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Shrestha J, Shrestha SK, Strand TA, Dudman S, Dembinski JL, Vikse R, Andreassen AK. Diversity of Rotavirus Strains in Children; Results From a Community-Based Study in Nepal. Front Med (Lausanne) 2021; 8:712326. [PMID: 34660624 PMCID: PMC8517221 DOI: 10.3389/fmed.2021.712326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/06/2021] [Indexed: 11/19/2022] Open
Abstract
Objective: The objectives of this study were to describe the incidence and genetic diversity of Rotavirus (RV) infection among children up to 3 years of age in a community in Nepal. Methods: We investigated community-acquired cases of asymptomatic and symptomatic RV infections in children from birth to 36 months of age in a community-based birth cohort in Bhaktapur, Nepal. Monthly surveillance and diarrheal stool samples were collected from 240 children enrolled at birth, of which 238 completed the 3 years of follow-up. Samples were screened for rotavirus by Enzyme Immuno Assay (EIA). All RV screened positives were further genotyped by reverse transcription-polymerase chain reaction for the capsid genes VP7 and VP4. Results: In total, 5,224 stool samples were collected from 238 children, followed from birth to 36 months of age. Diarrhea occurred in 92.4% (230/238) of all children in the cohort. During the 3 years study period, RV was more frequently seen in children with symptoms (7.6%) than in non-symptomatic children (0.8%). The highest RV detection rate was found in younger children between 3 and 21 months of age. Although rotavirus is known as winter diarrhea, it was detected throughout the year except in August. The highest positivity rate was observed in the months between December and March, with a peak in January. Four common G types were seen: G2 (30%), G1 (29%), G12 (19%), and G9 (16%). The most predominant genotypes seen were G2P[4] (30%), followed by G1P[8] (27.0%), G12P[6] (14.0%), G9P[8] (10%), and remaining were mixed, partial, and untyped. Conclusion: Our study confirms that rotavirus is a common cause of gastroenteritis in young children in the community. The prevalence and pathogenicity of rotavirus infection differed by age. There was substantial variability in circulating strains in the community samples compared to samples collected from hospitals. This shows the importance of including community-based surveillance systems to monitor the diversity of circulating rotavirus strains in Nepal.
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Affiliation(s)
- Jasmin Shrestha
- Center for International Health, University of Bergen, Bergen, Norway.,Walter Reed/AFRIMS Research Unit Nepal, Kathmandu, Nepal
| | - Sanjaya K Shrestha
- Center for International Health, University of Bergen, Bergen, Norway.,Walter Reed/AFRIMS Research Unit Nepal, Kathmandu, Nepal
| | - Tor A Strand
- Center for International Health, University of Bergen, Bergen, Norway.,Department of Research, Innlandet Hospital Trust, Lillehammer, Norway
| | - Susanne Dudman
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | - Rose Vikse
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
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Amit LN, Mori D, John JL, Chin AZ, Mosiun AK, Jeffree MS, Ahmed K. Emergence of equine-like G3 strains as the dominant rotavirus among children under five with diarrhea in Sabah, Malaysia during 2018-2019. PLoS One 2021; 16:e0254784. [PMID: 34320003 PMCID: PMC8318246 DOI: 10.1371/journal.pone.0254784] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/03/2021] [Indexed: 12/12/2022] Open
Abstract
Rotavirus infection is a dilemma for developing countries, including Malaysia. Although commercial rotavirus vaccines are available, these are not included in Malaysia's national immunization program. A scarcity of data about rotavirus genotype distribution could be partially to blame for this policy decision, because there are no data for rotavirus genotype distribution in Malaysia over the past 20 years. From January 2018 to March 2019, we conducted a study to elucidate the rotavirus burden and genotype distribution in the Kota Kinabalu and Kunak districts of the state of Sabah. Stool specimens were collected from children under 5 years of age, and rotavirus antigen in these samples was detected using commercially available kit. Electropherotypes were determined by polyacrylamide gel electrophoresis of genomic RNA. G and P genotypes were determined by RT-PCR using type specific primers. The nucleotide sequence of the amplicons was determined by Sanger sequencing and phylogenetic analysis was performed by neighbor-joining method. Rotavirus was identified in 43 (15.1%) children with watery diarrhea. The male:female ratio (1.9:1) of the rotavirus-infected children clearly showed that it affected predominantly boys, and children 12-23 months of age. The genotypes identified were G3P[8] (74% n = 31), followed by G1P[8] (14% n = 6), G12P[6](7% n = 3), G8P[8](3% n = 1), and GxP[8] (3% n = 1). The predominant rotavirus circulating among the children was the equine-like G3P[8] (59.5% n = 25) with a short electropherotype. Eleven electropherotypes were identified among 34 strains, indicating substantial diversity among the circulating strains. The circulating genotypes were also phylogenetically diverse and related to strains from several different countries. The antigenic epitopes present on VP7 and VP4 of Sabahan G3 and equine-like G3 differed considerably from that of the RotaTeq vaccine strain. Our results also indicate that considerable genetic exchange is occurring in Sabahan strains. Sabah is home to a number of different ethnic groups, some of which culturally are in close contact with animals, which might contribute to the evolution of diverse rotavirus strains. Sabah is also a popular tourist destination, and a large number of tourists from different countries possibly contributes to the diversity of circulating rotavirus genotypes. Considering all these factors which are contributing rotavirus genotype diversity, continuous surveillance of rotavirus strains is of utmost importance to monitor the pre- and post-vaccination efficacy of rotavirus vaccines in Sabah.
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Affiliation(s)
- Lia Natasha Amit
- Faculty of Medicine and Health Sciences, Department of Pathobiology and Medical Diagnostics, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Daisuke Mori
- Faculty of Medicine and Health Sciences, Department of Pathobiology and Medical Diagnostics, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Jecelyn Leaslie John
- Faculty of Medicine and Health Sciences, Borneo Medical and Health Research Centre, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Abraham Zefong Chin
- Faculty of Medicine and Health Sciences, Department of Community and Family Medicine, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Andau Konodan Mosiun
- Kunak District Health Office, Ministry of Health Malaysia, Kunak, Sabah, Malaysia
| | - Mohammad Saffree Jeffree
- Faculty of Medicine and Health Sciences, Department of Community and Family Medicine, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Kamruddin Ahmed
- Faculty of Medicine and Health Sciences, Department of Pathobiology and Medical Diagnostics, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
- Faculty of Medicine and Health Sciences, Borneo Medical and Health Research Centre, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
- * E-mail:
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3
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Arakaki L, Tollefson D, Kharono B, Drain PK. Prevalence of rotavirus among older children and adults with diarrhea: A systematic review and meta-analysis. Vaccine 2021; 39:4577-4590. [PMID: 34244008 DOI: 10.1016/j.vaccine.2021.06.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/10/2021] [Accepted: 06/23/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Older children and adults are susceptible to rotavirus, but the extent to which rotavirus affects this population is not fully understood, hindering accuracy of global rotavirus estimations. OBJECTIVE To determine what proportion of diarrhea cases are due to rotavirus among persons ≥ 5 years old and to estimate this proportion by age strata. METHODS We conducted a systematic review and meta-analysis using the PRISMA guidelines. We included studies that reported on conditional rotavirus prevalence (i.e., percent of diarrhea due to rotavirus) in persons ≥ 5 years old who were symptomatic with diarrhea/gastroenteritis and had laboratory confirmation for rotavirus infection. Studies on nosocomial infections and outbreak investigations were excluded. We collected age group-specific conditional rotavirus prevalence and other variables, such as study geography, study setting, and study type. We calculated pooled conditional rotavirus prevalence, corresponding 95% confidence intervals (95% CI), heterogeneity (I2) estimates, and prediction intervals (PI). RESULTS Sixty-six studies from 32 countries met the inclusion criteria. Conditional rotavirus prevalence ranged from 0% to 30% across the studies. The total pooled prevalence of rotavirus among persons ≥ 5 years old with diarrhea was 7.6% (95% CI: 6.2-9.2%, I2 = 99.6%, PI: 0-24%). The pooled prevalence of rotavirus among older children and adolescents was 8.7% (95% CI: 6.2-11.7%, I2 = 96%, PI:0-27%), among younger adults was 5.4% (95% CI: 1.4-11.8%, I2 = 96%, PI:0-31%), and among older adults was 4.7% (95% CI: 2.8-7.0%, I2 = 96%, PI:0-16%). Pooled conditional rotavirus prevalences did not differ by other variables. CONCLUSION In this systematic review and meta-analysis of rotavirus among persons ≥ 5 years old with diarrhea, we found relatively low pooled conditional rotavirus prevalence compared to what is typically reported for children < 5 years; however, results should be interpreted with caution as the wide prediction intervals suggest large heterogeneity.
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Affiliation(s)
- Lola Arakaki
- University of Washington, Strategic Analysis, Research, and Training (START) Center, 3980 15th Ave NE, Seattle, WA 98195, United States; University of Washington, Department of Epidemiology, 3980 15th Ave NE, Seattle, WA 98195, United States.
| | - Deanna Tollefson
- University of Washington, Strategic Analysis, Research, and Training (START) Center, 3980 15th Ave NE, Seattle, WA 98195, United States; University of Washington, Department of Global Health, 3980 15th Ave NE, Seattle, WA 98195, United States.
| | - Brenda Kharono
- University of Washington, Strategic Analysis, Research, and Training (START) Center, 3980 15th Ave NE, Seattle, WA 98195, United States; University of Washington, Department of Global Health, 3980 15th Ave NE, Seattle, WA 98195, United States.
| | - Paul K Drain
- University of Washington, Strategic Analysis, Research, and Training (START) Center, 3980 15th Ave NE, Seattle, WA 98195, United States; University of Washington, Department of Global Health, 3980 15th Ave NE, Seattle, WA 98195, United States; University of Washington, Department of Medicine, 1959 NE Pacific St, Seattle, WA 98195, United States.
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4
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Gupta S, Gauhar M, Bubber P, Ray P. Phylogenetic analysis of VP7 and VP4 genes of the most predominant human group A rotavirus G12 identified in children with acute gastroenteritis in Himachal Pradesh, India during 2013-2016. J Med Virol 2021; 93:6200-6209. [PMID: 34138482 DOI: 10.1002/jmv.27142] [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: 05/26/2021] [Accepted: 06/07/2021] [Indexed: 11/05/2022]
Abstract
G12 strains are now considered to be the sixth most prevalent human rotaviruses globally. India has introduced rotavirus vaccine Rotavac® into the national immunization program in 2016 and Himachal Pradesh (HP) is the first state to launch it. During epidemiological rotavirus surveillance in HP, predominance of G12 rotaviruses was observed. This study investigated the genetic variability and evolution of HP G12 strains (n = 15) associated with P-genotypes P[6], P[4], and P[8] identified between 2013 and 2016. Phylogenetic analysis of VP7 gene revealed that all characterized G12 strains clustered in lineage-III and diversified into three subclusters indicating that these strains may have originated from three different ancestral G12 strains. The comparative sequence analysis of HP strains with Rotavac® and Rotarix® vaccine strains revealed various amino acid substitutions in epitope regions of VP7 and VP4 proteins especially at the antibody neutralization sites. Only 12/29 VP7 epitope residues and 2/25 VP4 epitope residues were found to be conserved between HP rotavirus strains and vaccine strains. Both long and short electropherotypes were observed in G12P[4] strains, while a single long electropherotype was observed in G12P[6] strains. Children of ≤11 months were significantly infected with G12 rotaviruses. The frequency of vomiting episodes (≥5/day) was significantly higher in children infected with G12 rotavirus strains as compared to non-G12 rotaviruses (p = 0.0405). Our study provides the comprehensive data on clinical characteristics and evolutionary pattern of the G12 rotavirus, the most prevalent strain in HP and emphasizes the need to monitor these strains for inclusion in future vaccine.
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Affiliation(s)
- Shipra Gupta
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Mariyam Gauhar
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Parvesh Bubber
- Department of Biochemistry, School of Sciences, IGNOU, New Delhi, India
| | - Pratima Ray
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India.,Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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5
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Roczo-Farkas S, Bines JE. Australian Rotavirus Surveillance Program: Annual Report, 2018. ACTA ACUST UNITED AC 2021; 45. [PMID: 33573534 DOI: 10.33321/cdi.2021.45.6] [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] [Indexed: 12/14/2022]
Abstract
Abstract This report, from the Australian Rotavirus Surveillance Program and collaborating laboratories Australia-wide, describes the rotavirus genotypes identified in children and adults with acute gastroenteritis during the period 1 January to 31 December 2018. During this period, 690 faecal specimens were referred for rotavirus G- and P- genotype analysis, including 607 samples that were confirmed as rotavirus positive. Of these, 457/607 were wild-type rotavirus strains and 150/607 were identified as rotavirus vaccine-like. Genotype analysis of the 457 wild-type rotavirus samples from both children and adults demonstrated that G3P[8] was the dominant genotype nationally, identified in 52% of samples, followed by G2P[4] (17%). The Australian National Immunisation Program, which previously included both RotaTeq and Rotarix vaccines, changed to Rotarix exclusively on 1 July 2017. Continuous surveillance is needed to identify if the change in vaccination schedule could affect rotavirus genotype distribution and diversity in Australia.
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Affiliation(s)
| | - Julie E Bines
- Enteric Diseases Group, MCRI and the Australian Rotavirus Surveillance Group Enteric Diseases Group, Murdoch Children's Research Institute, Royal Children's Hospital
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6
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Chae SJ, Jung S, Cho SR, Choi W, Lee DY. Outbreak associated with Rotavirus G11,P[25] in Korea in 2018. Infect Chemother 2020; 52:616-620. [PMID: 33263243 PMCID: PMC7779978 DOI: 10.3947/ic.2020.52.4.616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/05/2020] [Indexed: 11/25/2022] Open
Abstract
We here report the first outbreak caused by rotavirus G11,P[25] in Korea in 2018, representing a case of re-assortment with pig-derived rotavirus. The genotype constellation was identical to the virus identified in Korea in 2012 as G11-P[25]-I12-R1-C1-M1-A1-N1-T1-E1-H1. The infection source was not known exactly but it must be considered infection from swine.
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Affiliation(s)
- Su Jin Chae
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Sunyoung Jung
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Seung Rye Cho
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Wooyoung Choi
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Deog Yong Lee
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Osong, Korea.
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7
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Giri S, Kumar CPG, Khakha SA, Chawla-Sarkar M, Gopalkrishna V, Chitambar SD, Ray P, Venkatasubramanian S, Borkakoty BJ, Roy S, Bhat J, Dwibedi B, Das P, Paluru V, Ramani S, Babji S, Arora R, Mehendale SM, Gupte MD, Kang G. Diversity of rotavirus genotypes circulating in children < 5 years of age hospitalized for acute gastroenteritis in India from 2005 to 2016: analysis of temporal and regional genotype variation. BMC Infect Dis 2020; 20:740. [PMID: 33036575 PMCID: PMC7547507 DOI: 10.1186/s12879-020-05448-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
Background From 2016, the Government of India introduced the oral rotavirus vaccine into the national immunization schedule. Currently, two indigenously developed vaccines (ROTAVAC, Bharat Biotech; ROTASIIL, Serum Institute of India) are included in the Indian immunization program. We report the rotavirus disease burden and the diversity of rotavirus genotypes from 2005 to 2016 in a multi-centric surveillance study before the introduction of vaccines. Methods A total of 29,561 stool samples collected from 2005 to 2016 (7 sites during 2005–2009, 3 sites from 2009 to 2012, and 28 sites during 2012–2016) were included in the analysis. Stools were tested for rotavirus antigen using enzyme immunoassay (EIA). Genotyping was performed on 65.8% of the EIA positive samples using reverse transcription- polymerase chain reaction (RT-PCR) to identify the G (VP7) and P (VP4) types. Multinomial logistic regression was used to quantify the odds of detecting genotypes across the surveillance period and in particular age groups. Results Of the 29,561 samples tested, 10,959 (37.1%) were positive for rotavirus. There was a peak in rotavirus positivity during December to February across all sites. Of the 7215 genotyped samples, G1P[8] (38.7%) was the most common, followed by G2P[4] (12.3%), G9P[4] (5.8%), G12P[6] (4.2%), G9P[8] (4%), and G12P[8] (2.4%). Globally, G9P[4] and G12P[6] are less common genotypes, although these genotypes have been reported from India and few other countries. There was a variation in the geographic and temporal distribution of genotypes, and the emergence or re-emergence of new genotypes such as G3P[8] was seen. Over the surveillance period, there was a decline in the proportion of G2P[4], and an increase in the proportion of G9P[4]. A higher proportion of mixed and partially typed/untyped samples was also seen more in the age group 0–11 months. Conclusions This 11 years surveillance highlights the high burden of severe rotavirus gastroenteritis in Indian children < 5 years of age before inclusion of rotavirus vaccines in the national programme. Regional variations in rotavirus epidemiology were seen, including the emergence of G3P[8] in the latter part of the surveillance. Having pre-introduction data is important to track changing epidemiology of rotaviruses, particularly following vaccine introduction.
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Affiliation(s)
- Sidhartha Giri
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, Tamil Nadu, India.,Indian Council of Medical Research, New Delhi, India
| | | | - Shainey Alokit Khakha
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - Mamta Chawla-Sarkar
- National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | | | | | | | | | | | - Subarna Roy
- National Institute of Traditional Medicine, Belgaum, Karnataka, India
| | - Jyothi Bhat
- National Institute for Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | | | - Pradeep Das
- Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Vijayachari Paluru
- Regional Medical Research Centre, Port Blair, Andaman & Nicobar Islands, India
| | - Sasirekha Ramani
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, Tamil Nadu, India.,Baylor College of Medicine, Houston, TX, USA
| | - Sudhir Babji
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rashmi Arora
- Indian Council of Medical Research, New Delhi, India.,Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | | | - Mohan D Gupte
- Indian Council of Medical Research, New Delhi, India
| | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, Tamil Nadu, India. .,Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India.
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8
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Zhou X, Wang YH, Pang BB, Chen N, Kobayashi N. Surveillance of Human Rotavirus in Wuhan, China (2011-2019): Predominance of G9P[8] and Emergence of G12. Pathogens 2020; 9:pathogens9100810. [PMID: 33023203 PMCID: PMC7600066 DOI: 10.3390/pathogens9100810] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children worldwide. To learn the shift of genotypes and genetic characteristics of Rotavirus A (RVA) causing diarrhea in children and adults, a hospital-based surveillance of rotavirus was conducted in Wuhan, China from June 2011 through May 2019, and representative virus strains were phylogenetically analyzed. Among a total of 6733 stool specimens collected from both children and adults with acute gastroenteritis, RVA was detected in 25.5% (1125/4409) and 12.3% (285/2324) of specimens, respectively. G9P[8] was the most common genotype (74.5%), followed by G1P[8] (8.7%), G2P[4] (8.4%), and G3P[8] (7.3%), with G9P[8] increasing rapidly during the study period. The predominant genotype shifted from G1P[8] to G9P[8] in 2012-2013 epidemic season. G12P[6] strain RVA/Human-wt/CHN/Z2761/2019/G12P[6] was detected in April 2019 and assigned to G12-P[6]-I1-R1-C1-M1-A1-N1-T2-E1-H1 genotypes. Phylogenetic analysis revealed that VP7, VP4, VP6, VP3, NSP1, NSP2, and NSP5 genes of Z2761 clustered closely with those of Korean G12P[6] strain CAU_214, showing high nucleotide identities (98.0-98.8%). The NSP3 gene of Z2761 was closely related to those of G2P[4] and G12P[6] rotaviruses in Asia. All the eleven gene segments of Z2761 kept distance from those of cocirculating G9P[8], G1P[8], and G3P[8] strains detected in Wuhan during this study period. This is the first identification of G12 rotavirus in China. It is deduced that Z2761 is a reassortant having DS-1-like NSP3 gene in the background of G12P[6] rotavirus genetically close to CAU_214.
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Affiliation(s)
- Xuan Zhou
- Division of Microbiology, Wuhan Centers for Disease Control and Prevention, Wuhan 430024, China; (X.Z.); (B.-B.P.)
| | - Yuan-Hong Wang
- Division of Microbiology, Wuhan Centers for Disease Control and Prevention, Wuhan 430024, China; (X.Z.); (B.-B.P.)
- Correspondence: ; Tel.: + 86-27-85801763
| | - Bei-Bei Pang
- Division of Microbiology, Wuhan Centers for Disease Control and Prevention, Wuhan 430024, China; (X.Z.); (B.-B.P.)
| | - Nan Chen
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China;
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan;
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9
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Bhattarai V, Sharma S, Rijal KR, Banjara MR. Co-infection with Campylobacter and rotavirus in less than 5 year old children with acute gastroenteritis in Nepal during 2017-2018. BMC Pediatr 2020; 20:68. [PMID: 32054497 PMCID: PMC7020500 DOI: 10.1186/s12887-020-1966-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/10/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diarrhoea, although easily curable, is a global cause of death for a half million children every year. Rotavirus and Campylobacter are the most common etiological agents of diarrhoea in children less than 5 years of age. However, in Nepal, these causative agents are not routinely examined for the diagnosis and treatment. The main objective of this study was to determine Campylobacter co-infection associated with rotavirus diarrhoea in children less than 5 years of age. METHODS A cross-sectional study was conducted at Kanti Children's Hospital (KCH), Kathmandu, Nepal from November 2017 to April 2018. A total of 303 stool specimens from children affected with diarrhoea were processed to detect rotavirus using a rapid rotavirus antigen detection test kit, and Campylobacter by microscopy, culture and biochemical tests. Antibiotic susceptibility tests of Campylobacter isolates were performed according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines 2015. RESULTS Of 303 samples, 91 (30.0%) were positive for co-infection with rotavirus and Campylobacter. Rotavirus mono-infection was detected in 61 (20.1%), and Campylobacter mono-infection was detected in 81 (26.7%) samples. Patient's age, month of infection, untreated water and frequent soil contact were the major risk factors for infections. Clinical features such as > 9 loose motions per day, fever, vomiting, mild to moderate dehydration, diarrhea persisting 6-9 days and presence of mucus in stool were significant (p < 0.05) clinical features, and were more severe in coinfection compared to mono-infections in multivariate analysis. CONCLUSION The study shows a high rate of rotavirus and Campylobacter coinfection in children with diarrhoea. Diagnosis based management of diarrhoeal cases can guide the specific treatment.
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Affiliation(s)
- Vishnu Bhattarai
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Saroj Sharma
- Kanti Children's Hospital, Maharajgunj, Kathmandu, Nepal
| | - Komal Raj Rijal
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Megha Raj Banjara
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal.
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10
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Bennour H, Bouazizi A, Fodha I, Ben Hadj Fredj M, Ben Hamida-Rebai M, Jerbi A, Dhiflaoui A, Abdelberi S, Abbassi F, Abroug S, Khlifa M, Fathallah A, Boujaafar N, Trabelsi A. Unexpected predominance of rotavirus G9P[8] strain in Tunisian adult diarrheal patients. J Med Microbiol 2020; 69:280-289. [PMID: 32003707 DOI: 10.1099/jmm.0.001156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Introduction. Group A Rotavirus (RVA) is known to be a major cause of acute gastroenteritis (AGE) in children but its role as a potential pathogen in immunocompetent adults is probably underestimated.Aim. To compare RVA infections in patients from different age groups.Methodology. Fecal samples were collected from patients aged from birth to 65 years, hospitalized or consulting for AGE between 2015 and 2017. All samples were screened by RT-PCR for the detection of VP6 gene specific of RVA. RVA-positive samples were VP7 and VP4 genotyped using multiplex semi-nested RT-PCR. Full-length VP7 gene of G9-positive strains were sequenced and submitted for phylogenetic analysis.Results. Of 1371 stool specimens collected from children (<5 years; n=454), older children (5 to <15 years; n=316) and adults (15-65 years; n=601), 165 (12.0 %) were RVA-positive. RVA detection rates were significantly higher in children and adults than in older children (15.8 % and 12.1 Vs 6.3 %, respectively; P<0.001). While RVA infections were mostly detected during the coldest months in children, they were observed all year-round in patients aged >5 years. Although G1P[8] remained the most prevalent combination (41.7 %) detected in children, G9P[8] strains widely predominated in adults (58.1 %), followed by G2P[4] (12.9 %). All characterized G9 strains clustered in the modern lineage III.Conclusion. RVA play an important role in AGE not only in children but also in adults. The findings of a wide G9 predominance in patients >5 years highlights the need for continuing surveillance in both pediatric and mature populations.
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Affiliation(s)
- Haifa Bennour
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Asma Bouazizi
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Imene Fodha
- Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia.,Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Mouna Ben Hadj Fredj
- Faculty of Sciences and Techniques, University of Kairouan, Kairouan, Tunisia.,Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Meriam Ben Hamida-Rebai
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Amira Jerbi
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Ameni Dhiflaoui
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Shada Abdelberi
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Fairouz Abbassi
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Saoussen Abroug
- Pediatric Unit, Sahloul University Hospital, Sousse, Tunisia
| | - Monia Khlifa
- Pediatric Unit, Regional Hospital of Msaken, Sousse, Tunisia
| | - Akila Fathallah
- Faculty of Medicine, University of Sousse, Sousse, Tunisia.,Parasitology Department, University Hospital Farhat Hached, Sousse, Tunisia
| | - Noureddine Boujaafar
- Microbiology Department, Sahloul University Hospital, Sousse, Tunisia.,Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Abdelhalim Trabelsi
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research laboratory for Epidemiology and immunogenetics of viral infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
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Prevalence of Rotavirus and Adenovirus in the Childhood Gastroenteritis in a Tertiary Care Teaching Hospital. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.2.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Shrestha S, Thakali O, Raya S, Shrestha L, Parajuli K, Sherchand JB. Acute gastroenteritis associated with Rotavirus A among children less than 5 years of age in Nepal. BMC Infect Dis 2019; 19:456. [PMID: 31117969 PMCID: PMC6532269 DOI: 10.1186/s12879-019-4092-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/15/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Rotavirus gastroenteritis is a major public health problem in Nepal. This study was conducted to obtain information associated with Rotavirus gastroenteritis and to perform genotyping of Rotavirus A. METHODS Hospital based cross sectional study was conducted from January to December 2017 among children less than 5 years of age attending Kanti Children's Hospital and Tribhuvan University Teaching Hospital. Rotavirus A antigen detection was performed by Enzyme Linked Immunosorbent Assay (ELISA) using ProSpecT Rotavirus Microplate Assay. Rotavirus A positive strains were further confirmed by genotyping using Reverse-Transcription Polymerase Chain Reaction (RT-PCR). RESULTS A total of 1074 stool samples were collected, of them 770 were hospitalized, and 304 were non-hospitalized cases. Rotavirus A infection was found in 28% of children with infection rate higher in hospitalized (34%) than in non-hospitalized (14%) children. Rotavirus A detection was higher in male (31%) than in female (24%), but this was statistically not significant (p > 0.05). Rotavirus A positivity was higher in children of age group 0-23 months, this result was statistically not significant (p > 0.05) with higher frequency found in the months of November, December, January, February and March (p < 0.05). On the basis of molecular analysis of Rotavirus A genotyping, G12P[6] (46.39%) was found to be the predominant followed by G1P[8] (35.05%), G3P[8] (7.21%) and G1P[6] (5.15%) while 4.12% was mixed infection and 1.03% was partially typed (p < 0.05). CONCLUSION Rotavirus A infection occurred throughout the year, but the infection was significantly higher during the month of March. The higher frequency of rotavirus infection was observed among children of age group 0-23 months; however this was not found to be statistically significant. In this study, G12P[6] is predominant genotype observed. The results of genotyping are essential for the introduction of Rotavirus vaccine in Nepal.
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Affiliation(s)
- Sony Shrestha
- Department of Clinical Microbiology and Public Health Research Laboratory, Maharajgunj Medical Campus, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Ocean Thakali
- Department of Clinical Microbiology and Public Health Research Laboratory, Maharajgunj Medical Campus, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Sunayana Raya
- Department of Clinical Microbiology and Public Health Research Laboratory, Maharajgunj Medical Campus, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Laxman Shrestha
- Department of Child Health, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Keshab Parajuli
- Department of Clinical Microbiology and Public Health Research Laboratory, Maharajgunj Medical Campus, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Jeevan Bahadhur Sherchand
- Department of Clinical Microbiology and Public Health Research Laboratory, Maharajgunj Medical Campus, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
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13
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Emergence of rotavirus G9 in 2012, as the dominant genotype in Turkish children with diarrhea, in a university hospital in Ankara. REV ROMANA MED LAB 2019. [DOI: 10.2478/rrlm-2019-0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Introduction: Rotavirus infection is a major cause of morbidity and mortality in infants and young children with diarrhea throughout the world.
Material and Methods: In this study, we aimed to determine the detection rate of rotavirus infection in 181 children less than 5 years of age presenting with acute gastroenteritis and admitted to a tertiary care hospital in Ankara, Turkey, from April to November 2012. We documented the epidemiological data by elucidating the prevalent genotypes. Stool specimens were collected, and rotavirus antigen in the samples was detected using ELISA. G and P genotypes were determined by RT-PCR via type specific primers. The nucleotide sequence of the concerned genes was determined by Sanger sequencing and phylogenetic analysis was performed by neighbor-joining method.
Results: Of the 181 samples, 28 (15.5%) were positive for the rotavirus antigen. Twenty-seven samples were positive for G genotypes and 21 were positive for P genotypes. Genotypes G1 (7.1%), G2 (7.1%), G3 (7.1%), G4 (3.6%), G9 (71.5%) and P4 (3.6%), P8 (71.4%) were identified. Genotype G9P[8] (50%) was predominant in the combination of G and P genotypes. Most of the G9 strains of this study formed an independent cluster in Lineage III, except two strains which clustered with an Ethiopian G9 strain of 2012.
Conclusions: It seems that during 2012 season, genotype G9P[8] increased significantly in Ankara due to a new circulating strain of G9.
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Takatsuki H, Agbemabiese CA, Nakagomi T, Pun SB, Gauchan P, Muto H, Masumoto H, Atarashi R, Nakagomi O, Pandey BD. Whole genome characterisation of G11P[25] and G9P[19] rotavirus A strains from adult patients with diarrhoea in Nepal. INFECTION GENETICS AND EVOLUTION 2019; 69:246-254. [DOI: 10.1016/j.meegid.2019.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 12/17/2022]
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Co-Infection by Waterborne Enteric Viruses in Children with Gastroenteritis in Nepal. Healthcare (Basel) 2019; 7:healthcare7010009. [PMID: 30642113 PMCID: PMC6473710 DOI: 10.3390/healthcare7010009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/22/2018] [Accepted: 01/08/2019] [Indexed: 12/20/2022] Open
Abstract
Enteric viruses are highly contagious and a major cause of waterborne gastroenteritis in children younger than five years of age in developing world. This study examined the prevalence of enteric virus infection in children with gastroenteritis to identify risk factors for co-infections. In total, 107 stool samples were collected from patients with acute gastroenteritis along with samples of their household drinking water and other possible contamination sources, such as food and hand. The presence of major gastroenteritis-causing enteric virus species (group A rotaviruses, enteroviruses, adenoviruses, and noroviruses of genogroup I) in stool and water samples was examined using quantitative polymerase chain reaction. Among the 107 stool samples tested, 103 (96%) samples contained at least one of the four tested enteric viruses, and the combination of group A rotaviruses and enteroviruses was the most common co-infection (52%, n = 54/103). At least one viral agent was detected in 16 (16%) of 103 drinking water samples. Identical enteric viruses were detected in both the stool and water samples taken from the same patients in 13% of cases (n = 13/103). Group A rotaviruses were most frequently found in children suffering from acute diarrhea. No socio-demographic and clinical factors were associated with the risk of co-infection compared with mono-infection. These less commonly diagnosed viral etiological agents in hospitals are highly prevalent in patients with acute gastroenteritis.
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Sherchand JB, Thakali O, Sherchan JB, Bhandari D, Tandukar S, Paudel KP, Shrestha BM, Rayamajhi A, Rai GK. Hospital based surveillance and molecular characterization of rotavirus in children less than 5 years of age with acute gastroenteritis in Nepal. Vaccine 2018; 36:7841-7845. [PMID: 30385057 DOI: 10.1016/j.vaccine.2018.07.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 03/11/2018] [Accepted: 07/17/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Rotavirus remains a significant causative agent of childhood acute gastroenteritis, particularly among children less than 5 years of age. Although precise data on childhood mortality associated with diarrheal disease in Nepal is not available, it is estimated that22% of all rotavirus deaths globally occurs in neighboring country of India. In spite of the substantial burden of rotavirus gastroenteritis in the Indian subcontinent, rotavirus vaccine has not been introduced in Nepal. Continuous surveillance for monitoring rotavirus disease burden and molecular characterization is needed prior to rotavirus vaccine introduction in Nepal. METHODS A total of 3310 stool samples (2849 hospitalized cases and 461 non-hospitalized cases), were collected from patients <5 years of age from January 2013 to December 2016 and tested for rotavirus antigen by ELISA (ProSpecT, USA). A subset of ELISA positive stool samples was genotyped. Demographic data were collected. RESULTS During the four-year surveillance period, the overall burden of rotavirus infection was 24% among hospitalized children which was much higher than among non-hospitalized children (12%). The majority of children hospitalized with rotavirus gastroenteritis were less than 2 years of age (86%). Rotavirus-associated gastroenteritis hospitalizations occur year-round in Nepal, but a distinct peak in winter (up to 40% among hospitalized) was observed. Of 735 ELISA positive samples, 492 were genotyped by RT-PCR. The most prevalent genotype was G12P[6] (45.3%), followed byG2P[4](12.2%), G1P[8] (9.6%), G9P[4](7.3%), and G9P[8](4.5%). Mixed infection accounted for 4.4% of cases, 6.2% were partially typed and 10.5% of the samples were G and P untypable. CONCLUSIONS A high burden of rotavirus gastroenteritis and a diversity of circulating rotavirus strains in Nepal were observed. Recommendation to introduce a rotavirus vaccine with known vaccine effectiveness would help in reducing the severity of Rotavirus diarrheal disease in children less than 5 years of age.
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Affiliation(s)
- Jeevan B Sherchand
- Public Health Research Laboratory, Institute of Medicine Tribhuvan University, Maharajgunj, Kathmandu, Nepal.
| | - Ocean Thakali
- Public Health Research Laboratory, Institute of Medicine Tribhuvan University, Maharajgunj, Kathmandu, Nepal
| | - Jatan B Sherchan
- Consultant Microbiologist - National Rotavirus Surveillance in Public Health Research Laboratory, Nepal
| | - Dinesh Bhandari
- Public Health Research Laboratory, Institute of Medicine Tribhuvan University, Maharajgunj, Kathmandu, Nepal
| | - Sarmila Tandukar
- Public Health Research Laboratory, Institute of Medicine Tribhuvan University, Maharajgunj, Kathmandu, Nepal
| | | | | | - Ajit Rayamajhi
- Kanti-children's Hospital, Maharajgunj, Kathmandu, Nepal
| | - Ganesh K Rai
- Kanti-children's Hospital, Maharajgunj, Kathmandu, Nepal
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Selvarajan S, Reju S, Pushpanathan P, Arumugam R, Padmanabhan R, Kothandaramanujam SM, Srikanth P, Kang G. Molecular characterisation and clinical correlates of rotavirus in children and adults in a tertiary care centre, Chennai, South India. Indian J Med Microbiol 2018; 35:221-227. [PMID: 28681810 DOI: 10.4103/ijmm.ijmm_16_51] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
AIMS This study was undertaken to determine the rate of detection of rotavirus causing diarrhoea among children and adults, identify the common genotypes circulating and determine clinical correlates. SETTINGS AND DESIGN This is a cross-sectional study in a tertiary care centre. MATERIALS AND METHODS Stool samples were collected from adults and children, transported on ice, aliquoted and stored at - 80°C. Rotavirus antigen detection enzyme-linked immunosorbent assay was performed on all samples. Representative samples were typed by conventional hemi-nested VP7 and VP4 reverse transcription-polymerase chain reaction. STATISTICAL ANALYSIS USED Test of proportion, Student's t-test and Chi-square test were used for statistical analysis. RESULTS A total of 444 stool samples were collected and tested over 14 months. Among these, 116 were paediatric with a rate of positivity of 36.21% and 328 were adults with rate of positivity of 20.73%. Among children under 5 years (n = 90), the rate of positivity was 41.11%. Vesikari scale was used for clinical assessment. The mean ± standard deviation Vesikari score in rotavirus-infected children and rotavirus-uninfected children was 11.2 ± 3.2 and 8.9 ± 3.6, respectively, and the difference was statistically significant. Nineteen samples were genotyped in children < 5 years, 94.7% were of G1P[8] and 5.3% were of G9P[4] genotype. Genotyping of 14 adult samples, G1P[8](85.7%) was found as the predominant genotype, two samples (14.3%) were partially typed (G9PUT and G12PUT). CONCLUSIONS The rate of positivity of rotavirus in children under 5 years was 41.11%. G1P[8] is the most common strain circulating across all age groups.
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Affiliation(s)
- Sribal Selvarajan
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Chennai, Tamil Nadu, India
| | - Sudhabharathi Reju
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Chennai, Tamil Nadu, India
| | - Premalatha Pushpanathan
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Chennai, Tamil Nadu, India
| | - Rajesh Arumugam
- Division of Gastrointestinal Sciences, The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, Tamil Nadu, India
| | - Ramachandran Padmanabhan
- Department of Paediatrics, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Chennai, Tamil Nadu, India
| | - Sudhakar Muthiah Kothandaramanujam
- Department of General Medicine, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Chennai, Tamil Nadu, India
| | - Padma Srikanth
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Chennai, Tamil Nadu, India
| | - Gagandeep Kang
- Division of Gastrointestinal Sciences, The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, Tamil Nadu, India
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Abstract
BACKGROUND In Asia, rotavirus accounts for approximately 45% of admissions due to acute gastroenteritis in children <5 years, and causes about 145,000 deaths every year. We studied the distribution of rotavirus strains from Myanmar, Sri Lanka, and Nepal during 2009-2015. METHODS Stool samples collected from children <5 years of age hospitalized with acute diarrhea in the three sites and positive for rotavirus antigen by enzyme immunoassay (EIA) were sent to the Christian Medical College, Vellore from 2009 to 2015. G and P typing of rotavirus strains were performed using reverse-transcription polymerase chain reaction (RT-PCR). RESULT Of the 2354 EIA positive samples tested, G12P[8] (36.8%), G1P[8] (30.1%), and G12P[6] (41.3%) were the most common strains isolated from Myanmar, Sri Lanka, and Nepal respectively. CONCLUSION There was substantial diversity of rotavirus genotypes, and continued surveillance in developing countries of Asia will help in understanding the epidemiology of rotavirus before and after introduction of vaccines.
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Azaran A, Makvandi M, Teimoori A, Ebrahimi S, Heydari F, Nikfar R. Distribution of Rotavirus Genotypes Ccirculating
in Ahvaz, Iran in 2016. IRANIAN BIOMEDICAL JOURNAL 2018; 22:107-16. [PMID: 28915725 PMCID: PMC5786656 DOI: 10.22034/ibj.22.2.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 05/06/2017] [Accepted: 05/08/2017] [Indexed: 02/06/2023]
Abstract
Background Group A rotavirus (RVA) mainly causes acute gastroenteritis, exclusively in young children in developing countries. The prevalence and determination of the molecular epidemiology of rotavirus genotypes will determine the dominant rotavirus genotypes in the region and provide a strategy for the development of appropriate vaccines. Methods A total of 100 fecal samples were collected from children below five years with acute gastroenteritis who referred to Aboozar Children’s Hospital of Ahvaz city during October 2015 to March 2016. All samples were screened by latex agglutination for the presence of rotavirus antigen. Rotavirus-positive samples were further analyzed by the semi-multiplex RT-PCR, and the sequencing was performed for G/P genotyping. Results Findings showed that 32% of the specimens were RVA-positive. Among the 32 VP7 genotyped strains, the predominant G genotype was G9 (37.5%), followed by G2 (21.9%), G1 (12.5%), G12 (9.4%), G4 (9.4%), G2G9 (6.3%), and G3 (3.1%). Among the 31 VP4 genotyped strains, P[8] genotype was the dominant (62.5%), followed by P[4] (31.3%) and P[4] P[8] (3.1%). The genotypes for G and P were identified for 31 rotaviruses (96.87%), but only one strain, G9, remained non-typeable for the P genotype. The most prevalent G/P combination was G9P[8] (28.5%), followed by G2P[4] (18.8%), G1P[8] (9.4%), G12P[8] (9.4%), G4P[8] (9.4%), G2G9P[4] (6.3%), G9P[4] P[8] (3.1%), G3P[8] (3.1%), G9P[4] (3.1%), G2P[8] (3.1%), and G9P[non-typeable] (3.1%). Conclusion A novel rotavirus strain, G12, was detected, for the first time, in patients from the southwest of Iran. Comprehensive investigations are required to evaluate the emergence of this strain.
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Affiliation(s)
- Azarakhsh Azaran
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Manoochehr Makvandi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Teimoori
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeedeh Ebrahimi
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farzad Heydari
- Cukurova University, Medicine Faculty, Medical Microbiology Department, Adana, Turkey
| | - Roya Nikfar
- Department of Infectious Diseases, Aboozar Children’s Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Shrestha S, Shrestha S, Shindo J, Sherchand JB, Haramoto E. Virological Quality of Irrigation Water Sources and Pepper Mild Mottle Virus and Tobacco Mosaic Virus as Index of Pathogenic Virus Contamination Level. FOOD AND ENVIRONMENTAL VIROLOGY 2018; 10:107-120. [PMID: 29098656 DOI: 10.1007/s12560-017-9324-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/28/2017] [Indexed: 05/04/2023]
Abstract
Irrigation water is a doorway for the pathogen contamination of fresh produce. We quantified pathogenic viruses [human adenoviruses, noroviruses of genogroups I and II, group A rotaviruses, Aichi virus 1 (AiV-1), enteroviruses (EnVs), and salivirus (SaliV)] and examined potential index viruses [JC and BK polyomaviruses (JCPyVs and BKPyVs), pepper mild mottle virus (PMMoV), and tobacco mosaic virus (TMV)] in irrigation water sources in the Kathmandu Valley, Nepal. River, sewage, wastewater treatment plant (WWTP) effluent, pond, canal, and groundwater samples were collected in September 2014, and in April and August 2015. Viruses were concentrated using an electronegative membrane-vortex method and quantified using TaqMan (MGB)-based quantitative PCR (qPCR) assays with murine norovirus as a molecular process control to determine extraction-reverse transcription-qPCR efficiency. Tested pathogenic viruses were prevalent with maximum concentrations of 5.5-8.8 log10 copies/L, and there was a greater abundance of EnVs, SaliV, and AiV-1. Virus concentrations in river water were equivalent to those in sewage. Canal, pond, and groundwater samples were found to be less contaminated than river, sewage, and WWTP effluent. Seasonal dependency was clearly evident for most of the viruses, with peak concentrations in the dry season. JCPyVs and BKPyVs had a poor detection ratio and correspondence with pathogenic viruses. Instead, the frequently proposed PMMoV and the newly proposed TMV were strongly predictive of the pathogen contamination level, particularly in the dry season. We recommend utilizing canal, pond, and groundwater for irrigation to minimize deleterious health effects and propose PMMoV and TMV as indexes to elucidate pathogenic virus levels in environmental samples.
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Affiliation(s)
- Sadhana Shrestha
- Interdisciplinary Centre for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan.
| | - Shankar Shrestha
- Interdisciplinary Centre for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan
| | - Junko Shindo
- Interdisciplinary Centre for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan
| | - Jeevan B Sherchand
- Institute of Medicine, Tribhuvan University, Maharajgunj, P.O.Box 1524, Kathmandu, Nepal
| | - Eiji Haramoto
- Interdisciplinary Centre for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan
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Cardemil CV, Sherchand JB, Shrestha L, Sharma A, Gary HE, Estivariz CF, Diez-Valcarce M, Ward ML, Bowen MD, Vinjé J, Parashar U, Chu SY. Pathogen-Specific Burden of Outpatient Diarrhea in Infants in Nepal: A Multisite Prospective Case-Control Study. J Pediatric Infect Dis Soc 2017; 6:e75-e85. [PMID: 28472489 PMCID: PMC10389588 DOI: 10.1093/jpids/pix009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/09/2017] [Indexed: 12/28/2022]
Abstract
BACKGROUND Nonsevere diarrheal disease in Nepal represents a large burden of illness. Identification of the specific disease-causing pathogens will help target the appropriate control measures. METHODS Infants aged 6 weeks to 12 months were recruited from 5 health facilities in eastern, central, and western Nepal between August 2012 and August 2013. The diarrhea arm included infants with mild or moderate diarrhea treatable in an outpatient setting; the nondiarrhea arm included healthy infants who presented for immunization visits or had a mild nondiarrheal illness. Stool samples were tested for 15 pathogens with a multiplex polymerase chain reaction (PCR) assay and real-time reverse-transcription (RT)-PCR assays for rotavirus and norovirus. Rotavirus- and norovirus-positive specimens were genotyped. We calculated attributable fractions (AFs) to estimate the pathogen-specific burden of diarrhea and adjusted for facility, age, stunting, wasting, and presence of other pathogens. RESULTS We tested 307 diarrheal and 358 nondiarrheal specimens. Pathogens were detected more commonly in diarrheal specimens (164 of 307 [53.4%]) than in nondiarrheal specimens (113 of 358 [31.6%]) (P < .001). Rotavirus (AF, 23.9% [95% confidence interval (CI), 14.9%-32.8%]), Salmonella (AF, 12.4% [95% CI, 6.6%-17.8%]), and Campylobacter (AF, 5.6% [95% CI, 1.3%-9.8%]) contributed most to the burden of disease. In these diarrheal specimens, the most common genotypes for rotavirus were G12P[6] (27 of 82 [32.9%]) and G1P[8] (16 of 82 [19.5%]) and for norovirus were GII.4 Sydney (9 of 26 [34.6%]) and GII.7 (5 of 26 [19.2%]). CONCLUSIONS The results of this study indicate that the introduction of a rotavirus vaccine in Nepal will likely decrease outpatient diarrheal disease burden in infants younger than 1 year, but interventions to detect and target other pathogens, such as Salmonella and Campylobacter spp, should also be considered.
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Affiliation(s)
- Cristina V Cardemil
- Global Immunization Division, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Laxman Shrestha
- Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Arun Sharma
- Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Howard E Gary
- Global Immunization Division, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Concepcion F Estivariz
- Global Immunization Division, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Marta Diez-Valcarce
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - M Leanne Ward
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Michael D Bowen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Umesh Parashar
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Susan Y Chu
- Global Immunization Division, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
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22
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Dhital S, Sherchand JB, Pokhrel BM, Parajuli K, Shah N, Mishra SK, Sharma S, Kattel HP, Khadka S, Khatiwada S, Parajuli N, Rijal B. Molecular epidemiology of Rotavirus causing diarrhea among children less than five years of age visiting national level children hospitals, Nepal. BMC Pediatr 2017; 17:101. [PMID: 28388889 PMCID: PMC5385007 DOI: 10.1186/s12887-017-0858-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/01/2017] [Indexed: 11/10/2022] Open
Abstract
Background Rotaviruses are the major cause of diarrhea among the infants and young children all over the world causing over 500,000 deaths and 2.4 million hospitalizations each year. In Nepal Rotavirus infection positivity rates ranges from 17.0 to 39.0% among children less than 5 years. However, little is known about the molecular genotypes of Rotavirus prevailing. The objective of this study was to estimate the burden of Rotavirus gastroenteritis and determine the genotypes of Rotavirus among children less than 5 years. Methods The cross sectional study was conducted from January to November 2014 among children less than 5 years old visiting Kanti Children’s Hospital and Tribhuvan University Teaching Hospital. Rotavirus antigen detection was performed by Enzyme Linked Immunosorbent Assay (ELISA) using ProSpecT Rotavirus Microplate Assay. Among the Rotavirus antigen positive samples, 59 samples were used for Rotavirus RNA extraction. Multiplex PCR was performed to identify G type comprising G1-G4, G8-G10 and G12 and P type comprising P[4], P[6], P[8], P[9], P[10], and P[11]. Results A total of 717 diarrheal stool samples were collected from patients ranging from 10 days to 59 months of age. Rotavirus antigen positive was found among (N = 164)22.9% of patients. The highest number of the diarrhea was seen in January. Molecular analysis of Rotavirus genotypes revealed that the predominant G-Type was G12 (36%) followed by G9 (31%), G1 (21%), G2 (8.6%). The predominant P- type was P6 (32.8%) followed by P8 (31%), P10 (14.8%), P4 (14.8%). A total of seven G/P type combinations were identified the most common being G12P [6] (35.8%), G1P [8] (15.1%), G9P [8] (15.1%). Conclusion Rotavirus diarrhea is, mostly affecting children from 7 to 24 months in Nepal, mostly occurring in winter. The circulating genotypes in the country are found to be primarily unusual genotypes and predominance of G12P[6]. It is recommended to conduct genotyping of Rotavirus on large samples before starting vaccination in the country. Electronic supplementary material The online version of this article (doi:10.1186/s12887-017-0858-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Subhash Dhital
- National Public Health Laboratory, HIV Reference Unit, Kathmandu, Nepal.
| | | | - Bharat Mani Pokhrel
- Department of Microbiology, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Keshab Parajuli
- Department of Microbiology, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Niranjan Shah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Shyam Kumar Mishra
- Department of Microbiology, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Sangita Sharma
- Department of Microbiology, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Hari Prasad Kattel
- Department of Microbiology, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Sundar Khadka
- National Public Health Laboratory, HIV Reference Unit, Kathmandu, Nepal
| | | | - Narayan Parajuli
- Department of Microbiology, ManMohan Memorial Institute of Health Sciences, Kathmandu, Nepal
| | - Basistha Rijal
- Department of Microbiology, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
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23
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Nakagomi T, Do LP, Agbemabiese CA, Kaneko M, Gauchan P, Doan YH, Jere KC, Steele AD, Iturriza-Gomara M, Nakagomi O, Cunliffe NA. Whole-genome characterisation of G12P[6] rotavirus strains possessing two distinct genotype constellations co-circulating in Blantyre, Malawi, 2008. Arch Virol 2016; 162:213-226. [PMID: 27718073 DOI: 10.1007/s00705-016-3103-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/30/2016] [Indexed: 10/20/2022]
Abstract
Rotavirus A strains detected in diarrhoeal children commonly possess any one of the genotypes G1, G2, G3, G4, and G9, with a recent increase in G12 detection globally. G12P[6] strains possessing short RNA (DS-1-like) and long RNA (Wa-like) migration patterns accounted for 27 % of the strains circulating in Blantyre, Malawi, between 2007 and 2008. To understand how the G12P[6] strains with two distinct genetic backgrounds emerged in Malawi, we conducted whole-genome analysis of two long-RNA and two short-RNA strains. While the former had a typical Wa-like genotype constellation of G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, the latter was found to have G12-P[6]-I2-R2-C2-M1-A2-N2-T2-E2-H2: a VP3 gene mono-reassortant on the DS-1-like backbone. Phylogenetic and Bayesian Markov chain Monte Carlo analyses showed that the short-RNA G12P[6] strains were generated around 2006 by reassortment between an African Wa-like G12P[6] strain donating three genes (the VP7, VP4, and VP3 genes) and a G2P[4] strain similar to the one circulating in Thailand or the United States of America that donated the remaining eight genes. On the other hand, the long-RNA strains were generated as a result of reassortment events within Wa-like G12 and non-G12 strains commonly circulating in Africa; only the VP4 gene was from a Malawian G8P[6] strain. In conclusion, this study uncovered the evolutionary pathways through which two distinct G12P[6] strains emerged in Malawi.
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Affiliation(s)
- T Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan. .,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - L P Do
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - C A Agbemabiese
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - M Kaneko
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - P Gauchan
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Y H Doan
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Department of Virology 2, National Institute of Infectious Diseases, Tokyo, Japan
| | - K C Jere
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.,Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - A D Steele
- Vaccines and Immunization, PATH, Seattle, WA, 98121, USA.,MRC Diarrhoeal Pathogens Research Unit, MEDUNSA, University of Limpopo, Pretoria, South Africa
| | - M Iturriza-Gomara
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - O Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - N A Cunliffe
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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24
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Yodmeeklin A, Khamrin P, Chuchaona W, Saikruang W, Kongkaew A, Vachirachewin R, Kumthip K, Okitsu S, Ushijima H, Maneekarn N. Great genetic diversity of rotaviruses detected in piglets with diarrhea in Thailand. Arch Virol 2016; 161:2843-9. [PMID: 27412716 DOI: 10.1007/s00705-016-2976-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/06/2016] [Indexed: 01/07/2023]
Abstract
A total of 491 fecal specimens collected from diarrheic piglets in Thailand from January 2011 to March 2014 were screened for group A rotavirus by RT-PCR assay. The G and P genotypes of the detected rotaviruses were determined by multiplex PCR or nucleotide sequencing. Group A rotaviruses were detected in 113 out of 491 (23.0 %) fecal specimens. A wide variety of G-P genotype combinations were identified, and G4P[13] was the most prevalent genotype combination (29.2 %), followed by G4P[23] (14.1 %), G5P[23] (11.5 %), G4P[6] (9.7 %), G3P[23] (7.0 %), G5P[13] (6.1 %), G3P[13] (4.4 %), G3P[6] (2.7 %), and G5P[6] (2.7 %). In addition, the other G-P combinations were also detected at a low percentage, including G3P[19], G4P[7], G9P[19], G9P[23], G9P[7], G4P[19], and G11P[13] strains. This study indicated that group A rotaviruses are a common causes of diarrhea in piglets and a great diversity of G and P genotype combinations are circulating in piglets in Thailand.
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Affiliation(s)
- Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Watchaporn Chuchaona
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Wilaiporn Saikruang
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Aphisek Kongkaew
- Animal House Unit, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Ratchaya Vachirachewin
- Department of Food Animal Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Shoko Okitsu
- 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
| | - 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
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
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25
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Moussa A, Ben Hadj Fredj M, Fodha I, BenHamida-Rebaï M, Kacem S, Argoubi A, Bennour H, Boujaafar N, Trabelsi A. Distribution of rotavirus VP7 and VP4 genotypes circulating in Tunisia from 2009 to 2014: Emergence of the genotype G12. J Med Microbiol 2016; 65:1028-1037. [PMID: 27375269 DOI: 10.1099/jmm.0.000305] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Group A rotavirus (RVA) represents the most important aetiological agent of diarrhoea in children worldwide. From January 2009 to December 2014, a multi-centre study realized through 11 Tunisian cities was undertaken among children aged <5 years consulting or hospitalized for acute gastroenteritis. A total of 1127 faecal samples were collected. All samples were screened by ELISA for the presence of RVA antigen. RVA-positive samples were further analyzed by PAGE and used for G/P-genotyping by semi-nested multiplex RT-PCR. Globally, 270 specimens (24 %) were RVA-positive, with peaks observed annually between November and March. Nine different electropherotypes could be visualized by PAGE, six with a long profile (173 cases) and two with a short one (seven cases). Mixed profiles were detected in two cases. Among the 267 VP7 genotyped strains, the predominant G- genotype was G1 (39.6 %) followed by G3 (22.2 %), G4 (13 %), G9 (11.5 %), G2 (5.2 %) and G12 (5.2 %). Among the 260 VP4 genotyped strains, P[8] genotype was the predominant (74.5 %) followed by P[6] (10.4 %) and P[4] (5.5 %). A total of 257 strains (95.2 %) could be successfully G- and P-genotyped. G1P[8] was the most prevalent combination (34.4 %), followed by G3P[8] (16.3 %), G9P[8] (10.3 %), G4P[8] (8.9 %), G2P[4] (4 %), G12P[6] (2.6 %) and G12P[8] (1.9 %). Uncommon G/Pgenotype combinations, mixed infections and untypeable strains were also detected. This is the first report, in Tunisia, of multiple detection of an emerging human RVA strain, G12 genotype. This study highlighted the need for maintaining active surveillance of emerging strains in Northern Africa.
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Affiliation(s)
- Amal Moussa
- LR14SP02, Epidemiology and Immunogenetics of Human Viral Infections, Laboratory of Microbiology, Sahloul University Hospital, 4054 Sousse, Tunisia
| | - Mouna Ben Hadj Fredj
- LR14SP02, Epidemiology and Immunogenetics of Human Viral Infections, Laboratory of Microbiology, Sahloul University Hospital, 4054 Sousse, Tunisia.,Faculty of Sciences and Techniques, University of Kairouan, Kairouan, Tunisia
| | - Imene Fodha
- LR14SP02, Epidemiology and Immunogenetics of Human Viral Infections, Laboratory of Microbiology, Sahloul University Hospital, 4054 Sousse, Tunisia.,Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Meriam BenHamida-Rebaï
- LR14SP02, Epidemiology and Immunogenetics of Human Viral Infections, Laboratory of Microbiology, Sahloul University Hospital, 4054 Sousse, Tunisia.,Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Saoussen Kacem
- LR14SP02, Epidemiology and Immunogenetics of Human Viral Infections, Laboratory of Microbiology, Sahloul University Hospital, 4054 Sousse, Tunisia.,Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Aida Argoubi
- LR14SP02, Epidemiology and Immunogenetics of Human Viral Infections, Laboratory of Microbiology, Sahloul University Hospital, 4054 Sousse, Tunisia.,Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Haifa Bennour
- LR14SP02, Epidemiology and Immunogenetics of Human Viral Infections, Laboratory of Microbiology, Sahloul University Hospital, 4054 Sousse, Tunisia
| | - Noureddine Boujaafar
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Laboratory of Microbiology, Sahloul University Hospital, 4054 Sousse, Tunisia
| | - Abdelhalim Trabelsi
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,LR14SP02, Epidemiology and Immunogenetics of Human Viral Infections, Laboratory of Microbiology, Sahloul University Hospital, 4054 Sousse, Tunisia
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26
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Agbemabiese CA, Nakagomi T, Doan YH, Nakagomi O. Whole genomic constellation of the first human G8 rotavirus strain detected in Japan. INFECTION GENETICS AND EVOLUTION 2015; 35:184-93. [PMID: 26275468 DOI: 10.1016/j.meegid.2015.07.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 12/25/2022]
Abstract
Human G8 Rotavirus A (RVA) strains are commonly detected in Africa but are rarely detected in Japan and elsewhere in the world. In this study, the whole genome sequence of the first human G8 RVA strain designated AU109 isolated in a child with acute gastroenteritis in 1994 was determined in order to understand how the strain was generated including the host species origin of its genes. The genotype constellation of AU109 was G8-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analyses of the 11 genome segments revealed that its VP7 and VP1 genes were closely related to those of a Hungarian human G8P[14] RVA strain and these genes shared the most recent common ancestors in 1988 and 1982, respectively. AU109 possessed an NSP2 gene closely related to those of Chinese sheep and goat RVA strains. The remaining eight genome segments were closely related to Japanese human G2P[4] strains which circulated around 1985-1990. Bayesian evolutionary analyses revealed that the NSP2 gene of AU109 and those of the Chinese sheep and goat RVA strains diverged from a common ancestor around 1937. In conclusion, AU109 was generated through genetic reassortment event where Japanese DS-1-like G2P[4] strains circulating around 1985-1990 obtained the VP7, VP1 and NSP2 genes from unknown ruminant G8 RVA strains. These observations highlight the need for comprehensive examination of the whole genomes of RVA strains of less explored host species.
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Affiliation(s)
- Chantal Ama Agbemabiese
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Toyoko Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yen Hai Doan
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Osamu Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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27
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Evolution of a G6P[6] rotavirus strain isolated from a child with acute gastroenteritis in Ghana, 2012. J Gen Virol 2015; 96:2219-2231. [DOI: 10.1099/vir.0.000174] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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28
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Ide T, Komoto S, Higo-Moriguchi K, Htun KW, Myint YY, Myat TW, Thant KZ, Thu HM, Win MM, Oo HN, Htut T, Wakuda M, Dennis FE, Haga K, Fujii Y, Katayama K, Rahman S, Nguyen SV, Umeda K, Oguma K, Tsuji T, Taniguchi K. Whole Genomic Analysis of Human G12P[6] and G12P[8] Rotavirus Strains that Have Emerged in Myanmar. PLoS One 2015; 10:e0124965. [PMID: 25938434 PMCID: PMC4418666 DOI: 10.1371/journal.pone.0124965] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/20/2015] [Indexed: 11/18/2022] Open
Abstract
G12 rotaviruses are emerging rotavirus strains causing severe diarrhea in infants and young children worldwide. However, the whole genomes of only a few G12 strains have been fully sequenced and analyzed. In this study, we sequenced and characterized the complete genomes of six G12 strains (RVA/Human-tc/MMR/A14/2011/G12P[8], RVA/Human-tc/MMR/A23/2011/G12P[6], RVA/Human-tc/MMR/A25/2011/G12P[8], RVA/Human-tc/MMR/P02/2011/G12P[8], RVA/Human-tc/MMR/P39/2011/G12P[8], and RVA/Human-tc/MMR/P43/2011/G12P[8]) detected in six stool samples from children with acute gastroenteritis in Myanmar. On whole genomic analysis, all six Myanmarese G12 strains were found to have a Wa-like genetic backbone: G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 for strains A14, A25, P02, P39, and P43, and G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 for strain A23. Phylogenetic analysis showed that most genes of the six strains examined in this study were genetically related to globally circulating human G1, G3, G9, and G12 strains. Of note is that the NSP4 gene of strain A23 exhibited the closest relationship with the cognate genes of human-like bovine strains as well as human strains, suggesting the occurrence of reassortment between human and bovine strains. Furthermore, strains A14, A25, P02, P39, and P43 were very closely related to one another in all the 11 gene segments, indicating derivation of the five strains from a common origin. On the other hand, strain A23 consistently formed distinct clusters as to all the 11 gene segments, indicating a distinct origin of strain A23 from that of strains A14, A25, P02, P39, and P43. To our knowledge, this is the first report on whole genome-based characterization of G12 strains that have emerged in Myanmar. Our observations will provide important insights into the evolutionary dynamics of spreading G12 rotaviruses in Asia.
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Affiliation(s)
- Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- * E-mail:
| | - Kyoko Higo-Moriguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Khaing Win Htun
- Nay Pyi Taw General Hospital (Central Myanmar), Nay Pyi Taw, Myanmar
| | - Yi Yi Myint
- Department of Medical Research (Upper Myanmar), Pyin Oo Lwin, Myanmar
| | | | - Kyaw Zin Thant
- Department of Medical Research (Lower Myanmar), Yangon, Myanmar
| | - Hlaing Myat Thu
- Department of Medical Research (Lower Myanmar), Yangon, Myanmar
| | - Mo Mo Win
- Department of Medical Research (Lower Myanmar), Yangon, Myanmar
| | - Htun Naing Oo
- Department of Traditional Medicine (Central Myanmar), Nay Pyi Taw, Myanmar
| | - Than Htut
- Ministry of Health (Central Myanmar), Nay Pyi Taw, Myanmar
| | - Mitsutaka Wakuda
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Francis Ekow Dennis
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Shofiqur Rahman
- Immunology Research Institute in Gifu, EW Nutrition Japan, Gifu, Japan
| | - Sa Van Nguyen
- Immunology Research Institute in Gifu, EW Nutrition Japan, Gifu, Japan
| | - Kouji Umeda
- Immunology Research Institute in Gifu, EW Nutrition Japan, Gifu, Japan
| | - Keiji Oguma
- Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Takao Tsuji
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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Zeller M, Heylen E, Damanka S, Pietsch C, Donato C, Tamura T, Kulkarni R, Arora R, Cunliffe N, Maunula L, Potgieter C, Tamim S, Coster SD, Zhirakovskaya E, Bdour S, O'Shea H, Kirkwood CD, Seheri M, Nyaga MM, Mphahlele J, Chitambar SD, Dagan R, Armah G, Tikunova N, Van Ranst M, Matthijnssens J. Emerging OP354-Like P[8] Rotaviruses Have Rapidly Dispersed from Asia to Other Continents. Mol Biol Evol 2015; 32:2060-71. [PMID: 25858434 DOI: 10.1093/molbev/msv088] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The majority of human group A rotaviruses possess the P[8] VP4 genotype. Recently, a genetically distinct subtype of the P[8] genotype, also known as OP354-like P[8] or lineage P[8]-4, emerged in several countries. However, it is unclear for how long the OP354-like P[8] gene has been circulating in humans and how it has spread. In a global collaborative effort 98 (near-)complete OP354-like P[8] VP4 sequences were obtained and used for phylogeographic analysis to determine the viral migration patterns. During the sampling period, 1988-2012, we found that South and East Asia acted as a source from which strains with the OP354-like P[8] gene were seeded to Africa, Europe, and North America. The time to the most recent common ancestor (TMRCA) of all OP354-like P[8] genes was estimated at 1987. However, most OP354-like P[8] strains were found in three main clusters with TMRCAs estimated between 1996 and 2001. The VP7 gene segment of OP354-like P[8] strains showed evidence of frequent reassortment, even in localized epidemics, suggesting that OP354-like P[8] genes behave in a similar manner on the evolutionary level as other P[8] subtypes. The results of this study suggest that OP354-like P[8] strains have been able to disperse globally in a relatively short time period. This, in combination with a relatively large genetic distance to other P[8] subtypes, might result in a lower vaccine effectiveness, underscoring the need for a continued surveillance of OP354-like P[8] strains, especially in countries where rotavirus vaccination programs are in place.
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Affiliation(s)
- Mark Zeller
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Elisabeth Heylen
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Susan Damanka
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | | | - Celeste Donato
- Enteric Virus Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Tsutomu Tamura
- Department of Virology, Niigata Prefectural Institute of Public Health and Environmental Sciences, Niigata, Japan
| | - Ruta Kulkarni
- Enteric Viruses Group, National Institute of Virology, Pune, Maharashtra, India
| | - Ritu Arora
- Enteric Viruses Group, National Institute of Virology, Pune, Maharashtra, India
| | - Nigel Cunliffe
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Leena Maunula
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Christiaan Potgieter
- Department of Biochemistry, Centre for Human Metabonomics, North-West University, Potchefstroom, South Africa Deltamune (Pty) Ltd, Lyttelton, Centurion, South Africa
| | - Sana Tamim
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sarah De Coster
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Elena Zhirakovskaya
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Salwa Bdour
- Department of Biological Sciences, Faculty of Science, The University of Jordan, Amman, Jordan
| | - Helen O'Shea
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - Carl D Kirkwood
- Enteric Virus Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Mapaseka Seheri
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Martin Monene Nyaga
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Jeffrey Mphahlele
- South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Shobha D Chitambar
- Enteric Viruses Group, National Institute of Virology, Pune, Maharashtra, India
| | - Ron Dagan
- Soroka University Medical Center and the Faculty of Health Sciences, Ben-Gurion University of Negev, Beer Sheva, Israel
| | - George Armah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Nina Tikunova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Marc Van Ranst
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Leuven, Belgium
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Wangchuk S, Dorji T, Tsheten, Tshering K, Zangmo S, Pem Tshering K, Dorji T, Nishizono A, Ahmed K. A Prospective Hospital-based Surveillance to Estimate Rotavirus Disease Burden in Bhutanese Children under 5 Years of Age. Trop Med Health 2014; 43:63-8. [PMID: 25859154 PMCID: PMC4361340 DOI: 10.2149/tmh.2014-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/06/2014] [Indexed: 11/18/2022] Open
Abstract
As part of efforts to develop an informed policy for rotavirus vaccination, this prospective study was conducted to estimate the burden of rotavirus diarrhea among children less than 5 years old attended to the Department of Pediatrics, Jigme Dorji Wangchuk National Referral Hospital (JDWNRH), Thimphu, Bhutan. The duration of the study was three years, extending from February 2010 through December 2012. We estimated the frequency of hospitalization in the pediatric ward and dehydration treatment unit (DTU) for diarrhea and the number of events attributable to rotavirus infection among children under 5 years of age. During the study period, a total of 284 children (1 in 45) were hospitalized in the pediatric ward, and 2,220 (1 in 6) in the DTU with diarrhea among children residing in the Thimphu district. Group A rotavirus was detected in 32.5% and 18.8% of the stool samples from children hospitalized in the pediatric ward, respectively. Overall, 22.3% of the stool samples were rotavirus-positive, and the majority (90.8%) of them was detected in children under 2 years of age. From this study, we estimated that the annual incidence of hospitalization in the pediatric ward and DTU due to rotavirus diarrhea was 2.4/1000 (95% CI 1.7–3.4) and 10.8/1000 (95% CI 9.1–12.7) children, respectively. This study revealed that rotavirus is a major cause of diarrhea in Bhutanese children in Thimphu district and since no study has been performed previously, represents an important finding for policy discussions regarding the adoption of a rotavirus vaccine in Bhutan.
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Affiliation(s)
- Sonam Wangchuk
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan , Thimphu, Bhutan
| | - Tshering Dorji
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan , Thimphu, Bhutan
| | - Tsheten
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan , Thimphu, Bhutan
| | - Karchung Tshering
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan , Thimphu, Bhutan
| | - Sangay Zangmo
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan , Thimphu, Bhutan
| | - Kunzang Pem Tshering
- Department of Pediatrics, Jigme Dorji Wangchuk National Referral Hospital , Thimphu, Bhutan
| | - Tandin Dorji
- Communicable Disease Division, Department of Public Health, Ministry of Health, Royal Government of Bhutan , Thimphu, Bhutan
| | - Akira Nishizono
- Department of Microbiology, Faculty of Medicine, Oita University , Yufu, Oita, Japan
| | - Kamruddin Ahmed
- Department of Microbiology, Faculty of Medicine, Oita University , Yufu, Oita, Japan ; Research Promotion Institute, Oita University , Yufu, Oita, Japan
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Shetty SA, Mathur M, Deshpande JM. Complete genome analysis of a rare group A rotavirus, G11P[25], isolated from a child in Mumbai, India, reveals interspecies transmission and reassortment with human rotavirus strains. J Med Microbiol 2014; 63:1220-1227. [PMID: 24951672 DOI: 10.1099/jmm.0.070524-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hospital-based rotavirus surveillance was carried out in Mumbai during 2005-2009. An isolate (B08299) with a rare genotype combination (G11P[25]) was detected. The present study was undertaken to characterize the complete genome of the isolate. B08299 exhibited a G11-P[25]-I12-R1-C1-M1-A1-N1-T1-E1-H1 genotype constellation. Phylogenetic analysis of the 11 gene segments of B08299 revealed that the VP2 and NSP5 genes of B08299 had a human origin, while the VP6 gene represented an I12 genotype of obscure origin. The remaining six genes formed a lineage distinct from human and porcine rotaviruses within genotype 1. Analysis of the structural and non-structural genes suggested that B08299 has evolved by gene reassortment. Our findings provide further evidence that interspecies transmission is an important mechanism involved in the evolution and genetic diversity of human rotaviruses in nature.
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Abstract
BACKGROUND The African Rotavirus Surveillance Network has been detecting and documenting rotavirus genotypes in the subcontinent since 1998, largely based on intercountry workshops conducted at Rotavirus Regional Reference Laboratories. This article reports on rotavirus genotypes generated at Regional Reference Laboratories, South Africa between 2007 and 2011 from 16 African countries. METHODS Stool samples were collected from <5-year-old children with diarrhea following World Health Organization criteria of hospital-based rotavirus surveillance. Enzyme immunoassay (EIA) was performed by National Laboratories. Regional Reference Laboratories retested 10% of randomly selected EIA positives and 10% of EIA negatives from each country as part of quality control. At least 50 rotavirus EIA positives from each country per year were subjected to reverse transcriptase polymerase chain reaction based on G-/P-types. Sequencing was conducted in 5-10% of each representative G or P genotype to confirm the genotype, as well as to type some of the samples that could not be genotyped with reverse transcriptase polymerase chain reaction-based methods. RESULTS A total of 2555 of rotavirus EIA positives were genotyped. G1 was the most predominant (28.8%), followed by G9 (17.3%), G2 (16.8%), G8 (8.2%), G12 (6.2%) and G3 (5.9%). Similarly, the P[8] strain was the most prevalent (40.6%), followed by P[6] (30.9%) and P[4] (13.9%). The top G/P combinations detected were G1P[8] (18.4%), G9P[8] (11.7%), G2P[4] (8.6%), G2P[6] (6.2%), G1P[6] (4.9%), G3P[6] (4.3%), G8P[6] (3.8%) and G12P[8] (3.1%). CONCLUSIONS There is high genetic diversity of rotavirus strains circulating in the subcontinent. Understanding the strain diversity pre- and postvaccine introduction are important in Africa to understand the broader impact of the rotavirus vaccines on regionally circulating strains.
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Mijatovic-Rustempasic S, Teel EN, Kerin TK, Hull JJ, Roy S, Weinberg GA, Payne DC, Parashar UD, Gentsch JR, Bowen MD. Genetic analysis of G12P[8] rotaviruses detected in the largest U.S. G12 genotype outbreak on record. INFECTION GENETICS AND EVOLUTION 2013; 21:214-9. [PMID: 24270016 DOI: 10.1016/j.meegid.2013.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/30/2013] [Accepted: 11/10/2013] [Indexed: 01/13/2023]
Abstract
In 2006-07, 77 cases of gastroenteritis in Rochester, NY, USA were associated with rotavirus genotype G12P[8]. Sequence analysis identified a high degree of genetic relatedness among the VP7 and VP4 genes of the Rochester G12P[8] strains and between these strains and currently circulating human G12P[8] strains. Out of 77 samples, two and seven unique nucleotide sequences were identified for VP7 and VP4 genes, respectively. Rochester strain VP7 genes were found to occupy the G12-III lineage and VP4 genes clustered within the P[8]-3 lineage. Six strains contained non-synonymous nucleotide substitutions that produced amino acid changes at 6 sites in the VP8(∗) region of the VP4 gene. Two sites (amino acids 242 and 246) were located in or near a described trypsin cleavage site. Selection analyses identified one positively selected VP7 site (107) and strong purifying selection at 58 sites within the VP7 gene as well as 2 of the 6 variant sites (79 and 218) in VP4.
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Affiliation(s)
- Slavica Mijatovic-Rustempasic
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Elizabeth N Teel
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tara K Kerin
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jennifer J Hull
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sunando Roy
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Geoffrey A Weinberg
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Daniel C Payne
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Umesh D Parashar
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jon R Gentsch
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael D Bowen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Motamedifar M, Amini E, Talezadeh Shirazi P. Frequency of rotavirus and adenovirus gastroenteritis among children in shiraz, iran. IRANIAN RED CRESCENT MEDICAL JOURNAL 2013; 15:729-33. [PMID: 24578843 PMCID: PMC3918200 DOI: 10.5812/ircmj.4415] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 01/07/2013] [Accepted: 06/14/2013] [Indexed: 11/22/2022]
Abstract
Background Viral pathogens are the main cause of acute gastroenteritis in developed and developing countries. Rotavirus and adenovirus are the two important agents associated with hospitalization for diarrhea especially in children. Limitation and control of diarrhea as a costly disease must be considered in national health programs. Objectives Epidemiological studies on viral diarrhea and collecting data for rotavirus and adenovirus prevalence, as two important viral agents of gastroenteritis, are valuable for planning of a prospective program. Materials and Methods 827 stool samples of pediatrics patients with gastroenteritis who were admitted to Dastgheib Hospital, Shiraz, Iran, from September 2008 to February 2010 were tested for presence of rotavirus and adenovirus using the EIA method. A demographic and clinical study was performed to determine the relationship between viral infection and clinical outcomes of patients. Results Rotavirus was identified in 347 patients out of 827 (42%), adenovirus was detected in 76 (9%) of samples and 34 (4%) of patients had rotavirus-adenovirus co-infection. Diarrhea was the most common symptom in viral infected patients. Conclusions Given the non-specific symptoms of these viruses and the high prevalence of viral diarrhea in our region, more laboratories should be equipped for virus detection and vaccination might be considered as a prevention strategy.
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Affiliation(s)
- Mohammad Motamedifar
- Shiraz HIV/Aids Research Center (SHARC), Medical Faculty, Shiraz University of Medical Sciences, Shiraz, IR Iran
- Department of Bacteriology and Virology, Medical Faculty, Shiraz University of Medical Sciences, Shiraz, IR Iran
- Corresponding Author: Mohammad Motamedifar, Shiraz HIV/Aids Research Center (SHARC), Medical Faculty, Shiraz University of Medical Sciences, Shiraz, IR Iran. Tel: +98-7112280916, Fax: +98-7112280916, E-mail:
| | - Elham Amini
- Department of Bacteriology and Virology, Medical Faculty, Shiraz University of Medical Sciences, Shiraz, IR Iran
| | - Pedram Talezadeh Shirazi
- Department of Bacteriology and Virology, Medical Faculty, Shiraz University of Medical Sciences, Shiraz, IR Iran
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Cunliffe N, Nakagomi O. Introduction of rotavirus vaccines in developing countries: remaining challenges. ACTA ACUST UNITED AC 2013; 27:157-67. [PMID: 17716443 DOI: 10.1179/146532807x220262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Rotavirus is the principal agent of severe, dehydrating gastro-enteritis in infants and young children worldwide. The main public health tool that can prevent hospitalisation and death from rotavirus is vaccination. One of two current rotavirus vaccines is now licensed in more than 80 countries and is incorporated into childhood immunisation schedules across several countries in the Americas and Europe. However, since the majority of childhood deaths from rotavirus occur in the developing countries of Africa and Asia, widespread use of vaccine in these two continents will be necessary before a major impact on global diarrhoea mortality is seen. Challenges in these latter settings which primarily relate to vaccine efficacy, safety and financing will be addressed within the next 3-5 years, and thus perhaps finally allow introduction of rotavirus vaccine into the populations in greatest need.
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Affiliation(s)
- Nigel Cunliffe
- Department of Medical Microbiology & Genitourinary Medicine, University of Liverpool, UK.
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Whole-genome sequence analysis of a Korean G11P[25] rotavirus strain identifies several porcine-human reassortant events. Arch Virol 2013; 158:2385-93. [DOI: 10.1007/s00705-013-1720-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/07/2013] [Indexed: 12/11/2022]
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A Survey on Rotavirus Associated Diarrhea in 5 Main Cities of Iran. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2013. [DOI: 10.5812/pedinfect.6431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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: 0.9] [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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Mullick S, Mukherjee A, Ghosh S, Pazhani GP, Sur D, Manna B, Nataro JP, Levine MM, Ramamurthy T, Chawla-Sarkar M. Genomic analysis of human rotavirus strains G6P[14] and G11P[25] isolated from Kolkata in 2009 reveals interspecies transmission and complex reassortment events. INFECTION GENETICS AND EVOLUTION 2012; 14:15-21. [PMID: 23219735 DOI: 10.1016/j.meegid.2012.11.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 11/02/2012] [Accepted: 11/04/2012] [Indexed: 11/19/2022]
Abstract
In a community based case-control study in Kolkata, India, in 2009, two human rotaviruses with uncommon genotypes G6P[14] and G11P[25] were identified, having bovine and porcine characteristics respectively. Strain N-1/2009 with G6P[14] and strain N-38/2009 with G11P[25] genotypes, were isolated from a 13months aged boy who was asymptomatic and a 10months old girl with severe diarrhea respectively. The remaining 9 gene segments of these two strains were analyzed to find the exact origin of these unusual rotaviruses, and the origin of these two strains from bovine/porcine rotaviruses was apparent. This study identifies zoonotic transmission and single and multiple reassortment events as mechanisms driving the diversity of human rotaviruses. This study indicates interspecies transmission between human and animal rotaviruses causes single or multiple reassortment and thus contribute to the genetic diversity of rotavirus.
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Affiliation(s)
- Satarupa Mullick
- National Institute of Cholera and Enteric Diseases, Kolkata, India
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Ansari S, Sherchand JB, Rijal BP, Parajuli K, Mishra SK, Dahal RK, Shrestha S, Tandukar S, Chaudhary R, Kattel HP, Basnet A, Pokhrel BM. Characterization of rotavirus causing acute diarrhoea in children in Kathmandu, Nepal, showing the dominance of serotype G12. J Med Microbiol 2012; 62:114-120. [PMID: 23038804 DOI: 10.1099/jmm.0.048124-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Diarrhoeal diseases are a major problem in developing countries. Though precise data on childhood mortality associated with diarrhoeal diseases in Nepal are not available, it has been estimated that approximately 25 % of child deaths are associated with diarrhoeal disease, particularly acute diarrhoea. The purpose of this study was to assess the incidence of rotavirus causing acute diarrhoea in children less than 5 years of age. A total of 525 children with acute diarrhoea in a children's hospital of Kathmandu, Nepal, were enrolled between April and September 2011. The incidence of acute diarrhoea due to rotavirus was 25.9 % (136/525) as determined by ELISA. The percentage of rotavirus-infected males was higher (64.5 %) than females (35.5 %). The frequency of rotavirus cases was higher in children less than 2 years of age, among which the majority of cases (80.2 %) were in children between 6 and 24 months old (P<0.01). Genotypic characterization by RT-PCR revealed that the serotype G12 represented 55.9 % of cases in this study associated with P-types of either P[6], P[4] or P[8]. Further to this, a total of eight G/P combinations were identified, G12P[6] being the most common strain type of rotavirus in Nepal, with a prevalence rate of 46.4 %. The aim of this study was to find out the major genotypes of rotavirus causing acute diarrhoea in children.
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Affiliation(s)
- Shamshul Ansari
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Jeevan Bahadur Sherchand
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Basista Prasad Rijal
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Keshab Parajuli
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Shyam Kumar Mishra
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Rajan Kumar Dahal
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Shovita Shrestha
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Sarmila Tandukar
- Public Health Research Laboratory, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Raina Chaudhary
- Nepalese Army Institute of Health Sciences, Kathmandu, Nepal
| | - Hari Prasad Kattel
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Amul Basnet
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Bharat Mani Pokhrel
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
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Sherchand JB, Schluter WW, Sherchan JBSB, Tandukar S, Dhakwa JR, Choudhary GR, Mahasethd C. Prevalence of group A genotype human rotavirus among children with diarrhoea in Nepal, 2009-2011. WHO South East Asia J Public Health 2012; 1:432-440. [PMID: 28615608 DOI: 10.4103/2224-3151.207045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Rotavirus as a causative agent of childhood diarrhea is known to cause serious illness among children less than 5 years of age. This study examined the epidemiology of rotavirus disease burden and diversity of G and P genotypes of rotavirus in Nepal. METHODS Stool samples were tested for rotavirus by Enzyme Immuno Assay and Group A rotaviruses were detected by using both ELISA and RT-PCR in 2718 samples between 2009 and 2011. RESULTS Rotavirus was more frequently detected among inpatients (28.5%) than outpatients (15.2%). Over the three-year study period, 653 (24.4%) cases were positive for rotavirus by ELISA. Genotyping by RT-PCR was done on 638 samples. The most prevalent genotype was G12P [6] (60.4%). Mixed infections were not uncommon (14% in 2009, 29% in 2010 an 7% in 2011). However, 41 were partially typed and 23 were completely untyped over the study period. CONCLUSIONS This study highlights the rotavirus disease burden and diversity of rotavirus strains circulating in Nepal. Continued sentinel surveillance will provide useful information to policy makers with regard to rotavirus vaccine introduction.
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Affiliation(s)
- Jeevan B Sherchand
- Tribhuvan University Institute of Medicine, Public Health Research Laboratory and Microbiology
| | | | | | - Sarmila Tandukar
- Tribhuvan University Institute of Medicine, Public Health Research Laboratory and Microbiology
| | - Jyoti R Dhakwa
- Kanti Children's Hospital, Maharajgunj, Kathmandu, Nepal
| | - Ganga R Choudhary
- Program for Immunization Preventable Diseases (IPD), Kathmandu, Nepal
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Mukherjee A, Mullick S, Kobayashi N, Chawla-Sarkar M. The first identification of rare human group A rotavirus strain G3P[10] with severe infantile diarrhea in eastern India. INFECTION GENETICS AND EVOLUTION 2012; 12:1933-7. [PMID: 22981998 DOI: 10.1016/j.meegid.2012.08.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/26/2012] [Accepted: 08/06/2012] [Indexed: 11/16/2022]
Abstract
During an ongoing surveillance for diarrheal pathogens, an unusual human group A rotavirus strain G3P[10] (RVA/Human-wt/IND/mcs60/2011/G3P[10]) was detected in a stool sample of a 14 months old girl child with acute diarrhea in Kolkata, eastern India. The VP7 nucleotide sequence of this strain revealed a close phylogenetic relationship to the prototype G3 strain AU-1 and Australian feline strain Cat2, whereas, the VP4 gene segment was closely related to the G8P[10] rotavirus 69M from Indonesia. Analysis of 11 gene segments of this unusual G3P[10] strain demonstrates a complex evolutionary pattern, with genes possibly derived from the group A rotaviruses of human DS-1-like and AU-1-like strains of simian and caprine host species. To our knowledge, this is the first complete genotyping report of any G3P[10] rotavirus, worldwide.
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Affiliation(s)
- Anupam Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33 CIT Road Scheme XM, Beliaghata, Kolkata 700 010, West Bengal, India
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Abugalia M, Cuevas L, Kirby A, Dove W, Nakagomi O, Nakagomi T, Kara M, Gweder R, Smeo M, Cunliffe N. Clinical features and molecular epidemiology of rotavirus and norovirus infections in Libyan children. J Med Virol 2012; 83:1849-56. [PMID: 21837804 DOI: 10.1002/jmv.22141] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Rotaviruses and noroviruses are leading viral causes of diarrhoea in children. A cross-sectional study was undertaken among children aged <5 years with acute gastroenteritis at Al-Jala Children's Hospital, Tripoli, Libya, from October 2007 to September 2008. Of 1,090 fecal samples collected, 260 from inpatients and 830 from outpatients, all inpatients and approximately a third of outpatients, selected systematically, were investigated for rotavirus and norovirus infection by ELISA and real-time RT-PCR, respectively. Of 520 fecal samples examined (inpatients = 260, outpatients = 260), 164 (31.5%) had rotavirus and 91 (17.5%) had norovirus detected. Rotavirus was identified more often among inpatients than outpatients (35.8% vs. 27.3% respectively, P = 0.038). Norovirus was detected more commonly among outpatients than inpatients (21.2% vs. 13.8% respectively, P = 0.028). The peak incidence of infection with both viruses was among children aged between 6 and 11 months. The number of rotavirus cases was highest between November and June with a peak detection rate of 50% in January. Norovirus occurred most commonly from May through August with a peak detection rate of 47% in August. The most prevalent rotavirus genotypes were P[8], G9 (n = 116, 65.9%), followed by P[8],G1 (n = 49, 27.8%); a single P[9], G3 strain was detected. There were seven distinct electropherotypes among the G9 strains and all belonged to VP7 Lineage III. Among 91 noroviruses identified, 90 were genogroup II. Of 26 genogroup II noroviruses examined, all were genotype GII.4. Rotaviruses and noroviruses are both important causes of gastrointestinal infection among young children in Libya.
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Kawai K, O'Brien MA, Goveia MG, Mast TC, El Khoury AC. Burden of rotavirus gastroenteritis and distribution of rotavirus strains in Asia: a systematic review. Vaccine 2011; 30:1244-54. [PMID: 22212128 DOI: 10.1016/j.vaccine.2011.12.092] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 12/12/2011] [Accepted: 12/19/2011] [Indexed: 02/07/2023]
Abstract
BACKGROUND Rotavirus is the leading cause of severe diarrhea in children worldwide. We systematically reviewed the burden of rotavirus gastroenteritis (RVGE) and distribution of rotavirus strains in Asia. METHODS We searched MEDLINE, EMBASE and the World Health Organization (WHO) website for the term "rotavirus" and the name of each country. We included studies that were conducted in children between 2000 and 2011 and that examined the epidemiology, health and/or economic burden of RVGE, and G and P-type distribution in Eastern, South East, Southern and Central Asia. Random effects models were used to pool the proportions of RVGE. We also estimated child mortality due to RVGE using the updated WHO and United Nations Children's Fund's mortality estimates in 2008. RESULTS The search identified 113 eligible articles. The incidence rates of rotavirus-related hospitalizations in children under 5 years of age ranged from 2.1 to 20.0 cases per 1000 children per year with the highest rates reported in Bangladesh, South Korea, Taiwan, Thailand, and Vietnam. Rotavirus accounted for 37.5% of year-round hospitalized gastroenteritis cases, with higher proportions reported in South East Asia. Rotavirus was associated with approximately 145,000 deaths every year in Asia, with the greatest numbers occurring in India, Pakistan, and Indonesia. The highest annual societal costs of treating RVGE were reported in China (US$365 million), followed by Japan (US$254 million) and India (US$41-72 million). A diversity of rotavirus G and P-types was observed across Asia and the distribution of strains differed by country and year. The most common strains were G1P[8] (23.6%), G2P[4] (11.8%), G3P[8] (18.9%), and G9P[8] (7.4%). CONCLUSIONS Rotavirus is associated with substantial hospitalizations and deaths among children and causes large healthcare expenditures throughout Asia. Safe and effective rotavirus vaccines could substantially reduce the burden of disease.
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Affiliation(s)
- Kosuke Kawai
- Temple University, School of Pharmacy, 3307N. Broad Street, Philadelphia, PA 19140, USA.
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Miyazaki A, Kuga K, Suzuki T, Kohmoto M, Katsuda K, Tsunemitsu H. Genetic diversity of group A rotaviruses associated with repeated outbreaks of diarrhea in a farrow-to-finish farm: identification of a porcine rotavirus strain bearing a novel VP7 genotype, G26. Vet Res 2011; 42:112. [PMID: 22067072 PMCID: PMC3245447 DOI: 10.1186/1297-9716-42-112] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 11/09/2011] [Indexed: 12/21/2022] Open
Abstract
Group A rotaviruses (GARs) are one of the most common causes of diarrhea in suckling pigs. Although a number of G and P genotypes have been identified in porcine GARs, few attempts have been made to study the molecular epidemiology of these viruses associated with diarrhea outbreaks within a farm over an extended period of time. Here, we investigated the molecular characteristics of GARs that caused four outbreaks of diarrhea among suckling pigs in a farrow-to-finish farm over the course of a year. G and P genotyping of GARs detected at each outbreak demonstrated genetic diversity in this farm as follows: G9P[23] was detected at the first outbreak, G9P[13]/[22] and G9P[23] at the second, G3P[7] at the third, and G9P[23], G5P[13]/[22], and P[7] combined with an untypeable G genotype at the fourth. Sequence analysis of the detected GARs revealed that such genetic diversity could have resulted not only from the introduction of new GAR strains, but also from gene reassortment between GAR strains within the farm. Further, the GAR strain carrying the untypeable G genotype was shown to be a novel porcine GAR bearing a new G26 genotype, as confirmed by the Rotavirus Classification Working Group.
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Affiliation(s)
- Ayako Miyazaki
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.
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Wu FT, Bányai K, Huang JC, Wu HS, Chang FY, Hsiung CA, Huang YC, Lin JS, Hwang KP, Jiang B, Gentsch JR. Human infection with novel G3P[25] rotavirus strain in Taiwan. Clin Microbiol Infect 2011; 17:1570-3. [PMID: 21851477 DOI: 10.1111/j.1469-0691.2011.03531.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Genotype P[25] rotaviruses are rare and to date have been reported to occur only in a few countries of mainland Asia. Here we report the molecular characterization of a novel human rotavirus genotype combination, G3P[25], detected in a 17-month-old child hospitalized due to severe gastroenteritis during 2009 in central Taiwan. Sequencing and phylogenetic analysis of the VP4 gene demonstrated a distinct origin from other strains bearing the P[25] VP4 gene, whereas the VP7, VP6 and NSP4 gene phylogenies identified common origins with cognate genes of other, presumed human-porcine reassortment Taiwanese strains. These results suggest that interactions between human and animal strains appear to contribute to the generation of genetic and antigenic diversity of rotavirus strains, with potential public health importance in Taiwan.
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Affiliation(s)
- F-T Wu
- Department of Health, Centre for Research and Diagnostics, Centres for Disease Control, Taiwan.
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Doan YH, Nakagomi T, Cunliffe NA, Pandey BD, Sherchand JB, Nakagomi O. The occurrence of amino acid substitutions D96N and S242N in VP7 of emergent G2P[4] rotaviruses in Nepal in 2004-2005: a global and evolutionary perspective. Arch Virol 2011; 156:1969-78. [DOI: 10.1007/s00705-011-1083-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 07/22/2011] [Indexed: 02/01/2023]
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Kim SY, Sweet S, Chang J, Goldie SJ. Comparative evaluation of the potential impact of rotavirus versus HPV vaccination in GAVI-eligible countries: a preliminary analysis focused on the relative disease burden. BMC Infect Dis 2011; 11:174. [PMID: 21679420 PMCID: PMC3129299 DOI: 10.1186/1471-2334-11-174] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 06/16/2011] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Immunization policymakers at global and local levels need to establish priorities among new vaccines competing for limited resources. However, comparison of the potential impact of single vaccination programs is challenging, primarily due to the limited number of vaccine analyses as well as their differing analytic approaches and reporting formats. The purpose of this study is to provide early insight into how the comparative impact of different new vaccines could be assessed in resource-poor settings with respect to affordability, cost-effectiveness, and distributional equity. METHODS We compared the health, economic, and financial consequences of introducing the two vaccines in 72 GAVI-eligible countries using a number of different outcome measures to evaluate affordability, cost-effectiveness, and distributional equity. We use simple static models to standardize the analytic framework and improve comparability between the two new vaccines. These simple models were validated by leveraging previously developed, more complex models for rotavirus and human papillomavirus (HPV). RESULTS With 70% coverage of a single-age cohort of infants and pre-adolescent girls, the lives saved with rotavirus (~274,000) and HPV vaccines (~286,000) are similar, although the timing of averted mortality differs; rotavirus-attributable deaths occur in close proximity to infection, while HPV-related cancer deaths occur largely after age 30. Deaths averted per 1000 vaccinated are 5.2 (rotavirus) and 12.6 (HPV). Disability-adjusted life years (DALYs) averted were ~7.15 million (rotavirus) and ~1.30 million (HPV), reflecting the greater influence of discounting on the latter, given the lagtime between vaccination and averted cancer. In most countries (68 for rotavirus and 66 for HPV, at the cost of I$25 per vaccinated individual) the incremental cost per DALY averted was lower than each country's GDP per capita. Financial resources required for vaccination with rotavirus are higher than with HPV since both genders are vaccinated. CONCLUSIONS While lifesaving benefits of rotavirus and HPV vaccines will be realized at different times, the number of lives saved over each target populations' lifetimes will be similar. Model-based analyses that use a standardized analytic approach and generate comparable outputs can enrich the priority-setting dialogue. Although new vaccines may be deemed cost-effective, other factors including affordability and distributional equity need to be considered in different settings. We caution that for priority setting in an individual country, more rigorous comparisons should be performed, using more comprehensive models and considering all relevant vaccines and delivery strategies.
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Affiliation(s)
- Sun-Young Kim
- Center for Health Decision Science, Harvard School of Public Health, Boston, MA, USA
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Ribas MDLA, Nagashima S, Calzado A, Acosta G, Tejero Y, Cordero Y, Piedra D, Kobayashi N. Emergence of G9 as a predominant genotype of human rotaviruses in Cuba. J Med Virol 2011; 83:738-44. [PMID: 21328392 DOI: 10.1002/jmv.22020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To study human rotaviruses in Cuban children up to 5 years old with acute diarrhea, a total of 64 faecal samples from two pediatric hospitals between 2006 and 2008 were analyzed. Thirty-nine samples (60.9%) were found positive for rotaviruses by enzyme-linked immunosorbent assay (ELISA) and polyacrylamide gel electrophoresis (PAGE), while four (6.2%) exhibited discordant results (ELISA positives/PAGE negatives). All the positive samples were genotyped by a reverse transcription-polymerase chain reaction (RT-PCR). The most prevalent G and P types were G1 (60.5%) and P[8] (90.6%), respectively. Among the rotaviruses detected, two long RNA patterns were identified by PAGE (L/A and L/B). The predominant genotype in 2006 and 2007 was G1/P[8] with detection rates 71.4% and 80%, respectively. In contrast, G9/P[8] was found at the highest rate (78.5%) in 2008. The phylogenetic analysis of VP7 genes of the ten representative strains indicated that Cuban G1/P[8] rotaviruses were close to those reported in the Americas, and G9/P[8] rotaviruses were located in the lineage of the emerging G9 strains spreading worldwide. This is the first molecular epidemiologic study of rotaviruses in Cuba, highlighting the current increase of the G9 rotavirus which has been recognized globally as an emerging genotype. The study reinforces the need for a systematic surveillance of the molecular epidemiology of rotaviruses.
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Than VT, Le VP, Lim I, Kim W. Complete genomic characterization of cell culture adapted human G12P[6] rotaviruses isolated from South Korea. Virus Genes 2011; 42:317-22. [DOI: 10.1007/s11262-011-0576-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 01/17/2011] [Indexed: 01/24/2023]
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