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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 2024:10.1007/s11262-024-02075-6. [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] [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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Li J, Yang L, Wang K, Gao Z, Li P, Lin Y, Jia L, Wang Q, Song H, Li P. Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols. Virol J 2023; 20:263. [PMID: 37964283 PMCID: PMC10647158 DOI: 10.1186/s12985-023-02224-7] [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: 06/16/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023] Open
Abstract
Human astroviruses (HAstV) are etiologic agents of acute gastroenteritis that most often afflict young children and elderly adults. Most studies of HAstV have focused on epidemiology. In this study, we collected 10 stool samples from a diarrhea outbreak from a diarrhea sentinel surveillance hospital in Beijing. Samples were evaluated immediately using parallel multiplex RT-qPCR and nanopore sequencing, and were then amplified by designed primers and Sanger sequencing to obtain whole genome sequences. Six isolates were categorized as HAstV-5 and subjected to whole genome analysis to characterize their genetic variation and evolution. Full genome analysis revealed low genetic variation (99.38-100% identity) among isolates. Phylogenetic analysis showed that all isolates were closely related to domestic strains Yu/1-CHN and 2013/Fuzhou/85. The recombination breakpoint of the six isolates was located at 2741 bp in the overlap region of ORF1a and ORF1b, similar to those of Yu/1-CHN and 2013/Fuzhou/85. Overall, our study highlights the combined use of RT-qPCR and sequencing as an important tool in rapid diagnosis and acquisition of whole genome sequences of HAstV.
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Affiliation(s)
- Jinhui Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Lang Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kaiying Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Zhiyong Gao
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Peihan Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Yanfeng Lin
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Leili Jia
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing, China.
| | - Hongbin Song
- Chinese PLA Center for Disease Control and Prevention, Beijing, China.
| | - Peng Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China.
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Lu L, Zhong H, Xu M, Jia R, Liu P, Su L, Cao L, Zhu X, Xu J. Diversity of classic and novel human astrovirus in outpatient children with acute gastroenteritis in Shanghai, China. Front Microbiol 2023; 14:1265843. [PMID: 38029144 PMCID: PMC10679754 DOI: 10.3389/fmicb.2023.1265843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Human astrovirus (HAstV) is an important pathogen of acute gastroenteritis (AGE) in children. This study was aimed at investigating the diversity and epidemiology of classic and novel HAstV in outpatient children aged 0-16 years old with AGE in Shanghai. Methods From May 2020 to December 2022, a total of 1,482 stool samples were collected from children diagnosed as AGE from the Children's Hospital of Fudan University. HAstV was identified using pan-astrovirus consensus primers by Reverse transcription PCR. Results During the study period, 3.3% (49/1,482) of specimens were identified as HAstV, with a detection rate of 2.5% (37/1,482) for classic HAstV and 0.8% (12/1,482) for novel HAstV. Among the 12 novel HAstV strains, 11 (91.7%) belonged to the HAstV-MLB and 1 (8.3%) was HAstV-VA. Genotyping revealed six circulating genotypes. Strain HAstV-1 was predominant in the study population with a detection rate of 1.8% (26/1,482) followed by HAstV-MLB1 (0.7%, 10/1,482) and HAstV-4 (0.6%, 9/1,482). Of note, all the HAstV-4 strains detected in this study were close to one astrovirus strain isolated from Bactrian camels with 99.0-100.0% amino acid sequences identity. In this study, HAstV was detected in all age groups with the highest detection rate of HAstV-positive specimens observed in children older than 73 months (5.7%, 12/209). Discussion This study provided useful information and contributed to the molecular epidemiology of both classic and novel HAstV, which were simultaneously characterized and reported for the first time in Shanghai.
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Affiliation(s)
- Lijuan Lu
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Huaqing Zhong
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Menghua Xu
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Ran Jia
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Pengcheng Liu
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Liyun Su
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Lingfeng Cao
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Xunhua Zhu
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Jin Xu
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
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Wang H, Churqui MP, Tunovic T, Enache L, Johansson A, Lindh M, Lagging M, Nyström K, Norder H. Measures against COVID-19 affected the spread of human enteric viruses in a Swedish community, as found when monitoring wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165012. [PMID: 37353026 PMCID: PMC10284612 DOI: 10.1016/j.scitotenv.2023.165012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/25/2023] [Accepted: 06/17/2023] [Indexed: 06/25/2023]
Abstract
The quantification of viral genomes in wastewater reflects the prevalence of viral infections within the community. Knowledge of how the spread of common enteric viruses in the community was affected by the Swedish COVID-19 interventions is limited. To investigate this, the weekly wastewater samples collected for monitoring SARS-CoV-2 throughout the COVID-19 pandemic at the Rya sewage treatment plant in Gothenburg were also analyzed for adenovirus, norovirus GII, astrovirus, and rotavirus. The amount of each viral genome was quantified by real-time-qPCR and compared with the quantity of these viral genomes in wastewater from 2017. The results showed that the winter seasonality of norovirus GII and rotavirus in wastewater observed in 2017 was interrupted shortly after the introduction of the COVID-19 interventions, and they remained at low level throughout the pandemic. The circulation pattern of astrovirus and adenovirus was less affected. When the COVID-19 restrictions were lifted in 2022, a dramatic increase was observed in the amount of norovirus GII, rotavirus, and adenovirus genomes in wastewater. The changes in abundance and seasonality of some viruses identified through wastewater monitoring were consistent with changes in the number of patients diagnosed with these viruses. These findings suggest that moderate intervention to prevent COVID-19 significantly reduced the spread of some enteric viruses in the community. The results show that wastewater monitoring is a valuable tool for detecting the spread and outbreaks of viral infections that may cause gastroenteritis also when people do not seek medical help, such as during the COVID-19 pandemic.
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Affiliation(s)
- Hao Wang
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, Gothenburg, Sweden.
| | - Marianela Patzi Churqui
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Timur Tunovic
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Magnus Lindh
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, Gothenburg, Sweden
| | - Martin Lagging
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, Gothenburg, Sweden
| | - Kristina Nyström
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, Gothenburg, Sweden
| | - Heléne Norder
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, Gothenburg, Sweden
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Rubinstein RJ, Reyes Y, González F, Gutiérrez L, Toval-Ruíz C, Hammond K, Bode L, Vinjé J, Vilchez S, Becker-Dreps S, Bucardo F, Vielot NA. Epidemiology of pediatric astrovirus gastroenteritis in a Nicaraguan birth cohort. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.24.23294584. [PMID: 37662285 PMCID: PMC10473812 DOI: 10.1101/2023.08.24.23294584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background Astrovirus is a leading cause of acute gastroenteritis in children worldwide. However, few prospective studies have analyzed astrovirus in community-dwelling pediatric populations in low-and-middle-income countries. Methods We assessed the incidence, risk factors, clinical characteristics, genotypes, viral coinfections and seasonality of astrovirus gastroenteritis in 443 healthy Nicaraguan children born in 2017-2018, followed for 36 months. Children were recruited from maternity hospitals and birth records in an economically-diverse neighborhood of León, the second-largest city in Nicaragua. Astrovirus-positive episodes and genotypes were identified from diarrheal specimens with reverse transcription quantitative polymerase chain reaction and Sanger sequencing. Results Of 1708 total specimens tested, eighty children (18%) experienced at least 1 astrovirus episode, and 9 experienced repeat episodes, mostly during the rainy season (May-October). The incidence of astrovirus episodes was 7.8/100 child-years (95% CI: 6.2, 9.8). Genotype-specific incidence of astrovirus also exhibited seasonality. Median age of astrovirus episode onset was 16 months (IQR 9, 23). Initial astrovirus episodes were not associated with protection against future episodes during the age span studied. Astrovirus cases were exclusively breastfed for a shorter period than uninfected children, and the human milk oligosaccharide lacto-N-fucopentaose-I was more concentrated in mothers of these children. Home toilets appeared to protect against future astrovirus episodes (HR=0.19, 95% CI 0.04-0.91). Human astrovirus-5 episodes, comprising 15% of all typed episodes, were associated with longer diarrhea and more symptomatic rotavirus co-infections. Conclusion Astrovirus was a common cause of gastroenteritis in this cohort, and future studies should clarify the role of astrovirus genotype in clinical infection severity.
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Affiliation(s)
- Rebecca J Rubinstein
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yaoska Reyes
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Fredman González
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Lester Gutiérrez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Christian Toval-Ruíz
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Kelli Hammond
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lars Bode
- Department of Pediatrics, University of California San Diego
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Samuel Vilchez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Sylvia Becker-Dreps
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Filemón Bucardo
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Nadja A Vielot
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Farahmand M, Khales P, Salavatiha Z, Sabaei M, Hamidzade M, Aminpanah D, Tavakoli A. Worldwide prevalence and genotype distribution of human astrovirus in gastroenteritis patients: A systematic review and meta-analysis. Microb Pathog 2023:106209. [PMID: 37385570 DOI: 10.1016/j.micpath.2023.106209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/17/2023] [Accepted: 06/18/2023] [Indexed: 07/01/2023]
Abstract
AIM Human astrovirus (HAstV) is an important causative agent of gastroenteritis in humans, which mainly infects young children and the elderly. The goal of this study was to conduct a meta-analytic review of the prevalence of HAstV amongst patients with gastroenteritis, and to shed light on the connection between HAstV infection and gastroenteritis. METHODS Systematic literature searches were conducted to identify all potentially relevant studies recorded up to April 8th, 2022. For study weighting, the inverse variance method was employed and the random-effects model was applied to evaluate data. For case-control studies, the pooled odds ratio (OR) and 95% confidence interval (CI) were calculated to establish the relationship between HAstV infection and gastroenteritis. RESULTS Among 302423 gastroenteritis patients from 69 different countries, the overall pooled prevalence of HAstV infection was 3.48% (95% CI: 3.11%-3.89%). Case-control approach was used in 39 investigations, and the overall prevalence of HAstV infection among the 11342 healthy controls was 2.01% (95% CI: 1.40%-2.89%). Gastroenteritis and HAstV infection were associated with a pooled OR of 2.16 (95% CI: 1.72-2.71; P < 0.0001; I2 = 33.7%). The most commonly found HAstV genotypes in gastroenteritis patients were HAstV1 (62.18%), HAstV7 (33.33%), and HAstV-MLB1 (17.43%). CONCLUSION The frequency of HAstV infection was the highest in children under the age of five, and in developing countries. The prevalence rate of HAstV was not influenced by gender. Semi-nested and nested RT-PCR were highly sensitive assays for detecting HAstV infections.
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Affiliation(s)
- Mohammad Farahmand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Pegah Khales
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Salavatiha
- Department of Medical Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Milad Sabaei
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Malihe Hamidzade
- Department of Medical Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Danesh Aminpanah
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran.
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Razizadeh MH, Pourrostami K, Kachooei A, Zarei M, Asghari M, Hamldar S, Khatami A. An annoying enteric virus: A systematic review and meta‐analysis of human astroviruses and gastrointestinal complications in children. Rev Med Virol 2022; 32:e2389. [DOI: 10.1002/rmv.2389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/22/2022] [Accepted: 07/21/2022] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kumars Pourrostami
- Department of Pediatrics School of Medicine Alborz University of Medical Sciences Karaj Iran
- Dietary Supplements and Probiotic Research Center Alborz University of Medical Sciences Karaj Iran
| | - Atefeh Kachooei
- Department of Virology Faculty of Medicine Iran University of Medical Sciences Tehran Iran
| | - Mohammad Zarei
- Renal Division Harvard Medical School Brigham and Women's Hospital Boston Massachusetts USA
- Harvard T.H. Chan School of Public Health John B. Little Center for Radiation Sciences Boston Massachusetts USA
| | - Milad Asghari
- Department of Microbiology Faculty of Basic Science Tabriz Branch Islamic Azad University Tabriz Iran
| | - Shahrzad Hamldar
- Department of Virology Faculty of Medicine Iran University of Medical Sciences Tehran Iran
| | - Alireza Khatami
- Department of Virology Faculty of Medicine Iran University of Medical Sciences Tehran Iran
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Mitra S, Lo M, Saha R, Deb AK, Debnath F, Miyoshi S, Dutta S, Chawla‐Sarkar M. Epidemiology of major entero‐pathogenic viruses and genetic characterization of Group A rotaviruses among children (≤5 years) with acute gastroenteritis in eastern India, 2018‐2020. J Appl Microbiol 2022; 133:758-783. [DOI: 10.1111/jam.15594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Suvrotoa Mitra
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
| | - Mahadeb Lo
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
| | - Ritubrita Saha
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
| | - Alok K. Deb
- Division of Epidemiology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Falguni Debnath
- Division of Epidemiology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Shin‐Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences Okayama University Okayama Japan
- Collaborative Research Centre of Okayama University for Infectious Disease ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Shanta Dutta
- Regional Virus Research and Diagnostic Laboratory, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Mamta Chawla‐Sarkar
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
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Tang X, Hu Y, Zhong X, Xu H. Molecular Epidemiology of Human Adenovirus, Astrovirus, and Sapovirus Among Outpatient Children With Acute Diarrhea in Chongqing, China, 2017-2019. Front Pediatr 2022; 10:826600. [PMID: 35311045 PMCID: PMC8929441 DOI: 10.3389/fped.2022.826600] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/09/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE To investigate the epidemiology of human adenovirus (HAdV), human astrovirus (HAstV), and sapovirus (SaV), children with acute diarrhea in Chongqing, China from 2017 to 2019 were enrolled. Improved surveillance could provide better guidance for diarrhea prevention. METHODS Between 2017 and 2019, fecal specimens were collected from children <14 years of age presenting with acute diarrhea for treatment at the outpatient department of the Children's Hospital, Chongqing Medical University. Human HAdV in the fecal specimens was detected by PCR, while RT-PCR was adopted for the detection of HAstV and SaV. RESULTS A total of 1,352 fecal specimens were screened in this study. The detection rate of HAdV was 4.44% (60/1352), HAstV was 2.81% (38/1352), and SaV was 1.04% (14/1352). The prevalence of enteric viruses in males was not significantly different to females (p > 0.05). We found 96.67% (58/60) of the HAdV-positive cases, 92.11% (35/38) of the HAstV-positive cases, and 100% (14/14) of the SaV-positive cases among the children under 4 years old. HAdV cases were identified throughout the year, while the infection of HAstV peaked from March to May every year. By contrast, SaV was detected in May, July, and from September to December. In total, 41 strains of HAdV-F were identified, including F41 (39/60) and F40 (2/60). Furthermore, A31, B3, B7, C1, C2, C5, and C6 were also detected in the study. In addition, we detected two genotypes of HAstV, HAstV-1 (34/38) and HAstV-5 (4/38), and two genotypes of SaV, GI0.1 (13/14), GI0.2 (1/14). CONCLUSION The enteric viruses HAdV, HAstV, and SaV contribute to the overall burden of diarrhea in Chongqing, especially in children <4 years of age. Two genotypes were identified for HAstV (HAstV-1 and HAstV-5) and SaV (GI.1 and GI.2) with an additional nine genotypes detected in HAdV cases. While the F41 HAdV strain was predominant, HAdV-A31 was also detected in 10% of cases. The study results along with continuous surveillance of enteric viruses will aid in the design and implementation of future enteric vaccines and diarrhea mitigation strategies.
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Affiliation(s)
- Xiang Tang
- Children's Hosptital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Yue Hu
- Children's Hosptital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Xiaoni Zhong
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Hongmei Xu
- Children's Hosptital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
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10
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Viral metagenomics reveals diverse viruses in the fecal samples of children with diarrhea. Virol Sin 2022; 37:82-93. [PMID: 35234620 PMCID: PMC8922427 DOI: 10.1016/j.virs.2022.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 12/06/2021] [Indexed: 01/12/2023] Open
Abstract
Diarrhea is the third leading cause of death in developing countries in children under the age of five. About half a million children die of diarrhea every year, most of which in developing countries. Viruses are the main pathogen of diarrhea. In China, the fecal virome of children with diarrhea has been rarely studied. Using an unbiased viral metagenomics approach, we analyzed the fecal virome in children with diarrhea. Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae, Astroviridae, Caliciviridae, Parvoviridae, Picornaviridae, and Reoviridae. Among them, the family of Caliciviridae accounts for the largest proportion of 78.42%, following with Adenoviridae (8.94%) and Picornaviridae (8.36%). In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea, the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus. This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area. Many DNA or RNA viruses associated with diarrhea were identified in this study. Viruses belonging to the family of Caliciviridae were the most main pathogen that induced children diarrhea. In addition to those diarrhea-related viruses, the viruses not associated with diarrhea were also identified.
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High divergence of human astrovirus genotypes circulating in pediatric patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, 2017-2020. Sci Rep 2021; 11:23266. [PMID: 34853390 PMCID: PMC8636499 DOI: 10.1038/s41598-021-02745-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/22/2021] [Indexed: 02/04/2023] Open
Abstract
Human astrovirus (HAstV) is one of the common causes of acute gastroenteritis in children. The investigation of molecular epidemiology of HAstV is essential for monitoring the emergence and/or re-emergence of new HAstV genotypes, as well as understanding the evolution of HAstV circulating in children suffering from acute gastroenteritis. The present study aimed to investigate the prevalence and distribution of HAstVs strains circulating in children hospitalized with acute gastroenteritis in Chiang Mai, Thailand during 2017-2020. A total of 1500 fecal specimens collected from children with acute gastroenteritis were screened for HAstV by RT-PCR that targeted the partial RdRp in ORF1b and strains were characterized by sequencing and phylogenetic analysis. Of the 1500 fecal samples, 39 (2.6%) were positive for HAstV. Of these, both classic and novel HAstV genotypes, including classic HAstV1-HAstV5, novel HAstV-MLB1, MLB2, and HAstV-VA2, were detected. The data in this study revealed a high divergence of HAstV genotypes circulating in pediatric patients admitted to the hospitals with acute gastroenteritis in Chiang Mai, Thailand during 2017-2020.
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