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Umair M, Rehman Z, Haider SA, Usman M, Rana MS, Ikram A, Salman M. First report of coinfection and whole-genome sequencing of norovirus and sapovirus in an acute gastroenteritis patient from Pakistan. J Med Virol 2023; 95:e28458. [PMID: 36597899 DOI: 10.1002/jmv.28458] [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: 11/28/2022] [Revised: 12/20/2022] [Accepted: 01/01/2023] [Indexed: 01/05/2023]
Abstract
Acute gastroenteritis is one of the most common diseases in infants and children in developing countries including Pakistan. In Pakistan, rotavirus (RVA) is known to contribute significantly to pediatric diarrheal illness, but the contribution of other viruses is still unclear. In the current study we have identified a case of mixed infection of norovirus (NoV) and sapovirus (SaV) in a 2-year-old child with acute gastroenteritis. The sample was initially processed for the detection of group A RVA through ELISA followed by NoV using RT-PCR assay. The sample tested positive for NoV RNA and was later subjected to whole-genome sequencing using meta-genome approach on Miseq (Illumina) platform. Sequencing results revealed GII.15 genotype of NoV that clustered with viruses from China and USA from 2017 to 2021. We also retrieved the complete genome of SaV (GI.1 genotype) from the same sample and phylogenetic analysis showed clustering with strains reported from Japan, South Korea, US, and Taiwan during 2012-2016. This is the first report from Pakistan that confirms coinfection of NoV and SaV and elucidates their whole genomes. We recommend initiation of NoV and SaV surveillance program to ascertain disease burden and explore genetic diversity, especially as RVA vaccines have been included in national immunization program.
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Affiliation(s)
- Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Zaira Rehman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Syed Adnan Haider
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Usman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | | | - Aamer Ikram
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
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Vaccine evaluation and genotype characterization in children infected with rotavirus in Qatar. Pediatr Res 2023:10.1038/s41390-023-02468-7. [PMID: 36658331 PMCID: PMC10382313 DOI: 10.1038/s41390-023-02468-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/29/2022] [Accepted: 12/14/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND We characterized and identified the genetic and antigenic variations of circulating rotavirus strains in comparison to used rotavirus vaccines. METHODS Rotavirus-positive samples (n = 231) were collected and analyzed. The VP7 and VP4 genes were sequenced and analyzed against the rotavirus vaccine strains. Antigenic variations were illustrated on the three-dimensional models of surface proteins. RESULTS In all, 59.7% of the hospitalized children were vaccinated, of which only 57.2% received two doses. There were no significant differences between the vaccinated and non-vaccinated groups in terms of clinical outcome. The G3 was the dominant genotype (40%) regardless of vaccination status. Several amino acid changes were identified in the VP7 and VP4 antigenic epitopes compared to the licensed vaccines. The highest variability was seen in the G3 (6 substitutions) and P[4] (11 substitutions) genotypes in comparison to RotaTeq®. In comparison to Rotarix®, G1 strains possessed three amino acid changes in 7-1a and 7-2 epitopes while P[8] strains possessed five amino acid changes in 8-1 and 8-3 epitopes. CONCLUSIONS The current use of Rotarix® vaccine might not be effective in preventing the infection due to the higher numbers of G3-associated cases. The wide range of mutations in the antigenic epitopes compared to vaccine strains may compromise the vaccine's effectiveness. IMPACT The reduced rotavirus vaccine effectiveness necessitate regular evaluation of the vaccine content to ensure optimal protection. We characterized and identified the genetic and antigenic variations of circulating rotavirus strains in comparison to the Rotarix vaccine strain that is used in Qatar. The study highlight the importance for regular monitoring of emerging rotavirus variants and their impact on vaccine effectiveness in young children.
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Fatima M, Khan DA, Amraiz D, Lodhi MA, Ghani E, Niazi SK, Ali S. Characterization of rotavirus strains isolated from children with acute gastroenteritis in Rawalpindi, Pakistan. J Med Virol 2022; 94:3312-3319. [PMID: 35274329 DOI: 10.1002/jmv.27711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 11/07/2022]
Abstract
Diarrhea is the leading cause of childhood morbidity and mortality particularly in developing countries and rotavirus has been identified as the major pathogen associated with diarrheal infections. The present study was conducted to detect genotypic distribution of predominant rotavirus strains circulating in children suffering from acute gastroenteritis in Rawalpindi, Pakistan. Stool specimens were collected from children ≤ 5 years of age, visiting Military Hospital, Rawalpindi, with signs and symptoms of acute gastroenteritis. 284 specimens were collected during the period from April 2017 to March 2018. Enzyme immunoassay was performed for detection of rotavirus and reverse transcription-PCR (RT-PCR) was carried out for amplification of VP7 and VP4 gene segments followed by multiplex PCR using genotype specific primers. Out of 284 children, 71 were found rotavirus positive and among them 54 % were females and 46 % males. Our findings showed 92% of infection among children ≤ 2 years of age, while, the peak age of rotavirus incidence was found to be6 to 12 months. Although, rotavirus infection was observed throughout the year but frequency increased in winter. Subtype G1P[8] was more prevalent followed by G2P[4], G3P[8] and G4P[6] subtypes. The results of the present study provide insight into the disease burden as well as information on rotavirus diversity which will be useful to develop future strategies to control and prevent diarrheal infections among children. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Munazza Fatima
- National University of Medical Sciences, Rawalpindi, Pakistan
| | | | - Deeba Amraiz
- National University of Medical Sciences, Rawalpindi, Pakistan
| | | | - Eijaz Ghani
- Armed Forces Institute of Pathology, Rawalpindi, Pakistan
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Babalola MO, Olaleye DO, Odaibo GN. Epidemiology of Group A Rotavirus Diarrhea among Children Hospitalized for Acute Gastroenteritis in Ondo State, Nigeria. JOURNAL OF CHILD SCIENCE 2021. [DOI: 10.1055/s-0040-1718543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractGlobally, infective group A rotavirus (RVA) enteric infection in children culminates in acute diarrheal disease, severe dehydration, and mortality in children under the age of 5 years, particularly in sub-Saharan Africa. This research sought to determine the prevalence of RVA diarrhea among children aged below 5 years in Ondo state, as one of the necessary frameworks before instituting a vaccine campaign, and to expand knowledge on the epidemiology of RVA diarrhea in Nigeria.In a cross-sectional descriptive study between October 2012 and September 2014, convenience sampling was adopted to obtain demographic information, clinical details, and stool samples from accented under five children who sought treatment for acute gastroenteritis at designated hospitals in Akure and Owo, Nigeria. A total of 390 stool samples were collected from children with acute diarrhea and tested for VP6 RVA antigen using enzyme immunoassay. Data generated were analyzed using descriptive statistics and chi-square at α
0.05.From the 390 children hospitalized for diarrhea, 240 samples (240/390; 61.5%) were from males, while 150 samples (150/390; 38.5%) were from females, representing a male:female ratio of 1.6:1. RVAs were found in 24.2% (58/240) males and 28% (42/150) females, giving a male-female ratio of 1:1.2 and total prevalence of 25.6% (100/390). RVA infection was inversely proportional to the age as a rate of 11.8% was observed in children aged above 36 months and 31.8% (35/110) in children 7 to 12 months, while the highest rate (45.7%) was among children ≤ 6 months old. No significant difference was found (chi-square = 0.712) in the induction of diarrhea in children from Akure and Owo, neither was there any significant difference in the rates of infection between the boys and girls in Akure (chi-square = 0.576) nor in Owo (chi-square = 0.333). Seasonal association (chi-square = 5.802) in RVA infection was observed in the rainy season of year 2013/2014 period.RVA diarrhea occurred year-round at a prevalence of 25.6%, predominantly in females. A seasonal fluctuation was observed in the rainy and dry seasons of the 2-year period. RVA diarrhea occurred predominantly in children aged below 18 months of age, and may thus help in determining the optimal period/schedule of any immunization program.
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Affiliation(s)
- Michael Oluyemi Babalola
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Microbiology, Division of Infectious Diseases Epidemiology, Virology and Special Pathogens Research, Adekunle Ajasin University, Ondo State, Nigeria
| | - David Olufemi Olaleye
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Georgina Njideka Odaibo
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Nigeria
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Khan MA. Epidemiological studies on gastroenteritis in children in the Bannu district, Khyber Pakhtunkhwa, Pakistan. JOURNAL OF PUBLIC HEALTH-HEIDELBERG 2021; 31:739-746. [PMID: 34036038 PMCID: PMC8138957 DOI: 10.1007/s10389-021-01592-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022]
Abstract
Aims Gastroenteritis is a digestive disorder among children with symptoms of abdominal cramps, diarrhoea, and vomiting. This study aimed to determine the prevalence of gastroenteritis in children in the Bannu district in 2019, and also contributed for adopting preventive measures to reduce mortality in children. Subject and methods A retrospective study was conducted to determine the prevalence of gastroenteritis in children in Bannu. The data were collected from official registers of admission maintained in the children wards in the Women and Children Hospital, Bannu. Patients with symptoms of gastroenteritis at the outpatient department were admitted to one of the children wards. Results Overall, 1456 children—897 (61.4%) males and 559 (38.6%) females—suffered from gastroenteritis during the study period. The age group ≤6 months demonstrated the highest share (37.8%), followed by >6 m ≤ 1y (35.5%), >1y ≤ 2y (15.8%), >2y ≤ 5y (7.3%), >5 ≤ 10y (3.2%), and > 10y ≤ 15y (0.4%). Overall, 89.1% of cases were from children ≤2 years old and 96.4% of cases were attributed to children ≤ 5 years of age. April demonstrated the highest percentage of prevalence of 17.7, followed by May (13.5%), November (13%), June (11.7%), September (10.4%), October (9.8%), July (9.5%), August (8.4%), March (3.4%), and February (2.6%). The age group ≤6 m was the dominant group during February through May and was replaced by the age group >6 m ≤ 1y during August through November. Conclusion Gastroenteritis showed a reduced prevalence when shifted from lower to higher age groups. Being male and age group ≤6 m showed the highest prevalence of gastroenteritis with the peak of disease in April. Further research is needed to determine the cause-based prevalence of different gastroenteritis cases in the study area.
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Affiliation(s)
- Muhammad Ashraf Khan
- Elementary and Secondary Education Department, Peshawar, Khyber Pakhtunkhwa Pakistan
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Basharat N, Sadiq A, Dawood M, Ali S, Khan A, Ullah R, Khan H, Aziz A, Ali H, Shah AA, Ali I, Khan J. Rotavirus gastroenteritis in Pakistan, 2018: updated disease burden. BMC Infect Dis 2021; 21:426. [PMID: 33957883 PMCID: PMC8103586 DOI: 10.1186/s12879-021-06123-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/28/2021] [Indexed: 11/10/2022] Open
Abstract
Objective Rotavirus A (RVA) is a significant cause of severe diarrheal illness and one of the common causes of death in children under the age of five. This study was aimed at detecting the prevalence of RVA in Pakistan after rotavirus vaccines were introduced. Fecal samples were obtained from 813 children from different hospitals in Rawalpindi and Islamabad, Pakistan, from January 2018 to December 2018. To obtain additional information from the parents / guardians of the children, a standard questionnaire was used. Results Using an enzyme-linked immunosorbent assay kit (ELISA), rotavirus antigen was detected and ELISA positive samples were subjected to reverse transcription PCR (RT-PCR). The findings showed 22% prevalence of RVA in children with acute gastroenteritis (AGE) via ELISA and 21% prevalence via RT-PCR in children with AGE. There was no statistically significant difference between gender, age and RVA infections. The winter, spring and fall/autumn seasons were statistically significant for RVA prevalence. Conclusion The present study will provide post vaccine prevalence data for the health policy makers. The implementation of rotavirus vaccines, along with adequate nutrition for babies, clean water supply and maternal hygienic activities during infant feeding, is recommended. Furthermore, continuous surveillance is mandatory in the whole country to calculate the disease burden caused by RVA.
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Affiliation(s)
- Nosheen Basharat
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Asma Sadiq
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Muhammad Dawood
- Department of Microbiology and Medical Laboratory Technology, COMWAVE Institute, Islamabad, Pakistan
| | - Shahid Ali
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Alam Khan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rooh Ullah
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hayat Khan
- Department of Microbiology, University of Swabi, Khyber Pakhtoonkhwa, Pakistan
| | - Aamir Aziz
- Institute of Biological Sciences, Sarhad University, Peshawar, Pakistan
| | - Hamid Ali
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Aamer Ali Shah
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ijaz Ali
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Jadoon Khan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
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Msolo L, Iweriebor BC, Okoh AI. Rotavirus and Cryptosporidium pathogens as etiological proxies of gastroenteritis in some pastoral communities of the Amathole District Municipality, Eastern Cape, South Africa. BMC Res Notes 2020; 13:187. [PMID: 32228662 PMCID: PMC7106725 DOI: 10.1186/s13104-020-05024-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/17/2020] [Indexed: 01/04/2023] Open
Abstract
Objective Cryptosporidium and Rotavirus agents have been associated with severe diarrheal illnesses and remain as one of the worst human health burdens in most developing regions. In the present study, we evaluated the incidences of Cryptosporidium and Rotavirus in diarrheal stool specimens of patients in some rural settlements of the Amathole District Municipality in the Eastern Cape Province, South Africa. Stool specimens from diarrheal children and elderly individuals were collected from clinics and hospitals within the rural communities of the region over a period of 21 months (February 2017–November 2018). Commercial enzyme-immuno-assays were used for the detection of Rotavirus and Cryptosporidium pathogens from processed diarrheal stool specimens. Results A total of 53 fresh stool samples from diarrheal patients were screened and 36% of the diarrheagenic stool specimens tested positive for Group A Rotavirus antigens, while 5.7% tested positive for Cryptosporidium antigens. Our findings reveal Rotavirus and Cryptosporidium pathogens as important etiological agents associated with diarrheal illnesses in children, among the rural hinterlands of the Amathole District Municipality.
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Affiliation(s)
- Luyanda Msolo
- SA-MRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Private Bag X1314, Alice, 5700, Eastern Cape, South Africa. .,Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, 5700, Eastern Cape, South Africa.
| | - Benson C Iweriebor
- Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria, Gauteng, South Africa
| | - Anthony I Okoh
- SA-MRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Private Bag X1314, Alice, 5700, Eastern Cape, South Africa.,Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, 5700, Eastern Cape, South Africa
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Sadiq A, Bokhari H, Noreen Z, Asghar RM, Bostan N. Magnitude of Rotavirus A and Campylobacter jejuni infections in children with diarrhea in Twin cities of Rawalpindi and Islamabad, Pakistan. BMC Infect Dis 2019; 19:978. [PMID: 31752744 PMCID: PMC6868847 DOI: 10.1186/s12879-019-4575-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/16/2019] [Indexed: 03/10/2023] Open
Abstract
Background Acute diarrhea is a leading cause of morbidity and mortality in children particularly in developing countries of Asia and Africa. The present study was conducted to detect the two most important pathogens, rotavirus and Campylobacter Jejuni in children suffering with diarrhea in Rawalpindi and Islamabad, Pakistan in 2014. The clinical and epidemiological aspects of the disease were also investigated. Methods A total of 500 stool samples were collected from children presented with clinical signs and symptoms of acute diarrhea. The samples were initially screened for the presence of rotavirus A (RVA) via ELISA (Enzyme-linked immunosorbent assay) and RT-PCR (Reverse Transcriptase PCR) and then were analysed for C. jejuni by using species specific PCR assay. Results The detection rate of RVA was 26.4% (132/500) while, Campylobacter was detected in 52% (260/500) of samples with C. jejuni accounted for 48.2% (241/500) of all study cases. Co-infection of C. jejuni with RVA was identified in 21.8% of all cases. Children with RVA and C. jejuni co-infection showed a higher probability (p = 0.01) to be dehydrated. A significant association (p = 0.02) was found between C. jejuni positive status and fever in children. The median age of children with both RVA and C. jejuni infection was 6–11 months. The RVA detection rate was high in winter months of the year while, C. jejuni infections were documented high in summer over 1 year study period. Conclusions The overall results have demonstrated the high prevalence of C. jejuni in Rawalpindi, Islamabad, Pakistan in 2014. The results of present study will not only help to calculate disease burden caused by C. jejuni and rotavirus but also will provide critical information to health authorities in planning public health care strategies against these pathogens.
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Affiliation(s)
- Asma Sadiq
- Department of Biosciences, COMSATS University (CUI), Tarlai Kalan, Chak Shahzad, Islamabad, 45550, Pakistan
| | - Habib Bokhari
- Department of Biosciences, COMSATS University (CUI), Tarlai Kalan, Chak Shahzad, Islamabad, 45550, Pakistan.
| | - Zobia Noreen
- Department of Biosciences, COMSATS University (CUI), Tarlai Kalan, Chak Shahzad, Islamabad, 45550, Pakistan
| | | | - Nazish Bostan
- Department of Biosciences, COMSATS University (CUI), Tarlai Kalan, Chak Shahzad, Islamabad, 45550, Pakistan.
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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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Badur S, Öztürk S, Pereira P, AbdelGhany M, Khalaf M, Lagoubi Y, Ozudogru O, Hanif K, Saha D. Systematic review of the rotavirus infection burden in the WHO-EMRO region. Hum Vaccin Immunother 2019; 15:2754-2768. [PMID: 30964372 PMCID: PMC6930073 DOI: 10.1080/21645515.2019.1603984] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Rotavirus gastroenteritis imposes a heavy burden on low- and middle-income countries. The World Health Organization defines the Eastern Mediterranean region (WHO-EMRO) as a diverse area in terms of socioeconomic status and health indicators. Rotavirus vaccination has been introduced, at least partially, in 19 out of the 22 EM countries; however, vaccine coverage remains low, and data on rotavirus disease burden is scarce.Available data on rotavirus prevalence, seasonality, vaccination status, and genotype evolution was systematically compiled following a literature review that identified 165 relevant WHO-EMRO epidemiology studies published between 1990 and 2017.Although the infectious agents responsible for acute gastroenteritis vary over time, rotavirus remained the leading cause of acute gastroenteritis in children, as seen in 76.3% of reviewed publications. Younger children (<2 years old) were at higher risk and thus increased vaccination coverage and surveillance systems are required to reduce the rotavirus gastroenteritis burden in WHO-EMRO countries.
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Affiliation(s)
- Selim Badur
- MENA, Medical & Clinical Emerging Markets, GSK, Istanbul, Turkey
| | - Serdar Öztürk
- MENA, Medical & Clinical Emerging Markets, GSK, Istanbul, Turkey
| | - Priya Pereira
- Global Medical Affairs Rota/MMRV, GSK, Wavre, Belgium
| | | | - Mansour Khalaf
- EM Central Vaccines Medical/Clinical, GSK, Jeddah, Saudi Arabia
| | - Youness Lagoubi
- EM Central Vaccines Medical/Clinical, GSK, Casablanca, Morocco
| | - Onur Ozudogru
- EM Central Vaccines Medical/Clinical, GSK, Dubai, United Arab Emirates
| | - Kashif Hanif
- EM Central Vaccines Medical/Clinical, GSK, Karachi, Pakistan
| | - Debasish Saha
- Epidemiology/Health Economics EM, GSK, Wavre, Belgium
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Almalki SSR. Circulating rotavirus G and P strains post rotavirus vaccination in Eastern Mediterranean Region. Saudi Med J 2018; 39:755-766. [PMID: 30106412 DOI: 10.15537/smj.2018.8.21394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVE To detect changes in circulating strains of rotavirus in the Eastern Mediterranean Region post rotavirus immunization drive. METHODS We searched MEDLINE, PubMed, ScienceDirect, and the Cochrane Library and specific database website (Nutrition and Food Sciences) for relevant articles. Our search included websites of a number of relevant organizations in addition to gray literature search. Of the 2198 articles found, we included only 35 studies after excluding irrelevant, ineligible, duplicated, and very low-quality papers. RESULTS Thirty pre-vaccination studies reported frequent rotavirus strains among children below 5 years of age. G1P[8] has been identified as the most dominant type prior to vaccination in Eastern Mediterranean Region (EMR) countries. Five post-vaccination studies conducted in 3 countries (Saudi Arabia, Morocco, and Yemen) illustrated that G1P[8] is the most prevalent strain in Saudi Arabia, and the incidence of G2P[4] has increased from 21.6% to 33.3%. In Yemen, G1P[4] is the most prevalent strain (87.5%), followed by G9P[8] (57%) and G1P[8] (18.5%). Furthermore, in Yemen, G9P[8] were the most prevalent strains accounting to 57% and 14% in G9P[4], post vaccination. Finally, in Morocco, G1P[8] was not reported 3 years post vaccination; however, incidence of G9P[8] was reported at 67% and G2P[4] at 33%. CONCLUSIONS Rotavirus circulating strain prevalence in EMR countries has changed post vaccination, and G9P[8], G2P[4], and G9P[4] have become more dominant. Proportion of rotavirus strains in these countries after vaccination has significantly reduced. There is an increase in circulating strain G2P[4] in the post-vaccination period, which needs further monitoring.
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Affiliation(s)
- Shaia S R Almalki
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Al Baha University, Kingdom of Saudi Arabia. E-mail.
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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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13
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High prevalence of G3 rotavirus in hospitalized children in Rawalpindi, Pakistan during 2014. PLoS One 2018; 13:e0195947. [PMID: 29708975 PMCID: PMC5927433 DOI: 10.1371/journal.pone.0195947] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/03/2018] [Indexed: 12/23/2022] Open
Abstract
Rotavirus A species (RVA) is the leading cause of severe diarrhea among children in both developed and developing countries. Among different RVA G types, humans are most commonly infected with G1, G2, G3, G4 and G9. During 2003-2004, G3 rotavirus termed as "new variant G3" emerged in Japan that later disseminated to multiple countries across the world. Although G3 rotaviruses are now commonly detected globally, they have been rarely reported from Pakistan. We investigated the genetic diversity of G3 strains responsible RVA gastroenteritis in children hospitalized in Rawalpindi, Pakistan during 2014. G3P[8] (18.3%; n = 24) was detected as the most common genotype causing majority of infections in children less than 06 months. Phylogenetic analysis of Pakistani G3 strains showed high amino acid similarity to "new variant G3" and G3 strains reported from China, Russia, USA, Japan, Belgium and Hungary during 2007-2012. Pakistani G3 strains belonged to lineage 3 within sub-lineage 3d, containing an extra N-linked glycosylation site compared to the G3 strain of RotaTeqTM. To our knowledge, this is the first report on the molecular epidemiology of G3 rotavirus strains from Pakistan and calls for immediate response measures to introduce RV vaccine in the routine immunization program of the country on priority.
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14
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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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15
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Esteves A, Nordgren J, Pereira J, Fortes F, Dimbu R, Saraiva N, Mendes C, Istrate C. Molecular epidemiology of rotavirus in four provinces of Angola before vaccine introduction. J Med Virol 2016; 88:1511-20. [DOI: 10.1002/jmv.24510] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Aida Esteves
- Global Health and Tropical Medicine (GHTM), Medical Microbiology Unit, Institute of Hygiene and Tropical Medicine; NOVA University of Lisbon; Lisbon Portugal
| | - Johan Nordgren
- Medical Faculty, Division of Molecular Virology, Department of Clinical and Experimental Medicine; Linkoping University; Linkoping Sweden
| | - Joana Pereira
- Global Health and Tropical Medicine (GHTM), Medical Microbiology Unit, Institute of Hygiene and Tropical Medicine; NOVA University of Lisbon; Lisbon Portugal
| | - Filomeno Fortes
- Department of Disease Control, National Institute of Public Health; National Program for Malaria Control; Luanda Angola
| | - Rafael Dimbu
- Department of Disease Control, National Institute of Public Health; National Program for Malaria Control; Luanda Angola
| | - Nilton Saraiva
- Department of Disease Control, National Institute of Public Health; National Program for Malaria Control; Luanda Angola
| | - Cristina Mendes
- Global Health and Tropical Medicine (GHTM), Medical Microbiology Unit, Institute of Hygiene and Tropical Medicine; NOVA University of Lisbon; Lisbon Portugal
| | - Claudia Istrate
- Global Health and Tropical Medicine (GHTM), Medical Microbiology Unit, Institute of Hygiene and Tropical Medicine; NOVA University of Lisbon; Lisbon Portugal
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16
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Azaran A, Makvandi M, Samarbafzadeh A, Neisi N, Hoseinzadeh M, Rasti M, Teymurirad M, Teimoori A, Varnaseri M, Makvandi K. Study on Rotavirus Infection and Its Genotyping in Children Below 5 Years in South West Iran. IRANIAN JOURNAL OF PEDIATRICS 2016; 26:e2080. [PMID: 27307959 PMCID: PMC4904489 DOI: 10.5812/ijp.2080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 11/11/2015] [Accepted: 11/23/2015] [Indexed: 11/16/2022]
Abstract
Background Human rotaviruses are the most important agents for severe dehydrating diarrhea in children below 5 years old. Rotaviruses (RV) is a serious public health problem in developing and developed countries. Objectives The aim of this study was to determine the prevalence of rotavirus infection and their genotypes in children younger than 5 years of age with acute diarrhea in Ahvaz, Iran. Materials and Methods For this study, 200 stool samples from children below 5 years of age with acute diarrhea were collected between October 2011 and March 2012. Initially all stool samples were tested for rotavirus antigen by ELISA, and positive samples were confirmed by RT-PCR targeting the VP6 rotavirus gene. Determination of rotavirus genotypes was carried out by performing RT-PCR for G and P types. Altogether, 15 samples were sequenced. Results Out of 200 stool samples, 100 (50%) had rotavirus antigen detected by ELISA and 73 (36.5%) were found positive by RT-PCR. Of the rotavirus strains identified, only 63 (86.3%) were positive for both VP7 and VP4 while 10 (13.7%) strains were found nontypeable. Rotavirus infection accounts for 36.5% of gastroenteritis cases in samples from symptomatic children. The most prevalent rotavirus genotypes were G1P [8] (80%) followed by G2P [4] (20%). Conclusions Our results suggest that group A rotavirus is a major pathogene of acute diarrhea in Ahvaz city. The genotypes circulating are similar with those of other countries.
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Affiliation(s)
- Azarakhsh Azaran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Manoochehr Makvandi
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
- Corresponding author: Manoochehr Makvandi, Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran; Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran. Tel: +98-6113738313, Fax: +98-6113738313, E-mail:
| | - Alireza Samarbafzadeh
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Niloofar Neisi
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Mohsen Hoseinzadeh
- Aboozar Children’s Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Mojtaba Rasti
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Majid Teymurirad
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Ali Teimoori
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Mehran Varnaseri
- Department of Infectious, Razi Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Kamyar Makvandi
- School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
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17
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Collins P, Mulherin E, O'Shea H, Cashman O, Lennon G, Pidgeon E, Coughlan S, Hall W, Fanning S. Changing patterns of rotavirus strains circulating in Ireland: Re-emergence of G2P[4] and identification of novel genotypes in Ireland. J Med Virol 2015; 87:764-73. [DOI: 10.1002/jmv.24095] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2014] [Indexed: 11/06/2022]
Affiliation(s)
- P.J. Collins
- Department of Biological Sciences; Cork Institute of Technology; Cork Ireland
| | - Emily Mulherin
- UCD-Centre for Food Safety; School of Public Health; Physiotherapy and Population Science; Dublin Ireland
| | - Helen O'Shea
- Department of Biological Sciences; Cork Institute of Technology; Cork Ireland
| | - Olivia Cashman
- Department of Biological Sciences; Cork Institute of Technology; Cork Ireland
| | - Grainne Lennon
- Department of Biological Sciences; Cork Institute of Technology; Cork Ireland
| | - Eugene Pidgeon
- National Virus Reference Laboratory; University College Dublin; Dublin Ireland
| | - Suzie Coughlan
- National Virus Reference Laboratory; University College Dublin; Dublin Ireland
| | - William Hall
- National Virus Reference Laboratory; University College Dublin; Dublin Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety; School of Public Health; Physiotherapy and Population Science; Dublin Ireland
- School of Veterinary Medicine; University College Dublin; Dublin Ireland
- Institute for Global Food Security; Queen's University Belfast; Belfast Ireland
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18
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Alam MM, Khurshid A, Shaukat S, Sharif S, Suleman RM, Angez M, Nisar N, Aamir UB, Naeem M, Zaidi SSZ. 'Human bocavirus in Pakistani children with gastroenteritis'. J Med Virol 2015; 87:656-63. [PMID: 25611467 DOI: 10.1002/jmv.24090] [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] [Accepted: 10/01/2014] [Indexed: 12/20/2022]
Abstract
Human Bocaviruses (HBoV) have been detected in human respiratory and gastrointestinal infections worldwide. Four genotypes of HBoV (HBoV1-4) have been described; HBoV-1 is associated with respiratory tract infections while HBoV-2, -3, and -4 genotypes are considered as entero-pathogenic although the exact role largely remains unclear. The global prevalence of HBoV has been reported, but the epidemiological data from Pakistan is largely unavailable to date. This study was conducted to understand the genetic diversity and disease prevalence of HBoV in hospitalized Pakistani children with acute diarrhea. During 2009, a total of 365 stool samples were collected from children hospitalized with gastrointestinal symptoms (as per WHO case definitions) at Rawalpindi General Hospital, Pakistan. Demographic and clinical data were recorded using a standardized questionnaire. The samples were tested for HBoV and rotavirus using real-time RT-PCR and ELISA, respectively. There were 47 (13%) samples positive for HBoV with 98% (n = 46) showing co-infection with rotavirus. HBoV-1 was the most frequently detected and was found in 94% samples followed by HBoV-2 and HBoV-3 genotypes. The mean age of infected children was 7.57 ± 5.4 months while detection was more frequent in males (n = 32, 68%). All cases recovered after 2.43 ± 1.0 mean days of treatment. On phylogenetic analysis, HBoV strains from Pakistan clustered closely with viruses from neighboring Bangladesh and China. These findings represent the first known epidemiological study in Pakistan to investigate the role of HBoV in acute gastroenteritis. The clinical data demonstrates that HBoV is not significantly associated with gastroenteritis alone and predominantly co-infections with rotavirus are found.
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Affiliation(s)
- Muhammad Masroor Alam
- Department of Virology, National Institute of Health, Islamabad, Pakistan; Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
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19
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Alam MM, Khurshid A, Shaukat S, Rana MS, Sharif S, Angez M, Nisar N, Aamir UB, Naeem M, Zaidi SSZ. Viral etiologies of acute dehydrating gastroenteritis in pakistani children: confounding role of parechoviruses. Viruses 2015; 7:378-93. [PMID: 25609308 PMCID: PMC4306844 DOI: 10.3390/v7010378] [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: 10/28/2014] [Accepted: 01/16/2015] [Indexed: 11/22/2022] Open
Abstract
Despite substantial interventions in the understanding and case management of acute gastroenteritis, diarrheal diseases are still responsible for a notable amount of childhood deaths. Although the rotavirus is known to cause a considerable burden of pediatric diarrheal cases, the roles of other viruses remain undefined for the Pakistani population. This study was based on tertiary care hospital surveillance, from January 2009 to December 2010, including the detection of rotavirus, norovirus, astrovirus, and human parechovirus in children under the age of five using serological or molecular assays. Rotavirus, human parechovirus, norovirus, and astrovirus were detected in 66%, 21%, 19.5%, and 8.5% subjects, respectively. Human parechovirus genotypes, determined through analysis of VP1 gene sequences, showed a great diversity among co-circulating strains. Eighty percent of hospitalized children had dual or multiple viral infections, while 98% parechovirus positive cases were co-infected with rotavirus. The remarkable diversity of viruses associated with the childhood diarrhea in Pakistan calls for large-scale epidemiological surveys, coupled with case control studies, to ascertain their role in clinical manifestations. In addition, these findings also highlight the need for the implementation of up-to-date health interventions, such as the inclusion of a rotavirus vaccine in routine immunization programs for the improvement of quality in child health care.
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Affiliation(s)
| | - Adnan Khurshid
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan.
| | - Shahzad Shaukat
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan.
| | - Muhammad Suleman Rana
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan.
| | - Salmaan Sharif
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan.
| | - Mehar Angez
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan.
| | - Nadia Nisar
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan.
| | - Uzma Bashir Aamir
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan.
| | - Muhammad Naeem
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Syed Sohail Zahoor Zaidi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 44000, Pakistan.
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20
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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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Kim JS, Kim HS, Hyun J, Kim HS, Song W, Lee KM, Shin SH. Analysis of rotavirus genotypes in Korea during 2013: an increase in the G2P[4] genotype after the introduction of rotavirus vaccines. Vaccine 2014; 32:6396-402. [PMID: 25312273 DOI: 10.1016/j.vaccine.2014.09.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 09/18/2014] [Accepted: 09/29/2014] [Indexed: 01/15/2023]
Abstract
BACKGROUND Group A rotavirus is the leading cause of acute gastroenteritis in children worldwide. We investigated G and P genotypes of group A rotavirus strains isolated from patients during 2013 and investigated which genotypes were identified from vaccinated patients. METHODS From January to December 2013, 2235 fecal specimens were tested for rotavirus antigen, of which 374 specimens (16.7%) showed positive results. Strains from 288 rotavirus-positive specimens were genotyped using PCR and sequencing, and individual patients' corresponding vaccine histories were investigated through the Korean Center for Disease Control website. RESULTS G2 (22.6%) and P[4] (24.0%) were the most frequently identified G and P genotypes, respectively; accordingly, G2P[4] (19.8%) was the most prevalent G/P genotype observed in this period. G4P[6] (10.1%) was the second most prevalent G/P genotype and was mostly detected in neonates. Other genotypes, G1P[8], G9P[8], G1P[6], and G3P[6], were also detected. Of 288 rotavirus-positive specimens, 48 specimens were obtained from previously vaccinated patients. G2P[4] was also the genotype most frequently isolated from vaccinated patients. VP7 epitope analysis of G1P[8] and G2P[4] strains showed at least one amino acid differences in comparison with Rotarix and RotaTeq vaccine strains. The genotypic distribution of rotavirus strains in Korea has been shown temporal and geographical differences. CONCLUSION This study showed that G2P[4] was the genotype most frequently isolated from both vaccinated and unvaccinated patients in Korea during 2013. However, it is unclear whether the change of predominant genotype is due to the effect of vaccination or due to natural variation.
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Affiliation(s)
- Jae-Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea.
| | - Jungwon Hyun
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea
| | - Han-Sung Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea
| | - Kyu Man Lee
- Department of Laboratory Medicine, Hallym University College of Medicine, Republic of Korea
| | - Seon-Hee Shin
- Department of Pediatrics, Hallym University College of Medicine, Republic of Korea
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22
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Kazi AM, Warraich GJ, Qureshi S, Qureshi H, Khan MMA, Zaidi AKM. Sentinel hospital-based surveillance for assessment of burden of rotavirus gastroenteritis in children in Pakistan. PLoS One 2014; 9:e108221. [PMID: 25295613 PMCID: PMC4189951 DOI: 10.1371/journal.pone.0108221] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 08/27/2014] [Indexed: 01/01/2023] Open
Abstract
Objectives To determine the burden and molecular epidemiology of rotavirus gastroenteritis in children hospitalized with severe acute watery diarrhea in Pakistan prior to introduction of rotavirus vaccine. Methods A cross-sectional study was carried out over a period of two years from 2006 – 2008 at five sentinel hospitals in the cities of Karachi, Lahore, Rawalpindi, and Peshawar. Stool samples collected from children under five years of age hospitalized with severe acute watery diarrhea were tested for rotavirus antigen via enzyme immunoassay (EIA) (IDEA REF K6020 Oxoid Ltd (Ely), Cambridge, United Kingdom). A subset of EIA positive stool samples were further processed for genotyping. Results 6679 children were enrolled and stool specimens of 2039 (30.5%) were positive for rotavirus. Rotavirus positivity ranged from 16.3% to 39.4% in the 5 hospitals with highest positivity in Lahore. 1241 (61%) of all rotavirus cases were in infants under one year of age. Among the strains examined for G-serotypes, the occurrence of G1, G2, G9 and G4 strains was found to be 28%, 24%, 14% and 13%, respectively. Among P-types, the most commonly occurring strains were P6 (31.5%) followed by P8 (20%) and P4 (12%). Prevalent rotavirus genotype in hospitalized children of severe diarrhea were G1P[8] 11.6% (69/593), followed by G2P[4] 10.4% (62/593), and G4P[6] 10.1% (60/593). Conclusions Approximately one third of children hospitalized with severe gastroenteritis in urban centers in Pakistan have rotavirus. Introduction of rotavirus vaccine in Pakistan's national immunization program could prevent many severe episodes and diarrheal deaths.
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Affiliation(s)
| | | | | | - Huma Qureshi
- Pakistan Medical Research Council, Islamabad, Pakistan
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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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Dhingra M, Kundu R, Gupta M, Kanungo S, Ganguly N, Singh M, Bhattacharya M, Ghosh R, Kumar R, Sur D, Chadha S, Saluja T. Evaluation of safety and immunogenicity of a live attenuated tetravalent (G1–G4) Bovine-Human Reassortant Rotavirus vaccine (BRV-TV) in healthy Indian adults and infants. Vaccine 2014; 32 Suppl 1:A117-23. [DOI: 10.1016/j.vaccine.2014.03.069] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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