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Kachooei A, Mirhoseinian M, Jalilvand S, Latifi T, Feizi M, Shahosseini Z, Arashkia A, Marashi SM, Shoja Z. Molecular characterization of human astrovirus infection in children under 5 years of age with acute gastroenteritis in Tehran, Iran, 2021-2022: co-infection with rotavirus. Virus Genes 2024; 60:357-369. [PMID: 38744749 DOI: 10.1007/s11262-024-02075-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024]
Abstract
Human astroviruses (HAstVs) are considered important causative pathogens of acute gastroenteritis (AGE) in children under 5 years of age worldwide, along with group A rotavirus (RVA), norovirus (NoV), and enteric adenovirus (EAdV). The present study was aimed to both detect HAstV and its co-infections and investigate genetic analysis of circulating HAstV and co-infected virus in hospitalized children under 5 years of age with AGE in Iran. Accordingly, a sum of 200 stool specimens were screened by PCR for HAstV during 2021-2022. The HAstV was found in 0.5% of 200 specimens (n = 1) while was co-infected with RVA. The genetic and phylogenetic analysis indicated HAstV1 genotype, which clustered with viruses from lineage 1b, which has not been previously reported in Iran. The detected RVA strain belonged to G1 lineage II/P[8]-lineage III, which has been reported previously in Iran as the most common strain. The further genetic analysis of RVA VP6 and NSP4 demonstrated an atypical genotype pattern G1P[8]-I1-E2, as a mono-reassortant of a Wa-like genogroup, which appeared to be reassorted with the NSP4 gene of E2 genotype of the G2P[4] DS-1 genogroup. Although the clinical outcomes of the AGE-causing viruses co-infection is not yet entirely clear, it seems that future studies will be helpful to merge clinical and epidemiological data of co-infecting viruses for a more accurate medical and clinical relevance in symptomatic children.
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Affiliation(s)
- Atefeh Kachooei
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahtab Mirhoseinian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Tayebeh Latifi
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Mahsa Feizi
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Arash Arashkia
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Sayed Mahdi Marashi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran.
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.
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Zhang P, Hao C, Di X, Chuizhao X, Jinsong L, Guisen Z, Hui L, Zhaojun D. Global prevalence of norovirus gastroenteritis after emergence of the GII.4 Sydney 2012 variant: a systematic review and meta-analysis. Front Public Health 2024; 12:1373322. [PMID: 38993708 PMCID: PMC11236571 DOI: 10.3389/fpubh.2024.1373322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/30/2024] [Indexed: 07/13/2024] Open
Abstract
Introduction Norovirus is widely recognized as a leading cause of both sporadic cases and outbreaks of acute gastroenteritis (AGE) across all age groups. The GII.4 Sydney 2012 variant has consistently prevailed since 2012, distinguishing itself from other variants that typically circulate for a period of 2-4 years. Objective This review aims to systematically summarize the prevalence of norovirus gastroenteritis following emergence of the GII.4 Sydney 2012 variant. Methods Data were collected from PubMed, Embase, Web of Science, and Cochrane databases spanning the period between January 2012 and August 2022. A meta-analysis was conducted to investigate the global prevalence and distribution patterns of norovirus gastroenteritis from 2012 to 2022. Results The global pooled prevalence of norovirus gastroenteritis was determined to be 19.04% (16.66-21.42%) based on a comprehensive analysis of 70 studies, which included a total of 85,798 sporadic cases with acute gastroenteritis and identified 15,089 positive cases for norovirus. The prevalence rate is higher in winter than other seasons, and there are great differences among countries and age groups. The pooled attack rate of norovirus infection is estimated to be 36.89% (95% CI, 36.24-37.55%), based on a sample of 6,992 individuals who tested positive for norovirus out of a total population of 17,958 individuals exposed during outbreak events. Conclusion The global prevalence of norovirus gastroenteritis is always high, necessitating an increased emphasis on prevention and control strategies with vaccine development for this infectious disease, particularly among the children under 5 years old and the geriatric population (individuals over 60 years old).
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Affiliation(s)
- Pan Zhang
- College of Public Health, Gansu University of Traditional Chinese Medicine, Lanzhou, Gansu, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infection Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Cai Hao
- College of Public Health, Gansu University of Traditional Chinese Medicine, Lanzhou, Gansu, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infection Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xie Di
- Chengdu Kanghua Biological Products Co., Ltd., Chengdu, China
| | - Xue Chuizhao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China
| | - Li Jinsong
- National Key Laboratory of Intelligent Tracking and Forecasting for Infection Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zheng Guisen
- College of Public Health, Gansu University of Traditional Chinese Medicine, Lanzhou, Gansu, China
| | - Liu Hui
- Chengdu Kanghua Biological Products Co., Ltd., Chengdu, China
| | - Duan Zhaojun
- National Key Laboratory of Intelligent Tracking and Forecasting for Infection Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Eftekhari M, Kachooei A, Jalilvand S, Latifi T, Habib Z, Ataei-Pirkoohi A, Marashi SM, Shoja Z. The predominance of recombinant Norovirus GII.4Sydney[P16] strains in children less than 5 years of age with acute gastroenteritis in Tehran, Iran, 2021-2022. Virus Res 2023; 334:199172. [PMID: 37459917 PMCID: PMC10388203 DOI: 10.1016/j.virusres.2023.199172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023]
Abstract
The present study was aimed to both detect emerging noroviruses and investigate RdRp and VP1-based dual typing of circulating noroviruses in hospitalized children less than 5 years of age with acute gastroenteritis (AGE) in Iran. For this purpose, a total of 200 stool specimens were screened during 2021-2022 by real-time RT-PCR for genogroup I and II (GI and GII) and dual-typed by sequence analysis of PCR products, using a web-based norovirus Typing Tool and phylogenetic analysis. The GI and GII noroviruses were detected in 20% of 200 specimens. The GII.4 norovirus was found to be the most common VP1 genotype (53%) followed by GII.8 (32%), GII.7 (6%), GII.17 (6%), and GII.3 (3%). The GII.P16 norovirus was also found as the predominant RdRp type (53%) followed by GII.P8 (32%), GII.P7 (6%), GII.P17 (6%), and GII.P31 (3%). To our knowledge, this is the first report that highlights the dominancy of recombinant norovirus GII.4Sydney[P16] and newly emerging of norovirus GII.8 [P8], GII.17 [P17] and GII.3 [P16] in Iran. These findings further indicate inter-genotype recombinant strains of noroviruses.
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Affiliation(s)
- Mahtab Eftekhari
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Atefeh Kachooei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Tayebeh Latifi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Habib
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Angila Ataei-Pirkoohi
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sayed Mahdi Marashi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran; Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.
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Elbashir I, Aldoos NF, Mathew S, Al Thani AA, Emara MM, Yassine HM. Molecular epidemiology, genetic diversity, and vaccine availability of viral acute gastroenteritis in the middle East and North Africa (MENA) region. J Infect Public Health 2022; 15:1193-1211. [PMID: 36240530 DOI: 10.1016/j.jiph.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022] Open
Abstract
Acute gastroenteritis is the cause of considerable mortality and morbidity worldwide, particularly among children under five years in underdeveloped countries. Most acute gastroenteritis (AGE) cases are attributed to viral etiologies, including rotavirus, norovirus, adenovirus, astrovirus, and sapovirus. This paper aimed to determine the prevalence rate of different viral etiologies of AGE in the Middle East and North Africa (MENA) region. Moreover, this paper explored rotavirus phylogenetic relatedness, compared VP7 and VP4 antigenic regions of rotavirus with vaccine strains, and explored the availability of vaccines in the MENA region. The literature search identified 160 studies from 18 countries from 1980 to 2019. The overall prevalence of rotavirus, norovirus, adenovirus, astrovirus, and sapovirus were 29.8 %, 13.9 %, 6.3 %, 3.5 %, and 3.2 % of tested samples, respectively. The most common rotavirus genotype combinations in the MENA region were G1P[8], G9P[9], and G2P[4], whereas GII.4 was the predominant norovirus genotype all of which were reported in almost all the studies with genotyping data. The comparison of VP7 and VP4 between circulating rotavirus in the MENA region and vaccine strains has revealed discrete divergent regions, including the neutralizing epitopes. Rotavirus vaccine was introduced to most of the countries of the MENA region; however, only a few studies have assessed the effectiveness of vaccine introduction. This paper provides a comprehensive update on the prevalence of the different viral agents of AGE in the MENA region.
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Affiliation(s)
- Israa Elbashir
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
| | - Noor F Aldoos
- Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.
| | - Shilu Mathew
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
| | - Asmaa A Al Thani
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar; Department of Biomedical Sciences, College of Health Science-QU Health, Qatar University, Doha 2713, Qatar
| | - Mohamed M Emara
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar.
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
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Li W, Yan H, Liu B, Tian Y, Chen Y, Jia L, Gao Z, Wang Q. Epidemiological characteristics and genetic diversity of norovirus infections among outpatient children with diarrhea under 5 years of age in Beijing, China, 2011-2018. Gut Pathog 2021; 13:77. [PMID: 34952625 PMCID: PMC8709959 DOI: 10.1186/s13099-021-00473-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background Human noroviruses are the leading cause of sporadic cases and outbreaks of viral acute gastroenteritis in all age groups worldwide. Methods Epidemiological data and fecal specimens were collected between January 2011 and December 2018 from 4911 children < 5 years of age with diarrhea in three districts of Beijing. From 2011 to 2013, One-Step Reverse Transcription Polymerase Chain Reaction (RT-PCR) was used to detect noroviruses, and from January 2014 to December 2018, norovirus GI and GII were screened using duplex quantitative real-time RT-PCR (qRT-PCR). One-Step RT-PCR and RT-seminested PCR were performed to amplify the RNA-dependent polymerase and capsid genes of noroviruses in positive sample. Amplified products were sequenced directly; norovirus was typed using the online Norovirus Genotyping Tool v2.0 and phylogenetic analyses were conducted using MEGA-X. Results From 2011 to 2018, noroviruses were detected in 16.5% of specimens from children with diarrhea. The highest prevalence was observed in children aged 12 to 23 months (22.4%, 319/1421), followed by children aged 6 to 11 months (17.6%, 253/1441). The highest prevalence of norovirus infections occurred in autumn followed by winter, spring, and summer. From 2011 to 2018, the most prevalent dual types (genotype and polymerase type) were GII.4 Sydney[P31] (51.6%, 239/463), followed by GII.3[P12] (24.0%, 111/463), GII.4 2006b[P4 2006b] (7.3%, 34/463), GII.2[P16] (5.0%, 23/463), GII.17[P17] (2.6%, 12/463) and GII.6[P7] (2.6%, 12/463). GII.4 2006b[P4 2006b] predominated in 2011 and 2012. GII.4 Sydney[P31] predominated from 2013 to 2018. In total, 15 genotypes, 15 P-types and 19 dual types were detected in this study, reflecting the genetic diversity. Conclusions There were significant epidemiological characteristics and genetic diversity among outpatient children with norovirus infections < 5 years of age in Beijing from 2011 to 2018. These characteristics differ from those of norovirus outbreaks in Beijing. The complete genome sequences of each genotype are needed to better understand norovirus evolutionary mechanisms.
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Affiliation(s)
- Weihong Li
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Hanqiu Yan
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Baiwei Liu
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Yi Tian
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Yanwei Chen
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Lei Jia
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China
| | - Zhiyong Gao
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China.
| | - Quanyi Wang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control and Beijing Research Center for Preventive Medicine, Beijing, China.
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Farahmand M, Moghoofei M, Dorost A, Shoja Z, Ghorbani S, Kiani SJ, Khales P, Esteghamati A, Sayyahfar S, Jafarzadeh M, Minaeian S, Khanaliha K, Naghdalipour M, Tavakoli A. Global prevalence and genotype distribution of norovirus infection in children with gastroenteritis: A meta-analysis on 6 years of research from 2015 to 2020. Rev Med Virol 2021; 32:e2237. [PMID: 33793023 DOI: 10.1002/rmv.2237] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022]
Abstract
In the post rotavirus vaccine era, norovirus (NoV) plays an increasingly important role in epidemic and sporadic gastroenteritis among children. This study was designed to provide an updated meta-analytic review of the prevalence of NoV among paediatric patients with gastroenteritis and to clarify the relationship between NoV infection and gastroenteritis. Systematic searches of the literature for potentially relevant studies were carried out from 1 January 2015 to 29 May 2020. The inverse variance method was chosen for weighting of the studies, and the random-effects model was used to analyse data. To determine the association between NoV infection and gastroenteritis in children, pooled odds ratio (OR) and its 95% confidence interval (CI) were computed for case-control studies. The pooled prevalence of NoV infection among 12,0531 children with gastroenteritis from 45 countries across the world was 17.7% (95% CI: 16.3%-19.2%). There were 28 studies with a case-control design, and the pooled prevalence of NoV infection among 11,954 control subjects was 6.7% (95% CI: 5.1%-8.8%). The pooled OR of the association of NoV infection and gastroenteritis was 2.7 (95% CI: 2.2-3.4). The most common NoV genotypes were GII.4 (59.3%) and GII.3 (14.9%). The highest frequency of NoV was found in the age group below 1 year. Our findings indicated a substantial burden of gastroenteritis caused by NoV globally, with GII.4 and GII.3 the major genotypes responsible for the majority of NoV-associated gastroenteritis cases among children. Younger age and male sex can be considered risk factors for NoV-associated gastroenteritis among children.
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Affiliation(s)
- Mohammad Farahmand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abolfazl Dorost
- Department of Health Economics and Management, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Saied Ghorbani
- Department of Medical Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Jalal Kiani
- Department of Medical Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Pegah Khales
- Department of Medical Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Abdoulreza Esteghamati
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Shirin Sayyahfar
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Mehrzad Jafarzadeh
- Institute of Endocrinology and Metabolism Research and Training Center, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Minaeian
- Antimicrobial Resistance Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Khanaliha
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Mehri Naghdalipour
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Tavakoli
- Department of Medical Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
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Farahmand M, Jalilvand S, Arashkia A, Izadi A, Forouzannia SM, Mollaei-Kandelous Y, Shoja Z. Estimation of genetic variation in the Secretor and Lewis genes in Iranian hospitalized children. Transfus Clin Biol 2021; 28:11-15. [PMID: 33301983 DOI: 10.1016/j.tracli.2020.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND The Secretor (FUT2) and lewis gene (FUT3) are in charge of the construction of histo-blood group antigens, which act as a receptor for some Pathogenes. This study aimed to estimate the prevalence of five significant single nucleotide polymorphisms (SNPs) in Iranian children. METHODS In this cross-sectional study, 102 blood samples collected from hospitalized children. The FUT2 gene region was amplified and sequenced to explore rs1047781 and rs601338, and the FUT3 gene region was amplified to explore rs28362459, rs812936, rs778986 SNPs. RESULTS In FUT2 gene, Se358,428 that produces Se phenotype with 63% (0.53 - 0.72) prevalence, was the most common genotype. For FUT3 gene Le59,202,314 with 80% prevalence was most common genotype (0.71 - 0.87). CONCLUSION This study genotyped Secretor and Lewis genes and designated SNPs' distinct distribution in Iran, and clarified at-risk groups for certain diseases.
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Affiliation(s)
- Mohammad Farahmand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Arash Arashkia
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Anahita Izadi
- Department of Pediatric Infectious diseases, Bahrami Children Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | - Zabihollah Shoja
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran.
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Lu L, Zhong H, Xu M, Su L, Cao L, Jia R, Xu J. Genetic diversity and epidemiology of Genogroup II noroviruses in children with acute sporadic gastroenteritis in Shanghai, China, 2012-2017. BMC Infect Dis 2019; 19:736. [PMID: 31438883 PMCID: PMC6704660 DOI: 10.1186/s12879-019-4360-1] [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: 05/10/2019] [Accepted: 08/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Noroviruses (NoVs) are considered an important cause of acute gastroenteritis (AGE) across all age groups, especially in children under 5 years of age. We investigated the epidemiology of noroviruses in outpatient children from the Children's Hospital of Fudan University in Shanghai, China. METHODS Stool specimens were collected between January 2012 and December 2017 from 1433 children under 5 years of age with acute gastroenteritis. All samples were analysed by conventional reverse transcription-polymerase chain reaction (RT-PCR) for genogroup II NoVs amplifying both the RNA-dependent RNA polymerase (RdRp) and partial capsid genes. The Norovirus Genotyping Tool v.2.0 ( https://www.rivm.nl/mpf/typingtool/norovirus/ ) was used for genotyping the strains, and phylogenetic analyses were conducted by MEGA 6.0. RESULTS From 2012 to 2017, GII NoVs were detected in 15.4% (220/1433) of the samples, with the highest detection rate in children aged 7-12 months (19.2%, 143/746). The seasons with the highest prevalence of GII NoVs infection were autumn and winter. Based on genetic analysis of RdRp, GII.Pe (74.5%%, 137/184) was the most predominant RdRp genotype from 2013 to 2017, while GII.P4 played a dominant role in 2012 (55.6%, 21/36). Among the capsid genotypes, the most prevalent NoV genotype from 2012 to 2017 was GII.4 (74.1%, 163/220). On the basis of genetic analysis of RdRp and capsid sequences, the strains were clustered into - 19 RdRp/capsid genotypes, and 12 of them were discordant, such as GII.Pe/GII.4-Sydney_2012, GII.P12/GII.3, GII.P7/GII.6, GII.Pe/GII.3, and GII.P16/GII.2. Starting with 2013, GII.Pe/GII.4-Sydney_2012 had completely replaced the pandemic GII.P4-2006b/GII.4-2006b subtype and was detected in children across all age groups. CONCLUSIONS The present study shows high detection rates and the genetic diversity of circulating NoV GII genotypes in paediatric AGE samples from Shanghai. The findings emphasize the importance of continuous molecular surveillance of emerging NoV strains.
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Affiliation(s)
- Lijuan Lu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Huaqing Zhong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Menghua Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Liyun Su
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Lingfeng Cao
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Ran Jia
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China.
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Arashkia A, Bahrami F, Farsi M, Nejati B, Jalilvand S, Nateghian A, Rahbarimanesh A, Shoja Z. Molecular analysis of human adenoviruses in hospitalized children <5 years old with acute gastroenteritis in Tehran, Iran. J Med Virol 2019; 91:1930-1936. [PMID: 31283018 DOI: 10.1002/jmv.25539] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 07/03/2019] [Indexed: 12/28/2022]
Abstract
Human adenoviruses (HAdVs), especially AdV-40 and 41, are common causes of nonbacterial sporadic and outbreak gastroenteritis in children. The present study aimed to describe the frequency and genetic analysis of HAdVs in hospitalized children <5 years old with acute gastroenteritis. A total of 376 stool samples obtained from June 2015 to December 2017 were investigated for the presence of HAdVs by polymerase chain reaction. The HAdV DNA was detected in 16 (4.3%) out of 376 stool samples. Based on the hexon hypervariable region (HVR), B, C, and F HADV species including five types HAdV-1, 2, 3, 6, and 41 were identified, among which enteric AdV species F (EAdV-41) was the most dominant. Moreover, our findings showed the presence of genomic type cluster 1 (GTC1) pattern in Iranian type 41 strains, which was closely similar to the D1 prototype strain (Tak) and D28. In this regard, a recombination was found in AdV-41 strains presenting the hexon sequence that belonged to GTC1, while fiber sequence clustered with GTC2.
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Affiliation(s)
- Arash Arashkia
- Virology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Ferial Bahrami
- Virology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Mahsa Farsi
- Biology Department, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
| | - Behrooz Nejati
- Biology Department, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
| | - Somayeh Jalilvand
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Nateghian
- Ali-Asghar Children's Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Aliakbar Rahbarimanesh
- Department of Pediatric Infectious Diseases, Bahrami Children Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Muhsen K, Kassem E, Rubenstein U, Goren S, Ephros M, Shulman LM, Cohen D. No evidence of an increase in the incidence of norovirus gastroenteritis hospitalizations in young children after the introduction of universal rotavirus immunization in Israel. Hum Vaccin Immunother 2019; 15:1284-1293. [PMID: 30945960 DOI: 10.1080/21645515.2019.1599522] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Following the introduction of universal immunization against rotavirus, concerns were raised regarding pathogen-replacement of rotavirus by norovirus. The study aim was to examine the incidence and characteristics and norovirus gastroenteritis before and after the introduction of universal rotavirus immunization in Israel. We studied 1179 stool samples collected between November 2007 and December 2014 for a prospective hospital-based surveillance study of children aged 0-59 months hospitalized for gastroenteritis. A real-time RT-PCR assay was used to identify genogroup II (GII) norovirus in extracted fecal RNA samples. Overall, the weighted percentage of norovirus positive patients was 10.9%. Norovirus positivity was similar in the pre-universal rotavirus immunisation years (2008-2010) and the universal years (2011-2014), the respective average annual incidence of norovirus gastroenteritis was 1.6 (95% CI 0.6-2.3) per 1000 and 1.1 (95% CI 0.8-1.4) per 1000 children. Rotavirus was detected in 36.8% and 19.6% of the patients in the pre-vaccine years and the universal vaccine years, with an estimated incidence of 5.5 (95% CI 3.4-7.6) per 1000 and 2.1 (95% CI 1.6-2.7) per 1000 children, respectively. Most patients (59.1%) with norovirus gastroenteritis were infants aged 0-11 months. Norovirus was detected all year round with a significant 3-month peak from September through November. In conclusion, norovirus continues to be a leading cause of acute gastroenteritis associated with hospitalizations in young children. Future norovirus vaccines should target young infants. There was no evidence of pathogen-replacement by norovirus following the introduction of universal rotavirus immunization in Israel.
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Affiliation(s)
- Khitam Muhsen
- a Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine , Tel Aviv University , Ramat Aviv, Tel Aviv , Israel
| | - Eias Kassem
- b Department of Pediatrics , Hillel Yaffe Medical Center , Hadera , Israel
| | - Uri Rubenstein
- c Department of Pediatrics , Laniado Medical Center , Netanya , Israel
| | - Sophy Goren
- a Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine , Tel Aviv University , Ramat Aviv, Tel Aviv , Israel
| | - Moshe Ephros
- d Department of Pediatrics , Carmel Medical Center , Haifa , Israel.,e Faculty of Medicine , Technion-Israel Institute of Technology , Haifa , Israel
| | - Lester M Shulman
- a Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine , Tel Aviv University , Ramat Aviv, Tel Aviv , Israel.,f Central Virology Laboratory , Ministry of Health , Tel Hashomer , Israel
| | - Dani Cohen
- a Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine , Tel Aviv University , Ramat Aviv, Tel Aviv , Israel
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Recombinant GII.P16/GII.4 Sydney 2012 Was the Dominant Norovirus Identified in Australia and New Zealand in 2017. Viruses 2018; 10:v10100548. [PMID: 30304780 PMCID: PMC6213408 DOI: 10.3390/v10100548] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/05/2018] [Accepted: 10/06/2018] [Indexed: 01/16/2023] Open
Abstract
For the past two decades, norovirus pandemic variants have emerged every 3–5 years, and dominate until they are replaced by alternate strains. However, this scenario changed in 2016 with the co-circulation of six prevalent viruses, three of which possessed the pandemic GII.4 Sydney 2012 capsid. An increased number of institutional gastroenteritis outbreaks were reported within the Oceania region in mid-2017. This study identified emerging noroviruses circulating in Australia and New Zealand in 2017 to assess the changing dynamics of the virus infection. RT-PCR-based methods, next generation sequencing, and phylogenetic analyses were used to genotype noroviruses from both clinical and wastewater samples. Antigenic changes were observed between the capsid of pandemic Sydney 2012 variant and the two new Sydney recombinant viruses. The combination of these antigenic changes and the acquisition of a new ORF1 through recombination could both facilitate their ongoing persistence in the population. Overall, an increased prevalence of GII.P16/GII.4 Sydney 2012 viruses was observed in 2017, replacing the GII.P16/GII.2 recombinant that dominated in the region at the end of 2016. This shift in strain dominance was also observed in wastewater samples, demonstrating the reliability of wastewater as a molecular surveillance tool.
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