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Trang UTH, Phuong HVM, Hoang NH, Son NV, Thanh LT, Hang NLK, Cuong VD, Huong TTT, Hien NT, Anh NP, Mai LQ. Circulation of human respiratory syncytial virus and new ON1 genotype in northern Viet Nam, 2017-2020. Western Pac Surveill Response J 2023; 14:1-9. [PMID: 38021214 PMCID: PMC10646430 DOI: 10.5365/wpsar.2023.14.4.990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Objective Human respiratory syncytial virus (RSV) is a primary cause of paediatric severe acute respiratory infection (SARI) worldwide, especially in developing countries. We investigated the genetic characteristics of RSV in northern Viet Nam to determine the prevalence and distribution of subtypes as well as the diversity and transmission patterns of genotypes. Methods In two facilities, from January 2017 to December 2020, 1563 clinical specimens were collected from paediatric patients hospitalized with SARI and tested for RSV. Selected positive samples underwent sequencing analysis targeting the second hypervariable region of the G gene using next-generation sequencing. Results The RSV positivity rate was 28.02% (438/1563 samples), and prevalence was highest in children aged < 1 year (43.84%; 192/438). Subtype RSV-A accounted for 53.42% (234/438) of cases, RSV-B for 45.89% (201/438), and there was coinfection in 0.68% (3/438). Both subtypes cocirculated and peaked during August-September in each year of the study. Phylogenetic analysis showed that RSV-A samples belonged to the ON1 genotype, which has three subgenotypes: ON1.1, ON1.2 and ON1.3. However, we did not find the 72-nucleotide duplication in the second hypervariable region of the G gene, a characteristic of genotype ON1, in any RSV-A samples. RSV-B samples belonged to genotype BA9. Discussion Our results provide additional molecular characterization of RSV infections in Viet Nam. Specially, our study is the first to report the absence of the 72-nucleotide duplication in the G gene of RSV-A genotype ON1 in Viet Nam, which may help in understanding the genetic evolution of RSV and be useful for vaccine development in the future.
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Affiliation(s)
- Ung Thi Hong Trang
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | | | - Nguyen Huy Hoang
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Nguyen Vu Son
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Le Thi Thanh
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | | | - Vuong Duc Cuong
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | | | - Nguyen Thi Hien
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | | | - Le Quynh Mai
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
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Laubscher F, Kaiser L, Cordey S. SCANellome: Analysis of the Genomic Diversity of Human and Non-Human Primate Anelloviruses from Metagenomics Data. Viruses 2023; 15:1575. [PMID: 37515261 PMCID: PMC10384568 DOI: 10.3390/v15071575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Anelloviruses are extremely prevalent in the human population and are considered to be commensal parts of the human virome. The best-known member in humans is the Torque teno virus. Recent metagenomic next-generation sequencing investigations have helped reveal the considerable number of species and genotypes from the same genus that can be co-detected within a single individual and that this diversity increases as a function of age during the first months/years of life. As a result, to date, the bioinformatics analysis of this genetic diversity remains complex and constraining for researchers. Here, we present SCANellome, a user-friendly tool to investigate the anellome composition at the genus, species, and genotype levels of samples from metagenomics data generated by the Illumina and Nanopore platforms. SCANellome is based on an in-house up-to-date database that includes all human and non-human primate anellovirus reference sequences available on GenBank and meets the latest classification criteria established by the International Committee on Taxonomy of Viruses.
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Affiliation(s)
- Florian Laubscher
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
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Chu FL, Li C, Chen L, Dong B, Qiu Y, Liu Y. Respiratory viruses among pediatric inpatients with acute lower respiratory tract infections in Jinan, China, 2016-2019. J Med Virol 2022; 94:4319-4328. [PMID: 35593042 DOI: 10.1002/jmv.27875] [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: 12/09/2021] [Revised: 04/16/2022] [Accepted: 05/17/2022] [Indexed: 11/06/2022]
Abstract
The viral etiologies responsible for acute lower respiratory tract infections (ALRI) are a major cause of pediatric hospitalization, and some develop severe diseases requiring pediatric intensive care unit (PICU) admission. The aim of this study was to determine the prevalence of viruses and risk factors associated with PICU admission among patients hospitalized for ALRI. Nasopharyngeal swabs were collected to detect human rhinovirus (HRV), influenza A and B viruses (IAV, IBV), parainfluenza viruses (PIV), and respiratory syncytial virus (RSV) by reverse transcription-polymerase chain reaction (RT-PCR) and adenovirus (ADV) by PCR. Of the 5590 pediatric inpatients enrolled, respiratory viral infection occurred in 2102 (37.60%) patients, including 1846 (33.02%) single and 256 (4.58%) mixed viral infections. Among the nasopharyngeal swabs from pediatric inpatients, HRV accounted for the highest detection rate (16.48%), followed by PIV (8.35%), RSV (7.41%), ADV (4.63%), IAV (3.51%), and IBV (2.08%). The positive rate of viral tests decreased with increasing age and was higher in males (39.29%) than females (34.67%). The prevalence of viral infection was the highest in winter (41.57%) and lowest in autumn (31.78%). Each virus had a seasonal pattern, with peaks occurring in months of their epidemic seasons. RSV infection and the presence of comorbidities including congenital tracheal stenosis, congenital heart disease, metabolic disorder, immunodeficiency, renal disease, gastrointestinal disease and neurological disorder might be associated with the need for PICU admission. Therefore, this study provides useful information for the prevention and control of virus-related respiratory diseases and the early identification of and the intervention in severe cases. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Fu-Lu Chu
- Department of Clinical Laboratory, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Chen Li
- Jinan hospital, Jinan, Shandong, PR China
| | - Li Chen
- Department of Ultrasound, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Bo Dong
- Department of Cardiology, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Yang Qiu
- Department of Clinical Laboratory, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Yiqing Liu
- Department of Clinical Laboratory, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong, PR China
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Abstract
Anelloviruses are small negative-sense single-stranded DNA viruses with genomes ranging in size from 1.6 to 3.9 kb. The family Anelloviridae comprised 14 genera before the present changes. However, in the last five years, a large number of diverse anelloviruses have been identified in various organisms. Here, we undertake a global analysis of mammalian anelloviruses whose full genome sequences have been determined and have an intact open reading frame 1 (ORF1). We established new criteria for the classification of anelloviruses, and, based on our analyses, we establish new genera and species to accommodate the unclassified anelloviruses. We also note that based on the updated species demarcation criteria, some previously assigned species (n = 10) merge with other species. Given the rate at which virus sequence data are accumulating, and with the identification of diverse anelloviruses, we acknowledge that the taxonomy will have to be dynamic and continuously evolve to accommodate new members.
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Evolutionary analysis of human respiratory syncytial virus collected in Myanmar between 2015 and 2018. INFECTION GENETICS AND EVOLUTION 2021; 93:104927. [PMID: 34020068 DOI: 10.1016/j.meegid.2021.104927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/24/2022]
Abstract
We studied genetic variation in the second hypervariable region (HVR) of the G gene of human respiratory syncytial virus (HRSV) from 1701 nasal swab samples collected from outpatients with acute respiratory infections at two general hospitals in the cities Yangon and Pyinmana in Myanmar from 2015 to 2018. HRSV genotypes were characterized using phylogenetic trees constructed using the maximum likelihood method. Time-scale phylogenetic tree analyses were performed using the Bayesian Markov chain Monte Carlo method. In total, 244 (14.3%) samples were HRSV-positive and were classified as HRSV-A (n = 84, 34.4%), HRSV-B (n = 158, 64.8%), and co-detection of HRSV-A/HRSV-B (n = 2, 0.8%). HRSV epidemics occurred seasonally between July (1.9%, 15/785) and August (10.5%, 108/1028), with peak infections in September (35.8%, 149/416) and October (58.2%, 89/153). HRSV infection rate was higher in children ≥1 year of age than in those <1 year of age (70.5% vs. 29.5%). The most common HRSV symptoms in children were cough (80%-90%) and rhinorrhea (70%-100%). The predominant genotypes were ON1for HRSV-A (78%) and BA9 for HRSV-B (64%). Time to the most recent common ancestor was 2014 (95% highest posterior density [HPD], 2012-2015) for HRSV-A ON1 and 2009 (95% HPD, 2004-2012) for HRSV-B BA9. The mean evolutionary rate (substitutions/site/year) for HRSV-B (2.12 × 10-2, 95% HPD, 8.53 × 10-3-3.63 × 10-2) was slightly higher than that for HRSV-A (1.39 × 10-2, 95% HPD, 6.03 × 10-3-2.12 × 10-2). The estimated effective population size (diversity) for HRSV-A increased from 2015 to 2016 and declined in mid-2018, whereas HRSV-B diversity was constant in 2015 and 2016 and increased in mid-2017. In conclusion, the dominant HRSV-A and HRSV-B genotypes in Myanmar were ON1 and BA9, respectively, between 2015 and 2018. HRSV-B evolved slightly faster than HRSV-A and exhibited unique phylogenetic characteristics.
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Duan Y, He J, Cui Y, Li W, Jiang Y. Characteristics and forecasting of respiratory viral epidemics among children in west China. Medicine (Baltimore) 2021; 100:e25498. [PMID: 33879683 PMCID: PMC8078258 DOI: 10.1097/md.0000000000025498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/15/2021] [Indexed: 02/05/2023] Open
Abstract
We aimed to assess the respiratory virus characteristics and forecasts among young children with acute respiratory tract infection (ARTI) in west China.This retrospective study investigated the epidemic characteristics of respiratory viruses among 11,813 paediatric ARTI patient samples (mean age, 2.25 years) between March 2018 and March 2020.The ratio of boys to girls was 1.36. The 2 predominant viruses were influenza (Flu) A and respiratory syncytial virus (RSV) in both years, with Flu A accounting for 47.3% and 47.5% in the first and second years and RSV accounting for 32.7% and 24.7% of the positive samples in the first and second years, respectively. The Flu B positive rates were 10.9% and 13.1%, and those of the other 4 viruses were <7%. The most common virus was RSV in children below 5 years and Flu A in those between 5 and 10 years. Flu A and RSV demonstrated pronounced seasonality, and their infection rates increased from October. During the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic, isolation measures led to a decline in the number of ARTI cases.This study provides surveillance data of the respiratory viruses in west China. It could guide medical staff in implementing necessary prevention and management strategies before future viral outbreaks.
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Affiliation(s)
- Yifei Duan
- Department of Laboratory Medicine, West China Second University Hospital
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
| | - Jinlan He
- Departments of Head and Neck Oncology and Radiation Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yali Cui
- Department of Laboratory Medicine, West China Second University Hospital
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
| | - Wensheng Li
- Department of Laboratory Medicine, West China Second University Hospital
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
| | - Yongmei Jiang
- Department of Laboratory Medicine, West China Second University Hospital
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
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Wang J, Xiao T, Xiao F, Hong S, Wang S, Lin J, Li Y, Wang X, Yan K, Zhuang D. Time Distributions of Common Respiratory Pathogens Under the Spread of SARS-CoV-2 Among Children in Xiamen, China. Front Pediatr 2021; 9:584874. [PMID: 33912516 PMCID: PMC8075055 DOI: 10.3389/fped.2021.584874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 03/15/2021] [Indexed: 11/18/2022] Open
Abstract
Objectives: The aim of this study was to observe the effect of COVID-19 prevention and control measures on the transmission of common respiratory viruses in a pediatric population. Methods: This was a retrospective observational study. The study population was selected from children with respiratory diseases who attended Xiamen Children's Hospital from January 1, 2018 to January 31, 2021. All children were screened for influenza virus, parainfluenza virus, respiratory syncytial virus (RSV), adenovirus, and Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The changes in respiratory virus detection rates before and after the SARS-CoV-2 intervention were analyzed using an interrupted time-series model. Polynomial curve fitting was also used to predict future short-term trends in respiratory virus detection. Results: A total of 56,859 children were seen at Xiamen Children's Hospital from January 1, 2018 to Jan 31, 2021, of which 32,120 were tested for respiratory viruses via pharyngeal swabs. The overall positive detection rates of the four respiratory viral infections decreased significantly (P = 0.0017) after the implementation of the quarantine and school suspension measures in January 2020. Among them, the detection rate of RSV decreased most significantly (P = 0.008), and although there was no statistically significant difference in the detection rates of the influenza virus, parainfluenza virus, and adenovirus, a downward trend in the graph was observed. The positive detection rates of RSV in the 0-1-, 1-3-, and 3-7-year-old groups all decreased significantly (P = 0.035, 0.016, and 0.038, respectively). The change in the positive detection rate of RSV was relatively stable in the 7-18-year-old group. A total of 10,496 samples were tested for SARS-CoV-2, and no positive cases were reported. Conclusions: The combination of preventive and control measures for COVID-19 reduced the detection rate of four common respiratory viruses, with the greatest impact on RSV. If prevention and control measures continue to be maintained, the overall detection rate or absolute number of detections for the four respiratory viruses will remain low in the short term. However, this trend is likely to vary with the changes in measures.
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Affiliation(s)
- Jinhui Wang
- Department of Clinical Laboratory, Xiamen Children's Hospital (Children's Hospital of Fudan University Xiamen Branch), Xiamen, China
| | - Tiantian Xiao
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai, China.,Department of Neonatology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Feifan Xiao
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai, China.,Center for Molecular Medicine, Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shaoxian Hong
- Pediatric Intensive Care Unit, Xiamen Children's Hospital (Children's Hospital of Fudan University Xiamen Branch), Xiamen, China
| | - Shunqin Wang
- Pediatric Intensive Care Unit, Xiamen Children's Hospital (Children's Hospital of Fudan University Xiamen Branch), Xiamen, China
| | - Jiancheng Lin
- Department of Clinical Laboratory, Xiamen Children's Hospital (Children's Hospital of Fudan University Xiamen Branch), Xiamen, China
| | - Yong Li
- Department of Medical Services, the Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Xiaochuan Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, China
| | - Kai Yan
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Deyi Zhuang
- Xiamen Key Laboratory of Neonatal Diseases, Xiamen Children's Hospital (Children's Hospital of Fudan University Xiamen Branch), Xiamen, China
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