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Novikova NA, Sashina TA, Epifanova NV, Kashnikov AU, Morozova OV. Long-term monitoring of G1P[8] rotaviruses circulating without vaccine pressure in Nizhny Novgorod, Russia, 1984-2019. Arch Virol 2020; 165:865-875. [DOI: 10.1007/s00705-020-04553-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/18/2020] [Indexed: 01/01/2023]
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Cuffia VI, Díaz Ariza MDC, Silvera A, Sabini LI, Cordoba PA. Comparison of Antigenic Dominants of VP7 in G9 and G1 Rotavirus Strains Circulating in La Rioja, Argentina, with the Vaccine Strains. Viral Immunol 2016; 29:367-71. [DOI: 10.1089/vim.2015.0126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Valeria I. Cuffia
- Laboratorio 1, Departamento de Investigación, IUCS, Fundación Barceló H.A. Sede La Rioja, La Rioja, Argentina
| | - María del Carmen Díaz Ariza
- Laboratorio 1, Departamento de Investigación, IUCS, Fundación Barceló H.A. Sede La Rioja, La Rioja, Argentina
| | - Alejandro Silvera
- Laboratorio 1, Departamento de Investigación, IUCS, Fundación Barceló H.A. Sede La Rioja, La Rioja, Argentina
| | - Liliana I. Sabini
- Laboratorio de Virología, Departamento de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Rio Cuarto, Cordoba, Argentina
| | - Patricia A. Cordoba
- Laboratorio 1, Departamento de Investigación, IUCS, Fundación Barceló H.A. Sede La Rioja, La Rioja, Argentina
- Laboratorio de Microbiología, Departamento de Ciencias Exactas Físicas y Naturales, Universidad Nacional de La Rioja, Argentina
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Jalilvand S, Afchangi A, Mohajel N, Roohvand F, Shoja Z. Diversity of VP7 genes of G1 rotaviruses isolated in Iran, 2009–2013. INFECTION GENETICS AND EVOLUTION 2016; 37:275-9. [DOI: 10.1016/j.meegid.2015.09.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 09/26/2015] [Accepted: 09/28/2015] [Indexed: 10/23/2022]
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Barril PA, Fumian TM, Prez VE, Gil PI, Martínez LC, Giordano MO, Masachessi G, Isa MB, Ferreyra LJ, Ré VE, Miagostovich M, Pavan JV, Nates SV. Rotavirus seasonality in urban sewage from Argentina: effect of meteorological variables on the viral load and the genetic diversity. ENVIRONMENTAL RESEARCH 2015; 138:409-15. [PMID: 25777068 DOI: 10.1016/j.envres.2015.03.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/05/2015] [Accepted: 03/08/2015] [Indexed: 05/15/2023]
Abstract
In Argentina, the rotavirus disease exhibits seasonal variations, being most prevalent in the fall and winter months. To deepen the understanding of rotavirus seasonality in our community, the influence of meteorological factors on the rotavirus load and the genetic diversity in urban raw sewage from Córdoba city, Argentina were evaluated. Wastewater samples were collected monthly during a three-year study period and viral particles were concentrated by polyethylene glycol precipitation. RT-nested PCR was applied for rotavirus detection, and VP7/VP4 characterization and real-time PCR for rotavirus quantification. Both molecular techniques showed relatively similar sensitivity rates and revealed rotavirus presence in urban wastewater in cold and warm seasons, indicating its circulation in the local community all year round. However, a slight trend for rotavirus circulation was noted by real-time PCR in the fall and winter seasons, showing a significantly higher peak of rotavirus concentration at mean temperatures lower than 18°C and also higher, although not statistically different during drier weather. VP7 and VP4 gene characterization showed that G1 and P[8] genotypes were dominant, and temporal variations in genotype distribution were not observed. Rotavirus spread is complex and our results point out that weather factors alone cannot explain the seasonal quantitative pattern of the rotavirus disease. Therefore, alternative transmission routes, changes in human behavior and susceptibility, and the stability and survivability of the virus might all together contribute to the seasonality of rotavirus. The results obtained here provide evidence regarding the dynamics of rotavirus circulation and maintenance in Argentina.
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Affiliation(s)
- P A Barril
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016 Córdoba, Argentina.
| | - T M Fumian
- Laboratório de Virologia Comparada e Ambiental, Pavilhão Hélio & Peggy Pereira, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Avenida Brasil, 4365 Manguinhos, 21040-360 Rio de Janeiro, Brazil
| | - V E Prez
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016 Córdoba, Argentina
| | - P I Gil
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016 Córdoba, Argentina
| | - L C Martínez
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016 Córdoba, Argentina
| | - M O Giordano
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016 Córdoba, Argentina
| | - G Masachessi
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016 Córdoba, Argentina
| | - M B Isa
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016 Córdoba, Argentina
| | - L J Ferreyra
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016 Córdoba, Argentina
| | - V E Ré
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016 Córdoba, Argentina
| | - M Miagostovich
- Laboratório de Virologia Comparada e Ambiental, Pavilhão Hélio & Peggy Pereira, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Avenida Brasil, 4365 Manguinhos, 21040-360 Rio de Janeiro, Brazil
| | - J V Pavan
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016 Córdoba, Argentina
| | - S V Nates
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, 5016 Córdoba, Argentina
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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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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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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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Mullick S, Mukherjee A, Ghosh S, Pazhani GP, Sur D, Manna B, Nataro JP, Levine MM, Ramamurthy T, Chawla-Sarkar M. Community based case-control study of rotavirus gastroenteritis among young children during 2008-2010 reveals vast genetic diversity and increased prevalence of G9 strains in Kolkata. PLoS One 2014; 9:e112970. [PMID: 25401757 PMCID: PMC4234499 DOI: 10.1371/journal.pone.0112970] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 10/17/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Group A Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children (<5 years) worldwide. Although rotavirus vaccines have been successfully administered in many countries, in India the introduction of rotavirus vaccine in national immunization program was approved in 2014. Since high disease burden and large number of genetic variants have been reported from low income countries including India, monitoring of rotavirus was initiated prior to implementation of the vaccine in the region. METHODS A total number of 3,582 stool samples were collected from an urban slum community in Kolkata, among which 1,568 samples were obtained from children of ≤ 5 years of age, with moderate to severe diarrhoea and 2,014 samples were collected from age-sex matched healthy neighbourhood controls. Rotavirus positive samples were typed by multiplex semi-nested PCR and nucleotide sequencing. Circulating strains were phylogenetically analyzed. RESULTS Among 1,568 children with diarrhoea, 395 (25.2%), and among 2,014 asymptomatic children, 42 (2%) were rotavirus positive. G1P[8] was identified as the most common strain (32%) followed by G9P[8] (16.9%), G2P[4] (13.5%) and G9P[4] (10.75%). G12 strains with combinations of P[4], P[6] and P[8] comprised 11.9% of total positive strains. The rest (<10%) were rare and uncommon strains like G1P[4], G1P[6], G2P[8] and animal-like strains G4P[6], G6P[14] and G11P[25]. The 42 rotavirus positive samples from asymptomatic children revealed common genotypes like G1, G2 and G9. CONCLUSION This community based case-control study showed increased predominance of genotype G9 in Kolkata. It also confirmed co-circulation of a large number of genetic variants in the community. Asymptomatic rotavirus positive children though low in number can also be a source of dispersal of infection in the community. This study provides background information to the policy makers for implementation of rotavirus vaccines in this region.
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Affiliation(s)
- Satarupa Mullick
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Anupam Mukherjee
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Santanu Ghosh
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Dipika Sur
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Byomkesh Manna
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - James P. Nataro
- Department of Paediatrics, University of Virginia, School of Medicine, Charlottesville, Virginia, United States of America
| | - Myron M. Levine
- Center for Vaccine Development, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
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Analysis of human rotaviruses from a single location over an 18-year time span suggests that protein coadaption influences gene constellations. J Virol 2014; 88:9842-63. [PMID: 24942570 DOI: 10.1128/jvi.01562-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
UNLABELLED Rotaviruses (RVs) are 11-segmented, double-stranded RNA viruses that cause severe gastroenteritis in children. In addition to an error-prone genome replication mechanism, RVs can increase their genetic diversity by reassorting genes during host coinfection. Such exchanges allow RVs to acquire advantageous genes and adapt in the face of selective pressures. However, reassortment may also impose fitness costs if it unlinks genes/proteins that have accumulated compensatory, coadaptive mutations and that operate best when kept together. To better understand human RV evolutionary dynamics, we analyzed the genome sequences of 135 strains (genotype G1/G3/G4-P[8]-I1-C1-R1-A1-N1-T1-E1-H1) that were collected at a single location in Washington, DC, during the years 1974 to 1991. Intragenotypic phylogenetic trees were constructed for each viral gene using the nucleotide sequences, thereby defining novel allele level gene constellations (GCs) and illuminating putative reassortment events. The results showed that RVs with distinct GCs cocirculated during the vast majority of the collection years and that some of these GCs persisted in the community unchanged by reassortment. To investigate the influence of protein coadaptation on GC maintenance, we performed a mutual information-based analysis of the concatenated amino acid sequences and identified an extensive covariance network. Unexpectedly, amino acid covariation was highest between VP4 and VP2, which are structural components of the RV virion that are not thought to directly interact. These results suggest that GCs may be influenced by the selective constraints placed on functionally coadapted, albeit noninteracting, viral proteins. This work raises important questions about mutation-reassortment interplay and its impact on human RV evolution. IMPORTANCE Rotaviruses are devastating human pathogens that cause severe diarrhea and kill >450,000 children each year. The virus can evolve by accumulating mutations and by acquiring new genes from other strains via a process called reassortment. However, little is known about the relationship between mutation accumulation and gene reassortment for rotaviruses and how it impacts viral evolution. In this study, we analyzed the genome sequences of human strains found in clinical fecal specimens that were collected at a single hospital over an 18-year time span. We found that many rotaviruses did not reassort their genes but instead maintained them as specific sets (i.e., constellations). By analyzing the encoded proteins, we discovered concurrent amino acid changes among them, which suggests that they are functionally coadapted to operate best when kept together. This study increases our understanding of how rotaviruses evolve over time in the human population.
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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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