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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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Ykema M, Ye K, Xun M, Harper J, Betancourt-Solis MA, Arias CF, McNew JA, Tao YJ. Human astrovirus capsid protein releases a membrane lytic peptide upon trypsin maturation. J Virol 2023; 97:e0080223. [PMID: 37504573 PMCID: PMC10506485 DOI: 10.1128/jvi.00802-23] [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: 05/26/2023] [Accepted: 06/13/2023] [Indexed: 07/29/2023] Open
Abstract
The human astrovirus (HAstV) is a non-enveloped, single-stranded RNA virus that is a common cause of gastroenteritis. Most non-enveloped viruses use membrane disruption to deliver the viral genome into a host cell after virus uptake. The virus-host factors that allow for HAstV cell entry are currently unknown but thought to be associated with the host-protease-mediated viral maturation. Using in vitro liposome disruption analysis, we identified a trypsin-dependent lipid disruption activity in the capsid protein of HAstV serotype 8. This function was further localized to the P1 domain of the viral capsid core, which was both necessary and sufficient for membrane disruption. Site-directed mutagenesis identified a cluster of four trypsin cleavage sites necessary to retain the lipid disruption activity, which is likely attributed to a short stretch of sequence ending at arginine 313 based on mass spectrometry of liposome-associated peptides. The membrane disruption activity was conserved across several other HAstVs, including the emerging VA2 strain, and effective against a wide range of lipid identities. This work provides key functional insight into the protease maturation process essential to HAstV infectivity and presents a method to investigate membrane penetration by non-enveloped viruses in vitro. IMPORTANCE Human astroviruses (HAstVs) are an understudied family of viruses that cause mild gastroenteritis but have recent cases associated with a more severe neural pathogenesis. Many important elements of the HAstV life cycle are not well understood, and further elucidating them can help understand the various forms of HAstV pathogenesis. In this study, we utilized an in vitro liposome-based assay to describe and characterize a previously unreported lipid disruption activity. This activity is dependent on the protease cleavage of key sites in HAstV capsid core and can be controlled by site-directed mutagenesis. Our group observed this activity in multiple strains of HAstV and in multiple lipid conditions, indicating this may be a conserved activity across the AstV family. The discovery of this function provides insight into HAstV cellular entry, pathogenesis, and a possible target for future therapeutics.
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Affiliation(s)
- Matthew Ykema
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Kai Ye
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Meng Xun
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Justin Harper
- Department of BioSciences, Rice University, Houston, Texas, USA
| | | | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - James A. McNew
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Yizhi Jane Tao
- Department of BioSciences, Rice University, Houston, Texas, USA
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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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Wei H, Kumthip K, Khamrin P, Yodmeeklin A, Jampanil N, Phengma P, Xie Z, Ukarapol N, Ushijima H, Maneekarn N. Triple Intergenotype Recombination of Human Astrovirus 5, Human Astrovirus 8, and Human Astrovirus 1 in the Open Reading Frame 1a, Open Reading Frame 1b, and Open Reading Frame 2 Regions of the Human Astrovirus Genome. Microbiol Spectr 2023; 11:e0488822. [PMID: 37017548 PMCID: PMC10269785 DOI: 10.1128/spectrum.04888-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/08/2023] [Indexed: 04/06/2023] Open
Abstract
Human astrovirus (HAstV) strains exhibit high levels of genetic diversity, and many recombinant strains with different recombination patterns have been reported. The aims of the present study were to investigate the emergence of HAstV recombinant strains and to characterize the recombination patterns of the strains detected in pediatric patients admitted to the hospital with acute gastroenteritis in Chiang Mai, Thailand. A total of 92 archival HAstV strains detected in 2011 to 2020 were characterized regarding their open reading frame 1a (ORF1a) genotypes in comparison with their ORF1b genotypes to identify recombinant strains. The recombination breakpoints of the putative recombinant strains were determined by whole-genome sequencing and were analyzed by SimPlot and RDP software. Three HAstV strains (CMH-N178-12, CMH-S059-15, and CMH-S062-15) were found to be recombinant strains of three different HAstV genotypes, i.e., HAstV5, HAstV8, and HAstV1 within the ORF1a, ORF1b, and ORF2 regions, respectively. The CMH-N178-12 strain displayed recombination breakpoints at nucleotide positions 2681 and 4357 of ORF1a and ORF1b, respectively, whereas the other two recombinant strains, CMH-S059-15 and CMH-S062-15, displayed recombination breakpoints at nucleotide positions 2612 and 4357 of ORF1a and ORF1b, respectively. This is the first study to reveal nearly full-length genome sequences of HAstV recombinant strains with a novel recombination pattern of ORF1a-ORF1b-ORF2 genotypes. This finding may be useful as a guideline for identifying other recombinant HAstV strains in other geographical regions and may provide a better understanding of their genetic diversity, as well as basic knowledge regarding virus evolution. IMPORTANCE Recombination is one of the mechanisms that plays a crucial role in the genetic diversity and evolution of HAstV. We wished to investigate the emergence of HAstV recombinant strains and to analyze the whole-genome sequences of the putative HAstV recombinant strains detected in pediatric patients with acute gastroenteritis in 2011 to 2020. We reported 3 novel intergenotype recombinant strains of HAstV5-HAstV8-HAstV1 at the ORF1a-ORF1b-ORF2 regions of the HAstV genome. The hot spots of recombination occur frequently near the ORF1a-ORF1b and ORF1b-ORF2 junctions of the HAstV genome. The findings indicate that intergenotype recombination of HAstV occurs frequently in nature. The emergence of a novel recombinant strain allows the new virus to adapt and successfully escape from the host immune system, eventually emerging as the predominant genotype to infect human populations that lack herd immunity against novel recombinant strains. The virus may cause an outbreak and needs to be monitored continually.
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Affiliation(s)
- Hongyu Wei
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Nutthawadee Jampanil
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phitchakorn Phengma
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Zhenfeng Xie
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Nuthapong Ukarapol
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
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Okitsu S, Khamrin P, Hikita T, Shimizu-Onda Y, Thongprachum A, Hayakawa S, Maneekarn N, Ushijima H. Molecular Epidemiology of Classic, MLB, and VA Astroviruses in Children with Acute Gastroenteritis, 2014-2021: Emergence of MLB3 Strain in Japan. Microbiol Spectr 2023; 11:e0070023. [PMID: 37140393 PMCID: PMC10269582 DOI: 10.1128/spectrum.00700-23] [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: 02/14/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Human astroviruses (HAstVs) are important causative pathogens of acute gastroenteritis (AGE) in children worldwide. MLB and VA HAstVs, which are genetically distinct from the previously known classic HAstVs, have been detected since 2008. To investigate the role of HAstVs in AGE, we conducted molecular detection and characterization of HAstVs circulating in children with AGE in Japan from 2014 to 2021. Out of 2,841 stool samples, HAstVs were detected in 130 (4.6%). MLB1 was the predominant genotype detected (45.4%), followed by HAstV1 (39.2%), MLB2 (7.4%), VA2 (3.1%), HAstV3 (2.3%), HAstV4, HAstV5, and MLB3 (0.8% each). The results demonstrated that HAstV infection in pediatric patients in Japan was dominated by the two major genotypes MLB1 and HAstV1, with a small proportion of other genotypes. The overall infection rates of MLB and VA HAstVs were higher than those of classic HAstVs. The HAstV1 strains detected in this study belonged solely to lineage 1a. The rare MLB3 genotype was detected for the first time in Japan. All three HAstV3 strains belonged to lineage 3c based on the ORF2 nucleotide sequence and were shown to be recombinant strains. IMPORTANCE HAstVs are one of the pathogens of viral AGE and are considered the third most common viral agents of AGE after rotavirus and norovirus. HAstVs are also suspected to be the causative agents of encephalitis or meningitis in immunocompromised patients and elderly persons. However, little is known about the epidemiology of HAstVs in Japan, especially that of MLBs and VA HAstVs. This study demonstrated epidemiological features and molecular characterization of human astroviruses encompassing a 7-year study period in Japan. This study highlights the genetic diversity of HAstV circulating in pediatric patients with acute AGE in Japan.
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Affiliation(s)
- Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | | | - Yuko Shimizu-Onda
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Aksara Thongprachum
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Public Health, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
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Ushijima H, Nishimura S, Shimizu-Onda Y, Thi Kim Pham N, Trinh QD, Okitsu S, Takano C, Kumthip K, Hoque SA, Komine-Aizawa S, Maneekarn N, Hayakawa S, Khamrin P. Outbreak of human astroviruses 1 and Melbourne 2 in acute gastroenteritis pediatric patients in Japan during the COVID-19 pandemic, 2021. J Infect Public Health 2023; 16:1301-1305. [PMID: 37336127 DOI: 10.1016/j.jiph.2023.05.034] [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: 01/22/2023] [Revised: 05/15/2023] [Accepted: 05/28/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Human astrovirus (HAstV) infection is one of the leading causes of acute gastroenteritis in young children. The present study reports the outbreak of HAstV in children with acute gastroenteritis in Kyoto, Japan, during the COVID-19 pandemic, 2021. METHODS A total of 61 stool samples were collected from children with acute gastroenteritis who visited a pediatric outpatient clinic in Maizuru city, Kyoto, Japan from July to October, 2021. HAstV was screened by RT-PCR, and the genotypes were identified by nucleotide sequence analysis. RESULTS Of 61 cases of acute gastroenteritis, 20 were mono-infected with HAstV alone. In addition, mixed infection of HAstV and NoV, and HAstV and RVA were also detected in 15 and 1 cases, respectively. Of 36 HAstV strains detected in this outbreak, 29 and 7 were HAstV1 and MLB2 genotypes, respectively. All HAstV1 strains were closely related to the HAstV1 reported from Thailand and Japan in 2021 and all of them belonged to subgenotype HAstV1a. Among MLB2, they were most closely related to the MLB2 strains reported from China in 2016 and 2018. CONCLUSIONS After the kindergartens and schools were re-opened at the middle of 2021 in Japan, an outbreak of HAstV was reported. Control measures against the COVID-19 pandemics might affect the spread of diarrheal virus infection. Here we report the outbreak of HAstV1 and MLB2 in Kyoto, Japan, during COVID-19 pandemic in 2021.
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Affiliation(s)
- Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.
| | | | - Yuko Shimizu-Onda
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Ngan Thi Kim Pham
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Quang Duy Trinh
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Chika Takano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Sheikh Ariful Hoque
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shihoko Komine-Aizawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan; Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand.
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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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毛 俊, 杨 娅, 石 长, 陈 竹, 李 春, 王 永, 李 琳, 陈 军. Molecular epidemiological characteristics of the virus in 96 children with acute diarrhea in Changdu of Tibet, China. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2022; 24:266-272. [PMID: 35351256 PMCID: PMC8974661 DOI: 10.7499/j.issn.1008-8830.2110012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/03/2022] [Indexed: 01/02/2023]
Abstract
OBJECTIVES To study the molecular epidemiological characteristics of the virus in children with acute viral diarrhea in Changdu of Tibet, China. METHODS Fecal specimens were collected from 96 children with acute diarrhea who visited the People's Hospital of Changdu, Tibet, from November 2018 to November 2020 and were tested for adenovirus, norovirus, astrovirus, sapovirus, and rotavirus. Gene sequencing was performed for the genotypes of these viruses. RESULTS The overall positive rate of the five viruses was 39% (37/96), among which astrovirus had the highest positive rate of 17%, followed by norovirus (9%), rotavirus (8%), adenovirus (7%), and sapovirus (5%). There was no significant difference in the positive rate of the five viruses among different age groups (P>0.05). Only the positive rate of astrovirus was significantly different among the four seasons (P<0.05). For adenovirus, 6 children had F41 type and 1 had C2 type; for norovirus, 6 had GⅠ.3 type, 1 had GⅠ.7 type, 1 had GⅡ.3 type, and 2 had GⅡ.4 Sydney_2012 type; HAstrV-1 type was observed in all children with astrovirus infection; for sapovirus, 1 child each had sporadic GⅠ.2, GⅠ.6, and GⅡ.1 sapovirus and 2 children had unknown type; 6 children had rotavirus G9[P8]. CONCLUSIONS Astrovirus and norovirus are important pathogens in children with acute diarrhea in Changdu, Tibet. The positive rate of adenovirus, norovirus, astrovirus, sapovirus, and rotavirus is not associated with age, and only the positive rate of astrovirus has obvious seasonality. F41 type is the dominant genotype of adenovirus; GⅠ.3 is the dominant genotype of norovirus; HAstrV-1 is the dominant genotype of astrovirus; sporadic GⅠ.2, GⅠ.6, and GⅡ.1 are the dominant genotypes of sapovirus; G9[P8] is the dominant genotype of rotavirus.
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Affiliation(s)
| | | | | | | | - 春 李
- 儿科学重庆市重点实验室重庆400016
- 重庆医科大学附属儿童医院新生儿科重庆400016
| | - 永明 王
- 儿科学重庆市重点实验室重庆400016
- 昌都市人民医院儿科,西藏昌都854000
- 重庆医科大学附属儿童医院新生儿科重庆400016
| | | | - 军华 陈
- 儿科学重庆市重点实验室重庆400016
- 昌都市人民医院儿科,西藏昌都854000
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10
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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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11
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Wei H, Khamrin P, Kumthip K, Yodmeeklin A, Maneekarn N. Emergence of Multiple Novel Inter-Genotype Recombinant Strains of Human Astroviruses Detected in Pediatric Patients With Acute Gastroenteritis in Thailand. Front Microbiol 2021; 12:789636. [PMID: 34966371 PMCID: PMC8710764 DOI: 10.3389/fmicb.2021.789636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/11/2021] [Indexed: 11/23/2022] Open
Abstract
Objective: Human astrovirus (HAstV) is recognized as an important cause of acute gastroenteritis in children. Recombination between different genotypes of HAstV can contribute to diversity and evolution of the virus. This study aimed to investigate the emergence of HAstV recombinant strains in pediatric patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, spanning 2011–2020. Methods: A total of 92 archival HAstV strains collected from pediatric patients with acute gastroenteritis during 2011–2020 were further characterized to identify the recombinant strains. The ORF1b and ORF2 junction region of each strain was amplified and sequenced. The obtained sequences were analyzed in comparison with the reference sequences retrieved from GenBank database. Their genotypes were assigned using MEGA X software based on the partial ORF1b (RdRp) and ORF2 (capsid) regions, and the recombination breakpoints of recombinant strains were determined by SimPlot and RDP4 analyses. Results: Five inter-genotype recombinant strains with three recombination patterns of ORF1b/ORF2 of classic HAstV, HAstV8/HAstV1, HAstV8/HAstV3, and HAstV3/HAstV2, were detected. The recombination breakpoints of all strains were located at the 3′-end region of ORF1b close to the ORF1b/ORF2 junction. Conclusion: Several novel inter-genotype recombinant strains of classic HAstV genotypes were detected in pediatric patients with acute gastroenteritis in Chiang Mai, Thailand, during the period of 10 years from 2011 to 2020.
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Affiliation(s)
- Hongyu Wei
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Department of Pathogenic Biology and Immunology, Youjiang Medical University for Nationalities, Baise, China
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
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12
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Luo X, Deng JK, Mu XP, Yu N, Che X. Detection and characterization of human astrovirus and sapovirus in outpatients with acute gastroenteritis in Guangzhou, China. BMC Gastroenterol 2021; 21:455. [PMID: 34861832 PMCID: PMC8642882 DOI: 10.1186/s12876-021-02044-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Human astrovirus (HAstV) and sapovirus (SaV) are common pathogens that can cause acute gastroenteritis (AGE). However, very few studies have reported the molecular epidemiology and clinical information on HAstV and SaV in China. This study aims to determine the molecular epidemiology and clinical features of HAstV and SaV in patients with AGE in Guangzhou, China. Methods For this study, 656 patients with AGE were enrolled. Their stool samples were screened for 15 enteropathogens using Luminex xTAG® Gastrointestinal Pathogen Panel. HAstV and SaV were detected through an in-house multiplex reverse transcriptase polymerase chain reaction followed by phylogenetic analysis. We described and compared clinical features of AGE in patients with HAstV and SaV. Results Of the 656 stool samples, 63.72% (418/656) were found to be positive, with 550 enteropathogens (296 bacteria and 254 viruses). HAstV and SaV were detected in 20 (3.0%) and 12 (1.8%) samples, respectively. Four genotypes (genotypes 1, 2, 3, and 8) of HAstV and three genotypes (GI.1, GI.2 and GIV) of SaV were identified. Coinfection was observed in ten HAstV-positive and two SaV-positive samples. HAstV was more likely to occur in winter, while SaV in early spring. The median age of the patients with single HAstV infection was higher than that of the patients with other viruses (rotavirus, norovirus, and enteric adenovirus; P = 0.0476) and unknown etiology (P = 0.006). Coinfection with HAstV or SaV were not associated with disease severity (P > 0.05). Conclusion HAstV and SaV are the common causes of AGE in Guangzhou, China.
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Affiliation(s)
- Xin Luo
- Department of Laboratory Medicine, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Jian-Kai Deng
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiao-Ping Mu
- Department of Laboratory Medicine, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Nan Yu
- Laboratory of Emerging Infectious Diseases and Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, No. 253 Gong-ye Avenue, Guangzhou, 510282, People's Republic of China.
| | - Xiaoyan Che
- Laboratory of Emerging Infectious Diseases and Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, No. 253 Gong-ye Avenue, Guangzhou, 510282, People's Republic of China
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13
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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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14
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Human Astrovirus in Symptomatic and Asymptomatic Children: A Cross-Sectional Study on Hospitalized and Outpatients from Rural Communities of South Africa between 2017-2021. Pathogens 2021; 10:pathogens10111398. [PMID: 34832554 PMCID: PMC8618259 DOI: 10.3390/pathogens10111398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/29/2022] Open
Abstract
Human astroviruses are considered acute gastroenteritis agents (AGE) and are largely reported in children worldwide. There are limited data on astrovirus prevalence in rural communities, especially in hospitalized and asymptomatic cases. This study was a cross-sectional survey aiming to investigate the prevalence of classic human astroviruses in symptomatic and asymptomatic cases and hospitalized and outpatient children in rural communities of the Vhembe District, South Africa. A total of 236 stool samples (166 symptomatic and 70 asymptomatic) were collected from young children under 5 years of age. Real-time RT-PCR for astrovirus detection, RT-PCR amplification of capsid and polymerase partial genes as well as Sanger sequencing were performed. The classic astrovirus prevalence in symptomatic patients (7.23%, 12/166) as compared to healthy controls (4.29%, 3/70) was not statistically different (t-value: 1.782, p = 0.141: 95% CI). We did not observe a significant difference of classic astrovirus prevalence rate between the hospitalized group (6.52%, 3/46) and outpatient group (7.5%, 9/120). Symptomatic children below 6 months old were the most affected group (18.18%, 6/33). This study characterized human astrovirus genotype 2 and a putative recombinant strain (polymerase genotype 1/capsid genotype 2). Phylogenetic analysis revealed these genotypes are closely related to the strains circulating elsewhere within the African continent. The findings suggest that astrovirus is a common enteric pathogen in the study area. The results highlight the exposure of children and the need to monitor astroviruses for their potential impact in diarrhoeal diseases.
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15
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Lu L, Zhong H, Xu M, Su L, Cao L, Jia R, Xu J. Molecular and epidemiological characterization of human adenovirus and classic human astrovirus in children with acute diarrhea in Shanghai, 2017-2018. BMC Infect Dis 2021; 21:713. [PMID: 34325664 PMCID: PMC8320412 DOI: 10.1186/s12879-021-06403-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 07/18/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In addition to rotavirus and norovirus, human adenovirus (HAdV) and classic human astrovirus (classic HAstV) are important pathogens of acute diarrhea in infants and young children. Here, we present the molecular epidemiology of HAdV and classic HAstV in children with acute diarrhea in Shanghai. METHODS Fecal specimens were collected from 804 outpatient infants and young children diagnosed with acute diarrhea in Shanghai from January 2017 to December 2018. All of the samples were screened for the presence of HAdV and classic HAstV. HAdV and classic HAstV were detected using traditional PCR and reverse-transcription PCR, respectively. All of the HAdV and classic HAstV positive samples were genotyped by phylogenetic analysis. RESULTS Among the 804 fecal samples, 8.58% (69/804) of samples were infected with either HAdV or classic HAstV, and five were co-infected with two diarrhea viruses. The overall detection rates of HAdV and classic HAstV were 3.47% (28/804) and 5.22% (42/804), respectively. Four subgroups (A, B, C, and F) and seven genotypes (HAdV-C1, -C2, -B3, -C5, -A31, -F40, and -F41) of HAdV were detected. Subgroup F had the highest constituent ratio at 64.29% (18/28), followed by non-enteric HAdV of subgroup C (21.43%, 6/28) and subgroup B 10.71% (3/28). HAdV-F41 (60.71%, 17/28) was the dominant genotype, followed by HAdV-C2 (14.29%, 4/28) and HAdV-B3 (10.71%, 3/28). Two genotypes of classic HAstV (HAstV-1 and HAstV-5) were identified in 42 samples during the study period; HAstV-1 (95.24%, 40/42) was the predominant genotype, and the other two strains were genotyped as HAstV-5. No significant differences were found between boys and girls in the detection rates of HAdV (P = 0.604) and classic HAstV (P = 0.275). Over half of the HAdV infections (82.14%, 23/28) and classic HAstV infections (66.67%, 28/42) occurred in children less than 36 months. Seasonal preferences of HAdV and classic HAstV infections were summer and winter, respectively. In this study, the common clinical symptoms of children with acute diarrhea were diarrhea, vomiting, fever and abdominal pain. CONCLUSIONS Our findings indicate that HAdV and classic HAstV play important roles in the pathogenesis of acute diarrhea in children in Shanghai. Systematic and long-term surveillance of HAdV and classic HAstV are needed to monitor their prevalence in children and prevent major outbreak.
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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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16
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Ykema M, Tao YJ. Structural Insights into the Human Astrovirus Capsid. Viruses 2021; 13:v13050821. [PMID: 34062934 PMCID: PMC8147390 DOI: 10.3390/v13050821] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Astroviruses (AstVs) are non-enveloped, positive single-stranded RNA viruses that cause a wide range of inflammatory diseases in mammalian and avian hosts. The T = 3 viral capsid is unique in its ability to infect host cells in a process driven by host proteases. Intercellular protease cleavages allow for viral egress from a cell, while extracellular cleavages allow for the virus to enter a new host cell to initiate infection. High-resolution models of the capsid core indicate a large, exposed region enriched with protease cleavage sites. The virus spike protein allows for binding to target cells and is the major target for naturally occurring and engineered neutralizing antibodies. During maturation, the capsid goes through significant structural changes including the loss of many surface spikes. The capsid interacts with host membranes during the virus life cycle at multiple stages such as assembly, host cell entry and exit. This review will cover recent findings and insights related to the structure of the capsid and its function. Further understanding of the viral capsid structure and maturation process can contribute to new vaccines, gastric therapeutics, and viral engineering applications.
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17
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Wu L, Teng Z, Lin Q, Liu J, Wu H, Kuang X, Cui X, Wang W, Cui X, Yuan ZA, Zhang X, Xie Y. Epidemiology and Genetic Characterization of Classical Human Astrovirus Infection in Shanghai, 2015-2016. Front Microbiol 2020; 11:570541. [PMID: 33101242 PMCID: PMC7546348 DOI: 10.3389/fmicb.2020.570541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/26/2020] [Indexed: 11/13/2022] Open
Abstract
Objective Human astroviruses (HAstVs) are single-stranded RNA viruses of the Astroviridae family. Infection of classic HAstVs is one of the most common causes of acute viral gastroenteritis (infectious viral diarrhea). There is a lack of data on the prevalence and genetic characterization of classic HAstVs in acute viral gastroenteritis in the whole population. This study aimed to investigate the epidemiological trend, genotypes, viral co-infections, and viral loads of classic HAstVs in Shanghai, China, from January 2015 to December 2016. Methods A total of 6,051 non-redundant stool samples were collected in outpatients with acute diarrhea in Shanghai from January 2015 to December 2016. One-step real-time RT-PCR was used for screening viral diarrhea, including rotavirus A, rotavirus B, rotavirus C, norovirus genotype I and II, classic human astroviruses, and sapovirus. Real-time PCR was used for screening human enteric adenoviruses. Conventional RT-PCR was used for the amplification of viral fragments for genotyping. PCR products were sequenced and used for the construction of phylogenetic trees. Results The detection rate of classic HAstVs was 1.55% (94/6,051). The prevalence of HAstV infection displayed a typical winter/spring (December to March) seasonality and was highest in the 5–14 age group. Eighty-six samples were genotyped, which revealed HAstV-1 as the most prevalent genotype, followed by HAstV-5, HAstV-4, HAstV- 2, HAstV-8, and HAstV-3. There was a dramatic rise in the prevalence of HAstV-4 from December 2015 to March 2016, and the viral loads of HAstV-4 were significantly higher than those of other genotypes. Among the mixed infection samples, noroviruses were found to be the most frequently co-infected enteric viruses with HAstV. Conclusion Multiple genotypes of classic HAstVs circulated in Shanghai from January 2015 to December 2016. For the first time, HAstV-3\4\5\8 were detected in Shanghai.
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Affiliation(s)
- Limeng Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China.,Shanghai Institute of Preventive Medicine, Shanghai, China
| | - Zheng Teng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Qingneng Lin
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Jing Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Huanyu Wu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaozhou Kuang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaoqing Cui
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Wei Wang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaoxian Cui
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zheng-An Yuan
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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18
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Vu DL, Sabrià A, Aregall N, Michl K, Sabrià J, Rodriguez Garrido V, Goterris L, Bosch A, Pintó RM, Guix S. A Spanish case-control study in <5 year-old children reveals the lack of association between MLB and VA astrovirus and diarrhea. Sci Rep 2020; 10:1760. [PMID: 32020041 PMCID: PMC7000717 DOI: 10.1038/s41598-020-58691-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/13/2020] [Indexed: 01/01/2023] Open
Abstract
Novel human astroviruses (HAstV) were discovered 10 years ago and have been associated with fatal cases of central nervous system infections. Their role in gastroenteritis is controversial, as they have been identified in symptomatic and asymptomatic subjects. The aim of the study was to investigate novel HAstV in a gastroenteritis case-control study including a pediatric population in Spain over a one-year period. We included stool samples from patients with gastroenteritis and negative results for viruses screened by routine diagnostics, and stool samples of control subjects who sought for a routine medical consultation. All samples were screened by real-time RT-PCR assays for novel HAstV. An additional screening for rotavirus, norovirus GI, GII, sapovirus, classic HAstV and adenovirus was also performed for the control group. Overall, 23/363 stool samples from case patients (6.3%) and 8/199 stool samples from control patients (4%) were positive for ≥1 novel HAstV. MLB1 was predominant (64.5% of positives). Seasonality was observed for the case group (p = 0.015), but not the control group (p = 0.95). No difference was observed in the prevalence of novel HAstV between the case and control groups (OR 1.78, 95% CI 0.68–5.45; p = 0.30). Nevertheless, MLB genome copy numbers/ml of fecal suspension was significantly higher in the control group than in the case group (p = 0.008). In our study, we identified a lack of association between novel HAstV and gastroenteritis in the studied population, which could indicate a potential role of reservoir for children, especially given the higher viral load observed in the asymptomatic group for some of them.
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Affiliation(s)
- Diem-Lan Vu
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain. .,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain. .,Department of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
| | - Aurora Sabrià
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Nuria Aregall
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Kristina Michl
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Jaume Sabrià
- Primary Health Care Center El Serral, Generalitat de Catalunya, Sant Vicenç dels Horts, Spain
| | | | - Lidia Goterris
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Rosa Maria Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain. .,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain.
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19
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Zhou N, Zhou L, Wang B. Molecular Evolution of Classic Human Astrovirus, as Revealed by the Analysis of the Capsid Protein Gene. Viruses 2019; 11:v11080707. [PMID: 31374999 PMCID: PMC6722597 DOI: 10.3390/v11080707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 01/17/2023] Open
Abstract
Classic human astroviruses (HAstV) are major global viral agents for gastroenteritis, but the molecular characteristics of classic HAstVs are not well understood. Here, we presented the molecular evolution of all classic HAstV serotypes by the analysis of the capsid protein sequences. Our results show that classic HAstVs can be divided into four groups with the most recent common ancestor (TMRCA) of 749. The overall evolutionary rate of classic HAstVs on the capsid gene was 4.509 × 10−4 substitutions/site/year, and most of the serotypes present a clock-like evolution with an amino acid accumulation of mutations over time. The mean effective population size of classic HAstVs is in a downward trend, and some positive and more than 500 negative selection sites were determined. Taken together, these results reveal that classic HAstVs evolve at the intra-serotype level with high genetic heterogeneity and are driven by strong purifying selection. Long-term surveillance of classic HAstVs are needed to enrich the genomic data for further analysis.
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Affiliation(s)
- Nan Zhou
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Statistics, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China.
| | - Lu Zhou
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, Jiangsu, China.
| | - Bei Wang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Statistics, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China.
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Novel Human Astroviruses: Prevalence and Association with Common Enteric Viruses in Undiagnosed Gastroenteritis Cases in Spain. Viruses 2019; 11:v11070585. [PMID: 31252663 PMCID: PMC6669616 DOI: 10.3390/v11070585] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022] Open
Abstract
A remarkable percentage of acute gastroenteritis cases remain etiologically undiagnosed. The aim of the study was to determine the prevalence of common and emerging enteric viruses, such as novel human astroviruses, among undiagnosed samples from children with acute gastroenteritis. Epidemiological studies for novel human astroviruses are still scarce. Stool samples collected over two consecutive winter seasons (2016–2017) from children with gastroenteritis in Spain, which were negative for bacteria, rotavirus, and adenovirus by routine diagnostics were screened by real-time RT-PCR assays for the presence of classical and novel astrovirus, rotavirus, norovirus GI and GII, sapovirus, and adenovirus. Overall, 220/384 stool samples (57.3%) were positive for at least one virus. Co-infections were identified in 21% of cases. Among a total of 315 viruses identified, adenovirus was the most prevalent (n = 103), followed by rotavirus (n = 51), sapovirus (n = 50), classical astrovirus (n = 43), novel astroviruses (n = 42), and norovirus (n = 26). Novel astroviruses were present in 13.3% of virus-positive cases. Most novel astroviruses were found in children <2-year-old (30/39 children, 77%, p = 0.01) and were found in co-infection (66%). Only classical astroviruses demonstrated significant differences in the Cq values during mono-infections compared to co-infections. In conclusion, common enteric viruses may be frequently found in children with undiagnosed gastroenteritis, indicating the need to implement more sensitive diagnostic methods. Novel astroviruses circulate in the community and could be the cause of gastroenteritis among young children.
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Human Astrovirus MLB Replication In Vitro: Persistence in Extraintestinal Cell Lines. J Virol 2019; 93:JVI.00557-19. [PMID: 31019055 DOI: 10.1128/jvi.00557-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 02/06/2023] Open
Abstract
MLB astroviruses were identified 10 years ago in feces from children with gastroenteritis of unknown etiology and have been unexpectedly detected in severe cases of meningitis/encephalitis, febrile illness of unknown etiology, and respiratory syndromes. The aim of this study was to establish a cell culture system supporting MLB astrovirus replication. We used two clinical strains to infect several cell lines, an MLB1 strain from a gastroenteritis case, and an MLB2 strain associated with a neurologic infection. Efforts to propagate the viruses in the Caco-2 cell line were unsuccessful. In contrast, we identified two human nonintestinal cell lines, Huh-7 and A549, permissive for both genotypes. After serial passages in the Huh-7.5 cell line, the adapted strains were able to establish persistent infections in the Huh-7.5, Huh-7AI, and A549 cell lines, with high viral loads (up to 10 log10 genome copies/ml) detected by quantitative reverse transcription-PCR (RT-qPCR) in the culture supernatant. Immunofluorescence assays demonstrated infection in about 10% of cells in persistently infected cultures. Electron microscopy revealed particles of 32 to 33 nm in diameter after negative staining of cell supernatants and capsid arrays in ultrathin sections with a particularly high production in Huh-7.5 cells. Interferon (IFN) expression by infected cells and effect of exogenous IFN varied depending on the type of infection and the cell line. The availability of a cell culture system to propagate MLB astroviruses represents a key step to better understand their replicative cycle, as well as a source of viruses to conduct a wide variety of basic virologic studies.IMPORTANCE MLB astroviruses are emerging viruses infecting humans. More studies are required to determine their exact epidemiology, but several reports have already identified them as the cause of unexpected clinical diseases, including severe neurologic diseases. Our study provides the first description of a cell culture system for the propagation of MLB astroviruses, enabling the study of their replicative cycle. Moreover, we demonstrated the unknown capacity of MLB astrovirus to establish persistent infections in cell culture. Whether these persistent infections are also established in vivo remains unknown, but the clinical consequences would be of high interest if persistence was confirmed in vivo Finally, our analysis of IFN expression provides some trails to understand the mechanism by which MLB astroviruses can cause persistent infections in the assayed cultures.
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Malasao R, Khamrin P, Kumthip K, Ushijima H, Maneekarn N. Molecular epidemiology and genetic diversity of human parechoviruses in children hospitalized with acute diarrhea in Thailand during 2011-2016. Arch Virol 2019; 164:1743-1752. [PMID: 30972593 DOI: 10.1007/s00705-019-04249-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/13/2019] [Indexed: 12/25/2022]
Abstract
Little is known about human parechovirus (HPeV) infection in Thailand. The genotype distribution of HPeV strains in children admitted to hospitals with acute gastroenteritis was investigated using polymerase chain reaction (PCR) and nucleotide sequencing of the VP1 region as the detection and genotype identification methods, respectively. Of a total of 2,002 stool samples, 49 (2.4%) were positive for HPeV. Of these, HPeV-1 was the most predominant genotype (40.8%), followed by HPeV-3 (16.3%) and HPeV-14 (16.3%), while HPeV-5, -6, -2, -4, and -8 strains were less frequently detected, at 10.2%, 8.2%, 2%, 2%, and 2%, respectively. HPeV infections were detected throughout the year with the biannual peaks of infection in the rainy (Jun-Jul-Aug) and winter (Nov-Dec-Jan) months in Thailand. Based on VP1 amino acid sequence alignment, the arginyl-glycyl-aspartic acid (RGD) motif was found in HPeV-1, -2, -4, and -6 strains. Additionally, an amino acid insertion at the N-terminus of VP1 was observed in HPeV-4 and HPeV-5 strains. Phylogenetic analysis revealed that small clades of HPeV-1 and HPeV-3 strains emerged in 2016 and 2015, respectively, and dominated in the year of their emergence. The HPeV strains detected in Thailand in this study were most closely related to reference strains from Asia and Europe. The evolutionary rate of HPeV strains was 2.87 × 10-4 (95% highest posterior density (HPD) 0.10-6.14 × 10-4) substitutions/site/year. These findings provide information about the genetic diversity and evolutionary dynamics of HPeV genotypes circulating in pediatric patients with acute gastroenteritis in Thailand.
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Affiliation(s)
- Rungnapa Malasao
- Department of Community Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Suthep Rd, Si Phum, Amphoe Muang, Chiang Mai, 50200, Thailand
| | - Kattareeya Kumthip
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Suthep Rd, Si Phum, Amphoe Muang, Chiang Mai, 50200, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand.
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Suthep Rd, Si Phum, Amphoe Muang, Chiang Mai, 50200, Thailand.
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