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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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2
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Makori TO, Bargul JL, Lambisia AW, Mwanga MJ, Murunga N, de Laurent ZR, Lewa CS, Mutunga M, Kellam P, Cotten M, Nokes DJ, Phan M, Agoti CN. Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012-8. Virus Evol 2023; 9:vead025. [PMID: 37207000 PMCID: PMC10190042 DOI: 10.1093/ve/vead025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/07/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
The introduction of rotavirus vaccines into the national immunization programme in many countries has led to a decline in childhood diarrhoea disease burden. Coincidentally, the incidence of some rotavirus group A (RVA) genotypes has increased, which may result from non-vaccine-type replacement. Here, we investigate the evolutionary genomics of rotavirus G2P[4] which has shown an increase in countries that introduced the monovalent Rotarix® vaccine. We examined sixty-three RVA G2P[4] strains sampled from children (aged below 13 years) admitted to Kilifi County Hospital, coastal Kenya, pre- (2012 to June 2014) and post-(July 2014 to 2018) rotavirus vaccine introduction. All the sixty-three genome sequences showed a typical DS-1-like genome constellation (G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2). Pre-vaccine G2 sequences predominantly classified as sub-lineage IVa-3 and co-circulated with low numbers of sub-lineage IVa-1 strains, whereas post-vaccine G2 sequences mainly classified into sub-lineage IVa-3. In addition, in the pre-vaccine period, P[4] sub-lineage IVa strains co-circulated with low numbers of P[4] lineage II strains, but P[4] sub-lineage IVa strains predominated in the post-vaccine period. On the global phylogeny, the Kenyan pre- and post-vaccine G2P[4] strains clustered separately, suggesting that different virus populations circulated in the two periods. However, the strains from both periods exhibited conserved amino acid changes in the known antigenic epitopes, suggesting that replacement of the predominant G2P[4] cluster was unlikely a result of immune escape. Our findings demonstrate that the pre- and post-vaccine G2P[4] strains circulating in Kilifi, coastal Kenya, differed genetically but likely were antigenically similar. This information informs the discussion on the consequences of rotavirus vaccination on rotavirus diversity.
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Affiliation(s)
- Timothy O Makori
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Kalimoni, PO Box 62000-00200, Juja, Kenya
| | - Joel L Bargul
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Kalimoni, PO Box 62000-00200, Juja, Kenya
- International Centre of Insect Physiology and Ecology, Animal Health Theme, ICIPE Road Kasarani, P.O BOX 30772-00100, Nairobi, Kenya
| | - Arnold W Lambisia
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Mike J Mwanga
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Clement S Lewa
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Martin Mutunga
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Paul Kellam
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, Exhibition Road, London SW7 2AZ, UK
- Kymab Ltd, The Bennet Building (B930), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Matthew Cotten
- Medical Research Centre (MRC)/Uganda Virus Research Institute, Plot No: 51-59 Nakiwogo Road, P.O.Box 49, Entebbe, Uganda
- MRC-University of Glasgow, Centre for Virus Research Glasgow, 464 Bearsden Road, Glasgow G61 1QH UK
| | - D James Nokes
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute (SBIDER), The University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - My Phan
- Medical Research Centre (MRC)/Uganda Virus Research Institute, Plot No: 51-59 Nakiwogo Road, P.O.Box 49, Entebbe, Uganda
- MRC-University of Glasgow, Centre for Virus Research Glasgow, 464 Bearsden Road, Glasgow G61 1QH UK
| | - Charles N Agoti
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi-Malindi Road, P.O BOX 195-80108, Kilifi, Kenya
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3
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Mwangi PN, Potgieter RL, Simwaka J, Mpabalwani EM, Mwenda JM, Mogotsi MT, Magagula N, Esona MD, Steele AD, Seheri ML, Nyaga MM. Genomic Analysis of G2P[4] Group A Rotaviruses in Zambia Reveals Positive Selection in Amino Acid Site 7 of Viral Protein 3. Viruses 2023; 15:501. [PMID: 36851715 PMCID: PMC9965253 DOI: 10.3390/v15020501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
The G2P[4] genotype is among the rotavirus strains that circulate commonly in humans. Several countries have reported its immediate upsurge after the introduction of rotavirus vaccination, raising concern about sub-optimal vaccine effectiveness against this genotype in the long term. This study aimed to gain insight into the evolution of post-vaccine Zambian G2P[4] group A rotavirus (RVA) strains and their overall genetic make-up by analysis of sequence alignments at the amino acid (AA) level. Twenty-nine Zambian G2P[4] rotavirus strains were subjected to whole-genome sequencing using the Illumina MiSeq® platform. All the strains exhibited the typical DS-1-like genotype constellation, and the nucleotide sequences of the 11 genome segments showed high nucleotide similarities (>97%). Phylogenetic analyses together with representative global G2P[4] RVA showed that Zambian strains clustered into human lineages IV (for VP2, VP4, VP7, NSP1, and NSP5), V (for VP1, VP3, VP6, NSP2, and NSP3), and XXIII (for NSP4). The AA differences between the lineages where the study strains clustered and lineages of global reference strains were identified and analyzed. Selection pressure analysis revealed that AA site seven in the Viral Protein 3 (VP3) genome segment was under positive selection. This site occurs in the region of intrinsic disorder in the VP3 protein, and Zambian G2P[4] strains could potentially be utilizing this intrinsically disordered region to survive immune pressure. The Zambian G2P[4] strains from 2012 to 2016 comprised the G2P[4] strains that have been circulating globally since the early 2000s, highlighting the epidemiological fitness of these contemporary G2P[4] strains. Continuous whole-genome surveillance of G2P[4] strains remains imperative to understand their evolution during the post-vaccination period.
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Affiliation(s)
- Peter N. Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Robyn-Lee Potgieter
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Julia Simwaka
- Institute of Basic and Biomedical Sciences, Department of Biomedical Sciences, The Levy Mwanawasa Medical University, Lusaka 10101, Zambia
| | - Evans M. Mpabalwani
- Department of Paediatrics and Child Health, School of Medicine, University of Zambia, Ridgeway, Lusaka RW50000, Zambia
| | - Jason M. Mwenda
- World Health Organization, Regional Office for Africa, Brazzaville P.O. Box 06, Congo
| | - Milton T. Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Nonkululeko Magagula
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - Mathew D. Esona
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - A. Duncan Steele
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - Mapaseka L. Seheri
- Diarrheal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
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4
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Mwangi PN, Page NA, Seheri ML, Mphahlele MJ, Nadan S, Esona MD, Kumwenda B, Kamng'ona AW, Donato CM, Steele DA, Ndze VN, Dennis FE, Jere KC, Nyaga MM. Evolutionary changes between pre- and post-vaccine South African group A G2P[4] rotavirus strains, 2003-2017. Microb Genom 2022; 8. [PMID: 35446251 PMCID: PMC9453071 DOI: 10.1099/mgen.0.000809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transient upsurge of G2P[4] group A rotavirus (RVA) after Rotarix vaccine introduction in several countries has been a matter of concern. To gain insight into the diversity and evolution of G2P[4] strains in South Africa pre- and post-RVA vaccination introduction, whole-genome sequencing was performed for RVA positive faecal specimens collected between 2003 and 2017 and samples previously sequenced were obtained from GenBank (n=103; 56 pre- and 47 post-vaccine). Pre-vaccine G2 sequences predominantly clustered within sub-lineage IVa-1. In contrast, post-vaccine G2 sequences clustered mainly within sub-lineage IVa-3, whereby a radical amino acid (AA) substitution, S15F, was observed between the two sub-lineages. Pre-vaccine P[4] sequences predominantly segregated within sub-lineage IVa while post-vaccine sequences clustered mostly within sub-lineage IVb, with a radical AA substitution R162G. Both S15F and R162G occurred outside recognised antigenic sites. The AA residue at position 15 is found within the signal sequence domain of Viral Protein 7 (VP7) involved in translocation of VP7 into endoplasmic reticulum during infection process. The 162 AA residue lies within the hemagglutination domain of Viral Protein 4 (VP4) engaged in interaction with sialic acid-containing structure during attachment to the target cell. Free energy change analysis on VP7 indicated accumulation of stable point mutations in both antigenic and non-antigenic regions. The segregation of South African G2P[4] strains into pre- and post-vaccination sub-lineages is likely due to erstwhile hypothesized stepwise lineage/sub-lineage evolution of G2P[4] strains rather than RVA vaccine introduction. Our findings reinforce the need for continuous whole-genome RVA surveillance and investigation of contribution of AA substitutions in understanding the dynamic G2P[4] epidemiology.
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Affiliation(s)
- Peter N Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Nicola A Page
- Centre for Enteric Disease, National Institute for Communicable Diseases, Private Bag X4, Sandringham, 2131, Johannesburg, South Africa.,Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007, Pretoria, South Africa
| | - Mapaseka L Seheri
- Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, Pretoria, South Africa
| | - M Jeffrey Mphahlele
- Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, Pretoria, South Africa.,Office of the Deputy Vice Chancellor for Research and Innovation, North-West University, Potchefstroom 2351, South Africa.,South African Medical Research Council, Pretoria 0001, South Africa
| | - Sandrama Nadan
- Centre for Enteric Disease, National Institute for Communicable Diseases, Private Bag X4, Sandringham, 2131, Johannesburg, South Africa
| | - Mathew D Esona
- Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, Pretoria, South Africa
| | - Benjamin Kumwenda
- Department of Biomedical Sciences, School of Life Sciences and Applied Health Professions, Kamuzu University of Health Sciences, Private Bag 360, Chichiri, Blantyre 3, Malawi
| | - Arox W Kamng'ona
- Department of Biomedical Sciences, School of Life Sciences and Applied Health Professions, Kamuzu University of Health Sciences, Private Bag 360, Chichiri, Blantyre 3, Malawi
| | - Celeste M Donato
- Department of Medical Laboratory Sciences, School of Life Sciences and Applied Health Professions, Kamuzu University of Health Sciences, Private Bag 360, Chichiri, Blantyre3, Malawi.,Enteric Diseases Group, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Melboune 3052, Australia.,Department of Paediatrics, the University of Melbourne, Parkville 3010, Australia
| | - Duncan A Steele
- Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, Pretoria, South Africa
| | - Valantine N Ndze
- Faculty of Health Sciences, University of Buea, P.O Box 63 Buea, Cameroon
| | - Francis E Dennis
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, P.O Box LG581, Legon, Ghana
| | - Khuzwayo C Jere
- Center for Global Vaccine Research, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L697BE, Liverpool, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre 312225, Malawi
| | - Martin M Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
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5
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Maringa WM, Simwaka J, Mwangi PN, Mpabalwani EM, Mwenda JM, Mphahlele MJ, Seheri ML, Nyaga MM. Whole Genome Analysis of Human Rotaviruses Reveals Single Gene Reassortant Rotavirus Strains in Zambia. Viruses 2021; 13:1872. [PMID: 34578453 PMCID: PMC8472975 DOI: 10.3390/v13091872] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 12/28/2022] Open
Abstract
Rotarix® vaccine was implemented nationwide in Zambia in 2013. In this study, four unusual strains collected in the post-vaccine period were subjected to whole genome sequencing and analysis. The four strains possessed atypical genotype constellations, with at least one reassortant genome segment within the constellation. One of the strains (UFS-NGS-MRC-DPRU4749) was genetically and phylogenetically distinct in the VP4 and VP1 gene segments. Pairwise analyses demonstrated several amino acid disparities in the VP4 antigenic sites of this strain compared to that of Rotarix®. Although the impact of these amino acid disparities remains to be determined, this study adds to our understanding of the whole genomes of reassortant strains circulating in Zambia following Rotarix® vaccine introduction.
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Affiliation(s)
- Wairimu M. Maringa
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (W.M.M.); (P.N.M.)
| | - Julia Simwaka
- Virology Laboratory, Department of Pathology and Microbiology, University Teaching Hospital, Adult and Emergency Hospital, Lusaka 10101, Zambia;
| | - Peter N. Mwangi
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (W.M.M.); (P.N.M.)
| | - Evans M. Mpabalwani
- Department of Paediatrics and Child Health, School of Medicine, University of Zambia, Ridgeway, Lusaka RW50000, Zambia;
| | - Jason M. Mwenda
- World Health Organization, Regional Office for Africa, Brazzaville P.O. Box 06, Congo;
| | - M. Jeffrey Mphahlele
- Office of the Deputy Vice Chancellor for Research and Innovation, The North-West University, Potchefstroom 2351, South Africa;
| | - Mapaseka L. Seheri
- Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa;
| | - Martin M. Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (W.M.M.); (P.N.M.)
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6
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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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Silva-Sales M, Leal E, Milagres FADP, Brustulin R, Morais VDS, Marcatti R, Araújo ELL, Witkin SS, Deng X, Sabino EC, Delwart E, Luchs A, Costa ACD. Genomic constellation of human Rotavirus A strains identified in Northern Brazil: a 6-year follow-up (2010-2016). Rev Inst Med Trop Sao Paulo 2020; 62:e98. [PMID: 33331517 PMCID: PMC7748031 DOI: 10.1590/s1678-9946202062098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/27/2020] [Indexed: 02/21/2023] Open
Abstract
Surveillance of Rotavirus A (RVA) throughout the national territory is important
to establish a more complete epidemiological-molecular scenario of this virus
circulation in Brazil. The aim of the present study was to investigate the
genetic diversity of RVA strains circulating in Tocantins State (Northern
Brazil) during six years of post-vaccination follow-up (2010-2016). A total of
248 stool samples were screened by next generation sequencing and 107 (43.1%)
nearly full length RVA genome sequences were obtained; one sample was
co-infected with two RVA strains (G2/G8P[4]). Six G and P genotypes combinations
were detected: G12P[8] strains (78.6%), as well as the G3P[8] (9.3%) and G1P[8]
(0.9%) were associated with a Wa-like genogroup backbone. All G2P[4] (5.6%) and
G8P[4] (2.8%) strains, including the mixed G2/G8P[4] infection (0.9%) showed the
DS-1-like genetic background. The two G12P[4] strains (1.9%) were associated
with distinct genetic backbones: Wa-like and DS-1-like. The phylogenetic
analysis revealed the circulation of lineages G1-I, G2-IV, G3-III, G8-I and
G12-III, and P[4]-V and P[8]-III of the VP7 and VP4 genes, respectively.
Conserved clustering pattern and low genetic diversity were observed regarding
VP1-VP3 and VP6, as well as NSP1-5 segments. We identified the same RVA
circulation pattern reported in other Brazilian regions in the period of
2010-2016, suggesting that rural and low-income areas may not have a different
RVA genotypic distribution compared to other parts of the country. The unique
presentation of whole-genome data of RVA strains detected in the Tocantins State
provides a baseline for monitoring variations in the genetic composition of RVA
in this area.
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Affiliation(s)
- Marcelle Silva-Sales
- Universidade Federal de Goiás, Instituto de Patologia Tropical e Saúde Pública, Laboratório de Virologia e Cultivo Celular, Goiânia, Goiás, Brazil
| | - Elcio Leal
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, Pará, Brazil
| | - Flavio Augusto de Pádua Milagres
- Universidade Federal do Tocantins, Palmas, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Estado de Tocantins, Palmas, Tocantins, Brazil
| | - Rafael Brustulin
- Universidade Federal do Tocantins, Palmas, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Estado de Tocantins, Palmas, Tocantins, Brazil
| | - Vanessa Dos Santos Morais
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Roberta Marcatti
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Emerson Luiz Lima Araújo
- Ministério da Saúde, Secretaria de Vigilância em Saúde, Departamento de Articulação Estratégica de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Brasília, Distrito Federal, Brazil
| | - Steven S Witkin
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil.,Weill Cornell Medicine, Department of Obstetrics and Gynecology, New York, New York, USA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, California, USA.,University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, USA
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, USA.,University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, USA
| | - Adriana Luchs
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
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8
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Morozova OV, Sashina TA, Epifanova NV, Kashnikov AY, Novikova NA. Increasing detection of rotavirus G2P[4] strains in Nizhny Novgorod, Russia, between 2016 and 2019. Arch Virol 2020; 166:115-124. [PMID: 33079276 DOI: 10.1007/s00705-020-04853-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/10/2020] [Indexed: 01/28/2023]
Abstract
Rotavirus infection is one of the leading causes of acute gastroenteritis in children in their first years of life. We studied the genotypic diversity of rotavirus A (RVA) strains in Nizhny Novgorod, Russia, during the period 2016-19. In total, 4714 samples of faeces from children admitted to the Nizhny Novgorod Hospital for Infectious Diseases with acute gastroenteritis were examined. The share of rotavirus-positive samples was 31.5% in 2016-17. It decreased to 21.6% in 2018-19. In Nizhny Novgorod, all six global types of RVA were detected (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]), as well as sporadic samples with genotypes G9P[4], G3P[9], G9P[9], G8P[8], G2P[8], G4P[4], G3P[9]. The fraction of strains with genotype G2P[4] gradually increased from 5.9% in 2016-17 to 39.1% in 2018-19. Simultaneously, the proportion of G9P[8] strains decreased from 63.2% to 27.7% in the same period. Phylogenetic analysis showed that rotaviruses with the G2P[4] genotype carried ubiquitous alleles of the VP7 and VP4 genes during the period of their prevalence: G2-IVa-1 and G2-IVa-3; P[4]-IVa and P[4]-IVb. As rotavirus vaccination is not widely used in the region because it is not included in the national vaccination calendar in Russia so far, the increase in the number of G2P[4] RVA is likely due to natural strain fluctuations.
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Affiliation(s)
- Olga V Morozova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russian Federation, 603950.
| | - Tatiana A Sashina
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russian Federation, 603950
| | - Natalia V Epifanova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russian Federation, 603950
| | - Alexander Yu Kashnikov
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russian Federation, 603950
| | - Nadezhda A Novikova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russian Federation, 603950
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9
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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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10
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Phylodynamics of G4P[8] and G2P[4] strains of rotavirus A isolated in Russia in 2017 based on full-genome analyses. Virus Genes 2020; 56:537-545. [PMID: 32472472 DOI: 10.1007/s11262-020-01771-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/22/2020] [Indexed: 01/08/2023]
Abstract
Rotavirus A is a dynamically evolving pathogen causing acute gastroenteritis in children during the first years of life. In the present study, we conducted a phylodynamic analysis based on the complete sequences of 11 segments of rotaviruses with the G4P[8] and G2P[4] genotypes isolated in Russia in 2017. Since rotavirus has a segmented genome, our analysis was performed using the Bayesian approach based on separate samples of nucleotide sequences for each gene of the strains studied. For the strain with the genotype G4P[8], the most likely geographical locations of the nearest common ancestor were Russia (VP7, VP4, VP6), China (VP1), Thailand (VP3), Belgium (NSP1), Hungary (VP2, NSP2, NSP3), Italy (NSP4) and Japan (NSP5). For the strain with the G2P[4] genotype, India (VP7, VP4, VP6, NSP1, NSP4), Malawi (VP2, NSP2, NSP3), Australia (VP1), Italy (NSP5) and Bangladesh (VP3). The closest common ancestor of the strain with the genotype G4P[8] circulated in 2001-2012, depending on the gene being analyzed. For the strain with the G2P[4] genotype, the closest common ancestor dates from 2006 to 2013.
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11
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Distribution of rotavirus genotypes in Japan from 2015 to 2018: Diversity in genotypes before and after introduction of rotavirus vaccines. Vaccine 2020; 38:3980-3986. [PMID: 32307276 DOI: 10.1016/j.vaccine.2020.03.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/18/2020] [Accepted: 03/05/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Diversity in group A rotavirus (RVA) strains after introduction of RV-vaccines remains an emerging concern worldwide. In this study, we investigated the prevalence and distribution of RVA genotypes in Japanese children with acute gastroenteritis (AGE) from 2015 to 2018. In addition, a comparison of the genotypes in pre-vaccination (2006-2012) and post-vaccination (2012-2018) periods was conducted to understand the impact of these vaccines on genotype distribution. METHODS Fecal samples were collected regularly from outpatient clinics in six localities: Hokkaido, Tokyo, Shizuoka, Osaka, Kyoto, and Saga. RVA were screened and genotyped by RT-PCR and sequence-based genotyping. RESULTS During the period 2015-2018, RVA was detected in 307 (19.7%) samples out of 1557 specimens: 29.9% (95% CI: 25.8% to 34.3%), 17.9% (95% CI: 14.7% to 21.5%), and 13% (95% CI: 10.3% to 16.0%) were detected RVA-positive in 2015-2016, 2016-2017 and 2017-2018, respectively. The average detection of RVA in pre-vaccination (2006-2012) and post-vaccination (2012-2018) era remained almost similar (18%-20%). The G2P[4]I2 (52.1%, 95% CI: 43.5%-60.6%) remained the most common genotype in 2015-2016, whereas G8P[8]I2 (55.9%, 95% CI: 45.2%-66.2%) dominated in 2016-2017. In 2017-2018, G9P[8]I2 (42.0%, 95% CI: 30.5%-53.9%) prevailed, followed by G9P[8]I1 (23.0%, 95% CI: 14.0%-34.2%). The detection rate of some common genotypes of pre-vaccination era like G1P[8] and G3P[8] has been reduced after introduction of RV-vaccine, whereas genotypes that were sporadic before the introduction of vaccines like G2P[4], G2P[8], G9P[8] and G8P[8] were emerged/reemerged in post-vaccination period. CONCLUSIONS Our study presented the diversity in circulating RVA genotypes in Japan before and after introduction of RV-vaccines. Sudden emergence of DS-1-like (I2) unusual strains in post-vaccination era remains alarming. Continuous monitoring of RVA genotypes is therefore indispensable to refine future vaccine strategy.
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12
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Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains. PLoS One 2019; 14:e0217422. [PMID: 31150425 PMCID: PMC6544246 DOI: 10.1371/journal.pone.0217422] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022] Open
Abstract
Recent increase in the detection of unusual G1P[8], G3P[8], G8P[8], and G9P[4] Rotavirus A (RVA) strains bearing the DS-1-like constellation of the non-G, non-P genes (hereafter referred to as the genotype 2 backbone) requires better understanding of their evolutionary relationship. However, within a genotype, there is lack of a consensus lineage designation framework and a set of common sequences that can serve as references. Phylogenetic analyses were carried out on over 8,500 RVA genotype 2 genes systematically retrieved from the rotavirus database within the NCBI Virus Variation Resource. In line with previous designations, using pairwise comparison of cogent nucleotide sequences and stringent bootstrap support, reference lineages were defined. This study proposes a lineage framework and provides a dataset ranging from 34 to 145 sequences for each genotype 2 gene for orderly lineage designation of global genotype 2 genes of RVAs detected in human and animals. The framework identified five to 31 lineages depending on the gene. The least number of lineages (five to seven) were observed in genotypes A2 (NSP1), T2 (NSP3) and H2 (NSP5) which are limited to human RVA whereas the most number of lineages (31) was observed in genotype E2 (NSP4). Sharing of the same lineage constellations of the genotype 2 backbone genes between recently-emerging, unusual G1P[8], G3P[8], G8P[8] and G9P[4] reassortants and many contemporary G2P[4] strains provided strong support to the hypothesis that unusual genotype 2 strains originated primarily from reassortment events in the recent past involving contemporary G2P[4] strains as one parent and ordinary genotype 1 strains or animal RVA strains as the other. The lineage framework with selected reference sequences will help researchers to identify the lineage to which a given genotype 2 strain belongs, and trace the evolutionary history of common and unusual genotype 2 strains in circulation.
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13
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Strydom A, João ED, Motanyane L, Nyaga MM, Christiaan Potgieter A, Cuamba A, Mandomando I, Cassocera M, de Deus N, O'Neill HG. Whole genome analyses of DS-1-like Rotavirus A strains detected in children with acute diarrhoea in southern Mozambique suggest several reassortment events. INFECTION GENETICS AND EVOLUTION 2019; 69:68-75. [PMID: 30641151 DOI: 10.1016/j.meegid.2019.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 01/10/2019] [Accepted: 01/10/2019] [Indexed: 11/20/2022]
Abstract
We report the first whole genome constellations of Mozambican rotavirus A strains detected between 2012 and 2013 in the Mavalane General Hospital in Maputo city and Manhiça District Hospital in the Manhiça district. Consensus sequences for ten DS-1-like strains (G2P[4] and G8P[4]) were identified with an Illumina Miseq platform using cDNA prepared from dsRNA extracted from stool samples, without genome amplification or prior adaptation to cell culture. Comparison of previously reported genotyping results and the consensus sequences described in this study, indicated that the genotype primers specific for G12 and P[4] might require revision. Phylogenetic analyses indicated diversity among the G2P[4] Mozambican strains and suggested reassortment between G2P[4] and G8P[4] Mozambican strains, as well as the intragenogroup reassortment of all the genome segments encoding VP1, 2, 3 and 6 for strain RVA/Human-wt/MOZ/0045/2012G8P[4]. These results highlight the necessity to determine whole genome constellations to confirm surveillance data in Africa and to monitor the growing diversity in DS-1-like strains.
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Affiliation(s)
- Amy Strydom
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Eva Dora João
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique; Institute of Hygiene and Tropical Medicine, Lisbon, Portugal
| | - Lithabiso Motanyane
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Martin M Nyaga
- Next Generation Sequencing Unit, Department of Medical Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - A Christiaan Potgieter
- Biochemistry, Focus Area Human Metabolomics, North-West University, Potchefstroom, South Africa; Deltamune (Pty.) Ltd., Lyttelton, Centurion, South Africa
| | - Assa Cuamba
- Faculdade de Medicina, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Inacio Mandomando
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique; Institute of Hygiene and Tropical Medicine, Lisbon, Portugal
| | - Marta Cassocera
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | | | - Hester G O'Neill
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa.
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14
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Hu L, Sankaran B, Laucirica DR, Patil K, Salmen W, Ferreon ACM, Tsoi PS, Lasanajak Y, Smith DF, Ramani S, Atmar RL, Estes MK, Ferreon JC, Prasad BVV. Glycan recognition in globally dominant human rotaviruses. Nat Commun 2018; 9:2631. [PMID: 29980685 PMCID: PMC6035239 DOI: 10.1038/s41467-018-05098-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/11/2018] [Indexed: 01/01/2023] Open
Abstract
Rotaviruses (RVs) cause life-threatening diarrhea in infants and children worldwide. Recent biochemical and epidemiological studies underscore the importance of histo-blood group antigens (HBGA) as both cell attachment and susceptibility factors for the globally dominant P[4], P[6], and P[8] genotypes of human RVs. How these genotypes interact with HBGA is not known. Here, our crystal structures of P[4] and a neonate-specific P[6] VP8*s alone and in complex with H-type I HBGA reveal a unique glycan binding site that is conserved in the globally dominant genotypes and allows for the binding of ABH HBGAs, consistent with their prevalence. Remarkably, the VP8* of P[6] RVs isolated from neonates displays subtle structural changes in this binding site that may restrict its ability to bind branched glycans. This provides a structural basis for the age-restricted tropism of some P[6] RVs as developmentally regulated unbranched glycans are more abundant in the neonatal gut. Human rotaviruses (RV) bind to histo-blood group antigens (HBGA) for attachment, but how different viral genotypes interact with HBGA isn’t known. Here, Hu et al. report crystal structures of a prevalent and a neonate-specific RV in complex with HBGA and provide insights into glycan recognition and age-restricted tropism of RVs.
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Affiliation(s)
- Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Daniel R Laucirica
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wilhelm Salmen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Phoebe S Tsoi
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yi Lasanajak
- Department of Biochemistry and the Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - David F Smith
- Department of Biochemistry and the Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Robert L Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Josephine C Ferreon
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
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15
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Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events. Sci Rep 2018; 8:6011. [PMID: 29662148 PMCID: PMC5902508 DOI: 10.1038/s41598-018-24511-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/05/2018] [Indexed: 01/02/2023] Open
Abstract
After the introduction of two global rotavirus vaccines, RotaTeq in 2007 and Rotarix in 2008 in South Korea, G1[P8] rotavirus was the major rotavirus genotype in the country until 2012. However, in this study, an emergence of G2P[4] as the dominant genotype during the 2013 to 2015 season has been reported. Genetic analysis revealed that these viruses had typical DS-1-like genotype constellation and showed evidence of re-assortment in one or more genome segments, including the incorporation of NSP4 genes from strains B-47/2008 from a cow and R4/Haryana/2007 from a buffalo in India, and the VP1 and VP3 genes from strain GO34/1999 from a goat in Bangladesh. Compared to the G2 RotaTeq vaccine strain, 17–24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.
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16
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Khandoker N, Thongprachum A, Takanashi S, Okitsu S, Nishimura S, Kikuta H, Yamamoto A, Sugita K, Baba T, Kobayashi M, Hayakawa S, Mizuguchi M, Ushijima H. Molecular epidemiology of rotavirus gastroenteritis in Japan during 2014-2015: Characterization of re-emerging G2P[4] after rotavirus vaccine introduction. J Med Virol 2018; 90:1040-1046. [PMID: 29488230 DOI: 10.1002/jmv.25067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 02/25/2018] [Indexed: 11/08/2022]
Abstract
Rotavirus vaccines have been available in Japan since 2011. This study conducted to monitor the trend of group A rotavirus (RVA) genotypes 3 years after vaccine introduction. A total of, 539 fecal samples were collected from children with acute gastroenteritis in six regions during July 2014-June 2015. Among them, 178 samples (33.0%) were positive for RVA. The most predominant genotype was G1P[8] (35.9%) followed by G2P[4] (26.4%), G9P[8] (21.3%), G3P[8] (4.5%), and G3P[9] (4.5%). The detection rate of G2P[4] was increased soon after vaccine introduction. Sequence analyses of VP7 and VP4 genes of the representative G2P[4] strains were found to be clustered in sub-lineage IVa of lineage IV. It is noteworthy that one amino acid substitution in the antigenic epitope (Q114P) of VP4 gene was found in representative G2P[4] strains of the current study. However, it is unclear whether the change in antigenic epitope is due to the effect of vaccination or due to natural variation, warranting further continuous monitoring of rotavirus evolution after vaccine introduction.
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Affiliation(s)
- Nusrat Khandoker
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Aksara Thongprachum
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoko Okitsu
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shuichi Nishimura
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hideaki Kikuta
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Atsuko Yamamoto
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Kumiko Sugita
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Tsuneyoshi Baba
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Masaaki Kobayashi
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Masashi Mizuguchi
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
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17
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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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18
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Bwogi J, Jere KC, Karamagi C, Byarugaba DK, Namuwulya P, Baliraine FN, Desselberger U, Iturriza-Gomara M. Whole genome analysis of selected human and animal rotaviruses identified in Uganda from 2012 to 2014 reveals complex genome reassortment events between human, bovine, caprine and porcine strains. PLoS One 2017. [PMID: 28640820 PMCID: PMC5480867 DOI: 10.1371/journal.pone.0178855] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Rotaviruses of species A (RVA) are a common cause of diarrhoea in children and the young of various other mammals and birds worldwide. To investigate possible interspecies transmission of RVAs, whole genomes of 18 human and 6 domestic animal RVA strains identified in Uganda between 2012 and 2014 were sequenced using the Illumina HiSeq platform. The backbone of the human RVA strains had either a Wa- or a DS-1-like genetic constellation. One human strain was a Wa-like mono-reassortant containing a DS-1-like VP2 gene of possible animal origin. All eleven genes of one bovine RVA strain were closely related to those of human RVAs. One caprine strain had a mixed genotype backbone, suggesting that it emerged from multiple reassortment events involving different host species. The porcine RVA strains had mixed genotype backbones with possible multiple reassortant events with strains of human and bovine origin.Overall, whole genome characterisation of rotaviruses found in domestic animals in Uganda strongly suggested the presence of human-to animal RVA transmission, with concomitant circulation of multi-reassortant strains potentially derived from complex interspecies transmission events. However, whole genome data from the human RVA strains causing moderate and severe diarrhoea in under-fives in Uganda indicated that they were primarily transmitted from person-to-person.
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Affiliation(s)
- Josephine Bwogi
- EPI laboratory, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Paediatrics and Child Health, College of Health Sciences, Makerere University, Kampala, Uganda
- * E-mail:
| | - Khuzwayo C. Jere
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme / Department of Medical Laboratory Sciences, University of Malawi, College of Medicine, Blantyre, Malawi
| | - Charles Karamagi
- Department of Paediatrics and Child Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Denis K. Byarugaba
- Department of Microbiology, College of Veterinary Medicine and Biosecurity, Makerere University, Kampala, Uganda
| | - Prossy Namuwulya
- EPI laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Frederick N. Baliraine
- Department of Biology and Kinesiology, LeTourneau University, Longview, Texas, United States of America
| | | | - Miren Iturriza-Gomara
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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Zeller M, Nuyts V, Heylen E, De Coster S, Conceição-Neto N, Van Ranst M, Matthijnssens J. Emergence of human G2P[4] rotaviruses containing animal derived gene segments in the post-vaccine era. Sci Rep 2016; 6:36841. [PMID: 27841357 PMCID: PMC5107926 DOI: 10.1038/srep36841] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/19/2016] [Indexed: 11/30/2022] Open
Abstract
The introduction of Rotarix into the Belgian immunization program in June 2006 coincided with an increase of the relative prevalence of G2P[4] strains. However, the genetic composition of these persistent G2P[4] strains has not been investigated. Therefore, we have investigated the NSP4 gene of 89 Belgian G2P[4] strains detected between 1999 and 2013, covering both pre- and post-vaccination periods. The NSP4 genes were divided over seven separate clusters of which six were more closely related to animal than to human strains. The NSP4 genes that clustered more closely to animal DS-1-like strains were isolated after 2004–2005 and were found throughout multiple seasons. Complete genome sequencing of 28 strains identified several other gene segments that clustered more closely to animal than to human DS-1-like strains. These findings suggest that frequent interspecies reassortments may have played a role in the spread of G2P[4] rotaviruses in the post-vaccination period in Belgium.
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Affiliation(s)
- Mark Zeller
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Valerie Nuyts
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Elisabeth Heylen
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Sarah De Coster
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Nádia Conceição-Neto
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium.,KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research, Leuven, Belgium
| | - Marc Van Ranst
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium.,KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research, Leuven, Belgium
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20
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Aida S, Nahar S, Paul SK, Hossain MA, Kabir MR, Sarkar SR, Ahmed S, Ghosh S, Urushibara N, Kawaguchiya M, Aung MS, Sumi A, Kobayashi N. Whole genomic analysis of G2P[4] human Rotaviruses in Mymensingh, north-central Bangladesh. Heliyon 2016; 2:e00168. [PMID: 27722206 PMCID: PMC5047856 DOI: 10.1016/j.heliyon.2016.e00168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 08/25/2016] [Accepted: 09/21/2016] [Indexed: 12/16/2022] Open
Abstract
Rotavirus A (RVA) is a dominant causative agent of acute gastroenteritis in children worldwide. G2P[4] is one of the most common genotypes among human rotavirus (HRV) strains, and has been persistently prevalent in South Asia including Bangladesh. In the present study, whole genome sequences of a total of 16 G2P[4] HRV strains (8 strains each in 2010 and 2013) detected in Mymensingh, north-central Bangladesh were determined. These strains had typical DS-1-like genotype constellation. Most of gene segments from DS-1 genogroup exhibited high level sequence identities to each other (>98%), while slight diversity was observed for VP1, VP3, and NSP4 genes. By phylogenetic analysis, individual RNA segments were classified into one (V) or two-three lineages (V–VI or V–VII). In terms of lineages (sublineages) of 11 gene segments, the 16 Bangladeshi strains could be further classified into four clades (A-D) containing 8 lineage constellations, revealing the presence of three clades (A-C) with three lineage constellations in 2010, and a single clade (D) with four constellations in 2013. Therefore, co-existence of multiple G2P[4] HRV strains with different lineage constellations, and change in clades for the study period were demonstrated. Although amino acids in the antigenic regions on VP7 and VP4 were mostly identical to those of global G2P[4] strains after 2000, VP4 of clade D RVAs in 2013 had alanine and proline at positions 88 and 114, respectively, which are novel substitutions compared with recent global G2P[4] strains. Replacement of lineage constellations associated with unique amino acid changes in the antigenic region in VP4 suggested continuous genetic evolutionary state for emerging new G2P[4] rotavirus strains in Bangladesh.
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Affiliation(s)
- Satoru Aida
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
- Corresponding author at: Satoru Aida, Department of Hygiene, Sapporo Medical University School of Medicine, S-1 W-17, Chuo-ku, Sapporo 060–8556, Japan.Department of HygieneSapporo Medical University School of MedicineSapporoJapan
| | - Samsoon Nahar
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Shyamal Kumar Paul
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | | | | | - Santana Rani Sarkar
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Salma Ahmed
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Souvik Ghosh
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts, West Indies
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mitsuyo Kawaguchiya
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Ayako Sumi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
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Agbemabiese CA, Nakagomi T, Doan YH, Do LP, Damanka S, Armah GE, Nakagomi O. Genomic constellation and evolution of Ghanaian G2P[4] rotavirus strains from a global perspective. INFECTION GENETICS AND EVOLUTION 2016; 45:122-131. [PMID: 27569866 DOI: 10.1016/j.meegid.2016.08.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/03/2016] [Accepted: 08/20/2016] [Indexed: 10/21/2022]
Abstract
Understanding of the genetic diversity and evolution of Rotavirus A (RVA) strains, a common cause of severe diarrhoea in children, needs to be based on the analysis at the whole genome level in the vaccine era. This study sequenced the whole genomes of six representative G2P[4] strains detected in Ghana from 2008 to 2013, and analysed them phylogenetically with a global collection of G2P[4] strains and African non-G2P[4] DS-1-like strains. The genotype constellation of the study strains was G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Strains from the same season were highly identical across the whole genome while strains from different seasons were more divergent from each other. The VP7, VP4, VP2, NSP1, and NSP5 genes belonged to lineage IVa; the VP6, VP1, NSP2, and NSP3 genes belonged to lineage V, and all these genes evolved in the same fashion as the global strains. In the NSP4 gene, lineages V (2008) and X (2009) were replaced by VI (2012/2013) whereas in the VP3 gene, lineage V (2008/2009) was replaced by VII (2012/2013) and these replacements coincided with the vaccine introduction period (2012). The evolutionary rate of the NSP4 gene was 1.2×10-3 substitutions/site/year and was rather comparable to that of the remaining 10 genes. The multiple NSP4 lineages were explained by intra-genotype reassortment with co-circulating African human DS-1-like strains bearing G2[6], G3P[6], G6[6] and G8. There was no explicit evidence of the contribution of animal RVA strains to the genome of the Ghanaian G2P[4] strains. In summary, this study revealed the dynamic evolution of the G2P[4] strains through intra-genotype reassortment events leading to African specific lineages such IX and X in the NSP4 gene. So far, there was no evidence of a recent direct involvement of animal RVA genes in the genome diversity of African G2P[4] strains.
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Affiliation(s)
- Chantal Ama Agbemabiese
- Leading Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan; Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Toyoko Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yen Hai Doan
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Loan Phuong Do
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Susan Damanka
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - George E Armah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Osamu Nakagomi
- Leading Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan; Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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22
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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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23
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Dong HJ, Qian Y, Zhang Y, Zhao LQ, Zhu RN, Nong Y, Mo ZJ, Li RC. G2 rotavirus within an emergent VP7 evolutionary lineage circulating in children with acute diarrhea in Guangxi Province of China, 2014. Arch Virol 2016; 161:1987-92. [PMID: 27101073 DOI: 10.1007/s00705-016-2852-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 03/30/2016] [Indexed: 01/21/2023]
Abstract
Routine surveillance revealed that the prevalence of P[4] rotaviruses circulating in children with acute diarrhea in Guangxi Province, China, increased in 2014. However, VP7 genotyping for these P[4] rotaviruses was unsuccessful. Exhaustive database searching and sequence analysis indicated that the G genotype of these P[4] rotaviruses was G2, and the VP7 genes clustered with recently emerging G2 strains in several countries within an emergent evolutionary lineage that was distinct from the previously designated lineages I-IV as well as lineage V including porcine rotaviruses. Further studies are essential to monitor the potential global spread of this emerging G2 rotavirus.
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Affiliation(s)
- Hui Jin Dong
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yuan Qian
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - You Zhang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Lin Qing Zhao
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Ru Nan Zhu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yi Nong
- Centers for Disease Control and Prevention of Guangxi Province, Nanning, 530028, Guangxi, China
| | - Zhao Jun Mo
- Centers for Disease Control and Prevention of Guangxi Province, Nanning, 530028, Guangxi, China
| | - Rong Cheng Li
- Centers for Disease Control and Prevention of Guangxi Province, Nanning, 530028, Guangxi, China
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Malik YS, Kumar N, Sharma K, Saurabh S, Dhama K, Prasad M, Ghosh S, Bányai K, Kobayashi N, Singh RK. Multispecies reassortant bovine rotavirus strain carries a novel simian G3-like VP7 genotype. INFECTION GENETICS AND EVOLUTION 2016; 41:63-72. [PMID: 27033751 DOI: 10.1016/j.meegid.2016.03.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 02/06/2023]
Abstract
Rotavirus-A (RVAs), are the major cause of severe gastroenteritis in the young of mammals and birds. RVA strains possessing G6, G8, and G10 genotypes in combination with P[1] or P[11] have been commonly detected in cattle. During a routine surveillance for enteric viruses in a bovine population on North-Western temperate Himalayan region of India, an uncommon bovine RVA strain, designated as RVA/Cow-wt/IND/M1/09/2009 was detected in a diarrhoeic crossbred calf. The examination of nearly complete genome sequence of this RVA strain revealed an unusual G-P combination (G3P[11]) on a typical bovine RVA genotype backbone (I2-R2-C2-M2-A11-N2-T6-E2-H3). The VP7 gene of M1/09 isolate displayed a maximum nucleotide sequence identity of 73.8% with simian strain (RVA/Simian-tc/USA/RRV/1975/G3P[3]). The VP4 and NSP5 genes clustered with an Indian pig strain, RVA/Pig-wt/IND/AM-P66/2012/G10P[11] (99.6%), and a caprine strain, RVA/Goat-tc/BGD/GO34/1999/G6P[1] (98.9%) from Bangladesh, respectively, whilst the, VP6, NSP1, NSP3 and NSP4 genes were identical or nearly identical to Indian bovine strains (RVA/Cow-wt/IND/B-72/2008/G10P[X], RVA/Cow-wt/IND/B85/2010/GXP[X], and RVA/Cow-wt/IND/C91/2011/G6P[X]). The remaining four genes (VP1, VP2, VP3 and NSP2) were more closely related to RVA/Human-wt/ITA/PAI11/1996/G2P[4] (93.5%), RVA/Sheep-wt/CHN/LLR/1985/G10P[15] (88.8%), RVA/Human-tc/SWE/1076/1983/G2P2A[6] (93.2%) and RVA/Human-wt/AUS/CK20003/2000/G2P[4] (91.2%), respectively. Altogether, these findings are suggestive of multiple independent interspecies transmission and reassortment events between co-circulating bovine, porcine, ovine and human rotaviruses. The complete genome sequence information is necessary to establish the evolutionary relationship, interspecies transmission and ecological features of animal RVAs from different geographical regions.
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Affiliation(s)
- Yashpal Singh Malik
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India.
| | - Naveen Kumar
- National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India.
| | - Kuldeep Sharma
- National Institute of Research in Tribal Health, Jabalpur -482 003, Madhya Pradesh, India.
| | - Sharad Saurabh
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India.
| | - Kuldeep Dhama
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India.
| | - Minakshi Prasad
- Department of Animal Biotechnology, LUVAS, Hisar 125 001, Haryana, India.
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, P. O. Box 334, Basseterre, Saint Kitts, West Indies.
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt 21, Budapest 1143, Hungary.
| | | | - Raj Kumar Singh
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India.
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Komoto S, Tacharoenmuang R, Guntapong R, Ide T, Haga K, Katayama K, Kato T, Ouchi Y, Kurahashi H, Tsuji T, Sangkitporn S, Taniguchi K. Emergence and Characterization of Unusual DS-1-Like G1P[8] Rotavirus Strains in Children with Diarrhea in Thailand. PLoS One 2015; 10:e0141739. [PMID: 26540260 PMCID: PMC4634990 DOI: 10.1371/journal.pone.0141739] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 10/12/2015] [Indexed: 12/11/2022] Open
Abstract
The emergence and rapid spread of unusual DS-1-like G1P[8] rotaviruses in Japan have been recently reported. During rotavirus surveillance in Thailand, three DS-1-like G1P[8] strains (RVA/Human-wt/THA/PCB-180/2013/G1P[8], RVA/Human-wt/THA/SKT-109/2013/G1P[8], and RVA/Human-wt/THA/SSKT-41/2013/G1P[8]) were identified in stool specimens from hospitalized children with severe diarrhea. In this study, we sequenced and characterized the complete genomes of strains PCB-180, SKT-109, and SSKT-41. On whole genomic analysis, all three strains exhibited a unique genotype constellation including both genogroup 1 and 2 genes: G1-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. This novel genotype constellation is shared with Japanese DS-1-like G1P[8] strains. Phylogenetic analysis revealed that the G/P genes of strains PCB-180, SKT-109, and SSKT-41 appeared to have originated from human Wa-like G1P[8] strains. On the other hand, the non-G/P genes of the three strains were assumed to have originated from human DS-1-like strains. Thus, strains PCB-180, SKT-109, and SSKT-41 appeared to be derived through reassortment event(s) between Wa-like G1P[8] and DS-1-like human rotaviruses. Furthermore, strains PCB-180, SKT-109, and SSKT-41 were found to have the 11-segment genome almost indistinguishable from one another in their nucleotide sequences and phylogenetic lineages, indicating the derivation of the three strains from a common origin. Moreover, all the 11 genes of the three strains were closely related to those of Japanese DS-1-like G1P[8] strains. Therefore, DS-1-like G1P[8] strains that have emerged in Thailand and Japan were assumed to have originated from a recent common ancestor. To our knowledge, this is the first report on whole genome-based characterization of DS-1-like G1P[8] strains that have emerged in an area other than Japan. Our observations will provide important insights into the evolutionary dynamics of emerging DS-1-like G1P[8] rotaviruses.
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Affiliation(s)
- Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- * E-mail:
| | | | - Ratigorn Guntapong
- Department of Medical Sciences, National Institute of Health, Nonthaburi, Thailand
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Yuya Ouchi
- Genome and Transcriptome Analysis Center, Fujita Health University, Toyoake, Aichi, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
- Genome and Transcriptome Analysis Center, Fujita Health University, Toyoake, Aichi, Japan
| | - Takao Tsuji
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Somchai Sangkitporn
- Department of Medical Sciences, National Institute of Health, Nonthaburi, Thailand
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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Doan YH, Nakagomi T, Agbemabiese CA, Nakagomi O. Changes in the distribution of lineage constellations of G2P[4] Rotavirus A strains detected in Japan over 32years (1980–2011). INFECTION GENETICS AND EVOLUTION 2015; 34:423-33. [DOI: 10.1016/j.meegid.2015.05.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 05/19/2015] [Accepted: 05/27/2015] [Indexed: 01/27/2023]
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27
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Sá ACC, Gómez MM, Lima IFN, Quetz JS, Havt A, Oriá RB, Lima AA, Leite JPG. Group a rotavirus and norovirus genotypes circulating in the northeastern Brazil in the post-monovalent vaccination era. J Med Virol 2015; 87:1480-90. [DOI: 10.1002/jmv.24144] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Ana Caroline C. Sá
- Laboratory of Comparative and Environmental Virology; Oswaldo Cruz Institute- Fiocruz; Rio de Janeiro Brazil
| | - Mariela M. Gómez
- Laboratory of Comparative and Environmental Virology; Oswaldo Cruz Institute- Fiocruz; Rio de Janeiro Brazil
| | - Ila Fernanda N. Lima
- Institute of Biomedicine for Brazilian Semi-Arid & Clinical Research Unit; Federal University of Ceara; Fortaleza Brazil
| | - Josiane S. Quetz
- Institute of Biomedicine for Brazilian Semi-Arid & Clinical Research Unit; Federal University of Ceara; Fortaleza Brazil
| | - Alexandre Havt
- Institute of Biomedicine for Brazilian Semi-Arid & Clinical Research Unit; Federal University of Ceara; Fortaleza Brazil
| | - Reinaldo B. Oriá
- Institute of Biomedicine for Brazilian Semi-Arid & Clinical Research Unit; Federal University of Ceara; Fortaleza Brazil
| | - Aldo A. Lima
- Institute of Biomedicine for Brazilian Semi-Arid & Clinical Research Unit; Federal University of Ceara; Fortaleza Brazil
| | - José Paulo G. Leite
- Laboratory of Comparative and Environmental Virology; Oswaldo Cruz Institute- Fiocruz; Rio de Janeiro Brazil
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28
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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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29
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Medici MC, Tummolo F, Bonica MB, Heylen E, Zeller M, Calderaro A, Matthijnssens J. Genetic diversity in three bovine-like human G8P[14] and G10P[14] rotaviruses suggests independent interspecies transmission events. J Gen Virol 2015; 96:1161-1168. [PMID: 25614586 DOI: 10.1099/vir.0.000055] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/13/2015] [Indexed: 11/18/2022] Open
Abstract
The group A rotavirus (RVA) P[14] genotype has been detected sporadically in humans and is thought to be acquired through zoonotic transmission. The present study describes the full-length genome analysis of two G8P[14] and one G10P[14] human RVAs detected in Italy. The strains possessed the typical bovine-like I2-R2-C2-M2-A3/A11-N2-T6-E2-H3 genotype constellation. All the segments of the two G8P[14] RVAs were most closely related to bovine(-like) strains but were relatively distant to each other, suggesting two independent interspecies transmission events. Likewise, the G10P[14] RVA gene segments were most similar to bovine(-like) RVAs but distinct from the G8 strains. The history of these strains probably involved the interspecies transmission of these viruses to humans from an as-yet-unidentified animal host, without evidence of reassortment events involving human RVAs. These results reinforce the potential of animal viruses to cross the host-species barrier, causing disease and increased viral genetic diversity in humans.
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Affiliation(s)
- Maria Cristina Medici
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Fabio Tummolo
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Melisa Berenice Bonica
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Elisabeth Heylen
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Mark Zeller
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Adriana Calderaro
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Jelle Matthijnssens
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
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30
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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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31
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Ndze VN, Esona MD, Achidi EA, Gonsu KH, Dóró R, Marton S, Farkas S, Ngeng MB, Ngu AF, Obama-Abena MT, Bányai K. Full genome characterization of human Rotavirus A strains isolated in Cameroon, 2010–2011: Diverse combinations of the G and P genes and lack of reassortment of the backbone genes. INFECTION GENETICS AND EVOLUTION 2014; 28:537-60. [DOI: 10.1016/j.meegid.2014.10.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/09/2014] [Accepted: 10/11/2014] [Indexed: 12/17/2022]
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32
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Gómez MM, Carvalho-Costa FA, de Mello Volotão E, Rose TL, da Silva MFM, Fialho AM, Assis RMS, da Silva Ribeiro de Andrade J, Sá ACC, Zeller M, Heylen E, Matthijnssens J, Leite JPG. Prevalence and genomic characterization of G2P[4] group A rotavirus strains during monovalent vaccine introduction in Brazil. INFECTION GENETICS AND EVOLUTION 2014; 28:486-94. [DOI: 10.1016/j.meegid.2014.09.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 11/15/2022]
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33
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De Grazia S, Bonura F, Colomba C, Cascio A, Di Bernardo F, Collura A, Terranova DM, Martella V, Giammanco GM. Data mining from a 27-years rotavirus surveillance in Palermo, Italy. INFECTION GENETICS AND EVOLUTION 2014; 28:377-84. [DOI: 10.1016/j.meegid.2014.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 02/07/2023]
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34
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Papp H, Marton S, Farkas SL, Jakab F, Martella V, Malik YS, Palya V, Bányai K. Classification and characterization of a laboratory chicken rotavirus strain carrying G7P[35] neutralization antigens on the genotype 4 backbone gene configuration. Biologicals 2014; 42:299-304. [PMID: 25284347 DOI: 10.1016/j.biologicals.2014.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/30/2014] [Accepted: 08/18/2014] [Indexed: 12/23/2022] Open
Abstract
The laboratory rotavirus strain, BRS/115, has been used for more than two decades to monitor rotaviruses in specific pathogen free flocks of laying hens. However, the virus strain has not been characterized in detail. Therefore we aimed at the description of molecular features of BRS115 by using random primed reverse transcription-PCR of the genomic RNA followed by massive parallel sequencing using the semiconductor sequencing technology. Over 64,000 trimmed reads mapped to reference sequences obtained from GenBank. The strain classified into the species Rotavirus A and genotyped G7-P[35]-I4-R4-C4-M4-A16-N4-T4-E11-H4 according to guidelines of the Rotavirus Classification Working Group. Phylogenetic analysis identified shared features with chicken, turkey and pigeon origin rotaviruses. This study demonstrates the robustness of next generation sequencing in the characterization of reference virus materials used in specialized laboratories.
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Affiliation(s)
- Hajnalka Papp
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
| | - Szilvia L Farkas
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
| | - Ferenc Jakab
- Institute of Biology, Faculty of Sciences, University of Pécs, Ifjúság útja 6., H-7624 Pécs, Hungary; János Szentágothai Research Center, University of Pécs, Ifjúság útja 20., H-7624 Pécs, Hungary
| | - Vito Martella
- Department of Veterinary Public Health, University of Bari, S.p. per Casamassima km 3, 70010 Valenzano, Bari, Italy
| | - Yashpal S Malik
- Division of Biological Standardisation, Indian Veterinary Research Institute (IVRI), Izatnagar, 243 122 Bareilly, Uttar Pradesh, India
| | - Vilmos Palya
- Ceva-Phylaxia Veterinary Biologicals Co. Ltd., Szállás u. 5., H-1107 Budapest, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary.
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35
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Wu FT, Bányai K, Jiang B, Wu CY, Chen HC, Fehér E, Huang YC, Lin JS, Huang FC, Hsiung CA, Huang JC, Wu HS. Molecular epidemiology of human G2P[4] rotaviruses in Taiwan, 2004-2011. INFECTION GENETICS AND EVOLUTION 2014; 28:530-6. [PMID: 25281207 DOI: 10.1016/j.meegid.2014.09.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/23/2014] [Accepted: 09/24/2014] [Indexed: 10/24/2022]
Abstract
In 2006, two rotavirus vaccines (Rotarix and RotaTeq) became available on the private market in Taiwan. Although vaccine coverage is currently low, molecular surveillance of rotavirus strains can provide pertinent information for evaluation of the potential impact of vaccine introduction and infection control. During January 2008-December 2011, children aged <5 years hospitalized with acute gastroenteritis were enrolled from sentinel surveillance hospitals in three geographic areas of Taiwan. Fecal specimens collected from enrolled patients were tested for rotavirus by enzyme immunoassay and reverse transcriptase-polymerase chain reaction. For genotyping, gene specific primer sets were used to amplify and sequence the genes encoding the neutralization antigens, VP7 and VP4. The resulting sequences were then subjected to phylogenetic analysis. In brief, a total of 4,052 fecal specimens were tested and 742 (18%) samples were positive for rotavirus. The annual range of rotavirus positive specimens varied between 16% and 20.7%. Of all specimens, genotype G1P[8] (63.3%) was the predominant strain, followed by G2P[4] (12.5%), G3P[8] (11.7%), and G9P[8] (5.1%). Uncommon strains were also detected in low percentages. We observed that the rotavirus positivity rate steadily decreased from 21% to 16% during 2008-2010, then slightly increased to 20% in 2011, when an increase in the number of G2P[4] cases was observed. Sequence and phylogenetic analysis was carried out to help understand any potential changes of G2P[4] rotaviruses over time. A number of G2P[4] strains collected between 2004 and 2011 were analyzed in detail and our analyses showed marked genetic and antigenic variability in the VP7 and VP4 genes. The Taiwanese strains could be classified into two major G2 VP7 lineages (IV and V) and two major P[4] VP4 lineages (IV and V) and several minor sublineages within lineage IV. Lineage V within both G2 and P[4] represented newly recognized genetic variants of the respective genotypes. The distribution of individual combinations of the G2 and P[4] (sub)lineages showed some temporal variations. This study provides further evidence for the great genetic diversity among G2P[4] strains and helps understand the epidemiological trends of these strains among children in Taiwan.
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Affiliation(s)
- Fang-Tzy Wu
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan; Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming University, Taipei, Taiwan.
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Baoming Jiang
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ching-Yi Wu
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Hsieh-Cheng Chen
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Enikő Fehér
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Yhu-Chering Huang
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Jen-Shiou Lin
- Division of Pediatric Infectious Disease and Department of Laboratory Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Fu-Chen Huang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chao A Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Jason C Huang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming University, Taipei, Taiwan; AIDS Prevention and Research Center, National Yang-Ming University, Taipei, Taiwan.
| | - Ho-Sheng Wu
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan.
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36
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Dóró R, Mihalov-Kovács E, Marton S, László B, Deák J, Jakab F, Juhász Á, Kisfali P, Martella V, Melegh B, Molnár P, Sántha I, Schneider F, Bányai K. Large-scale whole genome sequencing identifies country-wide spread of an emerging G9P[8] rotavirus strain in Hungary, 2012. INFECTION GENETICS AND EVOLUTION 2014; 28:495-512. [PMID: 25239526 DOI: 10.1016/j.meegid.2014.09.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 09/03/2014] [Accepted: 09/11/2014] [Indexed: 11/19/2022]
Abstract
With the availability of rotavirus vaccines routine strain surveillance has been launched or continued in many countries worldwide. In this study relevant information is provided from Hungary in order to extend knowledge about circulating rotavirus strains. Direct sequencing of the RT-PCR products obtained by VP7 and VP4 genes specific primer sets was utilized as routine laboratory method. In addition we explored the advantage of random primed RT-PCR and semiconductor sequencing of the whole genome of selected strains. During the study year, 2012, we identified an increase in the prevalence of G9P[8] strains across the country. This genotype combination predominated in seven out of nine study sites (detection rates, 45-83%). In addition to G9P[8]s, epidemiologically major strains included genotypes G1P[8] (34.2%), G2P[4] (13.5%), and G4P[8] (7.4%), whereas unusual and rare strains were G3P[8] (1%), G2P[8] (0.5%), G1P[4] (0.2%), G3P[4] (0.2%), and G3P[9] (0.2%). Whole genome analysis of 125 Hungarian human rotaviruses identified nine major genotype constellations and uncovered both intra- and intergenogroup reassortment events in circulating strains. Intergenogroup reassortment resulted in several unusual genotype constellations, including mono-reassortant G1P[8] and G9P[8] strains whose genotype 1 (Wa-like) backbone gene constellations contained DS1-like NSP2 and VP3 genes, respectively, as well as, a putative bovine-feline G3P[9] reassortant strain. The conserved genomic constellations of epidemiologically major genotypes suggested the clonal spread of the re-emerging G9P[8] genotype and several co-circulating strains (e.g., G1P[8] and G2P[4]) in many study sites during 2012. Of interest, medically important G2P[4] strains carried bovine-like VP1 and VP6 genes in their genotype constellation. No evidence for vaccine associated selection, or, interaction between wild-type and vaccine strains was obtained. In conclusion, this study reports the reemergence of G9P[8] strains across the country and indicates the robustness of whole genome sequencing in routine rotavirus strain surveillance.
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Affiliation(s)
- Renáta Dóró
- Hungarian Academy of Sciences, Budapest, Hungary
| | | | | | | | | | | | | | | | | | | | - Péter Molnár
- Combined Szent István and Szent László Hospital, Budapest, Hungary
| | - Ildikó Sántha
- Hungarian National Public Health and Medical Officer Service, Miskolc, Hungary
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37
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Semeiko GV, Yermalovich MA, Poliakova N, Mijatovic-Rustempasic S, Kerin TK, Wasley A, Videbaek D, Gentsch JR, Bowen MD, Samoilovich EO. Rotavirus genotypes in Belarus, 2008-2012. INFECTION GENETICS AND EVOLUTION 2014; 28:480-5. [PMID: 25218086 DOI: 10.1016/j.meegid.2014.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/21/2014] [Accepted: 09/03/2014] [Indexed: 12/19/2022]
Abstract
This study describes group A rotavirus (RVA) genotype prevalence in Belarus from 2008 to 2012. In 2008, data from 3 sites in Belarus (Brest, Mogilev, Minsk) indicated that G4P[8] was the predominant genotype. Data from Minsk (2008-2012) showed that G4P[8] was the predominant RVA genotype in all years except in 2011 when G3P[8] was most frequently detected. Other RVA genotypes common in Europe (G1P[8], G2P[4]) were detected each year of the study. This study reveals the dominance of genotype G4P[8] in Belarus and helps to establish the baseline genotype prevalence prior to RVA vaccine introduction in the country.
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Affiliation(s)
- Galina V Semeiko
- Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Marina A Yermalovich
- Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Nadezhda Poliakova
- Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Slavica Mijatovic-Rustempasic
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tara K Kerin
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Annemarie Wasley
- World Health Organization Regional Office for Europe, Copenhagen, Denmark
| | - Dovile Videbaek
- World Health Organization Regional Office for Europe, Copenhagen, Denmark
| | - Jon R Gentsch
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael D Bowen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Elena O Samoilovich
- Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
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Review of global rotavirus strain prevalence data from six years post vaccine licensure surveillance: is there evidence of strain selection from vaccine pressure? INFECTION GENETICS AND EVOLUTION 2014; 28:446-61. [PMID: 25224179 DOI: 10.1016/j.meegid.2014.08.017] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 11/23/2022]
Abstract
Comprehensive reviews of pre licensure rotavirus strain prevalence data indicated the global importance of six rotavirus genotypes, G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]. Since 2006, two vaccines, the monovalent Rotarix (RV1) and the pentavalent RotaTeq (RV5) have been available in over 100 countries worldwide. Of these, 60 countries have already introduced either RV1 or RV5 in their national immunization programs. Post licensure vaccine effectiveness is closely monitored worldwide. This review aimed at describing the global changes in rotavirus strain prevalence over time. The genotype distribution of the nearly 47,000 strains that were characterized during 2007-2012 showed similar picture to that seen in the preceding period. An intriguing finding was the transient predominance of heterotypic strains, mainly in countries using RV1. Unusual and novel antigen combinations continue to emerge, including some causing local outbreaks, even in vaccinated populations. In addition, vaccine strains have been found in both vaccinated infants and their contacts and there is evidence for genetic interaction between vaccine and wild-type strains. In conclusion, the post-vaccine introduction strain prevalence data do not show any consistent pattern indicative of selection pressure resulting from vaccine use, although the increased detection rate of heterotypic G2P[4] strains in some countries following RV1 vaccination is unusual and this issue requires further monitoring.
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39
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Molecular epidemiology of contemporary G2P[4] human rotaviruses cocirculating in a single U.S. community: footprints of a globally transitioning genotype. J Virol 2014; 88:3789-801. [PMID: 24429371 DOI: 10.1128/jvi.03516-13] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Group A rotaviruses (RVs) remain a leading cause of childhood gastroenteritis worldwide. Although the G/P types of locally circulating RVs can vary from year to year and differ depending upon geographical location, those with G1P[8], G2P[4], G3P[8], G4P[8], G9P[8], and G12P[8] specificities typically dominate. Little is known about the evolution and diversity of G2P[4] RVs and the possible role that widespread vaccine use has had on their increased frequency of detection. To address these issues, we analyzed the 12 G2P[4] RV isolates associated with a rise in RV gastroenteritis cases at Vanderbilt University Medical Center (VUMC) during the 2010-2011 winter season. Full-genome sequencing revealed that the isolates had genotype 2 constellations typical of DS-1-like viruses (G2P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2). Phylogenetic analyses showed that the genome segments of the isolates were comprised of two or three different subgenotype alleles; this enabled recognition of three distinct clades of G2P[4] viruses that caused disease at VUMC in the 2010-2011 season. Although the three clades cocirculated in the same community, there was no evidence of interclade reassortment. Bayesian analysis of 328 VP7 genes of G2 viruses isolated in the last 39 years indicate that existing G2 VP7 gene lineages continue to evolve and that novel lineages, as represented by the VUMC isolates, are constantly being formed. Moreover, G2 lineages are characteristically shaped by lineage turnover events that introduce new globally dominant strains every 7 years, on average. The ongoing evolution of G2 VP7 lineages may give rise to antigenic changes that undermine vaccine effectiveness in the long term. IMPORTANCE Little is known about the diversity of cocirculating G2 rotaviruses and how their evolution may undermine the effectiveness of rotavirus vaccines. To expand our understanding of the potential genetic range exhibited by rotaviruses circulating in postvaccine communities, we analyzed part of a collection of rotaviruses recovered from pediatric patients in the United States from 2010 to 2011. Examining the genetic makeup of these viruses revealed they represented three segregated groups that did not exchange genetic material. The distinction between these three groups may be explained by three separate introductions. By comparing a specific gene, namely, VP7, of the recent rotavirus isolates to those from a collection recovered from U.S. children between 1974 and 1991 and other globally circulating rotaviruses, we were able to reconstruct the timing of events that shaped their ancestry. This analysis indicates that G2 rotaviruses are continuously evolving, accumulating changes in their genetic material as they infect new patients.
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