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Prasetyo D, Ermaya YS, Sabaroedin IM, Widhiastuti D, Bachtiar NS, Kartasasmita CB. Genotype Profiles of Rotavirus Strains in Children under 5-year-old Outpatients with Diarrhea in Bandung, West Java, Indonesia. J Glob Infect Dis 2022; 14:142-146. [PMID: 36636306 PMCID: PMC9831209 DOI: 10.4103/jgid.jgid_101_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/25/2022] [Accepted: 09/30/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Diarrhea is a global leading cause of morbidity and mortality among children under five, with rotaviruses being the most common cause. This study aimed to determine the genotypes of rotavirus in children under 5 years with diarrhea in Bandung, Indonesia. Methods This cross-sectional study was conducted from 2014 to 2018 on 450 children under five with acute diarrhea in primary health centers in Bandung, Indonesia. Fecal samples were examined for rotavirus antigen using an enzyme-linked immunosorbent assay method, and genotype was determined through sequencing using polymerase chain reaction. Results were statistically analyzed using Pearson Chi-square in Epi Info version 3.5.4, with P < 0.05 considered statistically significant. Results Rotavirus was identified in 8.9% of the subjects, slightly higher in boys (n = 24, 9.8%) than girls (n = 16, 7.8%). We found that the most rotavirus positive in age group is >12-24 months and >24-59 months, while the highest percentage is at the age of ≤6 months (11.8%). Moderate malnutrition was observed in more subjects (12.8%). Vomiting was more frequent in patients positive (55%, P = 0.013) and fever was seen in 32.5% (P = 0.645). No signs of dehydration were seen in most subjects (75%), P = 0.227. Rotavirus genotypes identified were G1P[8] (18, 45%), G3P[8] (14, 35%), G3P[6] (4, 10%), G3P[9] (2, 5%), G2P[4] (1, 2.5%), and nontypeable (NT) (1, 2.5%). Conclusions The dominant rotavirus genotype is G1P[8], followed by G3P[8], G3P[6], G3P[9], G2P[4], and NT. The most common rotavirus positive in age group is >12-24 months and >24-59 months, while the highest percentage is at the age of ≤6 months.
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Affiliation(s)
- Dwi Prasetyo
- Department of Child Health, Faculty of Medicine, Universitas Padjadjaran, Dr. Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | - Yudith Setiati Ermaya
- Department of Child Health, Faculty of Medicine, Universitas Padjadjaran, Dr. Hasan Sadikin General Hospital, Bandung, West Java, Indonesia,Address for correspondence: Dr. Yudith Setiati Ermaya, Department of Child Health, Faculty of Medicine, Universitas Padjadjaran, Dr. Hasan Sadikin General Hospital, Jl. Pasteur No. 38, Bandung, West Java, Indonesia. E-mail:
| | - Iesje Martiza Sabaroedin
- Department of Child Health, Faculty of Medicine, Universitas Padjadjaran, Dr. Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | | | | | - Cissy Bana Kartasasmita
- Department of Child Health, Faculty of Medicine, Universitas Padjadjaran, Dr. Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
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Mwanga MJ, Verani JR, Omore R, Tate JE, Parashar UD, Murunga N, Gicheru E, Breiman RF, Nokes DJ, Agoti CN. Multiple Introductions and Predominance of Rotavirus Group A Genotype G3P[8] in Kilifi, Coastal Kenya, 4 Years after Nationwide Vaccine Introduction. Pathogens 2020; 9:pathogens9120981. [PMID: 33255256 PMCID: PMC7761311 DOI: 10.3390/pathogens9120981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/10/2020] [Accepted: 11/20/2020] [Indexed: 01/22/2023] Open
Abstract
Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use of vaccines in more than 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 stool samples from children aged less than 13 years admitted with diarrheal illness to Kilifi County Hospital, coastal Kenya. Antigen screening detected RVA in 55 samples (22.2%). Of these, VP7 (G) and VP4 (P) segments were successfully sequenced in 48 (87.3%) and phylogenetic analysis based on the VP7 sequences identified seven genetic clusters with six different GP combinations: G3P[8], G1P[8], G2P[4], G2P[8], G9P[8] and G12P[8]. The G3P[8] strains predominated the season (n = 37, 67.2%) and comprised three distinct G3 genetic clusters that fell within Lineage I and IX (the latter also known as equine-like G3 Lineage). Both the two G3 lineages have been recently detected in several countries. Our study is the first to document African children infected with G3 Lineage IX. These data highlight the global nature of RVA transmission and the importance of increasing global rotavirus vaccine coverage.
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Affiliation(s)
- Mike J. Mwanga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Jennifer R. Verani
- Centers for Disease Control and Prevention (CDC), KEMRI Complex, off Mbagathi Way, Village Market, Nairobi 00621, Kenya;
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Richard Omore
- KEMRI, Center for Global Health Research (KEMRI-CGHR), Kisumu 00202, Kenya;
| | - Jacqueline E. Tate
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Umesh D. Parashar
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Nickson Murunga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Elijah Gicheru
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Robert F. Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
| | - D. James Nokes
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
- School of Life Sciences and Zeeman Institute (SBIDER), The University of Warwick, Coventry CV4 7AL, UK
| | - Charles N. Agoti
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
- School of Health and Human Sciences, Pwani University, Kilifi 80108, Kenya
- Correspondence:
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3
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Satayarak J, Strauss ST, Duangdee C, Charunwatthana P, Jiamsomboon K, Kosoltanapiwat N, Srinukham S, Boonnak K. Prevalence and diversity of human rotavirus among Thai adults. J Med Virol 2020; 92:2582-2592. [PMID: 32470142 DOI: 10.1002/jmv.26076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/17/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022]
Abstract
Rotavirus infections have become one of the most common causes of infectious gastroenteritis in children. Although rotavirus infections have been intensively studied in infants and young children, the study in adults has been limited. As such, this study assessed the prevalence of rotaviruses and performed the molecular characterization of rotaviruses circulating in Thai adults experiencing acute gastroenteritis between January 2018 and December 2018. Group A human rotaviruses were detected in 100 feces samples by rapid immunochromatography. The peak incidence of infection occurred in February and began to decline in the summer months. From January 2018 to December 2018, there were 1344 acute gastroenteritis adult cases in the Hospital for Tropical Diseases, Bangkok, Thailand. Among these, 310 cases were rotavirus-suspected cases. Only 100 samples tested positive for rotavirus via an immunochromatography test. Twentynine out of the 100 rotavirus-positive samples were further characterized by real-time polymerase chain reaction. The G3[P8] strain was identified as the most prevalent (31.0%) followed by G1P[8], G8P[8] and G9P[8], and G2P[8], which accounted for 20.8%, 17.2%, and 13.8%, respectively. Because of the detection of rare rotavirus genotypes, such as G8, the surveillance of rotavirus epidemiology is crucial in monitoring new emergences of rotavirus strains, leading to a better understanding of the effects of strain variation for further vaccine development.
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Affiliation(s)
- Jantawan Satayarak
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Stefan Thomas Strauss
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chatnapa Duangdee
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Prakaykaew Charunwatthana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Nakhon Pathom, Thailand
| | - Kultida Jiamsomboon
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sompan Srinukham
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kobporn Boonnak
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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4
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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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5
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Nayak MK, Banerjee A, Sarkar R, Mitra S, Dutta K, Ganguly N, Ghosh C, Girish Kumar CP, Niyogi P, Panda S, Dutta S, Chawla-Sarkar M. Genetic characterization of group-A rotaviruses among children in eastern India during 2014-2016: Phylodynamics of co-circulating genotypes. Vaccine 2019; 37:6842-6856. [PMID: 31543416 DOI: 10.1016/j.vaccine.2019.06.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/08/2019] [Accepted: 06/19/2019] [Indexed: 11/15/2022]
Abstract
BACKGROUND Group-A human rotaviruses (GARV) are among the major cause of childhood diarrhea worldwide. In lieu of monitoring the circulatory GARV strains and underscoring the burden of GARV related hospitalization, a systematic surveillance was conducted in three hospitals of eastern India. In this hospital-based diarrheal disease surveillance (2014-2016), GARV was the most common cause of acute infantile gastroenteritis. The strains were genotyped and characterized to understand their prevalence and phylodynamics prior to the introduction of vaccine in eastern India. MATERIALS AND METHODS A total of 3652 stool samples were screened from children (≤5 years) hospitalized with acute diarrhea during 2014-2016. Initial screening for VP6 antigen was done by ELISA. GARV positive samples were genotyped by multiplex semi-nested PCR and DNA sequencing and phylogenetic analyses were based on the capsid proteins VP4 and VP7. RESULTS Of 3652 samples, 1817 (49.8%) were GARV positive. G1, G2, G3 and G9 in conjunction with P[4], P[6]and P[8]genotypes were seen to co-circulate in the population. A sharp deflection from G1 to G3 occurred since 2016; upsurge of G9 strains was seen in alternate years, whereas G2 strains had a low frequency. All the circulating genotypes depicted a low phylogenetic relatedness to the vaccine strains. Differences in antigenic epitopes of VP4 and VP7 proteins in local strains were seen when compared to the vaccine strains. A significant difference in the degree of dehydration, duration of mean hospital stay and frequency of vomiting/24 h between GARV positive and negative children was evident. CONCLUSION The study provides a relevant set of base-line data on high burden of rotaviral gastroenteritis and the varied genotypic diversity among children prior to the introduction of GARV vaccine in this endemic region. Continuous monitoring during post-vaccination era will be required to assess the impact of vaccination in this region.
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Affiliation(s)
- Mukti Kant Nayak
- ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India; B.B. College, Odisha, India
| | - Anindita Banerjee
- ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India
| | - Rakesh Sarkar
- ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India
| | - Suvrotoa Mitra
- ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India
| | | | | | | | | | | | | | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India
| | - Mamta Chawla-Sarkar
- ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata, India.
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6
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Banerjee A, Lo M, Indwar P, Deb AK, Das S, Manna B, Dutta S, Bhadra UK, Bhattacharya M, Okamoto K, Chawla-Sarkar M. Upsurge and spread of G3 rotaviruses in Eastern India (2014-2016): Full genome analyses reveals heterogeneity within Wa-like genomic constellation. INFECTION GENETICS AND EVOLUTION 2018; 63:158-174. [PMID: 29842980 DOI: 10.1016/j.meegid.2018.05.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 12/21/2022]
Abstract
Advent of new strains and shift in predominantly circulating genotypes are characteristics of group- A rotavirus (RVA), one of the major causes of childhood gastroenteritis. During diarrheal disease surveillance at Kolkata, India (2014-2016), a shift in circulating RVA strains from G1P[8] to G3P[8] was seen. Stool samples from children (n = 3048) with acute gastroenteritis were tested of which 38.7% were RVA positive. G1 was the predominant strain (65.3%) in 2014-2015 whereas in late 2015 and 2016, G3 became the preponderant strain (44.6%). In the past decade G3 strains were not observed in this region, we conducted whole genome sequencing of representative strains to gain insight into the phenomenon of emergence and genetic constellation of these circulating human G3 strains. The analyses revealed intergenogroup reassortment in G3P[4] strains (among Wa and DS-1-like genogroup) whereas G3P[8] strains were authentic Wa-like. Phylogenetic analysis revealed Kolkata G3 strains as polymorphic and thus they formed two sub-clusters due to antigenic differences in their VP7 protein. One of the sub-clusters had the wild-type threonine at 87 amino acid position while another sub-cluster had an isoleucine mutation. Presence of additional N-linked glycosylation site at amino acid 283 of VP7 glycoprotein suggests that the major neutralizing epitope on the VP7 (G3) of RotaTeq vaccine differs from the currently circulating G3 strains. The study is important as efficiency of rotavirus vaccine depends on the circulating heterogeneous genotype constellations. Continuous monitoring of circulating RVA strains in endemic settings like India is therefore important in pre- and post-vaccination period to monitor the emergence of new reassortant genotypes in addition to assessing vaccine efficacy.
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Affiliation(s)
- Anindita Banerjee
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India
| | - Mahadeb Lo
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India
| | - Pallavi Indwar
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India
| | - Alok K Deb
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India
| | - Santasabuj Das
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India
| | - Byomkesh Manna
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India
| | - Shanta Dutta
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India
| | - Uchhal K Bhadra
- Infectious diseases and Beliaghata General (ID & BG) Hospital, Beliaghata, Kolkata 700010, India
| | - Mala Bhattacharya
- Dr. B.C. Roy Post Graduate Institute of Pediatric Sciences, Kolkata 700054, India
| | - Keinosuke Okamoto
- Collaborative Research Center of Okayama University for Infectious Diseases at Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Mamta Chawla-Sarkar
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India.
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7
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High prevalence of G3 rotavirus in hospitalized children in Rawalpindi, Pakistan during 2014. PLoS One 2018; 13:e0195947. [PMID: 29708975 PMCID: PMC5927433 DOI: 10.1371/journal.pone.0195947] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/03/2018] [Indexed: 12/23/2022] Open
Abstract
Rotavirus A species (RVA) is the leading cause of severe diarrhea among children in both developed and developing countries. Among different RVA G types, humans are most commonly infected with G1, G2, G3, G4 and G9. During 2003-2004, G3 rotavirus termed as "new variant G3" emerged in Japan that later disseminated to multiple countries across the world. Although G3 rotaviruses are now commonly detected globally, they have been rarely reported from Pakistan. We investigated the genetic diversity of G3 strains responsible RVA gastroenteritis in children hospitalized in Rawalpindi, Pakistan during 2014. G3P[8] (18.3%; n = 24) was detected as the most common genotype causing majority of infections in children less than 06 months. Phylogenetic analysis of Pakistani G3 strains showed high amino acid similarity to "new variant G3" and G3 strains reported from China, Russia, USA, Japan, Belgium and Hungary during 2007-2012. Pakistani G3 strains belonged to lineage 3 within sub-lineage 3d, containing an extra N-linked glycosylation site compared to the G3 strain of RotaTeqTM. To our knowledge, this is the first report on the molecular epidemiology of G3 rotavirus strains from Pakistan and calls for immediate response measures to introduce RV vaccine in the routine immunization program of the country on priority.
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8
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Increasing predominance of G8P[8] species A rotaviruses in children admitted to hospital with acute gastroenteritis in Thailand, 2010-2013. Arch Virol 2018; 163:2165-2178. [DOI: 10.1007/s00705-018-3848-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 04/04/2018] [Indexed: 01/05/2023]
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9
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Umair M, Salman M, Alam MM, Rana MS, Zaidi SSZ, Bowen MD, Aamir UB, Abbasi BH. Rotavirus surveillance in Pakistan during 2015-2016 reveals high prevalence of G12P[6]. J Med Virol 2018; 90:1272-1276. [PMID: 29573357 DOI: 10.1002/jmv.25075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/06/2018] [Indexed: 11/09/2022]
Abstract
The G12 rotavirus genotype has emerged globally since their first detection in 1987 from the Philippines; however it remains a rare cause of gastroenteritis in Pakistan. Rotavirus surveillance conducted during 2015-2016, assessed 3446 children <5 years hospitalized for gastroenteritis and found 802 (23.2%) positive on ELISA. Genotyping of a subset of positive samples (n = 319) revealed G12P[6] (11.28%) as the third most common G/P combination following G3P[8] (28.5%) and G1P[8] (12.5%); G2P[4] (10.65%) and G3P[6] (8.15%) were other frequently detected strains. Phylogenetic analysis of G12 strains from Pakistan revealed high genetic similarity to G12 strains from Italy, Thailand, Korea, and Great Britain as well as local strains within G12 lineage III. In conclusion, G12P[6] was a major contributor of RVA gastroenteritis in Pakistani children. Robust surveillance after the introduction of rotavirus vaccines will help determine the evolution of G12 and other circulating genotypes in the country.
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Affiliation(s)
- Massab Umair
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.,Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Muhammad Masroor Alam
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Muhammad S Rana
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Syed S Z Zaidi
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Michael D Bowen
- Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Uzma B Aamir
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Bilal H Abbasi
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
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10
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Khandoker N, Thongprachum A, Takanashi S, Okitsu S, Nishimura S, Kikuta H, Yamamoto A, Sugita K, Baba T, Kobayashi M, Hayakawa S, Mizuguchi M, Ushijima H. Molecular epidemiology of rotavirus gastroenteritis in Japan during 2014-2015: Characterization of re-emerging G2P[4] after rotavirus vaccine introduction. J Med Virol 2018; 90:1040-1046. [PMID: 29488230 DOI: 10.1002/jmv.25067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 02/25/2018] [Indexed: 11/08/2022]
Abstract
Rotavirus vaccines have been available in Japan since 2011. This study conducted to monitor the trend of group A rotavirus (RVA) genotypes 3 years after vaccine introduction. A total of, 539 fecal samples were collected from children with acute gastroenteritis in six regions during July 2014-June 2015. Among them, 178 samples (33.0%) were positive for RVA. The most predominant genotype was G1P[8] (35.9%) followed by G2P[4] (26.4%), G9P[8] (21.3%), G3P[8] (4.5%), and G3P[9] (4.5%). The detection rate of G2P[4] was increased soon after vaccine introduction. Sequence analyses of VP7 and VP4 genes of the representative G2P[4] strains were found to be clustered in sub-lineage IVa of lineage IV. It is noteworthy that one amino acid substitution in the antigenic epitope (Q114P) of VP4 gene was found in representative G2P[4] strains of the current study. However, it is unclear whether the change in antigenic epitope is due to the effect of vaccination or due to natural variation, warranting further continuous monitoring of rotavirus evolution after vaccine introduction.
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Affiliation(s)
- Nusrat Khandoker
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Aksara Thongprachum
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoko Okitsu
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shuichi Nishimura
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hideaki Kikuta
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Atsuko Yamamoto
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Kumiko Sugita
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Tsuneyoshi Baba
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Masaaki Kobayashi
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Masashi Mizuguchi
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
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11
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Chan-It W, Chanta C. Emergence of G9P[8] rotaviruses in children with acute gastroenteritis in Thailand, 2015-2016. J Med Virol 2017; 90:477-484. [DOI: 10.1002/jmv.24985] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 09/27/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Wisoot Chan-It
- Biology Program; Faculty of Science and Technology; Pibulsongkram Rajabhat University; Phitsanulok Thailand
| | - Chulapong Chanta
- Pediatric Unit; Chiangrai Prachanukroh Hospital; Chiang Rai Thailand
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12
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The prevalence of enteric RNA viruses in stools from diarrheic and non-diarrheic people in southwestern Alberta, Canada. Arch Virol 2016; 162:117-128. [PMID: 27686073 DOI: 10.1007/s00705-016-3063-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/12/2016] [Indexed: 01/09/2023]
Abstract
Southwestern Alberta is a region of Canada that has high rates of enteritis as well as high densities of livestock. The presence of enteric RNA viruses, specifically norovirus (NoV) GI, GII, GIII, GIV; sapovirus (SaV); rotavirus (RV); and astrovirus (AstV), was evaluated in stools from diarrheic (n = 2281) and non-diarrheic (n = 173) people over a 1-year period in 2008 and 2009. Diarrheic individuals lived in rural (46.6 %) and urban (53.4 %) settings and ranged in age from less than 1 month to 102 years, and the highest prevalence of infection in these individuals was in November. In all, viruses were detected in diarrheic stools from 388 individuals (17.0 %). NoV GII was the most frequently detected virus (8.0 %; n = 182) followed by SaV (4.3 %; n = 97), RV (2.0 %; n = 46), AstV (1.8 %; n = 42), NoV GI (0.9 %; n = 20), and NoV GIV (0.1 %; n = 1). Animal NoV GIII was never detected. The prevalence of mixed viral infections in diarrheic individuals was 2.8 % (n = 11). Children from 1 to 5 years of age accounted for the highest prevalence of positive stools, followed by the elderly individuals (≥70 years). Only NoV GII (1.2 %; n = 2) and SaV (1.2 %; n = 2) were detected in stools from non-diarrheic people. Sequence analysis of a subset of stools revealed homology to NoV, SaV and RV sequences from humans but not to strains from non-human animals. The results of this study do not support the hypothesis that viruses of animal origin have a significant impact on the occurrence of acute gastroenteritis caused by RNA enteric viruses in people living in southwestern Alberta.
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Tort LFL, Victoria M, Lizasoain A, García M, Berois M, Cristina J, Leite JPG, Gómez MM, Miagostovich MP, Colina R. Detection of Common, Emerging and Uncommon VP4, and VP7 Human Group A Rotavirus Genotypes from Urban Sewage Samples in Uruguay. FOOD AND ENVIRONMENTAL VIROLOGY 2015; 7:342-353. [PMID: 26267835 DOI: 10.1007/s12560-015-9213-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/04/2015] [Indexed: 06/04/2023]
Abstract
Environmental approach has proven to be a useful tool for epidemiological studies demonstrating through environmental studies the diversity of viruses circulating in a given population. The aim of this study was to perform a phylogenetic characterization of the group A rotavirus (RVA) glycoprotein (G)- and protease-sensitive (P)-genotypes obtained from sewage samples (n = 116) collected in six cities of Uruguay during March 2011 to April 2013. A worldwide standardized semi-nested multiplex RT-PCR (SNM RT-PCR) protocol directed against VP4 and VP7 genes were conducted for RVA detection and consensual DNA fragments were submitted to nucleotide sequencing. P and/or G genotype was successfully determined by phylogenetic analysis in 61% (n = 37) of the positive samples obtained by SNM RT-PCR (n = 61). The RVA genotypes were as follow: G1 (n = 2), G2 (n = 14), G3 (n = 5), G12 (n = 2), P[4] (n = 4), P[8] (n = 16), and P[3] (n = 2). Interestingly, through phylogenetic analysis, emerging, and uncommon human genotypes could be detected. Results obtained from the comparison of RVA genotypes detected in the current study and Uruguayan RVA strains previously described for contemporary clinical pediatric cases showed that monitoring sewage may be a good screening option for a rapid and economical overview of the circulating genotypes in the surrounding human population and a useful approximation to study RVA epidemiology in a future vaccine monitoring program. The present study represents the first report in Uruguay that describes the phylogenetic diversity of RVA from urban sewage samples.
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Affiliation(s)
- Luis Fernando Lopez Tort
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte - CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - Matías Victoria
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte - CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - Andrés Lizasoain
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte - CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - Mariana García
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte - CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - Mabel Berois
- Sección Virología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - José Paulo Gagliardi Leite
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil 4365, Rio de Janeiro, 21040-360, Brazil
| | - Mariela Martínez Gómez
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil 4365, Rio de Janeiro, 21040-360, Brazil
| | - Marize Pereira Miagostovich
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil 4365, Rio de Janeiro, 21040-360, Brazil
| | - Rodney Colina
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte - CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay.
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Thongprachum A, Khamrin P, Maneekarn N, Hayakawa S, Ushijima H. Epidemiology of gastroenteritis viruses in Japan: Prevalence, seasonality, and outbreak. J Med Virol 2015; 88:551-70. [PMID: 26387663 DOI: 10.1002/jmv.24387] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 12/11/2022]
Abstract
Acute gastroenteritis has been recognized as one of the most common diseases in humans and continues to be a major public health problem worldwide. Several groups of viruses have been reported as the causative agents of acute gastroenteritis, including rotavirus, norovirus, sapovirus, human astrovirus, adenovirus, and an increasing number of others which have been reported more recently. The epidemiology, prevalence, seasonality, and outbreaks of these viruses have been reviewed in a number of studies conducted in Japan over three decades. Rotavirus and norovirus were the two most common viruses detected almost equally in children under 5 years of age who were suffering from acute gastroenteritis. Like many other countries, the main rotavirus strains circulating in pediatric patients in Japan are G1P[8], G2P[4], G3P[8], and G9P[8]. Norovirus GII.4 was involved in most outbreaks in Japan and found to be associated with the emergence of new variants Sydney_2012. The classic human astrovirus, MLB, and VA clades astroviruses were also commonly found in pediatric patients with acute diarrhea. The sapovirus and adenovirus have been identified as the minor viral causative agents for acute gastroenteritis in Japan.
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Affiliation(s)
- Aksara Thongprachum
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Pattara Khamrin
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Niwat Maneekarn
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Thongprachum A, Takanashi S, Kalesaran AFC, Okitsu S, Mizuguchi M, Hayakawa S, Ushijima H. Four-year study of viruses that cause diarrhea in Japanese pediatric outpatients. J Med Virol 2015; 87:1141-8. [DOI: 10.1002/jmv.24155] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Aksara Thongprachum
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University School of Medicine; Tokyo Japan
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
| | - Angela F. C. Kalesaran
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University School of Medicine; Tokyo Japan
| | - Shoko Okitsu
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University School of Medicine; Tokyo Japan
| | - Masashi Mizuguchi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
| | - Satoshi Hayakawa
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University School of Medicine; Tokyo Japan
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University School of Medicine; Tokyo Japan
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Tort LFL, Victoria M, Lizasoain A A, Castells M, Maya L, Gómez MM, Arreseigor E, López P, Cristina J, Leite JPG, Colina R. Molecular epidemiology of group a rotavirus among children admitted to hospital in Salto, Uruguay, 2011-2012: First detection of the emerging genotype G12. J Med Virol 2015; 87:754-63. [DOI: 10.1002/jmv.24123] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2014] [Indexed: 12/13/2022]
Affiliation(s)
| | - Matías Victoria
- Molecular Virology Laboratory, North Regional; University of Republic; Salto Uruguay
| | - Andrés Lizasoain A
- Molecular Virology Laboratory, North Regional; University of Republic; Salto Uruguay
| | - Matías Castells
- Molecular Virology Laboratory, North Regional; University of Republic; Salto Uruguay
| | - Leticia Maya
- Molecular Virology Laboratory, North Regional; University of Republic; Salto Uruguay
| | - Mariela Martínez Gómez
- Laboratory of Comparative and Environmental Virology; Oswaldo Cruz Institute; Rio de Janeiro Brazil
| | | | - Patricia López
- Pediatric Unit of Regional Public Hospital; Salto Uruguay
| | - Juan Cristina
- Molecular Virology Laboratory, Faculty of Sciences; University of Republic; Montevideo Uruguay
| | | | - Rodney Colina
- Molecular Virology Laboratory, North Regional; University of Republic; Salto Uruguay
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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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Human G3P[4] rotavirus obtained in Japan, 2013, possibly emerged through a human-equine rotavirus reassortment event. Virus Genes 2014; 50:129-33. [PMID: 25352228 PMCID: PMC4349953 DOI: 10.1007/s11262-014-1135-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/16/2014] [Indexed: 12/19/2022]
Abstract
Two novel G3P[4] rotavirus strains were detected from children with acute diarrhea in Sendai, Japan, identified as a G3–P[4]–I2–R2–C2–M2–A2–N2–T2–E2–H2 genotype constellation by whole-genome sequence analysis. The VP7 gene of the two strains displayed the highest nucleotide sequence identity (91 %) and showed a close genetic relationship (99 % bootstrap value) to an equine rotavirus reported in India. The other gene segments were related to human group A rotaviruses. This report suggests a possible reassortment event between human and equine rotaviruses.
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Degiuseppe JI, Parra GI, Stupka JA. Genetic diversity of G3 rotavirus strains circulating in Argentina during 1998-2012 assessed by full genome analyses. PLoS One 2014; 9:e110341. [PMID: 25337915 PMCID: PMC4206407 DOI: 10.1371/journal.pone.0110341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 09/19/2014] [Indexed: 12/28/2022] Open
Abstract
Seasonal shifts in the predominant strains and the periodic emergence of new strains are epidemiological features of human rotaviruses. After the sporadic detection in two samples in 1998, G3P[8] strains reemerged as the predominant rotavirus during 2008-2009 in Argentina. Notably, in 2011 6.3% (37/587) of samples presented the G3P[6] genotypes, which coincided with the recent detection of G3P[6] and G2P[6] strains in South America and Europe. Analyses of the 11 gene segments of four G3P[8] and two G3P[6] strains revealed that G3P[8] strains detected a decade apart (1998 and 2009) presented minor differences, while the G3P[6] strains presented a complete different genomic constellation albeit showing a similar VP7 gene. This study provides insights in the dynamics and evolution of one of the genotypes with the wider range of hosts and inter-species transmission potential.
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Affiliation(s)
- Juan Ignacio Degiuseppe
- Laboratorio de Gastroenteritis Virales, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Gabriel Ignacio Parra
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Juan Andrés Stupka
- Laboratorio de Gastroenteritis Virales, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
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Review of global rotavirus strain prevalence data from six years post vaccine licensure surveillance: is there evidence of strain selection from vaccine pressure? INFECTION GENETICS AND EVOLUTION 2014; 28:446-61. [PMID: 25224179 DOI: 10.1016/j.meegid.2014.08.017] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 11/23/2022]
Abstract
Comprehensive reviews of pre licensure rotavirus strain prevalence data indicated the global importance of six rotavirus genotypes, G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]. Since 2006, two vaccines, the monovalent Rotarix (RV1) and the pentavalent RotaTeq (RV5) have been available in over 100 countries worldwide. Of these, 60 countries have already introduced either RV1 or RV5 in their national immunization programs. Post licensure vaccine effectiveness is closely monitored worldwide. This review aimed at describing the global changes in rotavirus strain prevalence over time. The genotype distribution of the nearly 47,000 strains that were characterized during 2007-2012 showed similar picture to that seen in the preceding period. An intriguing finding was the transient predominance of heterotypic strains, mainly in countries using RV1. Unusual and novel antigen combinations continue to emerge, including some causing local outbreaks, even in vaccinated populations. In addition, vaccine strains have been found in both vaccinated infants and their contacts and there is evidence for genetic interaction between vaccine and wild-type strains. In conclusion, the post-vaccine introduction strain prevalence data do not show any consistent pattern indicative of selection pressure resulting from vaccine use, although the increased detection rate of heterotypic G2P[4] strains in some countries following RV1 vaccination is unusual and this issue requires further monitoring.
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Jeong S, Than VT, Lim I, Kim W. Whole-genome analysis of a rare human Korean G3P rotavirus strain suggests a complex evolutionary origin potentially involving reassortment events between feline and bovine rotaviruses. PLoS One 2014; 9:e97127. [PMID: 24818762 PMCID: PMC4018271 DOI: 10.1371/journal.pone.0097127] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/14/2014] [Indexed: 11/18/2022] Open
Abstract
A rare human rotavirus, G3P[9] strain RVA/Human-tc/KOR/CAU12-2-51/2013/G3P[9], was isolated from the stool of a 9-year-old female hospitalized with acute watery diarrhea in August 2012 in South Korea using a cell culture system, and its genome was analyzed. The complete genomic constellation of the CAU12-2-51 strain revealed a novel genotype constellation for human rotavirus, G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3. Phylogenetic analysis revealed that the CAU12-2-51 strain originated from feline- and bovine-like reassortment strains. The genes encoding VP4, VP7, NSP1, NSP3, NSP4, and NSP5 were related to human/feline-like and feline rotavirus strains, whereas the remaining five genes encoding VP1, VP2, VP3, VP6, and NSP2 were related to the human/bovine-like and bovine rotavirus strains. This novel strain was identified for the first time, providing evidence of feline/bovine-to-human transmission of rotavirus. The data presented herein provide information regarding rotavirus diversity and evolution.
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Affiliation(s)
- Sunyoung Jeong
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Van Thai Than
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Inseok Lim
- Department of Pediatrics, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- * E-mail:
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Wang YH, Pang BB, Ghosh S, Zhou X, Shintani T, Urushibara N, Song YW, He MY, Liu MQ, Tang WF, Peng JS, Hu Q, Zhou DJ, Kobayashi N. Molecular epidemiology and genetic evolution of the whole genome of G3P[8] human rotavirus in Wuhan, China, from 2000 through 2013. PLoS One 2014; 9:e88850. [PMID: 24676363 PMCID: PMC3967987 DOI: 10.1371/journal.pone.0088850] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/11/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children worldwide. Since the latter of the 1990s, G3 human rotaviruses referred to as "new variant G3" have emerged and spread in China, being a dominant genotype until 2010, although their genomic evolution has not yet been well investigated. METHODS The complete genomes of 33 G3P[8] human rotavirus strains detected in Wuhan, China, from 2000 through 2013 were analyzed. Phylogenetic trees of concatenated sequences of all the RNA segments and individual genes were constructed together with published rotavirus sequences. RESULTS Genotypes of 11 gene segments of all the 33 strains were assigned to G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, belonging to Wa genogroup. Phylogenetic analysis of the concatenated full genome sequences indicated that all the modern G3P[8] strains were assigned to Cluster 2 containing only one clade of G3P[8] strains in the US detected in the 1970s, which was distinct from Cluster 1 comprising most of old G3P[8] strains. While main lineages of all the 11 gene segments persisted during the study period, different lineages appeared occasionally in RNA segments encoding VP1, VP4, VP6, and NSP1-NSP5, exhibiting various allele constellations. In contrast, only a single lineage was detected for VP7, VP2, and VP3 genes. Remarkable lineage shift was observed for NSP1 gene; lineage A1-2 emerged in 2007 and became dominant in 2008-2009 epidemic season, while lineage A1-1 persisted throughout the study period. CONCLUSION Chinese G3P[8] rotavirus strains have evolved since 2000 by intra-genogroup reassortment with co-circulating strains, accumulating more reassorted genes over the years. This is the first large-scale whole genome-based study to assess the long-term evolution of common human rotaviruses (G3P[8]) in an Asian country.
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Affiliation(s)
- Yuan-Hong Wang
- Virology section, Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei Province, P.R. China
| | - Bei-Bei Pang
- Virology section, Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei Province, P.R. China
| | - Souvik Ghosh
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Xuan Zhou
- Virology section, Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei Province, P.R. China
| | - Tsuzumi Shintani
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yu-Wei Song
- College of Life Sciences, Central China Normal University, Wuhan, Hubei Province, P.R. China
| | - Ming-Yang He
- College of Life Sciences, Central China Normal University, Wuhan, Hubei Province, P.R. China
| | - Man-Qing Liu
- Virology section, Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei Province, P.R. China
| | - Wei-Feng Tang
- Virology section, Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei Province, P.R. China
| | - Jin-Song Peng
- Virology section, Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei Province, P.R. China
| | - Quan Hu
- Virology section, Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei Province, P.R. China
| | - Dun-Jin Zhou
- Virology section, Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei Province, P.R. China
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
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da Silva Soares L, de Fátima Dos Santos Guerra S, do Socorro Lima de Oliveira A, da Silva Dos Santos F, de Fátima Costa de Menezes EM, Mascarenhas JDP, Linhares AC. Diversity of rotavirus strains circulating in Northern Brazil after introduction of a rotavirus vaccine: high prevalence of G3P[6] genotype. J Med Virol 2013; 86:1065-72. [PMID: 24136444 DOI: 10.1002/jmv.23797] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2013] [Indexed: 12/29/2022]
Abstract
Rotavirus A (RVA) is the most common cause of severe acute gastroenteritis in infants and young children worldwide, causing 453,000 deaths annually. In Brazil, the most frequent genotype identified was G1 during almost three decades in the pre-vaccination period; however, after anti-rotavirus vaccine introduction, there was a predominance of G2 genotype. The aim of this study was to determine the G and P genotypes of rotaviruses isolated from children under 5 years of age with acute gastroenteritis in the Northern region of Brazil, and discuss the emergence of G3P[6] genotype. A total of 783 stool specimens were obtained between January 2011 and March 2012. RVA antigen was detected in 33% (272/783) of samples using a commercial enzyme-linked immunosorbent assay and type-specificity was determined by reverse-transcription polymerase chain reaction. The most common binary combination was G2P[4], representing 41% of cases, followed by G3P[6] (15%), G1P[8] (8%), G3P[8] (4%), G9P[8] (3%), and G12P[6] (2%). G3P[6] strains were analyzed further and phylogenetic analysis of VP7 gene showed that G3 strains clustered into lineage I and showed a high degree of amino acid identity with vaccine strain RV3 (95.1-95.6%). For VP4 sequences, G3P[6] clustered into lineage Ia. It was demonstrated by the first time the emergence of unusual genotype G3P[6] in the Amazon region of Brazil. This genotype shares neither VP7 nor VP4 specificity with the used vaccine and may represent a challenge to vaccination strategies. A continuous monitoring of circulating strains is therefore needed during the post-vaccine era in Brazil.
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Affiliation(s)
- Luana da Silva Soares
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Brazil
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Okitsu S, Khamrin P, Thongprachum A, Kongkaew A, Maneekarn N, Mizuguchi M, Hayakawa S, Ushijima H. Whole-genomic analysis of G3P[23], G9P[23] and G3P[13] rotavirus strains isolated from piglets with diarrhea in Thailand, 2006-2008. INFECTION GENETICS AND EVOLUTION 2013; 18:74-86. [PMID: 23681022 DOI: 10.1016/j.meegid.2013.05.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 05/01/2013] [Accepted: 05/06/2013] [Indexed: 11/30/2022]
Abstract
Group A rotavirus (RVA) is the most common cause of severe acute viral gastroenteritis in humans and animals worldwide. This study characterized the whole genome sequences of porcine RVAs, 2 G3P[23] strains (CMP40/08 and CMP48/08), 1 G9P[23] strain (CMP45/08), and 1 G3P[13] strain (CMP29/08). These strains were collected from diarrheic piglets less than 7weeks of age in 4 pig farms in Chiang Mai, Thailand, in 2008. The VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes of CMP40/08 and CMP48/08 strains were assigned as G3-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1 genotypes based on their nucleotide sequences and phylogenetic analyses. The CMP29/08 strain was different from the CMP40/08 and CMP48/08 strains only in the VP4 gene, since it was assigned as P[13] genotype. Furthermore, the VP7 gene of the CMP45/08 strain was classified as genotype G9, and the NSP3 gene as T7 genotype. The finding of this study supports the porcine-origin of T7 genotype, although the NSP3 gene of this strain was similar to the bovine UK strain at the highest nucleotide sequence identity of 92.6%. Whole genome sequence analysis of the porcine RVAs indicated that multiple inter-genotypic and intra-genotypic reassortment events had occurred among the porcine RVAs circulating in this studied area. Interestingly, the VP7 gene of the CMP45/08 strain, and the VP1, NSP2, and NSP4 genes of all four porcine RVAs strains described in this study revealed much similarity to those of two porcine-like human RVA strains (RVA/Human-tc/THA/Mc323/1989/G9P[19] and RVA/Human-tc/THA/Mc345/1989/G9P[19]) detected in Thailand in 1989. The present study provided important information on the evolution of porcine RVA.
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Affiliation(s)
- Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.
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