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Zou W, Yu Q, Liu Y, Li Q, Chen H, Gao J, Shi C, Wang Y, Chen W, Bai X, Yang B, Zhang J, Dong B, Ruan B, Zhou L, Xu G, Hu Z, Yang X. Genotype analysis of rotaviruses isolated from children during a phase III clinical trial with the hexavalent rotavirus vaccine in China. Virol Sin 2023; 38:889-899. [PMID: 37972894 PMCID: PMC10786658 DOI: 10.1016/j.virs.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
The oral hexavalent live human-bovine reassortant rotavirus vaccine (RV6) developed by Wuhan Institute of Biological Products Co., Ltd (WIBP) has finished a randomized, placebo-controlled phase III clinical trial in four provinces of China in 2021. The trail demonstrated that RV6 has a high vaccine efficacy against the prevalent strains and is safe for use in infants. During the phase III clinical trial (2019-2021), 200 rotavirus-positive fecal samples from children with RV gastroenteritis (RVGE) were further studied. Using reverse transcription-polymerase chain reaction and high-throughput sequencing, VP7 and VP4 sequences were obtained and their genetic characteristics, as well as the differences in antigenic epitopes of VP7, were analyzed in detail. Seven rotavirus genotypes were identified. The predominant rotavirus genotype was G9P [8] (77.0%), followed by prevalent strains G8P [8] (8.0%), G3P [8] (3.5%), G3P [9] (1.5%), G1P [8] (1.0%), G2P [4] (1.0%), and G4P [6] (1.0%). The amino acid sequence identities of G1, G2, G3, G4, G8, and G9 genotypes of isolates compared to the vaccine strains were 98.8%, 98.2%-99.7%, 88.4%-99.4%, 98.2%, 94.2%-100%, and 93.9%-100%, respectively. Notably, the vaccine strains exhibited high similarity in amino acid sequence, with only minor differences in antigenic epitopes compared to the Chinese endemic strains. This supports the potential application of the vaccine in preventing diseases caused by rotaviruses.
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Affiliation(s)
- Wenqi Zou
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Qingchuan Yu
- National Institutes for Food and Drug Control, Beijing, 100050, China
| | - Yan Liu
- National Institutes for Food and Drug Control, Beijing, 100050, China
| | - Qingliang Li
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Hong Chen
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Jiamei Gao
- National Institutes for Food and Drug Control, Beijing, 100050, China
| | - Chen Shi
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Ying Wang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Wei Chen
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Xuan Bai
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Biao Yang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Jiuwei Zhang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Ben Dong
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Bo Ruan
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Liuyifan Zhou
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Gelin Xu
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China
| | - Zhongyu Hu
- National Institutes for Food and Drug Control, Beijing, 100050, China.
| | - Xiaoming Yang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co., Ltd, Wuhan, 430207, China; China National Biotec Group, Beijing, 100024, China.
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2
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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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Elbashir I, Aldoos NF, Mathew S, Al Thani AA, Emara MM, Yassine HM. Molecular epidemiology, genetic diversity, and vaccine availability of viral acute gastroenteritis in the middle East and North Africa (MENA) region. J Infect Public Health 2022; 15:1193-1211. [PMID: 36240530 DOI: 10.1016/j.jiph.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022] Open
Abstract
Acute gastroenteritis is the cause of considerable mortality and morbidity worldwide, particularly among children under five years in underdeveloped countries. Most acute gastroenteritis (AGE) cases are attributed to viral etiologies, including rotavirus, norovirus, adenovirus, astrovirus, and sapovirus. This paper aimed to determine the prevalence rate of different viral etiologies of AGE in the Middle East and North Africa (MENA) region. Moreover, this paper explored rotavirus phylogenetic relatedness, compared VP7 and VP4 antigenic regions of rotavirus with vaccine strains, and explored the availability of vaccines in the MENA region. The literature search identified 160 studies from 18 countries from 1980 to 2019. The overall prevalence of rotavirus, norovirus, adenovirus, astrovirus, and sapovirus were 29.8 %, 13.9 %, 6.3 %, 3.5 %, and 3.2 % of tested samples, respectively. The most common rotavirus genotype combinations in the MENA region were G1P[8], G9P[9], and G2P[4], whereas GII.4 was the predominant norovirus genotype all of which were reported in almost all the studies with genotyping data. The comparison of VP7 and VP4 between circulating rotavirus in the MENA region and vaccine strains has revealed discrete divergent regions, including the neutralizing epitopes. Rotavirus vaccine was introduced to most of the countries of the MENA region; however, only a few studies have assessed the effectiveness of vaccine introduction. This paper provides a comprehensive update on the prevalence of the different viral agents of AGE in the MENA region.
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Affiliation(s)
- Israa Elbashir
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
| | - Noor F Aldoos
- Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.
| | - Shilu Mathew
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
| | - Asmaa A Al Thani
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar; Department of Biomedical Sciences, College of Health Science-QU Health, Qatar University, Doha 2713, Qatar
| | - Mohamed M Emara
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar.
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
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4
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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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5
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Donato CM, Pingault N, Demosthenous E, Roczo-Farkas S, Bines JE. Characterisation of a G2P[4] Rotavirus Outbreak in Western Australia, Predominantly Impacting Aboriginal Children. Pathogens 2021; 10:350. [PMID: 33809709 PMCID: PMC8002226 DOI: 10.3390/pathogens10030350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 01/13/2023] Open
Abstract
In May, 2017, an outbreak of rotavirus gastroenteritis was reported that predominantly impacted Aboriginal children ≤4 years of age in the Kimberley region of Western Australia. G2P[4] was identified as the dominant genotype circulating during this period and polyacrylamide gel electrophoresis revealed the majority of samples exhibited a conserved electropherotype. Full genome sequencing was performed on representative samples that exhibited the archetypal DS-1-like genome constellation: G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and phylogenetic analysis revealed all genes of the outbreak samples were closely related to contemporary Japanese G2P[4] samples. The outbreak samples consistently fell within conserved sub-clades comprised of Hungarian and Australian G2P[4] samples from 2010. The 2017 outbreak variant was not closely related to G2P[4] variants associated with prior outbreaks in Aboriginal communities in the Northern Territory. When compared to the G2 component of the RotaTeq vaccine, the outbreak variant exhibited mutations in known antigenic regions; however, these mutations are frequently observed in contemporary G2P[4] strains. Despite the level of vaccine coverage achieved in Australia, outbreaks continue to occur in vaccinated populations, which pose challenges to regional areas and remote communities. Continued surveillance and characterisation of emerging variants are imperative to ensure the ongoing success of the rotavirus vaccination program in Australia.
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Affiliation(s)
- Celeste M. Donato
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville 3052, Australia; (E.D.); (S.R.-F.); (J.E.B.)
- Department of Paediatrics, The University of Melbourne, Parkville 3010, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Australia
| | - Nevada Pingault
- Department of Health Western Australia, Communicable Disease Control Directorate, Perth 6004, Australia;
| | - Elena Demosthenous
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville 3052, Australia; (E.D.); (S.R.-F.); (J.E.B.)
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Australia
| | - Susie Roczo-Farkas
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville 3052, Australia; (E.D.); (S.R.-F.); (J.E.B.)
| | - Julie E. Bines
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville 3052, Australia; (E.D.); (S.R.-F.); (J.E.B.)
- Department of Paediatrics, The University of Melbourne, Parkville 3010, Australia
- Department of Gastroenterology and Clinical Nutrition, Royal Children’s Hospital, Parkville 3052, Australia
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6
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Rakau KG, Nyaga MM, Gededzha MP, Mwenda JM, Mphahlele MJ, Seheri LM, Steele AD. Genetic characterization of G12P[6] and G12P[8] rotavirus strains collected in six African countries between 2010 and 2014. BMC Infect Dis 2021; 21:107. [PMID: 33482744 PMCID: PMC7821174 DOI: 10.1186/s12879-020-05745-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia. METHODS The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains. RESULTS The findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related, irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 × 10- 3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s. CONCLUSIONS At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.
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Affiliation(s)
- Kebareng G Rakau
- Diarrhoeal Pathogens Research Unit, Department of Virology, WHO AFRO Rotavirus Regional Reference Laboratory, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Martin M Nyaga
- Diarrhoeal Pathogens Research Unit, Department of Virology, WHO AFRO Rotavirus Regional Reference Laboratory, Sefako Makgatho Health Sciences University, Pretoria, South Africa.,Next Generation Sequencing Unit and Department of Medical Microbiology and Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Maemu P Gededzha
- Diarrhoeal Pathogens Research Unit, Department of Virology, WHO AFRO Rotavirus Regional Reference Laboratory, Sefako Makgatho Health Sciences University, Pretoria, South Africa.,National Health Laboratory Service, Department of Molecular Medicine and Haematology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Jason M Mwenda
- African Rotavirus Surveillance Network, Immunization, Vaccines and Development Cluster, WHO African Regional Office, Brazzaville, Congo
| | - M Jeffrey Mphahlele
- Diarrhoeal Pathogens Research Unit, Department of Virology, WHO AFRO Rotavirus Regional Reference Laboratory, Sefako Makgatho Health Sciences University, Pretoria, South Africa.,South African Medical Research Council, Soutpansberg Road, Pretoria, South Africa
| | - L Mapaseka Seheri
- Diarrhoeal Pathogens Research Unit, Department of Virology, WHO AFRO Rotavirus Regional Reference Laboratory, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - A Duncan Steele
- Diarrhoeal Pathogens Research Unit, Department of Virology, WHO AFRO Rotavirus Regional Reference Laboratory, Sefako Makgatho Health Sciences University, Pretoria, South Africa. .,Present address: Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, WA, USA.
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7
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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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8
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Harastani HH, Reslan L, Sabra A, Ali Z, Hammadi M, Ghanem S, Hajar F, Matar GM, Dbaibo GS, Zaraket H. Genetic Diversity of Human Rotavirus A Among Hospitalized Children Under-5 Years in Lebanon. Front Immunol 2020; 11:317. [PMID: 32174920 PMCID: PMC7054381 DOI: 10.3389/fimmu.2020.00317] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/07/2020] [Indexed: 12/02/2022] Open
Abstract
Human rotavirus remains a major cause of gastroenteritis worldwide despite the availability of effective vaccines. In this study, we investigated the genetic diversity of rotaviruses circulating in Lebanon. We genetically characterized the VP4 and VP7 genes encoding the outer capsid proteins of 132 rotavirus-associated gastroenteritis specimens, previously identified in hospitalized children (<5 years) from 2011 to 2013 in Lebanon. These included 43 vaccine-breakthrough specimens and the remainder were from non-vaccinated subjects. Phylogenetic analysis of VP4 and VP7 genes revealed distinct clustering compared to the vaccine strains, and several substitutions were identified in the antigenic epitopes of Lebanese specimens. No unique changes were identified in the breakthrough specimens compared to non-breakthroughs that could explain the occurrence of infection in vaccinated children. Further, we report the emergence of a rare P[8] OP354-like strain with a G9 VP7 in Lebanon, possessing high genetic variability in their VP4 compared to vaccine strains. Therefore, human rotavirus strains circulating in Lebanon and globally have accumulated numerous substitutions in their antigenic sites compared to those currently used in the licensed vaccines. The successful spread and continued genetic drift of these strains over time might undermine the effectiveness of the vaccines. The effect of such changes in the antigenic sites on vaccine efficacy remains to be assessed.
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Affiliation(s)
- Houda H Harastani
- Faculty of Medicine, Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Lina Reslan
- Faculty of Medicine, Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Ahmad Sabra
- Faculty of Medicine, Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Zainab Ali
- Faculty of Medicine, Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon.,Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Moza Hammadi
- Faculty of Medicine, Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon.,Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Soha Ghanem
- Faculty of Medicine, Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon.,Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Farah Hajar
- Faculty of Medicine, Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon.,Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ghassan M Matar
- Faculty of Medicine, Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon.,Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ghassan S Dbaibo
- Faculty of Medicine, Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon.,Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hassan Zaraket
- Faculty of Medicine, Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon.,Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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9
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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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Vizzi E, Piñeros OA, Oropeza MD, Naranjo L, Suárez JA, Fernández R, Zambrano JL, Celis A, Liprandi F. Human rotavirus strains circulating in Venezuela after vaccine introduction: predominance of G2P[4] and reemergence of G1P[8]. Virol J 2017; 14:58. [PMID: 28320411 PMCID: PMC5359893 DOI: 10.1186/s12985-017-0721-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/01/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Rotavirus (RV) is the most common cause of severe childhood diarrhea worldwide. Despite Venezuela was among the first developing countries to introduce RV vaccines into their national immunization schedules, RV is still contributing to the burden of diarrhea. Concerns exist about the selective pressure that RV vaccines could exert on the predominant types and/or emergence of new strains. RESULTS To assess the impact of RV vaccines on the genotype distribution 1 year after the vaccination was implemented, a total of 912 fecal specimens, collected from children with acute gastroenteritis in Caracas from February 2007 to April 2008, were screened, of which 169 (18.5%) were confirmed to be RV positive by PAGE. Rotavirus-associated diarrhea occurred all year-round, although prevailed during the coolest and driest months among unvaccinated children under 24 months old. Of 165 RV strains genotyped for G (VP7) and P (VP4) by seminested multiplex RT-PCR, 77 (46.7%) were G2P[4] and 63 (38.2%) G1P[8]. G9P[8], G3P[8] and G2P[6] were found in a lower proportion (7.3%). Remarkable was also the detection of <5% of uncommon combinations (G8P[14], G8P[4], G1P[4] and G4P[4]) and 3.6% of mixed infections. A changing pattern of G/P-type distribution was observed during the season studied, with complete predominance of G2P[4] from February to June 2007 followed by its gradual decline and the reemergence of G1P[8], predominant since January 2008. Phylogenetic analysis of VP7 and VP4 genes revealed a high similarity among G2P[4] and global strains belonging to G2-II and P[4]-V lineages. The amino acid substitution 96D → N, related with reemergence of the G2 genotype elsewhere, was observed. The G1P[8] strains from Caracas were grouped into the lineages G1-I and P[8]-III, along with geographically remote G1P[8] rotaviruses, but they were rather distant from Rotarix® vaccine and pre-vaccine strains. Unique amino acid substitutions observed on neutralization domains of the VP7 sequence from Venezuelan post-vaccine G1P[8] could have conditioned their re-emergence and a more efficient dissemination into susceptible population. CONCLUSIONS The results suggest that natural fluctuations of genotypes in combination with forces driving the genetic evolution could determine the spread of novel strains, whose long-term effect on the efficacy of available vaccines should be determined.
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Affiliation(s)
- Esmeralda Vizzi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020-A, Venezuela.
| | - Oscar A Piñeros
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020-A, Venezuela
| | - M Daniela Oropeza
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020-A, Venezuela
| | | | | | - Rixio Fernández
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020-A, Venezuela
| | - José L Zambrano
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020-A, Venezuela
| | - Argelia Celis
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020-A, Venezuela
- Universidad de Carabobo-Sede Aragua, Maracay, Edo. Aragua, Venezuela
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020-A, Venezuela
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Wang Y, Zhang J, Liu P. Clinical and molecular epidemiologic trends reveal the important role of rotavirus in adult infectious gastroenteritis, in Shanghai, China. INFECTION GENETICS AND EVOLUTION 2017; 47:143-154. [DOI: 10.1016/j.meegid.2016.11.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 11/17/2016] [Accepted: 11/18/2016] [Indexed: 11/30/2022]
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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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13
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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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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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15
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Doan YH, Haga K, Fujimoto A, Fujii Y, Takai-Todaka R, Oka T, Kimura H, Yoshizumi S, Shigemoto N, Okamoto-Nakagawa R, Shirabe K, Shinomiya H, Sakon N, Katayama K. Genetic analysis of human rotavirus C: The appearance of Indian-Bangladeshi strain in Far East Asian countries. INFECTION GENETICS AND EVOLUTION 2016; 41:160-173. [PMID: 27071530 DOI: 10.1016/j.meegid.2016.03.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/17/2016] [Accepted: 03/25/2016] [Indexed: 11/30/2022]
Abstract
Rotaviruses C (RVCs) circulate worldwide as an enteric pathogen in both humans and animals. Most studies of their genetic diversity focus on the VP7 and VP4 genes, but the complete genomes of 18 human RVCs have been described in independent studies. The genetic background of the Far East Asian RVCs is different than other human RVCs that were found in India and Bangladesh. Recently, a RVC detected in 2010 in South Korea had genetic background similar to the Indian-Bangladeshi RVCs. This study was undertaken to determine the whole genome of eight Japanese RVCs detected in 2005-2012, and to compare them with other human and animal global RVCs to better understand the genetic background of contemporary Far East Asian RVC. By phylogenetic analysis, the human RVCs appeared to be distinct from animal RVCs. Among human RVCs, three lineage constellations had prolonged circulation. The genetic background of the Far East Asian RVC was distinguished from Indian-Bangladeshi RVC as reported earlier. However, we found one Japanese RVC in 2012 that carried the genetic background of Indian-Bangladeshi RVC, whereas the remaining seven Japanese RVCs carried the typical genetic background of Far East Asian RVC. This is the first report of the Indian-Bangladeshi RVC in Japan. With that observation and the reassortment event of human RVCs in Hungary, our study indicates that the RVCs are spreading from one region to another.
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Affiliation(s)
- Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Fujimoto
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Takai-Todaka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Naoki Shigemoto
- Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan
| | | | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Hiroto Shinomiya
- Ehime Prefectural Institute of Public Health and Environmental Science, Ehime, Japan
| | - Naomi Sakon
- Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
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16
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Abdel-Moneim AS, Al-Malky MIR, Alsulaimani AAA, Abuelsaad ASA, Mohamed I, Ismail AK. Sequence Diversity of VP4 and VP7 Genes of Human Rotavirus Strains in Saudi Arabia. Foodborne Pathog Dis 2015; 12:937-44. [PMID: 26356200 DOI: 10.1089/fpd.2015.1990] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Group A rotavirus is responsible for inducing severe diarrhea in young children worldwide. Rotavirus vaccines are used to control the disease in many countries. In the current study, the sequences of human rotavirus G and P types in Saudi Arabia are reported and compared to different relevant published sequences. In addition, the VP4 and VP7 genes of the G1P[8] strains are compared to different antigenic epitopes of the rotavirus vaccines. Stool samples were collected from children under 2 years suffering from severe diarrhea. Screening of the rotavirus-positive samples was performed with rapid antigen detection kit. RNA was amplified from rotavirus-positive samples by reverse transcriptase polymerase chain reaction assay for both VP4 and VP7 genes. Direct sequencing of the VP4 and VP7 genes was conducted and the obtained sequences were compared to each other and to the rotavirus vaccines. Both G1P[8] G1P[4] genotypes were detected. Phylogenetic analysis revealed that the detected strains belong to G1 lineage 1 and 2, P[8] lineage 3, and to P[4] lineage 5. Multiple amino acid substitutions were detected between the Saudi RVA strains and the commonly used vaccines. The current findings emphasize the importance of the continuous surveillance of the circulating rotavirus strains, which is crucial for monitoring virus evolution and helping in predicting the protection level afforded by rotavirus vaccines.
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Affiliation(s)
- Ahmed S Abdel-Moneim
- 1 College of Medicine, Taif University , Al-Taif, Saudi Arabia .,2 Department of Virology, Faculty of Veterinary Medicine, Beni-Suef University , Beni-Suef, Egypt
| | | | | | | | - Imad Mohamed
- 1 College of Medicine, Taif University , Al-Taif, Saudi Arabia
| | - Ayman K Ismail
- 1 College of Medicine, Taif University , Al-Taif, Saudi Arabia
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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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18
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Mullick S, Mandal P, Nayak MK, Ghosh S, De P, Rajendran K, Bhattacharya MK, Mitra U, Ramamurthy T, Kobayashi N, Chawla-Sarkar M. Hospital based surveillance and genetic characterization of rotavirus strains in children (<5 years) with acute gastroenteritis in Kolkata, India, revealed resurgence of G9 and G2 genotypes during 2011-2013. Vaccine 2015; 32 Suppl 1:A20-8. [PMID: 25091674 DOI: 10.1016/j.vaccine.2014.03.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION India accounts for an estimated 457,000-884,000 hospitalizations and 2 million outpatient visits for diarrhea. In spite of the huge burden of rotavirus (RV) disease, RV vaccines have not been introduced in national immunization programme of India. Therefore, continuous surveillance for prevalence and monitoring of the circulating genotypes is needed to assess the disease burden prior to introduction of vaccines in this region. METHODS During January 2011 through December 2013, 830 and 1000 stool samples were collected from hospitalized and out-patient department (OPD) patients, respectively, in two hospitals in Kolkata, Eastern India. After primary screening, the G-P typing was done by multiplex semi-nested PCR using type specific primers followed by sequencing. Phylogenetic analysis for the VP7 gene of 25 representative strains was done. RESULTS Among hospitalized and OPD patients, 53.4% and 47.5% cases were positive for rotaviruses, respectively. Unlike previous studies where G1 was predominant, in hospitalized cases G9 rotavirus strains were most prevalent (40%), followed by G2 (39.6%) whereas G1 and G12 occurred at 16.4% and 5.6% frequency. In OPD cases, the most prevalent strain was G2 (40.3%), followed by G1, G9 and G12 at 25.5%, 22.8%, 9.3%, respectively. Phylogenetically the G1, G2 and G9 strains from Kolkata did not cluster with corresponding genotypes of Rotarix, RotaTeq and Rotavac (116E) vaccine strains. CONCLUSION The study highlights the high prevalence of RV in children with gastroenteritis in Kolkata. The circulating genotypes have changed over the time with predominance of G9 and G2 strains during 2011-2013. The current G2, G9 and G1 Kolkata strains shared low amino acid homologies with current vaccine strains. Although there is substantial evidence for cross protection of vaccines against a variety of strains, still the strain variation should be monitored post vaccine introduction to determine if it has any impact on vaccine effectiveness.
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Affiliation(s)
- Satarupa Mullick
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Paulami Mandal
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Mukti Kant Nayak
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Souvik Ghosh
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Papiya De
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - K Rajendran
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Utpala Mitra
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
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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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Afrad MH, Matthijnssens J, Afroz SF, Rudra P, Nahar L, Rahman R, Hossain ME, Rahman SR, Azim T, Rahman M. Differences in lineage replacement dynamics of G1 and G2 rotavirus strains versus G9 strain over a period of 22 years in Bangladesh. INFECTION GENETICS AND EVOLUTION 2014; 28:214-22. [PMID: 25305473 DOI: 10.1016/j.meegid.2014.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/27/2014] [Accepted: 10/01/2014] [Indexed: 10/24/2022]
Abstract
Group A rotaviruses (RVAs) have been a major cause of severe gastroenteritis in Bangladesh, mainly in children below the age of five. At the icddr,b, RVA strains collection and characterization dates back for more than 20 years. This sample collection was used to study the molecular evolution of the VP7 gene of G1, G2 and G9 RVA strains, which have been circulating in Bangladesh for most of this study period. The evolutionary rates (95% HPD) for G1, G2 and G9 were calculated to be 0.93×10(-3) (0.68-1.18), 1.45×10(-3) (1.12-1.78) and 1.07×10(-3) (0.78-1.39), respectively, which is in line with previous data for the RVA VP7 outer capsid protein, which is under strong negative selective pressure. Bayesian analyses revealed that for the G1 and G2 genotypes, one or multiple lineages co-circulated for one or a few seasons, frequently followed by replacement with genetically different lineages. This can be explained by the existence of a large variety of G1 and G2 RVA lineages and the rapid dissemination of different lineages across the globe. In contrast, circulating G9 lineages were rather closely related to each other across the study period and they were usually derived from variants circulating in the previous season(s). This is consistent with the fact that G9 RVAs have circulated in the human population for less than 20 years, and therefore their genetic diversity is much smaller, not resulting in the replacement of circulating G9 strains by highly divergent G9 lineages from abroad. Such different evolutionary dynamics for different RVA genotypes may alter their response to the selective pressure that might be exerted by the introduction of RVA vaccines and therefore a continued close monitoring is warranted.
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Affiliation(s)
- Mokibul Hassan Afrad
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh.
| | - Jelle Matthijnssens
- Laboratory of Clinical & Epidemiological Virology, Department of Microbiology & Immunology, Rega Institute for Medical Research, University of Leuven, Belgium
| | - Syeda Farhana Afroz
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
| | - Pranab Rudra
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Lutfun Nahar
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
| | - Rajibur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
| | - Mohammad Enayet Hossain
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
| | | | - Tasnim Azim
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
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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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Characterization of G2P[4] rotavirus strains causing outbreaks of gastroenteritis in the Northern Territory, Australia, in 1999, 2004 and 2009. INFECTION GENETICS AND EVOLUTION 2014; 28:434-45. [PMID: 25152486 DOI: 10.1016/j.meegid.2014.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 08/01/2014] [Accepted: 08/11/2014] [Indexed: 01/18/2023]
Abstract
Outbreaks of rotavirus diarrhea cause a large disease burden in the Alice Springs region of the Northern Territory, Australia. The introduction of the rotavirus vaccine Rotarix® has been associated with an increase in detection of G2P[4] strains in many countries. However, G2P[4] emergence has also been observed in vaccine-naive countries, suggesting a general global increase in the circulation of G2P[4] strains. A G2P[4] rotavirus outbreak occurred in 2009, 28 months after the introduction of the Rotarix® vaccine and 43 children were hospitalized. Pre-vaccine introduction, G2P[4] strains were observed associated with large outbreaks in 1999 and 2004. To determine the genetic relationship between these strains whole genome sequence analysis was conducted on representative strains from each of the G2P[4] outbreaks, in 1999, 2004 and 2009. Phylogenetic analysis revealed the majority of genes from 2009 outbreak strain clustered with contemporary global strains, while the VP7 gene clustered with contemporary and older strains and was antigenically distinct to the majority of contemporary global G2P[4] strains; suggesting the strain was an intragenogroup reassortant. The 1999 and 2009 strains appear to share similar evolutionary origins, and both had a high degree of genetic identity to previously identified Australian and global strains. Conversely, the 2004 outbreak strain was more divergent in comparison to Australian and global strains. The 1999 and 2004 outbreaks likely occurred due to the accumulation of immunologically naïve children in the population following low levels of G2P[4] rotavirus disease in the community in the years prior to each outbreak. The 2009 outbreak was associated with moderate vaccine coverage in the population and vaccine efficacy against the strain was low. The circulation of this unusual strain in the population combined with low vaccine coverage and diminished vaccine efficacy likely contributed to the outbreak occurring in this population.
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Tatsumi M, Nagaoka Y, Tsugawa T, Yoto Y, Hori T, Tsutsumi H. Longitudinal analysis of VP7 gene of group A human rotavirus G2P[4] strains circulating in the pre-vaccine era in Sapporo, Japan from 1991 to 2011. Microbiol Immunol 2014; 58:540-4. [PMID: 25040726 DOI: 10.1111/1348-0421.12182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/03/2014] [Accepted: 07/14/2014] [Indexed: 11/27/2022]
Abstract
Sequence analysis of the VP7 gene in 23 group A human rotavirus G2P[4] strains obtained during 1991-2011, that is, the pre-vaccine era, in Sapporo, Japan showed considerable genetic diversity, mainly in variable regions. Recent G2P[4] epidemic strains were located in sublineage IVa with a distinctive substitution of D96N. This study provides background data on the genetic variability of G2P[4] rotavirus-VP7 gene prior to the widespread use of rotavirus vaccines in Japan.
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Affiliation(s)
- Masatoshi Tatsumi
- Department of Pediatrics, Sapporo Medical University School of Medicine, South-1, West-16, Sapporo, 060-8543, Japan; Otaru Kyokai Hospital, Otaru City, Japan
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24
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Characterization of G2P[4] rotavirus strains associated with increased detection in Australian states using the RotaTeq® vaccine during the 2010-2011 surveillance period. INFECTION GENETICS AND EVOLUTION 2014; 28:398-412. [PMID: 24861815 DOI: 10.1016/j.meegid.2014.05.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/15/2014] [Accepted: 05/17/2014] [Indexed: 11/20/2022]
Abstract
The introduction of rotavirus vaccines Rotarix® and RotaTeq® into the Australian National Immunisation Program in July 2007 has resulted in a dramatic decrease in the burden of rotavirus disease. G2P[4] strains became the dominant genotype Australia-wide during the 2010-2011 surveillance period and for the first time since vaccine introduction, a higher proportion were isolated in jurisdictions using RotaTeq® vaccine compared to locations using Rotarix®. Phylogenetic analysis of the VP7 gene of 32 G2P[4] strains identified six genetic clusters, these distinct clusters were also observed in the VP4 gene for a subset of 12 strains. The whole genome was determined for a representative strain of clusters; A (RVA/Human-wt/AUS/SA066/2010/G2P[4]), B (RVA/Human-wt/AUS/WAPC703/2010/G2P[4]), C (RVA/Human-wt/AUS/MON008/2010/G2P[4]) and E (RVA/Human-wt/AUS/RCH041/2010/G2P[4]). All of the strains possessed the archetypal DS-1 like genome constellation G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Three of the strains, SA066, MON008 and WAPC703 clustered together and were distinct to RCH041 for all 11 genes. The VP7 genes of 31/32 of the strains characterized in this study possessed five conserved amino acid substitutions when compared to the G2 VP7 gene present in the RotaTeq® vaccine. Three of the substitutions were in the VP7 antigenic regions A and C, the substitutions A87T, D96N and S213D have been reported in the majority of G2P[4] strains circulating globally over the previous decade. These changes may have improved the ability of strains to circulate in settings of high vaccine use.
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25
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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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26
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Theamboonlers A, Maiklang O, Thongmee T, Chieochansin T, Vuthitanachot V, Poovorawan Y. Complete genotype constellation of human rotavirus group A circulating in Thailand, 2008–2011. INFECTION GENETICS AND EVOLUTION 2014; 21:295-302. [DOI: 10.1016/j.meegid.2013.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 01/26/2023]
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27
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Giammanco GM, Bonura F, Zeller M, Heylen E, Van Ranst M, Martella V, Bányai K, Matthijnssens J, De Grazia S. Evolution of DS-1-like human G2P[4] rotaviruses assessed by complete genome analyses. J Gen Virol 2013; 95:91-109. [PMID: 24077298 DOI: 10.1099/vir.0.056788-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Group A rotaviruses (RVAs) are a leading cause of viral gastroenteritis in children, with G2P[4] RVA being one of the most common human strains worldwide. The complete genome sequences of nine G2P[4] RVA strains, selected from a 26-year archival collection (1985-2011) established in Palermo, Italy, were determined. A strain associated with a peak of G2P[4] RVA activity in 1996 resembled a reassortant strain identified in Kenya in 1982 and differed completely in genomic make up from more recent strains that circulated during 2004-2011. Conversely, the 2004-2011 G2P[4] RVAs were genetically more similar to contemporary RVA strains circulating globally. Recent G2P[4] strains possessed either single or multiple genome segments (VP1, VP3 and/or NSP4) likely derived from ruminant viruses through intra-genotype reassortment. Amino acid substitutions were selected and maintained over time in the VP7 and VP8* antigenic proteins, allowing the circulation of two contemporary G2P[4] variants to be distinguished. Altogether, these findings suggest that major changes in the genomic composition of recent G2P[4] RVAs occurred in the early 2000s, leading to the appearance of a novel variant of the DS-1-like genotype constellation. Whether the modifications observed in the neutralizing antigens and in the genome composition of modern G2P[4] RVAs may affect the long-term effectiveness of the vaccination programmes remains to be explored.
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Affiliation(s)
- Giovanni M Giammanco
- Dipartimento di Scienze per la Promozione della Salute 'G. D'Alessandro', Università di Palermo, Italy
| | - Floriana Bonura
- Dipartimento di Scienze per la Promozione della Salute 'G. D'Alessandro', Università di Palermo, Italy
| | - Mark Zeller
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Elisabeth Heylen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Vito Martella
- Dipartimento di Sanità Pubblica e Zootecnia, Università Aldo Moro di Bari, Valenzano, Italy
| | - Kristián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Jelle Matthijnssens
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Simona De Grazia
- Dipartimento di Scienze per la Promozione della Salute 'G. D'Alessandro', Università di Palermo, Italy
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28
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Comparative evaluation of commercially available manual and automated nucleic acid extraction methods for rotavirus RNA detection in stools. J Virol Methods 2013; 194:242-9. [PMID: 24036075 PMCID: PMC4603280 DOI: 10.1016/j.jviromet.2013.08.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 08/13/2013] [Accepted: 08/21/2013] [Indexed: 11/22/2022]
Abstract
Rotaviruses are a major cause of viral gastroenteritis in children. For accurate and sensitive detection of rotavirus RNA from stool samples by reverse transcription-polymerase chain reaction (RT-PCR), the extraction process must be robust. However, some extraction methods may not remove the strong RT-PCR inhibitors known to be present in stool samples. The objective of this study was to evaluate and compare the performance of six extraction methods used commonly for extraction of rotavirus RNA from stool, which have never been formally evaluated: the MagNA Pure Compact, KingFisher Flex and NucliSENS easyMAG instruments, the NucliSENS miniMAG semi-automated system, and two manual purification kits, the QIAamp Viral RNA kit and a modified RNaid kit. Using each method, total nucleic acid or RNA was extracted from eight rotavirus-positive stool samples with enzyme immunoassay optical density (EIA OD) values ranging from 0.176 to 3.098. Extracts prepared using the MagNA Pure Compact instrument yielded the most consistent results by qRT-PCR and conventional RT-PCR. When extracts prepared from a dilution series were extracted by the 6 methods and tested, rotavirus RNA was detected in all samples by qRT-PCR but by conventional RT-PCR testing, only the MagNA Pure Compact and KingFisher Flex extracts were positive in all cases. RT-PCR inhibitors were detected in extracts produced with the QIAamp Viral RNA Mini kit. The findings of this study should prove useful for selection of extraction methods to be incorporated into future rotavirus detection and genotyping protocols.
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29
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Do LP, Nakagomi T, Doan YH, Kitahori Y, Nakagomi O. Molecular evolution of the VP7 gene of Japanese G2 rotaviruses before vaccine introduction. Arch Virol 2013; 159:315-9. [PMID: 23925901 DOI: 10.1007/s00705-013-1804-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 06/20/2013] [Indexed: 01/01/2023]
Abstract
Changes in the prevalence of G2 rotavirus after vaccine introduction are an important issue. However, such changes in a given country should be interpreted in the global context over time. We determined 35 Japanese G2 sequences and compared them with 508 globally collected G2 sequences. The D96N substitution, a substitution known to be associated with an abrupt increase in G2 strains and antigenic changes, emerged in those strains that formed a nascent lineage outside of the currently predominant lineage (sublineage IVa). Further studies are warranted to monitor the potential of their global spread, since they also appeared in Europe and Australia.
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Affiliation(s)
- L P Do
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
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30
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Gauchan P, Nakagomi T, Sherchand JB, Yokoo M, Pandey BD, Cunliffe NA, Nakagomi O. Continued Circulation of G12P[6] Rotaviruses Over 28 Months in Nepal: Successive Replacement of Predominant Strains. Trop Med Health 2013; 41:7-12. [PMID: 23533063 PMCID: PMC3601201 DOI: 10.2149/tmh.2012-28] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 11/19/2012] [Indexed: 11/11/2022] Open
Abstract
Rotavirus A causes severe diarrhoea in infants and young children worldwide. The migration pattern (electropherotype) of the double-stranded RNA genome upon polyacrylamide gel electrophoresis has been used to define "strains" in molecular epidemiology. In temperate countries, distinct electropherotypes (strains) appear after the annual, off-seasonal interruption of rotavirus circulation. In Nepal, rotavirus circulated year-round and an uncommon genotype G12P[6] predominated and persisted, providing a unique opportunity to examine whether the same electropherotype (the same strain) persisted or new electropherotypes (new strains) emerged successively under the same G12P[6] predominance. A total of 147 G12P[6] rotaviruses, collected from diarrhoeal children in Nepal between 2007 and 2010, were classified into 15 distinct electropherotypes (strains). Of these, three electropherotypes (strains), LP1, LP24, and LP27, accounted for 10%, 32% and 38% of the G12P[6] rotaviruses, respectively. Each of the three major strains successively appeared, dominated, and disappeared. This study provided new evidence for the hypothesis that rotavirus constantly changes its strains to predominate in the local population even under conditions where a single genotype predominates and persists. Such dynamic strain replacement, the constant takeover of one predominant strain by another, fitter strain, is probably gives a competitive edge to the survival of rotavirus in nature.
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Affiliation(s)
- Punita Gauchan
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, and Global Center of Excellence, Nagasaki University, Nagasaki, Japan
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31
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Matthijnssens J, Van Ranst M. Genotype constellation and evolution of group A rotaviruses infecting humans. Curr Opin Virol 2012; 2:426-33. [PMID: 22683209 DOI: 10.1016/j.coviro.2012.04.007] [Citation(s) in RCA: 235] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 03/01/2012] [Accepted: 04/19/2012] [Indexed: 12/12/2022]
Abstract
Numerous rotavirus group A (RVA) strains with distinct G-genotype and P-genotype combinations have been described infecting humans worldwide. However, the increasing amount of complete RVA genome data which have become available, suggest that only RVA strains with 2 discrete genotype constellations have been successful in sustaining infection of humans worldwide over longer periods of time. Those genotype constellations have been designated I1-R1-C1-M1-A1-N1-T1-E1-H1 and I2-R2-C2-M2-A2-N2-T2-E2-H2 and are also known as Wa-like and DS-1-like, respectively. RVAs of other genotype constellations which were able to spread to a limited extent in the human population are AU-1-related RVA strains (I3-R3-C3-M3-A3/A12-N3-T3-E3-H3/H6) in combination with G3P[9] or G12P[9], and neonatal G10P[11] RVA strains in India (bovine×human Wa-like reassortants). On the basis of the analysis of complete genomes, it is suggested that the overall genetic diversity of epidemiologically widespread human RVA strains is more limited than generally assumed. This conclusion has consequences for how we look at host range restriction and the criteria according to which the effectiveness of RVA universal mass vaccination programs is assessed.
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Affiliation(s)
- Jelle Matthijnssens
- Laboratory of Clinical & Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium.
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32
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Desselberger U. Highlights of the 4th European Rotavirus Biology Symposium. Future Virol 2012. [DOI: 10.2217/fvl.11.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
After meetings in France, Sweden and Scotland, the 4th European Rotavirus Biology Symposium took place in southern Italy on 2–5 October 2011. The meeting was attended by 96 participants from 24 countries in four continents, demonstrating the increase in attention paid to this event, but also, more importantly, the high quality of virtually all contributions. The meeting was very ably organized by R Ruggeri and L Fiore (Rome, Italy), supported by L Svensson (Linköping, Sweden) in the beautiful environment of Villa San Giovanni, Reggio Calabria, Italy, with a direct view on Sicily over the Strait of Messina. An attractive social program comprised a visit to the local archaeological museum and to a museum devoted to the processing of the famous local bergamot fruit.
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Affiliation(s)
- Ulrich Desselberger
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
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