNRS, Immunology and New Concepts in Immunotherapy, INCIT, Nantes, France
| | - Fanny Henaff
- Department of Pediatrics, Centre Hospitalier Andrée Rosemon, Cayenne, France
| | - Tasnuva Ahmed
- Nantes Université, Inserm, CNRS, Immunology and New Concepts in Immunotherapy, INCIT, Nantes, France
- International Centre for Diarrheal Disease Research, Dhaka, Bangladesh
| | | | - Cécile Peltier
- Center for Research in Transplantation and Translational Immunology, Inserm, Nantes Université, Nantes, France
| | - Sarah S Marchand
- Virology Department, University Hospital of Nantes, Nantes, France
| | - Pauline Scherdel
- Clinical Investigation Center (CIC004), Inserm, University Hospital of Nantes, Nantes, France
| | - Marie-Anne Vibet
- Clinical Research Department, University Hospital of Nantes, Nantes, France
| | - Nathalie Ruvoën-Clouet
- Nantes Université, Inserm, CNRS, Immunology and New Concepts in Immunotherapy, INCIT, Nantes, France
- Ecole Nationale Vétérinaire, Agroalimentaire et de l'Alimentation, Oniris, Nantes, France
| | - Narcisse Elenga
- Department of Pediatrics, Centre Hospitalier Andrée Rosemon, Cayenne, France
| | - Berthe-Marie Imbert-Marcille
- Center for Research in Transplantation and Translational Immunology, Inserm, Nantes Université, Nantes, France
- Virology Department, University Hospital of Nantes, Nantes, France
| | | | - Jacques Le Pendu
- Nantes Université, Inserm, CNRS, Immunology and New Concepts in Immunotherapy, INCIT, Nantes, France
- *Correspondence: Jacques Le Pendu,
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Prevalence and Genetic Diversity of Group A Rotavirus Genotypes in Moscow (2019-2020). Pathogens 2021; 10:pathogens10060674. [PMID: 34070814 PMCID: PMC8228337 DOI: 10.3390/pathogens10060674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/20/2021] [Accepted: 05/28/2021] [Indexed: 11/23/2022] Open
Abstract
Group A rotavirus (RVA) infection is the leading cause of hospitalization of children under 5 years old, presenting with symptoms of acute gastroenteritis. The aim of our study was to explore the genetic diversity of RVA among patients admitted to Moscow Infectious Disease Clinical Hospital No. 1 with symptoms of acute gastroenteritis. A total of 653 samples were collected from May 2019 through March 2020. Out of them, 135 (20.67%) fecal samples were found to be positive for rotavirus antigen by ELISA. RT-PCR detected rotavirus RNA in 80 samples. Seven G-genotypes (G1, G2, G3, G4, G8, G9, and G12) and three P-genotypes (P[8], P[4], and P[6]) formed 9 different combinations. The most common combination was G9P[8]. However, for the first time in Moscow, the combination G3P[8] took second place. Moreover, all detected viruses of this combination belonged to Equine-like G3P[8] viruses that had never been detected in Russia before. The genotype G8P[8] and G9P[4] rotaviruses were also detected in Moscow for the first time. Among the studied rotaviruses, there were equal proportions of Wa and DS-1-like strains; previous studies showed that Wa-like strains accounted for the largest proportion of rotaviruses in Russia.
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Sashina TA, Morozova OV, Epifanova NV, Novikova NA. Genotype constellations of the rotavirus A strains circulating in Nizhny Novgorod, Russia, 2017-2018. INFECTION GENETICS AND EVOLUTION 2020; 85:104578. [PMID: 33010418 DOI: 10.1016/j.meegid.2020.104578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 11/27/2022]
Abstract
Currently, the full-genome-based classification is widely used to investigate rotavirus A (RVA) strains found in different countries around the world. However, the information on the full genotypes of rotaviruses circulating in Russia is limited. Using partial sequencing, this study determined the full genotype constellations of 15 RVA strains in total commonly detected in Nizhny Novgorod (European part of Russia) in 2017-2018, three from each of the following genotypes G1P[8], G4P[8], and G9P[8] and six from G2P[4]. There were two intergenogroup mono-reassortants possessing an identical genotype constellation of G4-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 with the DS-1-like NSP4 gene of probably local origin. A variety of subgenotype lineages and their combinations of Wa-like rotaviruses and genetic heterogeneity among G9P[8] and G1P[8] strains were shown on the basis of phylogenetic analysis of each gene. Moreover, two distinct co-circulating variants that differed in all 11 genome segments were found among DS-1-like rotaviruses.
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Affiliation(s)
- Tatiana A Sashina
- Laboratory of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation 603 950, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russia.
| | - Olga V Morozova
- Laboratory of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation 603 950, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russia
| | - Natalia V Epifanova
- Laboratory of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation 603 950, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russia
| | - Nadezhda A Novikova
- Laboratory of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation 603 950, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russia
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Pankov RC, Gondim RNDG, Prata MMG, Medeiros PHQS, Veras HN, Santos AKS, Havt A, da Silva MFM, Fumian TM, Miagostovich MP, Leite JPG, Lima AAM. Rotavirus A Infections in Community Childhood Diarrhea in the Brazilian Semiarid Region During Postvaccination Era. J Pediatr Gastroenterol Nutr 2019; 69:e91-e98. [PMID: 31568040 DOI: 10.1097/mpg.0000000000002416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
BACKGROUND Rotavirus A (RVA) is one of the leading causes of acute gastroenteritis worldwide; however, few studies assessed RVA genetics with community surveillance. OBJECTIVES This study aimed to investigate clinical data, genetic diversity, and coinfection patterns of RVA infections in children from 2 to 36 months old with or without community childhood diarrhea in the Brazilian semiarid region during postvaccination era. METHODS We enrolled and collected socioeconomic/clinical information using a standardized questionnaire and fecal samples from 291 children. Viral RNA samples were extracted and analyzed using quantitative reverse transcription polymerase chain reaction to establish the diagnosis of RVA. Sequencing of VP7 and VP4 (VP8*) regions and phylogenetic analysis were performed. RESULTS RVA-negative diagnosis was associated with children 24 to 36 months old with complete vaccination schedule. Genotype G1P[8] was the most prevalent (57%), whereas unusual genotypes including G1P[4], G2P[8], and G3P[9] were also detected. G1- and P[8]-positive samples showed high degrees of similarity with the vaccine strain. RVA coinfections were frequently observed, and enteroaggregative Escherichia coli was the most prevalent copathogen. CONCLUSIONS These results demonstrate that genotype G1P[8] is the most prevalent strain. VP7 and/or VP8* gene segments arising from RV1 vaccine strain were documented in these children, suggesting shedding or herd vaccination. Moreover, our study indicates full vaccination is important for protection against RVA infections.
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Affiliation(s)
- Rafaela C Pankov
- Institute of Biomedicine and Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE
| | - Rafhaella N D G Gondim
- Institute of Biomedicine and Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE
| | - Mara M G Prata
- Institute of Biomedicine and Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE
| | - Pedro H Q S Medeiros
- Institute of Biomedicine and Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE
| | - Herlice N Veras
- Institute of Biomedicine and Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE
| | - Ana K S Santos
- Institute of Biomedicine and Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE
| | - Alexandre Havt
- Institute of Biomedicine and Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE
| | | | | | | | | | - Aldo A M Lima
- Institute of Biomedicine and Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE
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Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens. PLoS Pathog 2019; 15:e1007865. [PMID: 31226167 PMCID: PMC6609034 DOI: 10.1371/journal.ppat.1007865] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 07/03/2019] [Accepted: 05/23/2019] [Indexed: 12/15/2022] Open
Abstract
Rotavirus is the leading agent causing acute gastroenteritis in young children, with the P[8] genotype accounting for more than 80% of infections in humans. The molecular bases for binding of the VP8* domain from P[8] VP4 spike protein to its cellular receptor, the secretory H type-1 antigen (Fuc-α1,2-Gal-β1,3-GlcNAc; H1), and to its precursor lacto-N-biose (Gal-β1,3-GlcNAc; LNB) have been determined. The resolution of P[8] VP8* crystal structures in complex with H1 antigen and LNB and site-directed mutagenesis experiments revealed that both glycans bind to the P[8] VP8* protein through a binding pocket shared with other members of the P[II] genogroup (i.e.: P[4], P[6] and P[19]). Our results show that the L-fucose moiety from H1 only displays indirect contacts with P[8] VP8*. However, the induced conformational changes in the LNB moiety increase the ligand affinity by two-fold, as measured by surface plasmon resonance (SPR), providing a molecular explanation for the different susceptibility to rotavirus infection between secretor and non-secretor individuals. The unexpected interaction of P[8] VP8* with LNB, a building block of type-1 human milk oligosaccharides, resulted in inhibition of rotavirus infection, highlighting the role and possible application of this disaccharide as an antiviral. While key amino acids in the H1/LNB binding pocket were highly conserved in members of the P[II] genogroup, differences were found in ligand affinities among distinct P[8] genetic lineages. The variation in affinities were explained by subtle structural differences induced by amino acid changes in the vicinity of the binding pocket, providing a fine-tuning mechanism for glycan binding in P[8] rotavirus. The interaction of viruses with host glycans has become an important topic in the study of enteric virus infectivity. This interaction modulates several aspects of the viral cycle, including viral attachment, which in most cases depends on the host glycobiology dictated by the secretor and Lewis genotypes. The capacity to synthesize secretory type-I antigen H (fucose-α1,2-galactose-β1,3-N-acetylglucosamine; H1) at the mucosae, dictated by the presence of one or two functional copies of the fucosyl-transferase FUT2 gene (secretor status), has been clearly linked to infectivity in important enteric viruses such as the noroviruses. However, a big controversy existed about the contribution of H1 antigen to infection in the leading cause of viral gastroenteritis in young children (rotavirus). It has not been until recently that epidemiological data evidenced a diminished incidence of rotavirus in non-secretor individuals unable to produce H1. In the present manuscript we offer the evidence that P[8] RV bind H1 via a binding site common for the P[II] RV genogroup and that the H1 precursor lacto-N-biose (galactose-β1,3-N-acetylglucosamine; LNB) is also bound to this pocket with diminished affinity. The P[8] VP8* structures show a marginal role for the L-fucose moiety from H1 in protein interaction. However, its presence provides conformational changes in the LNB moiety that increase the affinity of VP8* for the H1 ligand and would account for a stronger RV binding to mucosa in individuals expressing H1 (secretors). We thus offer a mechanistic explanation for the different incidence of P[8] RV infection in different secretor phenotypes.
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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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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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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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Wang Y, Zhang J, Liu P. Clinical and molecular epidemiologic trends reveal the important role of rotavirus in adult infectious gastroenteritis, in Shanghai, China. INFECTION GENETICS AND EVOLUTION 2017; 47:143-154. [DOI: 10.1016/j.meegid.2016.11.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 11/17/2016] [Accepted: 11/18/2016] [Indexed: 11/30/2022]
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da Silva MFM, Fumian TM, de Assis RMS, Fialho AM, Carvalho-Costa FA, da Silva Ribeiro de Andrade J, Leite JPG. VP7 and VP8* genetic characterization of group A rotavirus genotype G12P[8]: Emergence and spreading in the Eastern Brazilian coast in 2014. J Med Virol 2016; 89:64-70. [PMID: 27322509 DOI: 10.1002/jmv.24605] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2016] [Indexed: 11/07/2022]
Abstract
Group A rotavirus (RVA) genotype G12 is habitually associated with diarrhea disease (DD) in African children and recently its detection has increased worldwide. A total of 970 stool samples collected from individuals with DD in the Northeastern, Southeastern, and Southern Brazilian regions, Eastern coast, were analyzed and 321 (33%) were positive for RVA and of these, 241 (75%) genotyped as G12P[8]. The rate of RVA positivity was higher among children aged 5-10 years old (60%). All RVA infections observed in adults aged >21 years were G12P[8] (n = 27) showing that this genotype affected older age groups during the year of 2014 in Brazil. Phylogenetic analysis of VP7 and VP8* G12P[8] strains demonstrated an elevated similarity among Brazilian and G12-III prototypes strains circulating worldwide recently, suggesting that this lineage is associated with the global spread of the G12 genotype, considered as the 6th most prevalent human RVA genotype nowadays; while other G12 lineages remain sporadically detected and usually detected in association with other P genotypes. VP8* analysis revealed that Brazilian strains belong to P[8]-3 lineage, the single P[8] lineage presently detected in the country. No major nucleotide/amino acid disparities were observed among strains recovered from children and adults for VP7 and VP8* genes. These data are essential to support the surveillance studies, particularly in countries where the RVA vaccine was introduced in their National Immunization Program enabling identification of potential alterations in the epidemiological profile that can impact its efficacy in vaccination programs. J. Med. Virol. 89:64-70, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Marcelle Figueira Marques da Silva
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil.
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - Rosane Maria Santos de Assis
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - Alexandre Madi Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - Filipe Anibal Carvalho-Costa
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - Juliana da Silva Ribeiro de Andrade
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
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Dulgheroff ACB, Silva GAVD, Naveca FG, Oliveira AGD, Domingues ALDS. Diversity of group A rotavirus genes detected in the Triângulo Mineiro region, Minas Gerais, Brazil. Braz J Microbiol 2016; 47:731-40. [PMID: 27266629 PMCID: PMC4927641 DOI: 10.1016/j.bjm.2016.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 12/08/2015] [Indexed: 12/15/2022] Open
Abstract
Group A rotaviruses are the main causative agent of infantile gastroenteritis. The segmented nature of the viral genome allows reassortment of genome segments, which can generate genetic variants. In this study, we characterized the diversity of the VP7, VP4 (VP8*), VP6, NSP4, and NSP5 genes of the rotaviruses that circulated from 2005 to 2011 in the Triângulo Mineiro (TM) region of Brazil. Samples with genotypes G2 (sublineages IVa-1 and IVa-3), G1 (sublineage I-A), G9 (lineage III), G12 (lineages II and III), G8 (lineage II), G3 (lineage III), P[4] (sublineages IVa and IVb), P[8] (sublineages P[8]-3.6, P[8]-3.3, and P[8]-3.1), I2 (lineage VII), E2 (lineages VI, XII, and X), and H2 (lineage III) were identified. The associations found in the samples were G1, G9, or G12 with P[8]-I1-E1-H1; G2 or G8 with P[4]-I2-E2-H2; G12 with I3-E3-H6; and G3 with P[4]-I2-E3-H3 (previously unreported combination). Reassortment events in G2P[4] strains and an apparent pattern of temporal segregation within the lineages were observed. Five TM samples contained genes that exhibited high nucleotide and amino acid identities with strains of animal origin. The present study includes a period of pre- and post-introduction of rotavirus vaccination in all Brazilian territories, thereby serving as a basis for monitoring changes in the genetic constitution of rotaviruses. The results also contribute to the understanding of the diversity and evolution of rotaviruses in a global context.
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Affiliation(s)
- Ana Carolina Bernardes Dulgheroff
- Laboratory of Microbiology, Institute of Biological and Natural Science, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil; Health Technical School, Health Science Center, Federal University of Paraíba, João Pessoa, Paraíba, Brazil.
| | - George Allan Villarouco da Silva
- Laboratory of Infectious Disease Ecology in the Amazon, Leonidas e Maria Deane Institute, Oswaldo Cruz Foundation, Manaus, Amazonas, Brazil
| | - Felipe Gomes Naveca
- Laboratory of Infectious Disease Ecology in the Amazon, Leonidas e Maria Deane Institute, Oswaldo Cruz Foundation, Manaus, Amazonas, Brazil
| | - Adriana Gonçalves de Oliveira
- Laboratory of Microbiology, Institute of Biological and Natural Science, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - André Luiz da Silva Domingues
- Laboratory of Microbiology, Institute of Biological and Natural Science, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
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Bucardo F, Nordgren J. Impact of vaccination on the molecular epidemiology and evolution of group A rotaviruses in Latin America and factors affecting vaccine efficacy. INFECTION GENETICS AND EVOLUTION 2015; 34:106-13. [PMID: 26079278 DOI: 10.1016/j.meegid.2015.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/10/2015] [Accepted: 06/11/2015] [Indexed: 12/15/2022]
Abstract
Despite high rotavirus (RV) vaccine coverage (∼83%) and good effectiveness (∼77%) against RV-diarrhea hospitalization, RV is still contributing to the burden of diarrhea that persists in hospital settings in several Latin American countries, where RV vaccination is being implemented. Due to the extensive genomic and antigenic diversity, among co-circulating human RV, a major concern has been that the introduction of RV vaccination could exert selection pressure leading to higher prevalence of strains not included in the vaccines and/or emergence of new strains, thus, reducing the efficacy of vaccination. Here we review the molecular epidemiology of RV in Latin America and explore issues of RV evolution and selection in light of vaccination. We further explore etiologies behind the large burden of diarrhea remaining after vaccination in some countries and discuss plausible reasons for vaccine failures.
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Affiliation(s)
- Filemón Bucardo
- Department of Microbiology, National Autonomous University of León, Nicaragua (UNAN-León), Nicaragua.
| | - Johan Nordgren
- Division of Molecular Virology, Clinical and Experimental Medicine, Medical Faculty University of Linköping, 581 85 Linköping, Sweden
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Luchs A, Cilli A, Morillo SG, Ribeiro CD, Carmona RDCC, Timenetsky MDCST. Rotavirus genotypes and the indigenous children of Brazilian midwest in the vaccine era, 2008-2012: Footprints of animal genome. J Med Virol 2015; 87:1881-9. [PMID: 25963945 DOI: 10.1002/jmv.24241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2015] [Indexed: 01/28/2023]
Abstract
World group A rotavirus (RVA) surveillance data provides useful estimates of the disease burden, however, indigenous population might require special consideration. The aim of this study was to describe the results of G- and P-types from Brazilian native children ≤ 3 years. Furthermore, selected strains have been analyzed for the VP7, VP6, VP4, and NSP4 encoding genes in order to gain insight into genetic variability of Brazilian strains. A total of 149 samples, collected during 2008-2012, were tested for RVA using ELISA and PAGE, following by RT-PCR and sequencing. RVA infection was detected in 8.7% of samples (13/149). Genotype G2P[4] was detected in 2008 and 2010, G8P[6] in 2009, and G3P[8] in 2011. The phylogenetic analysis of the VP7 and VP4 genes grouped the Brazilian G2P[4] and G3P[8] strains within the lineages currently circulating in humans worldwide. However, the phylogenetic analysis of the VP6 and NSP4 from the Brazilian G2P[4] strains, and the VP7 and NSP4 from the Brazilian G3P[8] strains suggest a distant common ancestor with different animal strains (bovine, caprine, and porcine). The epidemiological and genetic information obtained in the present study is expected to provide an updated understanding of RVA genotypes circulating in the native infant population, and to formulate policies for the use of RVA vaccines in indigenous Brazilian people. Moreover, these results highlight the great diversity of human RVA strains circulating in Brazil, and an in-depth surveillance of human and animal RVA will lead to a better understanding of the complex dynamics of RVA evolution.
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Affiliation(s)
- Adriana Luchs
- Enteric Disease Laboratory, Adolfo Lutz Institute, São Paulo, Brazil
| | - Audrey Cilli
- Enteric Disease Laboratory, Adolfo Lutz Institute, São Paulo, Brazil
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Tort LFL, Victoria M, Lizasoain A A, Castells M, Maya L, Gómez MM, Arreseigor E, López P, Cristina J, Leite JPG, Colina R. Molecular epidemiology of group a rotavirus among children admitted to hospital in Salto, Uruguay, 2011-2012: First detection of the emerging genotype G12. J Med Virol 2015; 87:754-63. [DOI: 10.1002/jmv.24123] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2014] [Indexed: 12/13/2022]
Affiliation(s)
| | - Matías Victoria
- Molecular Virology Laboratory, North Regional; University of Republic; Salto Uruguay
| | - Andrés Lizasoain A
- Molecular Virology Laboratory, North Regional; University of Republic; Salto Uruguay
| | - Matías Castells
- Molecular Virology Laboratory, North Regional; University of Republic; Salto Uruguay
| | - Leticia Maya
- Molecular Virology Laboratory, North Regional; University of Republic; Salto Uruguay
| | - Mariela Martínez Gómez
- Laboratory of Comparative and Environmental Virology; Oswaldo Cruz Institute; Rio de Janeiro Brazil
| | | | - Patricia López
- Pediatric Unit of Regional Public Hospital; Salto Uruguay
| | - Juan Cristina
- Molecular Virology Laboratory, Faculty of Sciences; University of Republic; Montevideo Uruguay
| | | | - Rodney Colina
- Molecular Virology Laboratory, North Regional; University of Republic; Salto Uruguay
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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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Imbert-Marcille BM, Barbé L, Dupé M, Le Moullac-Vaidye B, Besse B, Peltier C, Ruvoën-Clouet N, Le Pendu J. A FUT2 gene common polymorphism determines resistance to rotavirus A of the P[8] genotype. J Infect Dis 2014; 209:1227-30. [PMID: 24277741 DOI: 10.1093/infdis/jit655] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Attachment to carbohydrates of the histo-blood group type of several human Rotavirus strains (RVA) has recently been described. Synthesis of these ligands requires a functional FUT2 enzyme, suggesting that FUT2 null homozygote (ie, nonsecretor) individuals may not be recognized by most human RVA strains. Whereas such individuals represent 20% of the control population, this retrospective study determined that none of 51 patients infected by P[8] rotavirus strains were nonsecretors. The lack of α1,2fucosylated carbohydrate motifs in the gut surface mucosa is thus associated with resistance to symptomatic infection and virus attachment to such motifs is essential to the infection process.
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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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