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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: 14] [Impact Index Per Article: 4.7] [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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KILIÇ AO, ATWAN HM, YAZAR A, AKIN F. Evaluation of children with acute gastroenteritis in Konya region. FAMILY PRACTICE AND PALLIATIVE CARE 2021. [DOI: 10.22391/fppc.762330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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3
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Epidemiological, molecular, and clinical features of rotavirus infections among pediatrics in Qatar. Eur J Clin Microbiol Infect Dis 2021; 40:1177-1190. [PMID: 33411172 DOI: 10.1007/s10096-020-04108-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022]
Abstract
Acute gastroenteritis (AGE) remains a major cause of diarrhea in developing and developed countries. Rotavirus (RV) is a leading cause of severe pediatric diarrhea worldwide. Here we report on the prevalence of circulating genotypes in association with demographics and clinical manifestations outcomes in Qatar. A total of 231 RV-positive fecal samples were collected from children suffering from AGE during 3 years study period between June 2016 and June 2019. The age of the subjects ranged between 2 months and 14 years (median of 16 months). The VP4 and VP7 were amplified and sequenced. Phylogenetic analyses were performed using MEGA7.0. Pearson's chi-squared test was used to determine significant differences for comparisons of general categorical variables. RV infections were most common in children between 1 and 3 years of age (49%), followed by those < 1 year and > 3 years of age (33% and 28%, respectively). RV infections were more frequent in males than females, with a ratio of 1.4:1. RV infections occurred throughout the year, with a noticeable increase in summer (42.8%) and a drop in winter (20.1%). RV genotypes G3P[8] (30.8%), G2P[8] (12.3%), G4P[8] (11.7%), and G1P[8] (10.4%) were the common genotypes during the study period. The G3P[8] strain detected in our study revealed similarities to the equine-like G3P[8] (10.3%; 24/231) (KT988229.1), Wa-like genomic constellation (9%; 21/231) (MF563894.1), and DS-1-like strains (6.4%; 15/231) (LC386081.1). Based on the Vesikari score system, severe clinical illness including diarrhea and vomiting (average frequency: 4 to 5 times/day) was recorded for G3P[8] group, followed by G9P[8], G4P[8], and G1P[8]. Higher incidence for G3P[8], G2P[8], G4P[8], and G1P[8] were reported in Qatari subjects compared to other nationalities. The multinational status of a small country explains the wide diversity of circulating RV genotypes in Qatar. The highest prevalence and severe illnesses were recorded to G3P[8], which is different from other surrounding countries/global levels.
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Gikonyo JN, Mbatia B, Okanya PW, Obiero GFO, Sang C, Steele D, Nyangao J. Post-vaccine rotavirus genotype distribution in Nairobi County, Kenya. Int J Infect Dis 2020; 100:434-440. [PMID: 32898668 PMCID: PMC7670220 DOI: 10.1016/j.ijid.2020.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Rotaviruses are primary etiological agents of gastroenteritis in young children. In Kenya, G1P8 monovalent vaccine (Rotarix) was introduced in July 2014 for mandatory vaccination of all newborns at 6 and 10 weeks of age. Since then, no studies have been done to identify the rotavirus genotypes circulating in Nairobi County, Kenya, following the vaccine introduction, hence the post-vaccine genotype distribution is not known. OBJECTIVES The aim of this study was to determine the post-vaccine occurrence of rotavirus genotypes in children <5 years of age in Nairobi County, Kenya. METHODS Stool samples were collected from children presenting with diarrhea for whom the vaccination status was card-confirmed. Fecal samples were analyzed for rotavirus antigen using a commercial enzyme immunoassay (EIA) kit, followed by characterization by polyacrylamide gel electrophoresis, RT-PCR, and nested PCR genotyping, targeting the most medically important genotypes. RESULTS The strains observed included G1P[8] (38.8%), G9P[8] (20.4%), G2P[4] (12.2%), G3[P4] (6.1%), G2P[6] (4.1%), and G9P[6] (4.1%). Mixed genotype constellations G3P[4][8] were also detected (4.1%). Remarkably, an increased prevalence of G2 genotypes was observed, revealing a change in genetic diversity of rotavirus strains. While the dominance of G1P[8] decreased after vaccination, an upsurge in G2P[4] (12.2%) and G9P[8] (20.4%) was observed. Additionally, G3[P4] (6.1%) and G2P[6] (4.1%) prevalence increased over the 3 years of study. CONCLUSIONS The results inform the need for robust longitudinal surveillance and epidemiological studies to assess the long-term interaction between rotavirus vaccine and strain ecology.
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Affiliation(s)
- Joshua Ndung'u Gikonyo
- Department of Biochemistry and Biotechnology, The Technical University of Kenya (TU-K), PO Box 52428-00200, Nairobi, Kenya.
| | - Betty Mbatia
- School of Pharmacy and Health Sciences, United States International University (USIU) - Africa, PO Box 14634-00800, Nairobi, Kenya.
| | - Patrick W Okanya
- Department of Biochemistry and Biotechnology, The Technical University of Kenya (TU-K), PO Box 52428-00200, Nairobi, Kenya.
| | - George F O Obiero
- Department of Biochemistry and Biotechnology, The Technical University of Kenya (TU-K), PO Box 52428-00200, Nairobi, Kenya.
| | - Carlene Sang
- Kenya Medical Research Institute (KEMRI), PO Box 43640-00100, Nairobi, Kenya.
| | - Duncan Steele
- Enteric and Diarrhoeal Diseases, Global Health Bill and Melinda Gates Foundation PO Box 23350, Seattle, WA98102, USA.
| | - James Nyangao
- Kenya Medical Research Institute (KEMRI), PO Box 43640-00100, Nairobi, Kenya.
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Satayarak J, Strauss ST, Duangdee C, Charunwatthana P, Jiamsomboon K, Kosoltanapiwat N, Srinukham S, Boonnak K. Prevalence and diversity of human rotavirus among Thai adults. J Med Virol 2020; 92:2582-2592. [PMID: 32470142 DOI: 10.1002/jmv.26076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/17/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022]
Abstract
Rotavirus infections have become one of the most common causes of infectious gastroenteritis in children. Although rotavirus infections have been intensively studied in infants and young children, the study in adults has been limited. As such, this study assessed the prevalence of rotaviruses and performed the molecular characterization of rotaviruses circulating in Thai adults experiencing acute gastroenteritis between January 2018 and December 2018. Group A human rotaviruses were detected in 100 feces samples by rapid immunochromatography. The peak incidence of infection occurred in February and began to decline in the summer months. From January 2018 to December 2018, there were 1344 acute gastroenteritis adult cases in the Hospital for Tropical Diseases, Bangkok, Thailand. Among these, 310 cases were rotavirus-suspected cases. Only 100 samples tested positive for rotavirus via an immunochromatography test. Twentynine out of the 100 rotavirus-positive samples were further characterized by real-time polymerase chain reaction. The G3[P8] strain was identified as the most prevalent (31.0%) followed by G1P[8], G8P[8] and G9P[8], and G2P[8], which accounted for 20.8%, 17.2%, and 13.8%, respectively. Because of the detection of rare rotavirus genotypes, such as G8, the surveillance of rotavirus epidemiology is crucial in monitoring new emergences of rotavirus strains, leading to a better understanding of the effects of strain variation for further vaccine development.
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Affiliation(s)
- Jantawan Satayarak
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Stefan Thomas Strauss
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chatnapa Duangdee
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Prakaykaew Charunwatthana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Nakhon Pathom, Thailand
| | - Kultida Jiamsomboon
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sompan Srinukham
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kobporn Boonnak
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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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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El C, Celikkaya ME. Akut viral gastroenteritlerde oral çinko kullanımının hastalığın semptomları ve süresine etkisinin değerlendirilmesi. FAMILY PRACTICE AND PALLIATIVE CARE 2019. [DOI: 10.22391/fppc.471460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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8
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Tapisiz A, Bedir Demirdag T, Cura Yayla BC, Gunes C, Ugraş Dikmen A, Tezer H, Baran Aksakal N, Bozdayi G, Ozkan S. Rotavirus infections in children in Turkey: A systematic review. Rev Med Virol 2018; 29:e2020. [PMID: 30511804 DOI: 10.1002/rmv.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/17/2018] [Accepted: 10/18/2018] [Indexed: 11/11/2022]
Abstract
We aimed to describe rotavirus epidemiology and clinical findings including extraintestinal manifestations in a setting that has yet to introduce rotavirus vaccines in the national immunization program. A literature search was performed by using the key words "Turkey" and "rotavirus." Ninety-eight studies published between 1987 and 2016 including epidemiological, clinical, and genotypical data at least 1 year duration were included. There were a total of 117 741 children with diarrhea and 26 566 rotavirus gastroenteritis with a median detection rate 31.8% (95% CI, 31.3-32.4) under 5 years of age. The rate of dehydration was 47% (95% CI, 23.4-91.6). There were 328 cases reported to be presenting with a various complication related to rotavirus in 2750 children in eight studies. The overall complication rate was 11.7% (95% CI, 10.7-12.9). The cumulative incidence of the most common genotypical combinations circulating worldwide was only 59.7% (G9[P8], 25%; G1[P8], 22%; G2[P4], 5.6%; G3[P8], 2.6%; G4[P8], 4.5%) whereas mixed, untypeable, and other genotypes were 2.4%, 15%, and 22.9% respectively. Our results point out the importance of rotavirus vaccination by presenting that rotavirus may cause severe complications besides severe gastroenteritis. The role of strain diversity in the variability of clinical presentations of rotavirus infections needs to be further investigated.
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Affiliation(s)
- Anil Tapisiz
- Department of Pediatric Infectious Diseases, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Tugba Bedir Demirdag
- Department of Pediatric Infectious Diseases, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Burcu Ceylan Cura Yayla
- Department of Pediatric Infectious Diseases, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Cemalettin Gunes
- Department of Pediatric Infectious Diseases, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Asiye Ugraş Dikmen
- Department of Public Health, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Hasan Tezer
- Department of Pediatric Infectious Diseases, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Nur Baran Aksakal
- Department of Public Health, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Gulendam Bozdayi
- Department of Medical Microbiology, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Secil Ozkan
- Department of Public Health, Gazi University Faculty of Medicine, Ankara, Turkey
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Islamuddin M, Khan WH, Gupta S, Tiku VR, Khan N, Akdag AI, Chaudhary S, Upadhyay A, Kumar P, Ghatwala G, Ray P. Surveillance and genetic characterization of rotavirus strains circulating in four states of North Indian children. INFECTION GENETICS AND EVOLUTION 2018; 62:253-261. [DOI: 10.1016/j.meegid.2018.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/15/2018] [Accepted: 04/22/2018] [Indexed: 12/16/2022]
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Bulut Y, Yenişehirli G, Durmaz R. Molecular Epidemiology of Rotavirus Strains in Under Five Children. Indian J Pediatr 2018; 85:364-368. [PMID: 29185230 DOI: 10.1007/s12098-017-2540-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/20/2017] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To determine the prevalence and genotype distribution of rotaviruses in children presenting to authors' hospital in Middle Black Sea region of Turkey. The results may supply important information about vaccine studies in Turkey. METHODS Rotavirus antigen was detected by latex agglutination test and rotavirus RNA was detected by RT-PCR test. On the other hand, rotavirus positive samples were genotyped by semi-nested multiplex polymerase chain reaction. RESULTS The highest rate of rotavirus positivity (46.9%) was observed among children in the 13 to 24 mo age group. All the positive-strains were in G1-4, G8-9, P [4], P [8], and P [9] genotypes. The most common G and P combination in present study was G9P[8] (n = 24, 28.9%). CONCLUSIONS The present results indicated that the most prevalent genotypes were G1, G9, P8, G9P[8] and G1P[8] in authors' region. Rotavirus vaccines used in this region must include mainly these genotypes.
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Affiliation(s)
- Yunus Bulut
- Department of Medical Microbiology, Gaziosmanpaşa University Faculty of Medicine, 60100, Tokat, Turkey.
| | - Gülgün Yenişehirli
- Department of Medical Microbiology, Gaziosmanpaşa University Faculty of Medicine, 60100, Tokat, Turkey
| | - Rıza Durmaz
- Department of Medical Microbiology, Yıldırım Beyazıt University Faculty of Medicine, Ankara, Turkey
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Zaraket H, Charide R, Kreidieh K, Dbaibo G, Melhem NM. Update on the epidemiology of rotavirus in the Middle East and North Africa. Vaccine 2017; 35:6047-6058. [PMID: 28986034 DOI: 10.1016/j.vaccine.2017.09.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/07/2017] [Accepted: 09/22/2017] [Indexed: 12/16/2022]
Abstract
Rotavirus (RV) is the leading cause of severe acute gastroenteritis (AGE) worldwide. Consequently, we conducted a systematic literature review on articles studying RV in the 25 countries of the MENA region during the past 15years (2000-2015). The methods and reporting were set according to the 2015 preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) and based on the elements from the international prospective register of systematic reviews (PROSPERO). Our literature search identified 169 studies meeting our predefined inclusion criteria. Studies reporting on RV were conducted in 19 out of the 24 countries of the MENA region. The largest number of studies was reported in Turkey (n=32), Iran (n=31), Saudi Arabia (n=19) and Egypt (n=17). The majority of studies reporting on RV gastroenteritis rates were clinical observational studies. In 115 studies out of 169, RV was reported among in-patients whereas 35 studies reported RV among outpatients. The predominantly reported RV genotype in the region was G1[P8] followed by G2[P4] and G9[P8]. The majority of studies (n=108) were conducted among children less than 5years of age whereas the remaining studies reported on AGE among other age groups and rarely adults. In MENA countries, RV infection was reported all year round with peaks described in cold as well as hot months. This systematic review provides a current update on the epidemiology of RV-associated gastroenteritis in countries of the MENA region and draws attention to the major gaps existing in the continuous monitoring of RV.
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Affiliation(s)
- Hassan Zaraket
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Rana Charide
- Department of Epidemiology and Population Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Khalil Kreidieh
- Department of Epidemiology and Population Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon; Medical Laboratory Sciences Program, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Ghassan Dbaibo
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Department of Pediatrics and Adolescent Medicine, Division of Pediatric Infectious Diseases, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Nada M Melhem
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Medical Laboratory Sciences Program, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon.
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Durmaz R, Bakkaloglu Z, Unaldi O, Karagoz A, Korukluoglu G, Kalaycioglu AT, Acar S, Kilic S. Prevalence and diversity of rotavirus A genotypes cirulating in Turkey during a 2-year sentinel surveillance period, 2014-2016. J Med Virol 2017; 90:229-238. [PMID: 28892173 DOI: 10.1002/jmv.24945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/01/2017] [Indexed: 12/29/2022]
Abstract
Human rotavirus A (RVA) is the main etiological agent of watery diarrhea among children under 5 years of age worldwide. The aims of this study were to investigate the prevalence and diversity of RVA genotypes circulating in Turkey during a 2-year sentinel surveillance study. A total of 1639 rotavirus antigen-positive stool samples were obtained from children younger than 5 years of age hospitalized with acute gastroenteritis. Rotavirus G and P genotypes were determined by reverse transcription polymerase chain reaction (RT-PCR) with consensus primers for the VP7 and VP4 genes, followed by semi-nested type-specific multiplex PCR. Rotavirus RNA was detected in 1396 (85.3%) of the samples tested. The highest detection rate (38.2%) was obtained among children in the 0-12 months age group, followed by children in the 13-24 months age group (36.2%). The most prevalent genotype was G1P[8] (24.6%) followed by G3P[8] (19.6%), G9P[8] (12.2%), G2P[4] (9.5%), G2P[8] (6.5%), and G4P[8] (4.8%). The proportions of uncommon and mixed genotypes were 21.5% and 1.14%, respectively. The large number of genotypes observed, including common, uncommon, and mixed types, indicates a high heterogeneity of RVA strains circulating in Turkey. The current study also exhibited dramatic fluctuations on the prevalences of the common genotypes, with increases in G3 and G1 and decreases in G9 and G2 from 2014-2016.
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Affiliation(s)
- Riza Durmaz
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey.,Department of Medical Microbiology, Faculty of Medicine Yildirim Beyazit University, Ankara, Turkey
| | - Zekiye Bakkaloglu
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Ozlem Unaldi
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Alper Karagoz
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Gulay Korukluoglu
- Virology Reference Central Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Atila T Kalaycioglu
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey.,Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Karadeniz Technical University, Trabzon, Turkey
| | - Sumeyra Acar
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Selcuk Kilic
- Microbiology Reference Laboratories, Public Health Agency of Turkey, Ankara, Turkey
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Rotavirus genotypes in children with gastroenteritis in Erzurum: first detection of G12P[6] and G12P[8] genotypes in Turkey. GASTROENTEROLOGY REVIEW 2016; 12:122-127. [PMID: 28702101 PMCID: PMC5497125 DOI: 10.5114/pg.2016.59423] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/24/2015] [Indexed: 02/06/2023]
Abstract
Introduction Rotavirus is one of the leading pathogens which cause acute gastroenteritis in children and is responsible for a substantial proportion of childhood deaths worldwide. Aim To determine the group A rotavirus (RVA) prevalence and genotypes of circulating RVA strains in 0–5-year-old children with complaints of vomiting and diarrhoea in Eastern Anatolia in Turkey. Material and methods RNA extracted from stool specimens of 329 children aged 0–5 years with acute diarrhoea was subjected to reverse transcription polymerase reaction (RT-PCR) and multiplex-nested PCR. The genotypes were identified based on the expected size of the amplicon, which was amplified with a genotype-specific primer. Results Out of 329 stool samples analyzed, 109 (33.1%) were positive for RVA. G1P[8] was the dominant genotype combination (42.2%), followed by G9P[8] (21.1%) and G12P[6] (11.0%). Mixed infections were identified in 5 cases: G3,9 in 2 cases, G1,9 in 1 case, P[4,8] in 1 case, and P[6,8] in 1 case. The P genotype could not be typed in two patients. Conclusions In the study, we detected six different rotavirus G genotypes, 3 different P genotypes, 11 different G-P combinations and 5 different mixed genotypes combinations. G1, G9, G12 and P[8] were found to be the predominant genotypes. G12P[6] and G12P[8] genotypes, showing an increase as new rotavirus genotypes in the world, are reported for the first time for our regions. We determined the dominant genotypes, mixed genotypes and unconventional genotypes of rotavirus in our region.
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Re-emergence of genotype G9 during a five-and-a-half-year period in Turkish children with rotavirus diarrhea. Arch Virol 2016; 161:2879-84. [DOI: 10.1007/s00705-016-2986-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 07/11/2016] [Indexed: 10/21/2022]
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15
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Dereci S, Çopur Çiçek A, Savaş Acar S, Bakkaloğlu Z, Özkasap S, Kanber K, Hacisalihoğlu Ş, Albayrak Y, Durmaz R. Prevalence and genotype distribution of rotaviruses in children with gastroenteritis in Rize province. Bosn J Basic Med Sci 2015; 15:35-9. [PMID: 26295292 DOI: 10.17305/bjbms.2015.469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 04/29/2015] [Accepted: 04/29/2015] [Indexed: 01/08/2023] Open
Abstract
Determination of the distribution of rotavirus genotypes is essential for understanding the epidemiology of this virus responsible for nearly half a million of deaths in patients with gastroenteritis worldwide. In the present study, we aimed to genotype the rotavirus strains isolated from diarrheal stool samples in children under 5 years old. A total of 1297 fecal samples were collected, and rotavirus antigen was detected in 73 of these samples. Antigen-positive samples were transferred to the Public Health Agency of Turkey, Molecular Microbiology Research Laboratory, and were tested for determination of genotypes G and P using semi-nested multiplex polymerase chain reaction method performed with consensus- and genotype-specific primers. Twelve specimens were found to be negative for rotavirus in genotyping method. All the positive-strains were in G1-4, G8-9, P(4), P(8), and P(9) genotypes. The most frequent GP genotype combinations were found to be G9P(8) in 21 strains (34.4%), G2P(4) in 14 strains (23.0%), and G1P(8) in 12 strains (19.7%). We found 10 distinct genotypes amongst a total of 61 strains. Among the strains isolated and genotyped in our study, 90.2% (55/61) and 67.2% (41/61) have already been included in the two existing commercial vaccines. In conclusion, these findings implicate the necessity of development of region-specific vaccines after evaluation of the local genotype distribution. Further studies on the large number of rotavirus strains would contribute to this process.
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Affiliation(s)
- Selim Dereci
- Department of Pediatrics, School of Medicine Recep Tayyip Erdogan University Rize.
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16
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Altay A, Yahiro T, Bozdayi G, Matsumoto T, Sahin F, Ozkan S, Nishizono A, Söderlund-Venermo M, Ahmed K. Bufavirus genotype 3 in Turkish children with severe diarrhoea. Clin Microbiol Infect 2015; 21:965.e1-4. [PMID: 26086570 DOI: 10.1016/j.cmi.2015.06.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 05/31/2015] [Accepted: 06/04/2015] [Indexed: 10/23/2022]
Abstract
Recently a parvovirus called bufavirus (BuV) has been implicated as a causative agent of diarrhoea. To further reveal the epidemiology and genetic characteristics of BuV, this study was performed in Turkish children with diarrhoea. BuV was detected in 1.4% (8/583) of stool samples. All stool samples from healthy children (n = 148) were negative for BuV. Diarrhoea in BuV-positive patients was severe and occurred mainly during the colder months of the year. Complete genome sequences were generated from four BuVs. Only BuV3 was found, which was genetically and phylogenetically similar to Bhutanese BuV3, indicating that BuV3 is prevalent in Asian countries.
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Affiliation(s)
- A Altay
- Department of Medical Microbiology, Gazi University, Ankara, Turkey
| | - T Yahiro
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - G Bozdayi
- Department of Medical Microbiology, Gazi University, Ankara, Turkey
| | - T Matsumoto
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan
| | - F Sahin
- Department of Paediatrics, Turkey
| | - S Ozkan
- Department of Public Health, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - A Nishizono
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan
| | | | - K Ahmed
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia; Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan; Research Promotion Institute, Oita University, Yufu, Japan.
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17
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Durmaz R, Kalaycioglu AT, Acar S, Bakkaloglu Z, Karagoz A, Korukluoglu G, Ertek M, Torunoglu MA. Prevalence of rotavirus genotypes in children younger than 5 years of age before the introduction of a universal rotavirus vaccination program: report of rotavirus surveillance in Turkey. PLoS One 2014; 9:e113674. [PMID: 25437502 PMCID: PMC4249891 DOI: 10.1371/journal.pone.0113674] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/29/2014] [Indexed: 02/01/2023] Open
Abstract
Background Group A rotaviruses are the most common causative agent of acute gastroenteritis among children less than 5 years of age throughout the world. This sentinel surveillance study was aimed to obtain baseline data on the rotavirus G and P genotypes across Turkey before the introduction of a universal rotavirus vaccination program. Methods Rotavirus antigen-positive samples were collected from 2102 children less than 5 years of age who attended hospitals participating in the Turkish Rotavirus Surveillance Network. Rotavirus antigen was detected in the laboratories of participating hospitals by commercial serological tests such as latex agglutination, immunochromatographic test or enzyme immunoassay. Rotavirus G and P genotypes were determined by reverse transcription polymerase chain reaction (RT-PCR) using consensus primers detecting the VP7 and VP4 genes, followed by semi-nested type-specific multiplex PCR. Results RT-PCR found rotavirus RNA in 1644 (78.2%) of the samples tested. The highest rate of rotavirus positivity (38.7%) was observed among children in the 13 to 24 month age group, followed by children in the age group of 25 to 36 months (28.3%). A total of eight different G types, six different P types, and 42 different G–P combinations were obtained. Four common G types (G1, G2, G3, and G9) and two common P types (P[8] and P[4]) accounted for 95.1% and 98.8% of the strains, respectively. G9P[8] was the most common G/P combination found in 40.5% of the strains followed by G1P[8] (21.6%), G2P[8] (9.3%), G2P[4] (6.5%), G3P[8] (3.5%), and finally, G4P[8] (3.4%). These six common genotypes included 83.7% of the strains tested in this study. The rate of uncommon genotypes was 14%. Conclusion The majority of the strains analyzed belonged to the G1–G4 and G9 genotypes, suggesting high coverage of current rotavirus vaccines. This study also demonstrates a dramatic increase in G9 genotype across the country.
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Affiliation(s)
- Riza Durmaz
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
- Department of Medical Microbiology, Faculty of Medicine Yıldırım Beyazıt University, Ankara, Turkey
- * E-mail:
| | - Atila Taner Kalaycioglu
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Sumeyra Acar
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Zekiye Bakkaloglu
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Alper Karagoz
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Gulay Korukluoglu
- Virology Reference Central Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Mustafa Ertek
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Mehmet Ali Torunoglu
- Molecular Microbiology Research and Applied Laboratory, Public Health Agency of Turkey, Ankara, Turkey
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18
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Mladenova Z, Nawaz S, Ganesh B, Iturriza-Gomara M. Increased detection of G3P[9] and G6P[9] rotavirus strains in hospitalized children with acute diarrhea in Bulgaria. INFECTION GENETICS AND EVOLUTION 2014; 29:118-26. [PMID: 25461849 DOI: 10.1016/j.meegid.2014.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 09/23/2014] [Accepted: 11/12/2014] [Indexed: 11/30/2022]
Abstract
Rotavirus severe disease in children is now vaccine-preventable and the roll-out of vaccination programs globally is expected to make a significant impact in the reduction of morbidity and mortality in children <5 years of age. Rotavirus is also a pathogen of other mammals and birds, and its segmented RNA genome can lead to the emergence of new or unusual strains in human population via interspecies transmission and reassortment events. Despite the efficacy and impact of rotavirus vaccine in preventing severe diarrhea, the correlates of protection remain largely unknown. Therefore, rotavirus strain surveillance before, during and after the introduction of immunization programs remains a crucial for monitoring rotavirus vaccine efficacy and impact. In this context, molecular characterization of 1323 Bulgarian rotavirus strains collected between June 2010 and May 2013 was performed. A total of 17 strains of interest were analyzed by partial sequence analysis. Twelve strains were characterized as G3P[9] and G6P[9] of potential animal origin. Phylogenetic analysis and comparisons with the same specificity strains detected sporadically between 2006 and 2010 revealed the constant circulation of these unusual human strains in Bulgaria, although in low prevalence, and their increased potential for person-to-person spread.
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Affiliation(s)
- Zornitsa Mladenova
- National Center for Infectious and Parasitic Diseases, Sofia, Bulgaria; Public Health of England, London, United Kingdom.
| | | | | | - Miren Iturriza-Gomara
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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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: 0.8] [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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20
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Wangchuk S, Mitui MT, Tshering K, Yahiro T, Bandhari P, Zangmo S, Dorji T, Tshering K, Matsumoto T, Nishizono A, Ahmed K. Dominance of emerging G9 and G12 genotypes and polymorphism of VP7 and VP4 of rotaviruses from Bhutanese children with severe diarrhea prior to the introduction of vaccine. PLoS One 2014; 9:e110795. [PMID: 25330070 PMCID: PMC4203849 DOI: 10.1371/journal.pone.0110795] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/12/2014] [Indexed: 11/19/2022] Open
Abstract
A prospective study was performed to determine the molecular characteristics of rotaviruses circulating among children aged <5 years in Bhutan. Stool samples were collected from February 2010 through January 2011 from children who attended two tertiary care hospitals in the capital Thimphu and the eastern regional headquarters, Mongar. The samples positive for rotavirus was mainly comprised genotype G1, followed by G12 and G9. The VP7 and VP4 genes of all genotypes clustered mainly with those of neighboring countries, thereby indicating that they shared common ancestral strains. The VP7 gene of Bhutanese G1 strains belonged to lineage 1c, which differed from the lineages of vaccine strains. Mutations were also identified in the VP7 gene of G1 strains, which may be responsible for neutralization escape strains. Furthermore, we found that lineage 4 of P[8] genotype differed antigenically from the vaccine strains, and mutations were identified in Bhutanese strains of lineage 3. The distribution of rotavirus genotypes varies among years, therefore further research is required to determine the distribution of rotavirus strain genotypes in Bhutan.
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Affiliation(s)
- Sonam Wangchuk
- Public Health Laboratory, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Marcelo T. Mitui
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan
| | - Kinlay Tshering
- Department of Pediatrics, Jigme Dorji Wangchuk National Referral Hospital, Thimphu, Bhutan
| | - Takaaki Yahiro
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan
| | | | - Sangay Zangmo
- Public Health Laboratory, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Tshering Dorji
- Public Health Laboratory, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Karchung Tshering
- Public Health Laboratory, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Takashi Matsumoto
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan
| | - Akira Nishizono
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan
| | - Kamruddin Ahmed
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan
- Research Promotion Institute, Oita University, Yufu, Japan
- * E-mail:
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21
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Mitui MT, Bozdayi G, Ahmed S, Matsumoto T, Nishizono A, Ahmed K. Detection and molecular characterization of diarrhea causing viruses in single and mixed infections in children: a comparative study between Bangladesh and Turkey. J Med Virol 2013; 86:1159-68. [PMID: 24105741 DOI: 10.1002/jmv.23744] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2013] [Indexed: 01/06/2023]
Abstract
The incidence and mortality caused by diarrhea differ among countries. The prevalence of different enteric viruses, their molecular characteristics, and infections with multiple viruses might affect the disease incidence and mortality caused by diarrhea. The objective of this study was to determine the distribution and molecular characteristics of enteric viruses in children with diarrhea in Turkey and Bangladesh. A total of 288 stool samples that were negative for group A rotavirus were collected from children aged <5 years with acute diarrhea who presented to hospitals in Turkey and Bangladesh. The samples were screened for human bocavirus (HBoV), astrovirus (HAstV), norovirus (NoV), and adenovirus (AdV). Phylogenetic analyses of the targeted virus genes were performed. In Turkey, viruses were detected in 87/150 samples (58%), which included 69 (79.3%) with single viruses and 18 (20.7%) with multiple viruses. AdV was the most common virus, followed by HBoV. In Bangladesh, viruses were detected in 123/138 samples (89.1%), which included 29 (23.6%) with single viruses and 94 (76.4%) with multiple viruses. NoV GII was the most common, followed by AdV. The dominant genotypes among the virus species were HBoV 2A, HAstV 1, NoV GI type 1, and AdV 40. For NoV GII, the Hunter variant of genotype 4 in Turkey and genotype 17 in Bangladesh were the most common among the sequenced strains. It was concluded that the distribution of the viruses associated with diarrhea in Turkish and Bangladeshi children was different. Enteric viruses and mixed infections were more prevalent in Bangladesh than in Turkey.
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Sharma R, Bora DP, Chakraborty P, Das S, Barman NN. Circulation of group A rotaviruses among neonates of human, cow and pig: study from Assam, a north eastern state of India. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2013; 24:250-5. [PMID: 24426283 DOI: 10.1007/s13337-013-0153-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 07/26/2013] [Indexed: 11/29/2022]
Abstract
Rotavirus (RV) infections are worldwide in distribution causing high morbidity and mortality in human and animal neonates. Human settlements in close proximity of animals aids for genetic re-assortment of the virus by interspecies transmission and consequent emergence of new viral antigenic strain. Therefore, the present study was designed to explore RV incidence in a single approach from human and animal neonates sharing similar environment. Altogether, 200 diarrheal samples from children (50), piglets (80) and calves (70) were collected during the year of 2010-2012 from various locality, farms and hospitals, initially screened through monoclonal antibody based enzyme immunoassay followed by RNA-PAGE and VP7 gene amplification by Reverse transcription PCR. The overall prevalence of rotavirus was found to be 41.5 % (83/200) where maximum numbers of positive cases were found in piglets (46.3 %) followed by human (40 %) and cow (37.1 %). Majority of samples demonstrated characteristic group A rotavirus (RVA) electropherotype of 4:2:3:2 pattern. Moreover, RNA profiles of seven samples from piglets and calves revealed variation in the migration pattern of class II, III and class IV segments. The study, for the first time from the valley, detected 43.7 % of neonatal RVA positive cases from human and animal sharing similar setting. The variation in RNA migration pattern in seven cases signifies tentative cases of gene re-assortment that warrant further evaluation.
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Affiliation(s)
- Rinky Sharma
- Department of Microbiology, College of Veterinary Sciences, Assam Agricultural University, Khanapara, Guwahati, 781022 Assam India
| | - Durlav Prasad Bora
- Department of Microbiology, College of Veterinary Sciences, Assam Agricultural University, Khanapara, Guwahati, 781022 Assam India
| | - Paromita Chakraborty
- Department of Microbiology, College of Veterinary Sciences, Assam Agricultural University, Khanapara, Guwahati, 781022 Assam India
| | - Sushmita Das
- Department of Microbiology, College of Veterinary Sciences, Assam Agricultural University, Khanapara, Guwahati, 781022 Assam India
| | - Nagendra Nath Barman
- Department of Microbiology, College of Veterinary Sciences, Assam Agricultural University, Khanapara, Guwahati, 781022 Assam India
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Complete Genome Sequence of an MLB2 Astrovirus from a Turkish Child with Diarrhea. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00619-13. [PMID: 23950127 PMCID: PMC3744683 DOI: 10.1128/genomea.00619-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Only two complete genome sequences of MLB2 astroviruses are available, one from an Indian child with diarrhea and another from plasma of an American child. Here we report the complete MLB2 genome sequence from a Turkish child with diarrhea. This MLB2 astrovirus genome sequence shows high nucleotide identity with the American MLB2.
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24
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Than VT, Baek IH, Kim W. Whole genomic analysis reveals the co-evolutionary phylodynamics of Korean G9P[8] human rotavirus strains. Arch Virol 2013; 158:1795-803. [DOI: 10.1007/s00705-013-1662-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 02/04/2013] [Indexed: 12/14/2022]
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Ahmed K, Bozdayi G, Mitui MT, Ahmed S, Kabir L, Buket D, Bostanci I, Nishizono A. Circulating rotaviral RNA in children with rotavirus antigenemia. J Negat Results Biomed 2013; 12:5. [PMID: 23369078 PMCID: PMC3564870 DOI: 10.1186/1477-5751-12-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 01/18/2013] [Indexed: 12/02/2022] Open
Abstract
Background Rotavirus antigenemia is a common phenomenon in children with rotavirus diarrhea, but information is scarce on aspects of this phenomenon, such as genotype specificity, presence of intact viruses and correlation between genomic RNA and antigen concentration. Such information may help in understanding rotavirus pathogenesis and eventually be useful for diagnosis, treatment and prevention. Methods and findings Serum samples were collected from children who presented at hospitals with diarrhea. Antigenemia was present in 162/250 (64.8%) samples from children with rotavirus diarrhea. No specific rotavirus genotype was found to be associated with antigenemia. Rotavirus particles could not be found by electron microscopy in concentrated serum from children with high levels of antigenemia. In passaged rotavirus suspension a significant correlation (r = 0.9559; P = 0.0029) was found between antigen level and viral copy number, but no significant correlation (r = 0.001480; P = 0.9919) was found between antigenemia level and viral copy number in serum. When intact rotavirus was treated with benzonase endonuclease, genomic double-stranded (ds) RNA was not degraded, but when sera of patients with antigenemia were treated with benzonase endonuclease, genomic dsRNA was degraded, indicating genomic dsRNA was free in sera and not inside virus capsid protein. Conclusions Antigenemia is present in a significant number of patients with rotavirus diarrhea. Rotavirus viremia was absent in the children with rotavirus diarrhea who participated in our study, and was not indicated by the presence of antigenemia. The significance of circulating rotavirus antigen and genomic dsRNA in serum of patients with diarrhea deserves further study.
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Than VT, Kang H, Lim I, Kim W. Molecular characterization of serotype G9 rotaviruses circulating in South Korea between 2005 and 2010. J Med Virol 2012; 85:171-8. [DOI: 10.1002/jmv.23436] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Mitui MT, Chandrasena TN, Chan PK, Rajindrajith S, Nelson EAS, Leung TF, Nishizono A, Ahmed K. Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch. Virol J 2012; 9:144. [PMID: 22862784 PMCID: PMC3422167 DOI: 10.1186/1743-422x-9-144] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 07/30/2012] [Indexed: 12/02/2022] Open
Abstract
Reverse transcription (RT)-PCR is now the standard method for typing group A rotaviruses (RVA) to monitor the circulating genotypes in a population. Selection of primers that can accurately type the circulating genotypes is crucial in the context of vaccine introduction and correctly interpreting the impact of vaccination on strain distribution. To our knowledge this study is the first report from Asia of misidentification of genotype G9 as G3 due to a primer-template mismatch. We tested two published G-genotype specific primers sets, designed by Gouvea and colleagues (Set A) and Iturriza‐Gomara and colleagues (Set B) on RVA from Hong Kong and Sri Lanka. Among 52 rotaviruses typed as G3 by set A primers, 36 (69.2%) were identified as G9 by nucleotide sequencing and set B primers. Moreover, of 300 rotaviruses tested, 28.3% were untypable by set A primers whereas only 12.3% were untypable by set B primers. Our findings reinforce the need to periodically monitor the primers used for RVA genotyping.
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The comparition of the efficacy of two different probiotics in rotavirus gastroenteritis in children. J Trop Med 2012; 2012:787240. [PMID: 22778754 PMCID: PMC3388355 DOI: 10.1155/2012/787240] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/20/2012] [Accepted: 05/03/2012] [Indexed: 12/12/2022] Open
Abstract
Objectives. The aim of the study is to compare the clinical effectiveness of the probiotics—Saccharomyces boulardii and Bifidobacterium lactis—in children who had been diagnosed with rotavirus gastroenteritis. Materials and methods. Seventy five patients aged between 5 months–5 years diagnosed as rotavirus gastroenteritis were included in the study. The patients diagnosed as rotavirus gastroenteritis by latex agglutination test in stool were divided into 3 groups of twenty-five patients each: First group was given oral rehydration therapy and rapid refeeding with a normal diet with Saccharomyces boulardii (spp. I-745), second group was given oral rehydration therapy and rapid refeeding with a normal diet with Bifidobacterium lactis (spp. B94, culture number:N°118529) and third group received only oral rehydration therapy and rapid refeeding with a normal diet. Results. The duration of diarrhea was shorter in the group given oral rehydration therapy and rapid refeeding with a normal diet with Bifidobacterium lactis and Saccharomyces boulardii than the group given only oral rehydration therapy and rapid refeeding with a normal diet. Conclusion. Bifidobacterium lactis has a complemental role in the treatment of rotavirus gatroenteritis and other probiotics may also have a beneficial effect in rotavirus gastroenteritis compared with the therapy included only oral rehydration therapy and rapid refeeding with a normal diet.
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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: 4.2] [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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Shin JW, Le VP, Than VT, Lim I, Yoon Y, Kim K, Chung SI, Myung SC, Kim W. Genomic characterization of a cell-culture-adapted Korean human G9P[8] rotavirus, CAU05-202. Arch Virol 2012; 157:753-9. [DOI: 10.1007/s00705-012-1232-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Accepted: 12/13/2011] [Indexed: 11/29/2022]
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Tapisiz A, Karahan ZC, Çiftçi E, İnce E, Doğru Ü. Changing patterns of rotavirus genotypes in Turkey. Curr Microbiol 2011; 63:517-22. [PMID: 21938522 DOI: 10.1007/s00284-011-0014-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 09/12/2011] [Indexed: 11/26/2022]
Abstract
To describe the circulation dynamics of human rotavirus genotypes and to understand the epidemiological changes of rotavirus infection in Turkey, one of the countries where the highest mortality rates are seen due to rotavirus in Europe. Stool samples of children under 5 years of age which gave positive results for rotavirus antigen were stored at -20°C and then genotyped using multiplex reverse transcription polymerase-chain reaction. Of the 494 stool samples, 137 (28.1%) were positive for rotavirus antigen and 100 (73%) samples which could be genotyped successfully were included in the study. 42 (42%) samples were from inpatients, and 58 (58%) were from outpatients. The median age of the children was 16 months (5 days-59 months). G9 and P[8] were the most frequent G and P genotypes, and were detected in 30 (30%) and 55 patients (55%), respectively. In 90 samples for which both G and P genotypes could be determined, 34 different combinations were found. G9P[8] was the most frequent genotype detected in 19 patients (19%), followed by G1P[8] and G4P[6] each in 7 (7%) patients. The incidence of mixed infection was found to be 26%. Novel strains like P2A[6] and P[5] and unusual reassortant strains were detected. Distribution of rotavirus genotypes exhibited distinctive changes in this study. When the ever-changing epidemiology of rotaviruses is taken into account, ongoing surveillance studies are important before the inclusion of rotavirus vaccines in national immunization program of Turkey.
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Affiliation(s)
- Anil Tapisiz
- Department of Pediatric Infectious Disease, Ankara University Medical School, 06100 Dikimevi, Ankara, Turkey.
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Salem K, Bdour S, Zeller M, Van Ranst M, Matthijnssens J. Genotypes of rotavirus strains circulating in Amman, Jordan, in 2006/07 and their significance for the potential effectiveness of future rotavirus vaccination. Arch Virol 2011; 156:1543-50. [PMID: 21614437 DOI: 10.1007/s00705-011-1028-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 05/10/2011] [Indexed: 12/21/2022]
Abstract
The prevalence, seasonality and genotypes of rotavirus circulating in Jordan were determined to provide data useful for the implementation of a rotavirus vaccine in the national childhood vaccination program. During 2006/07, rotavirus was detected in 35% of hospitalized children, and 88% of the cases occurred in children aged between 6 and 23 months. Rotavirus infection persisted throughout the year and peaked in winter. Seven genotypes were identified by RT-PCR and sequencing: G1P[8], G9P[8], G2P[4], G1P[4], G3P[8], G4P[8] and G9P[6], which represented 69%, 8.8%, 2.4%, 2.0%, 1.2%, 0.4% and 0.4% of the rotavirus strains, respectively. Thirteen percent and 2.8% of the total strains were partially typed or untypeable, respectively. Eighty-eight percent and 12% of the rotavirus strains possessed a long and short electropherotype, respectively. As more than 90% of the rotavirus strains circulating in Jordan possessed the G1 or P[8]-genotype, it is concluded that the implementation of the rotavirus vaccine in the framework of the national childhood vaccination program of Jordan would most likely be very effective. Continuous monitoring of the currently circulating genotypes in Jordan should be encouraged.
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Affiliation(s)
- Khitam Salem
- Department of Biological Sciences, Faculty of Science, University of Jordan, Amman, Jordan
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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: 1.2] [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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Khoury H, Ogilvie I, El Khoury AC, Duan Y, Goetghebeur MM. Burden of rotavirus gastroenteritis in the Middle Eastern and North African pediatric population. BMC Infect Dis 2011; 11:9. [PMID: 21214934 PMCID: PMC3022719 DOI: 10.1186/1471-2334-11-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 01/07/2011] [Indexed: 12/27/2022] Open
Abstract
Background Rotavirus gastroenteritis (RVGE) is the most common cause of severe childhood diarrhea worldwide. Objectives were to estimate the burden of RVGE among children less than five years old in the Middle East (Bahrain, Iran, Iraq, Israel, Jordan, Kuwait, Oman, Qatar, Saudi Arabia, Syria, UAE, Yemen), North Africa (Algeria, Egypt, Libya, Morocco, Tunisia) and Turkey. Methods A comprehensive literature search was conducted in major databases on the epidemiology and burden of rotavirus among children less than five years old between 1999 and 2009. Data from each country was extracted and compared. Results The search identified 43 studies. RVGE was identified in 16-61% of all cases of acute gastroenteritis, with a peak in the winter. RVGE-related hospitalization rates ranged from 14% to 45%, compared to 14%-28% for non-RVGE. Annually, RVGE caused up to 112 fatalities per 100,000 in certain countries in the region. Hospitalization costs ranged from $1.8 to $4.6 million annually, depending on the country. The most recent literature available showed that G1P[8] was the most prevalent genotype combination in 8 countries (range 23%-56%). G2P[4] was most prevalent in 4 countries (26%-48%). G9P[8] and G4P[8] were also frequently detected. Conclusions RVGE is a common disease associated with significant morbidity, mortality, and economic burden. Given the variety and diverse rotavirus types in the region, use of a vaccine with broad and consistent serotype coverage would be important to help decrease the burden of RVGE in the Middle East and North Africa.
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Affiliation(s)
- Hanane Khoury
- BioMedCom Consultants inc,, 1405 TransCanada Highway, Suite 310, Montreal, Quebec H9P 2V9, Canada.
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Molecular characterization of rotaviruses in mid-western Turkey, 2006–2007. Open Med (Wars) 2010. [DOI: 10.2478/s11536-009-0130-6] [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] Open
Abstract
AbstractVaccines against rotaviruses are now available in numerous countries, including Turkey. As the vaccines may show various efficiencies against different type specificities and routine vaccination in infants might result in selection and immune escape of wild-type rotavirus strains, strain surveillance has been initiated before and during the vaccine introduction. We aimed to provide corresponding information on local strain prevalence in Anatolia, mid-western Turkey during the introduction of rotavirus vaccines. Stool samples positive for group A rotavirus by commercial enzyme immunoassay were subjected to reverse transcription-polymerase chain reaction based genotyping of the outer capsid antigens, VP7 and VP4, determining G and P type specificities respectively. Among 36 fully and 5 partially typeable strains we detected genotype G1, G2, and G9 VP7 specificities and genotype P[4], P[6] and P[8] VP4 specificities in 5 individual and 4 mixed combinations. The most common strain was G2P[4] (n=17), followed by G9P[8] (n=9). Other strains were G1P[8] (n=2), G2P[8] (n=2), G1+2P[8] (n=2), G9P[4] (n=1), G2+9P[8] (n=1), G4+9P[6] (n=1), and G2P[4+8] (n=1). Partially typed strains included 2 G1P[NT] and 3 G2P[NT] strains. Our data may help determine a baseline of the rotavirus genotype prevalence in Turkey and see if changes in the incidence of individual strains will be observed after routine use of vaccine.
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Molecular characterization of VP7 gene of human rotaviruses from Bangladesh. Virus Genes 2010; 40:347-56. [DOI: 10.1007/s11262-010-0463-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2009] [Accepted: 02/20/2010] [Indexed: 11/25/2022]
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Rotavirus infections with multiple emerging genotypes in Sri Lanka. Arch Virol 2009; 155:71-5. [DOI: 10.1007/s00705-009-0552-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 10/22/2009] [Indexed: 10/20/2022]
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Mitui MT, Bozdayi G, Dalgic B, Bostanci I, Nishizono A, Ahmed K. Molecular characterization of a human group C rotavirus detected first in Turkey. Virus Genes 2009; 39:157. [DOI: 10.1007/s11262-009-0420-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 06/10/2009] [Indexed: 02/04/2023]
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