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Sthapit N, Malla B, Tandukar S, Thakali O, Sherchand JB, Haramoto E. Evaluating acute gastroenteritis-causing pathogen reduction in wastewater and the applicability of river water for wastewater-based epidemiology in the Kathmandu Valley, Nepal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170764. [PMID: 38331291 DOI: 10.1016/j.scitotenv.2024.170764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/16/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
Rapid urbanization and population growth without the implementation of proper waste management are capable of contaminating water sources, which can lead to acute gastroenteritis. This study examined the detection and reduction of five gastroenteritis-causing enteropathogens, Salmonella, Campylobacter coli, Campylobacter jejuni, Clostridium perfringens, and genogroup IV norovirus, and one respiratory pathogen, influenza A virus, in two municipal wastewater treatment plants (WWTP) using an oxidation ditch system (WWTP A; n = 20) and a stabilization pond system (WWTP B; n = 18) in the Kathmandu Valley, Nepal, collected between August 2017 and August 2019. All enteropathogens were detected in wastewater via quantitative PCR. The concentrations of the pathogens ranged from 5.7 to 7.9 log10 copies/L in WWTP A and from 4.9 to 8.1 log10 copies/L in WWTP B. The log10 reduction values of the pathogens ranged from 0.3 to 1.0 in WWTP A and from -0.1 to 0.2 in WWTP B. The association between the pathogen concentrations and the number of clinical cases in the corresponding week could not be evaluated; however, the consistent detection of pathogens in the wastewater despite low number of case reports suggested the use of wastewater-based epidemiology (WBE) for early warning of acute gastroenteritis (AGE) in the Kathmandu Valley. The pathogens were also detected in river water at approximately 7.0 log10 copies/L and exhibited no significant difference in concentration compared to wastewater, suggesting the applicability of river water for WBE of AGE. Insufficient treatment of all pathogens in the wastewater was observed, suggesting the need for full rehabilitation of the treatment plants. However, the influent may be utilized for early detection of AGE-causing pathogens in the city, whereas the river water may serve as an alternative in areas without connection to the WWTPs.
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Affiliation(s)
- Niva Sthapit
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sarmila Tandukar
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Ocean Thakali
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Jeevan B Sherchand
- Institute of Medicine, Tribhuvan University, Maharajgunj, Kathmandu 1524, Nepal
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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Malakalinga JJ, Misinzo G, Msalya GM, Shayo MJ, Kazwala RR. Genetic diversity and Genomic analysis of G3P[6] and equine-like G3P[8] in Children Under-five from Southern Highlands and Eastern Tanzania. Acta Trop 2023; 242:106902. [PMID: 36948234 DOI: 10.1016/j.actatropica.2023.106902] [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: 11/06/2022] [Revised: 03/12/2023] [Accepted: 03/18/2023] [Indexed: 03/24/2023]
Abstract
Rotavirus group A genomic characterization is critical for understanding the mechanisms of rotavirus diversity, such as reassortment events and possible interspecies transmission. However, little is known about the genetic diversity and genomic relationship of the rotavirus group A strains circulating in Tanzania. The genetic and genomic relationship of RVA genotypes was investigated in children under the age of five. A total of 169 faecal samples were collected from under-five with diarrhea in Mbeya, Iringa and Morogoro regions of Tanzania. The RVA were screened in children under five with diarrhea using reverse transcription PCR for VP7 and VP4, and the G and P genotypes were determined using Sanger dideoxynucleotide cycle sequencing. Whole-genome sequencing was performed on selected genotypes. The overall RVA rate was 4.7% (8/169). The G genotypes were G3 (7/8) and G6 (1/8) among the 8 RVA positives, while the P genotypes were P[6] (4/8) and P[8] (2), and the other two were untypeable. G3P[6] and G3P[8] were the identified genotype combinations. The genomic analysis reveals that the circulating G3P[8] and G3P[6] isolates from children under the age of five with diarrhea had a DS-1-like genome configuration (I2-R2-C2-M2-Ax-N2-T2-E2-H2). The phylogenic analysis revealed that all 11 segments of G3P[6] were closely related to human G3P[6] identified in neighboring countries such as Uganda, Kenya, and other African countries, implying that G3P[6] strains descended from a common ancestor. Whereas, G3P[8] were closely related to previously identified equine-like G3P[P8] from Kenya, Japan, Thailand, Brazil, and Taiwan, implying that this strain was introduced rather than reassortment events. We discovered amino acid differences at antigenic epitopes and N-linked glycosylation sites between the wild type G3 and P[8] compared to vaccine strains, implying that further research into the impact of these differences on vaccine effectiveness is warranted. The phylogenic analysis of VP7 also identified a bovine-like G6. For the first time in Tanzania, we report the emergence of novel equine-like G3 and bovine-like G6 RVA strains, highlighting the importance of rotavirus genotype monitoring and genomic analysis of representative genotypes.
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Affiliation(s)
- Joseph J Malakalinga
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3021, Morogoro, Tanzania; SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro, Tanzania; Food and Microbiology Laboratory, Tanzania Bureau of Standards, Ubungo Area, Morogoro Road/Sam Nujoma Road, P.O. Box 9524, Dar es Salaam, Tanzania.
| | - Gerald Misinzo
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro, Tanzania; Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3019, Morogoro, Tanzania
| | - George M Msalya
- Department of Animal, Aquaculture and Range Sciences, College of Agriculture, Sokoine University of Agriculture, P.O. Box 3004, Morogoro, Tanzania
| | - Mariana J Shayo
- Muhimbili University of Health and Allied sciences, Department of Biological and Pre-clinical Studies, PO Box 65001, Dar es Salaam, Tanzania
| | - Rudovick R Kazwala
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3021, Morogoro, Tanzania
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Shrestha SK, Shrestha J, Mason CJ, Sornsakrin S, Dhakhwa JR, Shrestha BR, Sakha B, Rana JC, Srijan A, Serichantalergs O, Sethabutr O, Demons S, Bodhidatta L. Etiology of Acute Diarrheal Disease and Antimicrobial Susceptibility Pattern in Children Younger Than 5 Years Old in Nepal. Am J Trop Med Hyg 2023; 108:174-180. [PMID: 36509064 PMCID: PMC9833095 DOI: 10.4269/ajtmh.21-1219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/13/2022] [Indexed: 12/12/2022] Open
Abstract
Diarrhea is a common cause of morbidity and mortality among children younger than 5 years in developing countries. Children from 3 to 60 months of age were recruited from two hospitals in Nepal- Bharatpur Hospital, Bharatpur, and Kanti Children's Hospital, Kathmandu-in 2006 to 2009. Stool specimens collected from 1,200 children with acute diarrhea (cases) and 1,200 children without diarrhea (control subjects) were examined for a broad range of enteropathogens by standard microbiology, including microscopy, enzyme immunoassay for viral pathogens (adenovirus, astrovirus, and rotavirus) and protozoa (Giardia, Cryptosporidium, and Entamoeba histolytica), as well as by using reverse transcription real-time polymerase for norovirus. Antimicrobial susceptibility testing was performed using the disk diffusion method. Overall, rotavirus (22% versus 2%), norovirus (13% versus 7%), adenovirus (3% versus 0%), Shigella (6% versus 1%), enterotoxigenic Escherichia coli (8% versus 4%), Vibrio (7% versus 0%), and Aeromonas (9% versus 3%) were identified significantly more frequently in cases than control subjects. Campylobacter, Plesiomonas, Salmonella, and diarrheagenic E. coli (enteropathogenic, enteroinvasive, enteroaggregative) were identified in similar proportions in diarrheal and non-diarrheal stools. Campylobacter was resistant to second-generation quinolone drugs (ciprofloxacin and norfloxacin), whereas Vibrio and Shigella were resistant to nalidixic acid and trimethoprim/sulfamethoxazole. This study documents the important role of rotavirus and norovirus in acute diarrhea in children younger than 5 years, followed by the bacteria Shigella, enterotoxigenic E. coli, Vibrio cholera, and Aeromonas. Data on the prevalence and epidemiology of enteropathogens identify potential pathogens for public health interventions, whereas pathogen antibiotic resistance pattern data may provide guidance on choice of therapy in clinical settings.
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Affiliation(s)
- Sanjaya K. Shrestha
- Walter Reed/AFRIMS Research Unit Nepal (WARUN), Kathmandu, Nepal;,Centre for International Health, University of Bergen, Bergen, Norway
| | - Jasmin Shrestha
- Walter Reed/AFRIMS Research Unit Nepal (WARUN), Kathmandu, Nepal;,Centre for International Health, University of Bergen, Bergen, Norway;,Address correspondence to Jasmin Shrestha, Walter Reed/AFRIMS Research Unit Nepal (WARUN), Kathmandu, Nepal. E-mail:
| | - Carl J. Mason
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Siriporn Sornsakrin
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Bhola Ram Shrestha
- Shree Mahendra Adarsa Chikitsalaya, Bharatpur Hospital, Bharatpur, Nepal
| | - Bina Sakha
- Walter Reed/AFRIMS Research Unit Nepal (WARUN), Kathmandu, Nepal
| | - Jid Chani Rana
- Walter Reed/AFRIMS Research Unit Nepal (WARUN), Kathmandu, Nepal
| | - Apichai Srijan
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Oralak Serichantalergs
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Orntipa Sethabutr
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Samandra Demons
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Ladaporn Bodhidatta
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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4
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Prevalence and genomic characterization of rotavirus group A genotypes in piglets from in southern highlands and eastern Tanzania. Heliyon 2022; 8:e11750. [DOI: 10.1016/j.heliyon.2022.e11750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/27/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [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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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: 3.0] [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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7
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Gutierrez MB, Fialho AM, Maranhão AG, Malta FC, de Andrade JDSR, de Assis RMS, Mouta SDSE, Miagostovich MP, Leite JPG, Machado Fumian T. Rotavirus A in Brazil: Molecular Epidemiology and Surveillance during 2018-2019. Pathogens 2020; 9:pathogens9070515. [PMID: 32605014 PMCID: PMC7400326 DOI: 10.3390/pathogens9070515] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 02/06/2023] Open
Abstract
Rotavirus A (RVA) vaccines succeeded in lowering the burden of acute gastroenteritis (AGE) worldwide, especially preventing severe disease and mortality. In 2019, Brazil completed 13 years of RVA vaccine implementation (Rotarix™) within the National Immunization Program (NIP), and as reported elsewhere, the use of Rotarix™ in the country has reduced childhood mortality and morbidity due to AGE. Even though both marketed vaccines are widely distributed, the surveillance of RVA causing AGE and the monitoring of circulating genotypes are important tools to keep tracking the epidemiological scenario and vaccines impact. Thus, our study investigated RVA epidemiological features, viral load and G and P genotypes circulation in children and adults presenting AGE symptoms in eleven states from three out of five regions in Brazil. By using TaqMan®-based one-step RT-qPCR, we investigated a total of 1536 stool samples collected from symptomatic inpatients, emergency department visits and outpatients from January 2018 to December 2019. G and P genotypes of RVA-positive samples were genetically characterized by multiplex RT-PCR or by nearly complete fragment sequencing. We detected RVA in 12% of samples, 10.5% in 2018 and 13.7% in 2019. A marked winter/spring seasonality was observed, especially in Southern Brazil. The most affected age group was children aged >24-60 months, with a positivity rate of 18.8% (p < 0.05). Evaluating shedding, we found a statistically lower RVA viral load in stool samples collected from children aged up to six months compared to the other age groups (p < 0.05). The genotype G3P[8] was the most prevalent during the two years (83.7% in 2018 and 65.5% in 2019), and nucleotide sequencing of some strains demonstrated that they belonged to the emergent equine-like G3P[8] genotype. The dominance of an emergent genotype causing AGE reinforces the need for continuous epidemiological surveillance to assess the impact of mass RVA immunization as well as to monitor the emergence of novel genotypes.
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8
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Shrivastava AK, Reddy NS, Giri S, Sahu PS, Das M, Mohakud NK, Das RR. Burden and Molecular Epidemiology of Rotavirus Causing Diarrhea among Under-Five Children: A Hospital-based Study from Eastern India. J Glob Infect Dis 2019; 11:147-152. [PMID: 31849435 PMCID: PMC6906892 DOI: 10.4103/jgid.jgid_16_19] [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: 02/11/2019] [Revised: 04/17/2019] [Accepted: 11/12/2019] [Indexed: 01/18/2023] Open
Abstract
Background Rotavirus (RVA) causes severe gastroenteritis in under-five children, and there are many diverse strains of the virus that are localized to different parts of the world. Objectives To study the burden and molecular epidemiology of RVA causing gastroenteritis among children from Eastern India. Materials and Methods This hospital-based cross-sectional study included children under-five with gastroenteritis. Demographic and clinical parameters were recorded in a predesigned pro forma. Stool samples collected from these children were initially screened for RVA VP6 antigen by enzyme immunoassay (EIA). Each EIA-positive sample was then subjected to RNA extraction, followed by reverse transcription, and heminested multiplex polymerase chain reaction for genotyping of RVA strains. Results Of 320 included children, RVA was detected in 30.62% (98/320) cases by EIA. The highest incidence for RVA-positive cases (34.61%) was observed among children in the age group of 24-36 months, followed by 0-12 months (33.04%). Of the 97 completely typed samples, single genotype was detected in 85 (87.62%) samples with either G (VP7) or P (VP4) types. However, mixed genotypes were detected in 12 (11.21%) samples. G3P[8] (44.09%) was the most common genotype, followed by G1P[8] (32.65%), G2[P4] (5.10%), G1[P6] (3.06%), and G9[P4] (1.02%). Conclusions The present study found RVA positivity in 30.62% of children with gastroenteritis, with the highest burden among 24-36 months old. The predominant genotypes were G1, G3, and P[8]. Further large-scale/multicentric studies should be conducted to document the diversity of circulating RVA genotypes in this region for giving inputs for vaccination strategy.
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Affiliation(s)
- Arpit Kumar Shrivastava
- Department of Biotechnology, Infection Biology Laboratory, KIIT Deemed to be University, Vellore, Tamil Nadu, India
| | - N Samarasimha Reddy
- Division of Gastrointestinal Sciences, The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, Tamil Nadu, India
| | - Sidhartha Giri
- Division of Gastrointestinal Sciences, The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Mirabai Das
- Department of Health, Kalinga Institute of Social Sciences, KISS University, Bhubaneswar, Odisha, India
| | - Nirmal Kumar Mohakud
- Department of Paediatrics, Kalinga Institute of Medical Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha, India
| | - Rashmi Ranjan Das
- Department of Pediatrics, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
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9
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Vrdoljak M, Gužvinec M, Trkulja V, Butić I, Ivić I, Krželj V, Tonkić M, Hegeduš Jungvirth M, Payerl Pal M, Tešović G. Distribution of rotavirus genotypes in three Croatian regions among children ≤5 years of age (2012-2014). Int J Infect Dis 2019; 89:3-9. [PMID: 31521853 DOI: 10.1016/j.ijid.2019.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/17/2019] [Accepted: 09/09/2019] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Rotavirus is the major cause of severe diarrhea in young children worldwide. In countries like Croatia, where rotavirus vaccine has not been introduced in the national immunization program, prospective surveillance is necessary to establish the diversity of rotavirus strains. The aim of this study was to describe the prevalence and geographical distribution of rotavirus strains in Croatia and to detect the possible emergence of novel strains. METHODS The study was conducted among children ≤5 years of age with acute gastroenteritis at three hospitals located in different geographical regions of Croatia, during the years 2012 to 2014. Rotavirus was detected in stools using an immunochromatographic assay and then sent for further molecular analysis. RESULTS Genotyping of 822 rotaviruses showed that the predominant circulating strain was G1P[8] (61.9%), followed by G2P[4] (19.5%), G1P[4] (3.9%), and G3P[8] (2.9%). A high prevalence of reassortants among common human rotavirus genotypes was detected (7.7%). Possible zoonotic reassortants were found, including G8 and G6 strains. The latter is described for the first time in Croatia. CONCLUSIONS This study represents pre-vaccination data that are important for decisions regarding immunization strategies in Croatia. The high prevalence of 'common' rotavirus strains circulating in Croatia may advocate for rotavirus vaccine introduction, but further surveillance is necessary to monitor the possible emergence of novel genotypes.
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Affiliation(s)
- Maja Vrdoljak
- Department of Pediatric Infectious Diseases, University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Mirogojska 8, 10000 Zagreb, Croatia.
| | - Marija Gužvinec
- Department of Clinical Microbiology, University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Mirogojska 8, 10000 Zagreb, Croatia
| | - Vladimir Trkulja
- Department of Pharmacology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
| | - Iva Butić
- Department of Clinical Microbiology, University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Mirogojska 8, 10000 Zagreb, Croatia
| | - Ivo Ivić
- Department of Infectious Diseases, University Hospital of Split, Spinčićeva 1, 21000 Split, Croatia; School of Medicine, University of Split, Šoltanska ulica 2, 21000 Split, Croatia
| | - Vjekoslav Krželj
- School of Medicine, University of Split, Šoltanska ulica 2, 21000 Split, Croatia; Department of Pediatrics, University Hospital of Split, Spinčićeva 1, 21000 Split, Croatia
| | - Marija Tonkić
- School of Medicine, University of Split, Šoltanska ulica 2, 21000 Split, Croatia; Department of Clinical Microbiology, University Hospital of Split, Spinčićeva 1, 21000 Split, Croatia
| | - Marija Hegeduš Jungvirth
- Department of Pediatrics, County Hospital Čakovec, Ivana Gorana Kovačića 1E, 40000 Čakovec, Croatia
| | - Marina Payerl Pal
- Institute of Public Health, County Međimurje, Ivana Gorana Kovačića 1E, 40000 Čakovec, Croatia
| | - Goran Tešović
- Department of Pediatric Infectious Diseases, University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Mirogojska 8, 10000 Zagreb, Croatia; School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
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Sadiq A, Bostan N, Bokhari H, Matthijnssens J, Yinda KC, Raza S, Nawaz T. Molecular characterization of human group A rotavirus genotypes circulating in Rawalpindi, Islamabad, Pakistan during 2015-2016. PLoS One 2019; 14:e0220387. [PMID: 31361761 PMCID: PMC6667158 DOI: 10.1371/journal.pone.0220387] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 07/15/2019] [Indexed: 01/17/2023] Open
Abstract
Group A rotaviruses (RVA) are one of the major causes of acute gastroenteritis (AGE) in young children worldwide. Owing to lack of proper surveillance programs and health facilities, developing countries of Asia and Africa carry a disproportionately heavy share of the RVA disease burden. The aim of this hospital-based study was to investigate the circulation of RVA genotypes in Rawalpindi and Islamabad, Pakistan in 2015 and 2016, prior to the implementation of RVA vaccine. 639 faecal samples collected from children under 10 years of age hospitalized with AGE were tested for RVA antigen by ELISA. Among 171 ELISA positive samples, 143 were successfully screened for RT-PCR and sequencing. The prevalence of RVA was found to be 26.8% with the highest frequency (34.9%) found among children of age group 6-11 months. The most predominant circulating genotypes were G3P[8] (22.4%) followed by G12P[6] (20.3%), G2P[4] (12.6%), G1P[8] (11.9%), G9P[6] (11.9%), G3P[4] (9.1%), G1P[6] (4.2%), G9P[8] (4.2%), and G3P[6] (0.7%). A single mixed genotype G1G3P[8] was also detected. The findings of this study provide baseline data, that will help to assess if future vaccination campaigns using currently available RVA vaccine will reduce RVA disease burden and instigate evolutionary changes in the overall RVA biology. The high prevalence of RVA infections in Pakistan require to improve and strengthen the surveillance and monitoring system for RVA. This will provide useful information for health authorities in planning public health care strategies to mitigate the disease burden caused by RVA.
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Affiliation(s)
- Asma Sadiq
- Department of Biosciences, COMSATS University (CUI), Tarlai Kalan, Chak Shahzad, Islamabad, Pakistan
| | - Nazish Bostan
- Department of Biosciences, COMSATS University (CUI), Tarlai Kalan, Chak Shahzad, Islamabad, Pakistan
- * E-mail:
| | - Habib Bokhari
- Department of Biosciences, COMSATS University (CUI), Tarlai Kalan, Chak Shahzad, Islamabad, Pakistan
| | - Jelle Matthijnssens
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Kwe Claude Yinda
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Saqlain Raza
- Department of Biosciences, COMSATS University (CUI), Tarlai Kalan, Chak Shahzad, Islamabad, Pakistan
| | - Tayyab Nawaz
- Department of Biosciences, COMSATS University (CUI), Tarlai Kalan, Chak Shahzad, Islamabad, Pakistan
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Ghaju Shrestha R, Tanaka Y, Sherchand JB, Haramoto E. Identification of 16S rRNA and Virulence-Associated Genes of Arcobacter in Water Samples in the Kathmandu Valley, Nepal. Pathogens 2019; 8:pathogens8030110. [PMID: 31357473 PMCID: PMC6789466 DOI: 10.3390/pathogens8030110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/23/2022] Open
Abstract
This study aimed to determine the prevalence of Arcobacter and five associated virulence genes (cadF, ciaB, mviN, pldA, and tlyA) in water samples in the Kathmandu Valley, Nepal. A total of 286 samples were collected from deep tube wells (n = 30), rivers (n = 14), a pond (n = 1), shallow dug wells (n = 166), shallow tube wells (n = 33), springs (n = 21), and stone spouts (n = 21) in February and March (dry season) and August (wet season), 2016. Bacterial DNA was extracted from the water samples and subjected to SYBR Green-based quantitative PCR for 16S rRNA and virulence genes of Arcobacter. The 16S rRNA gene of Arcobacter was detected in 36% (40/112) of samples collected in the dry season, at concentrations ranging from 5.7 to 10.2 log copies/100 mL, and 34% (59/174) of samples collected in the wet season, at concentrations of 5.4–10.8 log copies/100 mL. No significant difference in Arcobacter 16S rRNA gene-positive results was observed between samples collected in the two seasons (p > 0.05). Seventeen (17%), 84 (84%), 19 (19%), 23 (23%), and 17 (17%) of the 99 Arcobacter 16S rRNA gene-positive samples were also positive for cadF, ciaB, mviN, pldA, and tlyA, respectively. At least one virulence gene was detected in 87 (88%) of the 99 Arcobacter 16S rRNA gene-positive samples. The presence of Arcobacter and the virulence genes in these samples illustrates the persistence of pathogenic bacteria in the environment and highlights the importance of regular monitoring of water for pathogens.
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Affiliation(s)
- Rajani Ghaju Shrestha
- Division of Sustainable Energy and Environmental Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Yasuhiro Tanaka
- Department of Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Jeevan B Sherchand
- Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu 1524, Nepal
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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Detection of Pathogenic Viruses, Pathogen Indicators, and Fecal-Source Markers within Tanker Water and Their Sources in the Kathmandu Valley, Nepal. Pathogens 2019; 8:pathogens8020081. [PMID: 31248180 PMCID: PMC6630610 DOI: 10.3390/pathogens8020081] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 11/17/2022] Open
Abstract
Tanker water is used extensively for drinking as well as domestic purposes in the Kathmandu Valley of Nepal. This study aimed to investigate water quality in terms of microbial contamination and determine sources of fecal pollution within these waters. Thirty-one samples from 17 tanker filling stations (TFSs) and 30 water tanker (WT) samples were collected during the dry and wet seasons of 2016. Escherichia coli was detected in 52% of the 31 TFS samples and even more frequently in WT samples. Of the six pathogenic viruses tested, enteroviruses, noroviruses of genogroup II (NoVs-GII), human adenoviruses (HAdVs), and group A rotaviruses were detected using quantitative PCR (qPCR) at 10, five, four, and two TFSs, respectively, whereas Aichi virus 1 and NoVs-GI were not detected at any sites. Index viruses, such as pepper mild mottle virus and tobacco mosaic virus, were detected using qPCR in 77% and 95% out of 22 samples, respectively, all of which were positive for at least one of the tested pathogenic viruses. At least one of the four human-associated markers tested (i.e., BacHum, HAdVs, and JC and BK polyomaviruses) was detected using qPCR in 39% of TFS samples. Ruminant-associated markers were detected at three stations, and pig- and chicken-associated markers were found at one station each of the suburbs. These findings indicate that water supplied by TFSs is generally of poor quality and should be improved, and proper management of WTs should be implemented.
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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: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [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. Electronic supplementary material The online version of this article (10.1186/s12879-019-4092-2) contains supplementary material, which is available to authorized users.
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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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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: 1.0] [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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Tian Y, Chughtai AA, Gao Z, Yan H, Chen Y, Liu B, Huo D, Jia L, Wang Q, MacIntyre CR. Prevalence and genotypes of group A rotavirus among outpatient children under five years old with diarrhea in Beijing, China, 2011-2016. BMC Infect Dis 2018; 18:497. [PMID: 30285635 PMCID: PMC6168998 DOI: 10.1186/s12879-018-3411-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/24/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Rotavirus is a leading cause of severe diarrheal disease, and one of the common causes of death in children aged under five years old. The dominant epidemic strains may change in different years in the same area. In order to provide evidence for rotavirus epidemic control and inform vaccine development, we analyzed epidemiological patterns and genetic characteristics of rotavirus in Beijing during 2011-2016. METHODS Stool specimens of outpatient children under five years old were collected from three children's hospitals on a weekly basis. Group A rotavirus antigens were detected using enzyme-linked immunosorbent assay (ELISA) kit. The partial VP4 genes and VP7 genes of rotavirus were both amplified and sequenced. Genotyping and phylogenetic analyses were performed. Logistic regression and Chi-square tests were performed to determine differences across age groups, districts and years in rotavirus prevalence and genotype distribution. RESULTS A total of 3668 stool specimens from children with acute diarrhea identified through hospital-based surveillance were collected from 2011 to 2016 in Beijing. A total of 762 (20.8%) specimens tested positive for rotavirus. The rotavirus-positive rate was highest among the 1-2 years old age group (29.0%, 310/1070). November, December and January were the highest rotavirus-positive rate months each year. G9 was the most common G genotype (64.4%, 461/716), and P [8] was the most common P genotype (87.0%, 623/716) among the 716 rotavirus-positive specimens. G9P [8], G3P [8] and G2P [4] were the most common strains. The rotavirus-positive rates of samples in 2012 and 2013 were higher than that in 2011, and the dominant genotype changed from G3P [8] to G9P [8] in 2012 and 2013. VP7 gene sequences of G9 strains in this study clustered into two main lineages. Most of the G9 strains exhibited the highest nucleotide similarity (99.1%~ 100.0%) to the strain found in Japan (MI1128). VP4 gene sequences of P [8] strains were almost P[8]b. CONCLUSIONS Rotavirus accounted for more than one fifth of childhood diarrhea in Beijing during the study period. Targeted measures such as immunization with effective rotavirus vaccines should be carried out to reduce the morbidity and mortality due to rotavirus.
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Affiliation(s)
- Yi Tian
- Institute for Infectious Disease and Endemic Disease Control, Beijing Municipal Center for Disease Prevention and Control, Beijing, China
- Institute for Infectious Disease and Endemic Disease Control, Beijing Research Center for Preventive Medicine, Beijing, China
| | - Abrar Ahmad Chughtai
- School of Public Health and Community Medicine, University of New South Wales, Sydney, Australia
| | - Zhiyong Gao
- Institute for Infectious Disease and Endemic Disease Control, Beijing Municipal Center for Disease Prevention and Control, Beijing, China
- Institute for Infectious Disease and Endemic Disease Control, Beijing Research Center for Preventive Medicine, Beijing, China
| | - Hanqiu Yan
- Institute for Infectious Disease and Endemic Disease Control, Beijing Municipal Center for Disease Prevention and Control, Beijing, China
- Institute for Infectious Disease and Endemic Disease Control, Beijing Research Center for Preventive Medicine, Beijing, China
| | - Yanwei Chen
- Institute for Infectious Disease and Endemic Disease Control, Beijing Municipal Center for Disease Prevention and Control, Beijing, China
- Institute for Infectious Disease and Endemic Disease Control, Beijing Research Center for Preventive Medicine, Beijing, China
| | - Baiwei Liu
- Institute for Infectious Disease and Endemic Disease Control, Beijing Municipal Center for Disease Prevention and Control, Beijing, China
- Institute for Infectious Disease and Endemic Disease Control, Beijing Research Center for Preventive Medicine, Beijing, China
| | - Da Huo
- Institute for Infectious Disease and Endemic Disease Control, Beijing Municipal Center for Disease Prevention and Control, Beijing, China
- Institute for Infectious Disease and Endemic Disease Control, Beijing Research Center for Preventive Medicine, Beijing, China
| | - Lei Jia
- Institute for Infectious Disease and Endemic Disease Control, Beijing Municipal Center for Disease Prevention and Control, Beijing, China
- Institute for Infectious Disease and Endemic Disease Control, Beijing Research Center for Preventive Medicine, Beijing, China
| | - Quanyi Wang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Municipal Center for Disease Prevention and Control, Beijing, China
- Institute for Infectious Disease and Endemic Disease Control, Beijing Research Center for Preventive Medicine, Beijing, China
| | - Chandini Raina MacIntyre
- School of Public Health and Community Medicine, University of New South Wales, Sydney, Australia
- College of Public Service and Community Solutions, and College of Health Solutions, Arizona State University, Phoenix, USA
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Rotavirus infection among hospitalized children under five years of age with acute watery diarrhea in Sri Lanka. Vaccine 2018; 36:7846-7850. [PMID: 29945833 DOI: 10.1016/j.vaccine.2018.03.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/24/2018] [Accepted: 03/22/2018] [Indexed: 12/29/2022]
Abstract
BACKGROUND Rotavirus is the leading cause of acute watery diarrhoea among children and is vaccine preventable. The aim of this hospital-based sentinel surveillance was to study the prevalence, demographic and clinical characteristics of rotavirus infections and to describe rotavirus genotype distribution patterns among children under five years of age hospitalized for acute watery diarrhea during the period of 2009-2016. METHODS Prospective, sentinel hospital-based surveillance was conducted in Lady Ridgeway Hospital (LRH) from 2009 to 2016. Stool samples of children admitted with acute watery diarrhea were tested by rotavirus antigen detection 'ProSpecT' Enzyme Immunoassay (EIA) at Department of Virology, Medical Research Institute, Colombo. Specimens that tested positive for rotavirus were further analyzed at the Regional Reference Laboratory (RRL) participating in the World Health Organization (WHO)-coordinated Global Rotavirus Surveillance Network (GRSN) to determine the genotype of strains by reverse-transcriptase polymerase chain reaction. RESULTS Of the 6090 children with diarrhea admitted, 1801 (29.5%) had stools taken and tested. In years with at least 11 months of data (2010 and 2013) rotavirus was detected in 36.5% (228/624) of specimens. Genotype G1P[8] was the most common genotype detected throughout the surveillance period (30.1%; 123/408) with G2P [8], G9P[8] and G3P[8] also detected. CONCLUSIONS Rotavirus is a common cause of pediatric diarrhea hospitalizations in Sri Lanka. National introduction of rotavirus vaccine could reduce the burden of pediatric diarrhea.
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Adhikari R, Thapa S. Changing Trend of Infectious Diseases in Nepal. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1052:19-38. [PMID: 29785478 PMCID: PMC7122567 DOI: 10.1007/978-981-10-7572-8_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Many infectious/communicable diseases (IDs) are endemic in Nepal. Until a decade and half ago, IDs were the major cause of both morbidity and mortality accounting 70% for both. However, as a result of various preventive measures implemented by both the state and non-state actors, the overall IDs have shown a changing (declining) trend. The most impressive decline has been seen in the intestinal helminth infection. Though the overall burden of IDs is decreasing, several newer infectious diseases (emerging infections) namely, dengue fever, scrub typhus, influenza (H5N1 and H1N1), and others are posing a great public health problem. On the other hand, though sporadic, outbreaks of endemic diseases together with HIV-TB coinfection and infection with drug resistance microbes during recent years have constituted a serious public health as well as medical problem. On the contrary, with the decline of IDs, noninfectious diseases (noncommunicable disease, NCD) namely, diabetes, cancer (and cancer therapy), and others are on the rise particularly in urban areas. Hence, currently Nepal is trapped in "double burden" of diseases. Risk of opportunistic infection has increased in immunocompromised person with NCD. To address the present situation, the multi-sectoral plan and strategies developed must be implemented effectively.
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Affiliation(s)
- Rameshwar Adhikari
- Research Center for Applied Science and Technology (RECAST), Tribhuvan University, Kathmandu, Nepal
| | - Santosh Thapa
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas USA
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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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Pellegrinelli L, Ianiro G, Pariani E, Monini M, Ruggeri FM, Binda S. Molecular characterization of rotavirus disclosed the first introduction of G12P[8] strain in northern Italy. Future Virol 2018. [DOI: 10.2217/fvl-2017-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: This paper discusses the unexpected findings from the RotaNet-Italy hospital-based surveillance study carried out in northern Italy. Materials & methods: From September 2015 to August 2016, 51 rotavirus-A (RVA) positive fecal samples were collected from children aged less than 15 years, who were hospitalized for acute gastroenteritis in Lombardy, northern Italy. Results: Molecular characterization revealed the predominance of the uncommon G12P[8] RVA strain, which was detected in 49% of cases. Phylogenetic analysis showed that these G12 strains clustered into lineage 3. Conclusion: To our knowledge, this is the first study on the G12P[8] genotype’s introduction in northern Italy. Our findings emphasize the importance of the surveillance of RVA gastroenteritis with the aim of obtaining new insight into the unusual newly emerging RVA strains.
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Affiliation(s)
- Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Giovanni Ianiro
- Department of Veterinary Public Health & Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Marina Monini
- Department of Veterinary Public Health & Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Franco Maria Ruggeri
- Department of Veterinary Public Health & Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
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Mchaile DN, Philemon RN, Kabika S, Albogast E, Morijo KJ, Kifaro E, Mmbaga BT. Prevalence and genotypes of Rotavirus among children under 5 years presenting with diarrhoea in Moshi, Tanzania: a hospital based cross sectional study. BMC Res Notes 2017; 10:542. [PMID: 29084598 PMCID: PMC5661935 DOI: 10.1186/s13104-017-2883-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 10/27/2017] [Indexed: 12/03/2022] Open
Abstract
Background Diarrhoea is a main cause of morbidity and mortality in children under 5 responsible for approximately four billion cases and 1.1 million deaths annually. In developing countries, it causes two million deaths each year. The major causative organism responsible is Rotavirus which is responsible for one-third of hospitalizations with approximately 40% mortality. Results The prevalence of Rotavirus infection was 26.4% (73/277). The predominant strain of Rotavirus found was G1 21/73 (53.8%), followed by G8 9/73 (23.1%), G12 5/73 (12.8%), G9 3/73(7.7%) and G4 1/73 (2.6%). All serotypes identified were in children who had completed Rotavirus vaccination except for one who had G8 in whom the vaccine was introduced after they had completed immunizations. Conclusion The overall prevalence of rotavirus has reduced from 33.2% in 2009 to 26.4% in 2016. We have found G1 to be the predominant serotype as well as other circulating serotypes namely G4, G8, G9 and G12. Despite a reduction in prevalence, there is a need for further rotavirus surveillance in the region. Electronic supplementary material The online version of this article (10.1186/s13104-017-2883-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deborah N Mchaile
- Department of Pediatrics and Child Health, Kilimanjaro Christian Medical Centre, Moshi, Tanzania. .,Kilimanjaro Christian Medical University College, Moshi, Tanzania.
| | - Rune N Philemon
- Department of Pediatrics and Child Health, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Sonia Kabika
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Evelyn Albogast
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Kikoti J Morijo
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Emmanuel Kifaro
- Department of Veterinary Microbiology and Parasitology, Sokoine University of Agriculture (SUA), Morogoro, Tanzania
| | - Blandina T Mmbaga
- Department of Pediatrics and Child Health, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Kilimanjaro Clinical Research Institute, Moshi, Tanzania
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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: 1.3] [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: 2.9] [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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Leshem E, Parashar U. Use of Surveillance Data to Assess the Impact of Vaccination on Circulating Rotavirus Strains. J Pediatric Infect Dis Soc 2015; 4:e90-2. [PMID: 26582888 DOI: 10.1093/jpids/piu114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/03/2014] [Indexed: 11/13/2022]
Affiliation(s)
- Eyal Leshem
- 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
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24
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Tong Y, Lee BE, Pang XL. Rapid genotyping of human rotavirus using SYBR green real-time reverse transcription-polymerase chain reaction with melting curve analysis. World J Virol 2015; 4:365-371. [PMID: 26568918 PMCID: PMC4641228 DOI: 10.5501/wjv.v4.i4.365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/01/2015] [Accepted: 09/30/2015] [Indexed: 02/05/2023] Open
Abstract
AIM: To develop a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay to genotype rotavirus (G and P) in Alberta from January 2012 to June 2013.
METHODS: We developed and validated a different approach to perform rotavirus G and P genotyping using a two-step SYBR green RT-PCR (rt-gPCR) by selecting genotype-specific primers of published conventional RT nested PCR (cnRT-PCR) assay and optimizing the amplification conditions. cDNA was first synthesized from total RNA with SuperScript™ II reverse transcriptase kit followed by amplication step using monoplex SYBR green real-time PCR. After the PCR reaction, melting curve analysis was used to determine specific genotype. Sixteen samples previously genotyped using cnRT-PCR were tested using the new assay and the genotyping results were compared as sensitivity analysis. Assay specificity was evaluated by testing other gastroenteritis viruses with the new assay. The amplicon size of each available genotype was determined by gel-electrophoresis and DNA sequences were obtained using Sanger-sequencing method. After validation and optimization, the new assay was used to genotype 122 pediatric clinical stool samples previously tested positive for rotavirus using electron microscopy between January 2012 and June 2013.
RESULTS: The new rt-gPCR assay was validated and optimized. The assay detected G1 to G4, G9, G12 and P[4] and P[8] that were available as positive controls in our laboratory. A single and clear peak of melting curve was generated for each of specific G and P genotypes with a Tm ranging from 80 °C to 82 °C. The sensitivity of rt-gPCR was comparable to cnRT-PCR with 100% correlation of the 16 samples with known G and P genotypes. No cross reaction was found with other gastroenteritis viruses. Using the new rt-gPCR assay, genotypes were obtained for 121 of the 122 pediatric clinical samples tested positive for rotavirus: G1P[8] (42.6%), G2P[4] (4.9%), G3P[8] (10.7%), G9P[8] (10.7%), G9P[4] (6.6%), G12P[8] (23.0%), and unknown GP[8] (0.8%). For the first time, G12 rotavirus strains were found in Alberta and G12 was the second most common genotype during the study period. Gel electrophoresis of all the genotypes showed expected amplicon size for each genotype. The sequence data of the two G12 samples along with other genotypes were blasted in NCBI BLAST or analyzed with Rota C Genotyping tool (http://rotac.regatools.be/). All genotyping results were confirmed to be correct.
CONCLUSION: rt-gPCR is a useful tool for the genotyping and characterization of rotavirus. Monitoring of rotavirus genotypes is important for the identification of emerging strains and ongoing evaluation of rotavirus vaccination programs.
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Ide T, Higo-Moriguchi K, Komoto S, Htun KW, Myint YY, Myat TW, Thant KZ, Thu HM, Win MM, Oo HN, Htut T, Rahman S, Nguyen SV, Umeda K, Oguma K, Tsuji T, Taniguchi K. High Prevalence of G12 Human Rotaviruses in Children with Gastroenteritis in Myanmar. Jpn J Infect Dis 2015; 69:326-7. [PMID: 26370431 DOI: 10.7883/yoken.jjid.2015.267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Human rotavirus samples from 54 children with acute gastroenteritis in Myanmar in 2011 were subjected to reverse transcription-PCR to determine their G and P types. On G typing, G2 (24/54; 44.4%) was found to be the most prevalent, followed by G12 (17/54; 31.5%) and G1 (1/54; 1.9%). Mixed cases with G2 and G12 were found in 12 of the 54 (22.2%) samples. On P typing, P[4] was found to be the most predominant (29/54; 53.7%), followed by P[8] (17/54; 31.5%) and P[6] (4/54; 7.4%). Mixed cases with P[4] and P[8] were detected in 4 of 54 (7.4%) samples. Thus, occurrence of G2 and unusual G12 in high proportions was characteristic of human rotaviruses in Myanmar in this study setting.
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Affiliation(s)
- Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine
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26
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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: 2.8] [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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Tiku VR, Sharma S, Verma A, Kumar P, Raghavendhar S, Aneja S, Paul VK, Bhan MK, Ray P. Rotavirus diversity among diarrheal children in Delhi, India during 2007-2012. Vaccine 2015; 32 Suppl 1:A62-7. [PMID: 25091683 DOI: 10.1016/j.vaccine.2014.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rotavirus is the leading cause of severe gastroenteritis in young children worldwide and is responsible for around 100,000 deaths in India annually. Vaccination against rotavirus (RV) is a high priority: 'ROTAVAC' an indigenous vaccine will soon be licensed in India. Surveillance to determine the impact of vaccines on emerging RV strains is required. In this study we compared the pattern of RV strains circulating in Delhi over a 5 year period with the strains over the past 12 years. The most commonly detected G genotypes were G1 (22.4%), G2 (17.2%), and G9 (25.2%) with P[4] (25.5%), P[6] (20%) and P[8] (16.9%) specificity. G12 genotype was found to be the fourth common G-type with 14.8% prevalence. Among the G-P combinations; G1P[8], G2P[4], G9P[8] and G12P[6] were detected at 7.2%, 7.2%, 5.2% and 10%, respectively. Of note, G9P[4] and G2P[6] that were rarely detected during 2000-2007 in Delhi, were observed quite frequently with prevalence of 6.5% and 3.4%, respectively. In total, 16 different G-P combinations were detected in the present study demonstrating the rich diversity of rotavirus strains in Delhi. Our data from the 12 year period indicate wide circulation of G1 and G9 genotypes in combination with P[8], G2 with P[4] and G12 with P[6] with high frequency of RV strains having rare G-P combinations in Delhi. Since the indigenous vaccine 'ROTAVAC' has a monovalent formulation, the impact of vaccines on strains and the effect of strain diversity on the efficacy of the vaccine should be monitored.
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Affiliation(s)
- Vasundhara Razdan Tiku
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sumit Sharma
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Anil Verma
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Praveen Kumar
- Kalawati Saran Children's Hospital, Lady Hardinge Medical College, New Delhi 110001, India
| | - Siva Raghavendhar
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Satinder Aneja
- Kalawati Saran Children's Hospital, Lady Hardinge Medical College, New Delhi 110001, India
| | - Vinod Kumar Paul
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Maharaj Kishan Bhan
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pratima Ray
- Department of Biotechnology, Faculty of Science, Jamia Hamdard, Hamdard Nagar New Delhi 110062, India.
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28
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Review of global rotavirus strain prevalence data from six years post vaccine licensure surveillance: is there evidence of strain selection from vaccine pressure? INFECTION GENETICS AND EVOLUTION 2014; 28:446-61. [PMID: 25224179 DOI: 10.1016/j.meegid.2014.08.017] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 11/23/2022]
Abstract
Comprehensive reviews of pre licensure rotavirus strain prevalence data indicated the global importance of six rotavirus genotypes, G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]. Since 2006, two vaccines, the monovalent Rotarix (RV1) and the pentavalent RotaTeq (RV5) have been available in over 100 countries worldwide. Of these, 60 countries have already introduced either RV1 or RV5 in their national immunization programs. Post licensure vaccine effectiveness is closely monitored worldwide. This review aimed at describing the global changes in rotavirus strain prevalence over time. The genotype distribution of the nearly 47,000 strains that were characterized during 2007-2012 showed similar picture to that seen in the preceding period. An intriguing finding was the transient predominance of heterotypic strains, mainly in countries using RV1. Unusual and novel antigen combinations continue to emerge, including some causing local outbreaks, even in vaccinated populations. In addition, vaccine strains have been found in both vaccinated infants and their contacts and there is evidence for genetic interaction between vaccine and wild-type strains. In conclusion, the post-vaccine introduction strain prevalence data do not show any consistent pattern indicative of selection pressure resulting from vaccine use, although the increased detection rate of heterotypic G2P[4] strains in some countries following RV1 vaccination is unusual and this issue requires further monitoring.
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