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Hikmat H, Le Targa L, Boschi C, Py J, Bedotto M, Morand A, Cassir N, Aherfi S, La Scola B, Colson P. Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022. J Med Virol 2024; 96:e29706. [PMID: 38888111 DOI: 10.1002/jmv.29706] [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: 02/07/2024] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024]
Abstract
The diversity and evolution of the genomes of human bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next-generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in-house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypic clusters determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotypic cluster α tended to be correlated with HAdV co-infection. Subsequent HAdV typing for HBoV1-positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1-associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.
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Affiliation(s)
- Houmadi Hikmat
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Lorlane Le Targa
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Biosellal, Lyon, France
| | - Celine Boschi
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Justine Py
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Marielle Bedotto
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Aurélie Morand
- Service d'Accueil des Urgences Pédiatriques, Hôpital Nord, AP-HM, Marseille, France
- Service de Pédiatrie Générale, Hôpital Timone, AP-HM, Marseille, France
| | - Nadim Cassir
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Sarah Aherfi
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Bernard La Scola
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Philippe Colson
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
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Qian W, Wang X, Wang T, Huang J, Zhang Q, Li Y, Chen S. Development of RPA-Cas12a-fluorescence assay for rapid and reliable detection of human bocavirus 1. Animal Model Exp Med 2024; 7:179-188. [PMID: 36794352 PMCID: PMC11079142 DOI: 10.1002/ame2.12298] [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: 07/23/2022] [Accepted: 11/24/2022] [Indexed: 02/17/2023] Open
Abstract
Human bocavirus (HBoV) 1 is considered an important pathogen that mainly affects infants aged 6-24 months, but preventing viral transmission in resource-limited regions through rapid and affordable on-site diagnosis of individuals with early infection of HBoV1 remains somewhat challenging. Herein, we present a novel faster, lower cost, reliable method for the detection of HBoV1, which integrates a recombinase polymerase amplification (RPA) assay with the CRISPR/Cas12a system, designated the RPA-Cas12a-fluorescence assay. The RPA-Cas12a-fluorescence system can specifically detect target gene levels as low as 0.5 copies of HBoV1 plasmid DNA per microliter within 40 min at 37°C without the need for sophisticated instruments. The method also demonstrates excellent specificity without cross-reactivity to non-target pathogens. Furthermore, the method was appraised using 28 clinical samples, and displayed high accuracy with positive and negative predictive agreement of 90.9% and 100%, respectively. Therefore, our proposed rapid and sensitive HBoV1 detection method, the RPA-Cas12a-fluorescence assay, shows promising potential for early on-site diagnosis of HBoV1 infection in the fields of public health and health care. The established RPA-Cas12a-fluorescence assay is rapid and reliable method for human bocavirus 1 detection. The RPA-Cas12a-fluorescence assay can be completed within 40 min with robust specificity and sensitivity of 0.5 copies/μl.
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Affiliation(s)
- Weidong Qian
- School of Food and Biological EngineeringShaanxi University of Science and TechnologyXi'anP. R. China
| | - Xuefei Wang
- School of Food and Biological EngineeringShaanxi University of Science and TechnologyXi'anP. R. China
| | - Ting Wang
- School of Food and Biological EngineeringShaanxi University of Science and TechnologyXi'anP. R. China
| | - Jie Huang
- School of Food and Biological EngineeringShaanxi University of Science and TechnologyXi'anP. R. China
| | - Qian Zhang
- Department of DermatologyHuazhong University of Science and Technology Union Shenzhen HospitalShenzhenP. R. China
| | - Yongdong Li
- Ningbo Municipal Center for Disease Control and PreventionNingboP. R. China
| | - Si Chen
- Medical College of Shenzhen UniversityShenzhenP. R. China
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Caporizzi A, Ravidà F, Barneschi S, Moriondo M, Nieddu F, Boscia S, Stinco M, Ricci S, Trapani S. Analysis of a Cohort of 165 Pediatric Patients with Human Bocavirus Infection and Comparison between Mono-Infection and Respiratory Co-Infections: A Retrospective Study. Pathogens 2024; 13:55. [PMID: 38251362 PMCID: PMC10821073 DOI: 10.3390/pathogens13010055] [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: 12/15/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
INTRODUCTION Human Bocavirus (HBoV) is mainly associated with respiratory tract infections. However, its role as respiratory pathogen is not fully understood for a high co-infection rate in symptomatic patients and a significant HBoV detection rate in asymptomatic subjects. This study aimed to describe a large cohort of children with HBoV infection and to compare HBoV mono-infection and co-infections. METHODS We retrospectively reviewed data from 165 children admitted to Meyer Children's Hospital IRCCS from March 2022 to March 2023 with the diagnosis of HBoV infection, detected using Reverse Transcription qPCR from nasal swabs. Thereafter, we compared patients with HBoV mono-infection (Group A) and those with HBoV co-infections (Group B) in terms of disease severity, established by the length of stay (LOS), the requirement of Pediatric Intensive Care Unit (PICU), and advanced respiratory support (ARS). RESULTS The median age was 1.5 years; 80% of patients presented with respiratory symptoms. The discharge rate from the emergency department (ED) within 24 h was 42.4%. Most cases (57.6%) were hospitalized, and 7.3% were admitted to PICU due to respiratory failure. Group A comprised 69 patients, and Group B 96 children (95% viral co-infections, 2% bacterial, 3% viral and bacterial). Group A and Group B were similar in hospitalization rate but differed significantly in LOS (median 3 vs. 5 days) and requirement of PICU admission (0 vs. 12 patients, p < 0.001). Patients with a respiratory disease history (17.5%) showed significantly longer LOS and more necessity of inhaled bronchodilator therapy. CONCLUSIONS HBoV should be considered a relevant respiratory pathogen especially in viral co-infections. Patients with HBoV co-infections have a higher risk of necessitating advanced respiratory support with more PICU admission and longer LOS; a previous respiratory disease puts them at a higher risk of longer hospitalization.
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Affiliation(s)
- Alice Caporizzi
- Postgraduate School of Pediatrics, University of Florence, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy; (F.R.); (S.B.)
| | - Federica Ravidà
- Postgraduate School of Pediatrics, University of Florence, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy; (F.R.); (S.B.)
| | - Sara Barneschi
- Postgraduate School of Pediatrics, University of Florence, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy; (F.R.); (S.B.)
| | - Maria Moriondo
- Division of Immunology, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy; (M.M.); (F.N.); (S.B.); (S.R.)
| | - Francesco Nieddu
- Division of Immunology, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy; (M.M.); (F.N.); (S.B.); (S.R.)
| | - Silvia Boscia
- Division of Immunology, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy; (M.M.); (F.N.); (S.B.); (S.R.)
| | - Mariangela Stinco
- Pediatric Unit, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy; (M.S.); (S.T.)
| | - Silvia Ricci
- Division of Immunology, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy; (M.M.); (F.N.); (S.B.); (S.R.)
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Sandra Trapani
- Pediatric Unit, Meyer Children’s Hospital IRCCS, Viale Pieraccini 24, 50139 Florence, Italy; (M.S.); (S.T.)
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
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Jalving HT, Heimdal I, Valand J, Risnes K, Krokstad S, Nordbø SA, Døllner H, Christensen A. The Burden of Human Bocavirus 1 in Hospitalized Children With Respiratory Tract Infections. J Pediatric Infect Dis Soc 2023; 12:282-289. [PMID: 37099765 PMCID: PMC10231390 DOI: 10.1093/jpids/piad027] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/27/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Human bocavirus 1 (HBoV1) is frequently codetected with other viruses, and detected in asymptomatic children. Thus, the burden of HBoV1 respiratory tract infections (RTI) has been unknown. Using HBoV1-mRNA to indicate true HBoV1 RTI, we assessed the burden of HBoV1 in hospitalized children and the impact of viral codetections, compared with respiratory syncytial virus (RSV). METHODS Over 11 years, we enrolled 4879 children <16 years old admitted with RTI. Nasopharyngeal aspirates were analyzed with polymerase chain reaction for HBoV1-DNA, HBoV1-mRNA, and 19 other pathogens. RESULTS HBoV1-mRNA was detected in 2.7% (130/4850) samples, modestly peaking in autumn and winter. Forty-three percent with HBoV1 mRNA were 12-17 months old, and only 5% were <6 months old. A total of 73.8% had viral codetections. It was more likely to detect HBoV1-mRNA if HBoV1-DNA was detected alone (odds ratio [OR]: 3.9, 95% confidence interval [CI]: 1.7-8.9) or with 1 viral codetection (OR: 1.9, 95% CI: 1.1-3.3), compared to ≥2 codetections. Codetection of severe viruses like RSV had lower odds for HBoV1-mRNA (OR: 0.34, 95% CI: 0.19-0.61). The yearly lower RTI hospitalization rate per 1000 children <5 years was 0.7 for HBoV1-mRNA and 8.7 for RSV. CONCLUSIONS True HBoV1 RTI is most likely when HBoV1-DNA is detected alone, or with 1 codetected virus. Hospitalization due to HBoV1 LRTI is 10-12 times less common than RSV.
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Affiliation(s)
- Hedda Trømborg Jalving
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Inger Heimdal
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jonas Valand
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Kari Risnes
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Children’s Department, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Sidsel Krokstad
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Svein Arne Nordbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Henrik Døllner
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Children’s Department, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Andreas Christensen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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Trapani S, Caporizzi A, Ricci S, Indolfi G. Human Bocavirus in Childhood: A True Respiratory Pathogen or a "Passenger" Virus? A Comprehensive Review. Microorganisms 2023; 11:1243. [PMID: 37317217 DOI: 10.3390/microorganisms11051243] [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: 03/31/2023] [Revised: 05/04/2023] [Accepted: 05/08/2023] [Indexed: 06/16/2023] Open
Abstract
Recently, human bocavirus (HBoV) has appeared as an emerging pathogen, with an increasing number of cases reported worldwide. HBoV is mainly associated with upper and lower respiratory tract infections in adults and children. However, its role as a respiratory pathogen is still not fully understood. It has been reported both as a co-infectious agent (predominantly with respiratory syncytial virus, rhinovirus, parainfluenza viruses, and adenovirus), and as an isolated viral pathogen during respiratory tract infections. It has also been found in asymptomatic subjects. The authors review the available literature on the epidemiology of HBoV, the underlying risk factors associated with infection, the virus's transmission, and its pathogenicity as a single pathogen and in co-infections, as well as the current hypothesis about the host's immune response. An update on different HBoV detection methods is provided, including the use of quantitative single or multiplex molecular methods (screening panels) on nasopharyngeal swabs or respiratory secretions, tissue biopsies, serum tests, and metagenomic next-generations sequencing in serum and respiratory secretions. The clinical features of infection, mainly regarding the respiratory tract but also, though rarely, the gastrointestinal one, are extensively described. Furthermore, a specific focus is dedicated to severe HBoV infections requiring hospitalization, oxygen therapy, and/or intensive care in the pediatric age; rare fatal cases have also been reported. Data on tissue viral persistence, reactivation, and reinfection are evaluated. A comparison of the clinical characteristics of single infection and viral or bacterial co-infections with high or low HBoV rates is carried out to establish the real burden of HBoV disease in the pediatric population.
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Affiliation(s)
- Sandra Trapani
- Department of Health Sciences, University of Florence, Viale Pieraccini, 24, 50139 Florence, Italy
- Pediatric Unit, Meyer Children's Hospital IRCCS, Viale Pieraccini, 24, 50139 Florence, Italy
| | - Alice Caporizzi
- Pediatric Unit, Meyer Children's Hospital IRCCS, Viale Pieraccini, 24, 50139 Florence, Italy
| | - Silvia Ricci
- Department of Health Sciences, University of Florence, Viale Pieraccini, 24, 50139 Florence, Italy
- Division of Immunology, Meyer Children's Hospital IRCCS, Viale Pieraccini, 24, 50139 Florence, Italy
| | - Giuseppe Indolfi
- Pediatric Unit, Meyer Children's Hospital IRCCS, Viale Pieraccini, 24, 50139 Florence, Italy
- NEUROFARBA Department, University of Florence, Viale Pieraccini, 24, 50139 Florence, Italy
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Prevalence and Genetic Characteristics of Human Bocaviruses Detected in Patients with Acute Respiratory Infections in Bulgaria. Int J Microbiol 2021; 2021:7035081. [PMID: 34819956 PMCID: PMC8608525 DOI: 10.1155/2021/7035081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/28/2021] [Indexed: 12/16/2022] Open
Abstract
Нuman bocaviruses (hBoVs) are often associated with acute respiratory infections (ARIs). Information on the distribution and molecular epidemiology of hBoVs in Bulgaria is currently limited. The objectives of this study were to investigate the prevalence and genetic characteristics of hBoVs detected in patients with ARIs in Bulgaria. From October 2016 to September 2019, nasopharyngeal/oropharyngeal swabs were prospectively collected from 1842 patients of all ages and tested for 12 common respiratory viruses using a real-time RT-PCR. Phylogenetic and amino acid analyses of the hBoV VP1/VP2 gene/protein were performed. HBoV was identified in 98 (5.3%) patients and was the 6th most prevalent virus after respiratory-syncytial virus (20.4%), influenza A(H1N1)pdm09 (11.1%), A(H3N2) (10.5%), rhinoviruses (9.9%), and adenoviruses (6.8%). Coinfections with other respiratory viruses were detected in 51% of the hBoV-positive patients. Significant differences in the prevalence of hBoVs were found during the different study periods and in patients of different age groups. The detection rate of hBoV was the highest in patients aged 0-4 years (6.9%). In this age group, hBoV was the only identified virus in 9.7%, 5.8%, and 1.1% of the children diagnosed with laryngotracheitis, bronchiolitis, and pneumonia, respectively. Among patients aged ≥5 years, hBoV was detected as a single agent in 2.2% of cases of pneumonia. Phylogenetic analysis showed that all Bulgarian hBoV strains belonged to the hBoV1 genotype. A few amino acid substitutions were identified compared to the St1 prototype strain. This first study amongst an all-age population in Bulgaria showed a significant rate of hBoV detection in some serious respiratory illnesses in early childhood, year-to-year changes in the hBoV prevalence, and low genetic variability in the circulating strains.
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Nichols GL, Gillingham EL, Macintyre HL, Vardoulakis S, Hajat S, Sarran CE, Amankwaah D, Phalkey R. Coronavirus seasonality, respiratory infections and weather. BMC Infect Dis 2021; 21:1101. [PMID: 34702177 PMCID: PMC8547307 DOI: 10.1186/s12879-021-06785-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 10/12/2021] [Indexed: 12/23/2022] Open
Abstract
Background The survival of coronaviruses are influenced by weather conditions and seasonal coronaviruses are more common in winter months. We examine the seasonality of respiratory infections in England and Wales and the associations between weather parameters and seasonal coronavirus cases. Methods Respiratory virus disease data for England and Wales between 1989 and 2019 was extracted from the Second-Generation Surveillance System (SGSS) database used for routine surveillance. Seasonal coronaviruses from 2012 to 2019 were compared to daily average weather parameters for the period before the patient’s specimen date with a range of lag periods. Results The seasonal distribution of 985,524 viral infections in England and Wales (1989–2019) showed coronavirus infections had a similar seasonal distribution to influenza A and bocavirus, with a winter peak between weeks 2 to 8. Ninety percent of infections occurred where the daily mean ambient temperatures were below 10 °C; where daily average global radiation exceeded 500 kJ/m2/h; where sunshine was less than 5 h per day; or where relative humidity was above 80%. Coronavirus infections were significantly more common where daily average global radiation was under 300 kJ/m2/h (OR 4.3; CI 3.9–4.6; p < 0.001); where average relative humidity was over 84% (OR 1.9; CI 3.9–4.6; p < 0.001); where average air temperature was below 10 °C (OR 6.7; CI 6.1–7.3; p < 0.001) or where sunshine was below 4 h (OR 2.4; CI 2.2–2.6; p < 0.001) when compared to the distribution of weather values for the same time period. Seasonal coronavirus infections in children under 3 years old were more frequent at the start of an annual epidemic than at the end, suggesting that the size of the susceptible child population may be important in the annual cycle. Conclusions The dynamics of seasonal coronaviruses reflect immunological, weather, social and travel drivers of infection. Evidence from studies on different coronaviruses suggest that low temperature and low radiation/sunlight favour survival. This implies a seasonal increase in SARS-CoV-2 may occur in the UK and countries with a similar climate as a result of an increase in the R0 associated with reduced temperatures and solar radiation. Increased measures to reduce transmission will need to be introduced in winter months for COVID-19. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06785-2.
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Affiliation(s)
- G L Nichols
- Climate Change and Health Group, Centre for Radiation Chemicals and Environmental Hazards, UK Health Security Agency (Formerly Public Health England), Chilton, Oxon, OX11 0RQ, UK. .,European Centre for Environment and Human Health, University of Exeter Medical School, C/O Knowledge Spa RCHT, Truro, Cornwall, TR1 3HD, UK. .,School of Environmental Sciences, UEA, Norwich, NR4 7TJ, UK.
| | - E L Gillingham
- Climate Change and Health Group, Centre for Radiation Chemicals and Environmental Hazards, UK Health Security Agency (Formerly Public Health England), Chilton, Oxon, OX11 0RQ, UK
| | - H L Macintyre
- Climate Change and Health Group, Centre for Radiation Chemicals and Environmental Hazards, UK Health Security Agency (Formerly Public Health England), Chilton, Oxon, OX11 0RQ, UK.,School of Geography Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - S Vardoulakis
- European Centre for Environment and Human Health, University of Exeter Medical School, C/O Knowledge Spa RCHT, Truro, Cornwall, TR1 3HD, UK.,National Centre for Epidemiology and Population Health, Research School of Population Health, Australian National University, Canberra, ACT, 2601, Australia
| | - S Hajat
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, UK
| | - C E Sarran
- Met Office, Fitzroy Road, Exeter, EX1 3PB, UK.,Institute of Health Research, University of Exeter, Saint Luke's Campus, Heavitree Road, Exeter, EX1 2LU, UK
| | - D Amankwaah
- Climate Change and Health Group, Centre for Radiation Chemicals and Environmental Hazards, UK Health Security Agency (Formerly Public Health England), Chilton, Oxon, OX11 0RQ, UK
| | - R Phalkey
- Climate Change and Health Group, Centre for Radiation Chemicals and Environmental Hazards, UK Health Security Agency (Formerly Public Health England), Chilton, Oxon, OX11 0RQ, UK.,Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany.,Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
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Ljubin-Sternak S, Slović A, Mijač M, Jurković M, Forčić D, Ivković-Jureković I, Tot T, Vraneš J. Prevalence and Molecular Characterization of Human Bocavirus Detected in Croatian Children with Respiratory Infection. Viruses 2021; 13:v13091728. [PMID: 34578309 PMCID: PMC8473146 DOI: 10.3390/v13091728] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/16/2022] Open
Abstract
Human bocavirus (HBoV) 1 is considered an important respiratory pathogen, while the role of HBoV2-4 in clinical disease remains somewhat controversial. Since, they are characterized by a rapid evolution, worldwide surveillance of HBoVs’ genetics is necessary. This study explored the prevalence of HBoV genotypes in pediatric patients with respiratory tract infection in Croatia and studied their phylogeny. Using multiplex PCR for 15 respiratory viruses, we investigated 957 respiratory samples of children up to 18 years of age with respiratory tract infection obtained from May 2017 to March 2021 at two different hospitals in Croatia. Amplification of HBoV near-complete genome or three overlapping fragments was performed, sequenced, and their phylogenetic inferences constructed. HBoV was detected in 7.6% children with a median age of 1.36 years. Co-infection was observed in 82.2% samples. Sequencing was successfully performed on 29 HBoV positive samples, and all belonged to HBoV1. Croatian HBoV1 sequences are closely related to strains isolated worldwide, and no phylogenetic grouping based on mono- or co-infection cases or year of isolation was observed. Calculated rates of evolution for HBoV1 were 10−4 and 10−5 substitutions per site and year. Recombination was not detected among sequences from this study.
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Affiliation(s)
- Sunčanica Ljubin-Sternak
- Molecular Microbiology Department, Dr. Andrija Štampar Teaching Institute of Public Health, 10000 Zagreb, Croatia; (M.M.); (J.V.)
- Medical Microbiology Department, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
- Correspondence:
| | - Anamarija Slović
- Center of Excellence for Virus Immunology and Vaccines, Center for Research and Knowledge Transfer in Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (A.S.); (M.J.); (D.F.)
| | - Maja Mijač
- Molecular Microbiology Department, Dr. Andrija Štampar Teaching Institute of Public Health, 10000 Zagreb, Croatia; (M.M.); (J.V.)
- Medical Microbiology Department, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Mirna Jurković
- Center of Excellence for Virus Immunology and Vaccines, Center for Research and Knowledge Transfer in Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (A.S.); (M.J.); (D.F.)
| | - Dubravko Forčić
- Center of Excellence for Virus Immunology and Vaccines, Center for Research and Knowledge Transfer in Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (A.S.); (M.J.); (D.F.)
| | - Irena Ivković-Jureković
- Department of Pulmonology, Allergy, Immunology and Rheumatology, Children’s Hospital Zagreb, 10000 Zagreb, Croatia;
- Faculty for Dental Medicine and Healthcare/School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Tatjana Tot
- Microbiology Department, General hospital Karlovac, Karlovac, 47000 Karlovac, Croatia;
| | - Jasmina Vraneš
- Molecular Microbiology Department, Dr. Andrija Štampar Teaching Institute of Public Health, 10000 Zagreb, Croatia; (M.M.); (J.V.)
- Medical Microbiology Department, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
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Huang XB, Yuan L, Ye CX, Zhu X, Lin CJ, Zhang DM, He KS, Niu RX, Cao KY, Xu L. Epidemiological characteristics of respiratory viruses in patients with acute respiratory infections during 2009-2018 in southern China. Int J Infect Dis 2020; 98:21-32. [PMID: 32562851 DOI: 10.1016/j.ijid.2020.06.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Acute respiratory infections (ARIs) remain a significant public threat with high morbidity and mortality worldwide; viruses are significant pathogens that cause ARIs. This study was conducted to better understand the epidemiological characteristics of respiratory viruses circulating in southern China. METHODS We collected 22,680 respiratory samples from ARI patients in 18 hospitals in southern China during 2009-2018; seven common respiratory viruses including Flu, RSV, PIV, hMPV, ADV, HCoV, and HBoV were screened using in-house real-time PCR. RESULTS Of all samples, 9760 ARI cases (9760/22680, 43.03%) tested positive for the seven common respiratory viruses. The most detected virus was Flu (14.15%), followed by RSV (10.33%) and PIV (5.43%); Flu-A, PIV3, and HCoV-OC43 were the predominant subtypes. Although most of the viruses were detected in male inpatients, Flu was more likely detected in female outpatients. Flu infection was more likely to cause URTI (upper respiratory tract infection), whereas RSV infection was more likely to cause pneumonia and bronchitis. The prevalence of Flu was particularly high in 2009. The epidemic level was found notably high in 2014-2018 for RSV, in 2016-2018 for PIV, in the summer of 2018 for ADV, in the summer of 2016 and winter of 2018 for HCoV, and in the summer of 2011 and autumn of 2018 for HBoV. The co-detection rate of the seven viruses was 4.70%; RSV, PIV, and Flu were the most commonly co-detected viruses. CONCLUSIONS This work demonstrates the epidemiological characteristics of seven common respiratory viruses in ARI patients in southern China.
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Affiliation(s)
- Xu-Bin Huang
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lei Yuan
- Clinical laboratory, First Affiliated Hospital of Nanchang University, Nanchang University, Jiangxi, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China; Research Center for Clinical Laboratory Standard, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Cong-Xiu Ye
- Department of Dermatovenereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xun Zhu
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China; Research Center for Clinical Laboratory Standard, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Cui-Ji Lin
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China; Research Center for Clinical Laboratory Standard, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ding-Mei Zhang
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Kai-Shu He
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China; Research Center for Clinical Laboratory Standard, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ruo-Xi Niu
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China; Research Center for Clinical Laboratory Standard, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kai-Yuan Cao
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China; Research Center for Clinical Laboratory Standard, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Lin Xu
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China; Research Center for Clinical Laboratory Standard, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
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Inagaki A, Kitano T, Nishikawa H, Suzuki R, Onaka M, Nishiyama A, Kitagawa D, Oka M, Masuo K, Yoshida S. The Epidemiology of Admission-Requiring Pediatric Respiratory Infections in a Japanese Community Hospital Using Multiplex PCR. Jpn J Infect Dis 2020; 74:23-28. [PMID: 32611977 DOI: 10.7883/yoken.jjid.2020.154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Respiratory tract infections (RTIs) are the most common diseases globally among children. This study aimed to assess the epidemiology of admission-requiring pediatric RTI cases and evaluate the effect of the pathogen type on the length of hospital stay (LOS) using the FilmArray® respiratory panel, a multiplex PCR test. The age-specific distribution and seasonality of viruses were investigated between March 26, 2018 and April 12, 2019. Multivariable linear regression analyses were performed to evaluate the effect of pathogen type and coinfection on LOS. Among 153 hospitalized RTI patients, respiratory syncytial virus was the leading cause of hospitalization in infants < 12 months of age (27.7%). Human metapneumovirus and parainfluenza virus were also major causes of hospitalization in patients aged 2-3 years (22.6% and 22.6%, respectively). In the multivariable linear regression model excluding rhinovirus/enterovirus, there was a significant association between viral coinfection and longer LOS (p = 0.012), while single viral infection of any type was not positively correlated with LOS. This study revealed the epidemiology of admission-requiring pediatric RTIs.
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Affiliation(s)
- Atsushi Inagaki
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
| | - Taito Kitano
- Division of Infectious Diseases, The Hospital for Sick Children, Canada
| | - Hiroki Nishikawa
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
| | - Rika Suzuki
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
| | - Masayuki Onaka
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
| | - Atsuko Nishiyama
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
| | - Daisuke Kitagawa
- Department of Microbiology, Nara Prefecture General Medical Center, Japan
| | - Miyako Oka
- Department of Microbiology, Nara Prefecture General Medical Center, Japan
| | - Kazue Masuo
- Department of Microbiology, Nara Prefecture General Medical Center, Japan
| | - Sayaka Yoshida
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
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Cao LT, Liu HH, Li J, Yin XD, Duan Y, Wang J. Relationship of meteorological factors and human brucellosis in Hebei province, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:135491. [PMID: 31740063 DOI: 10.1016/j.scitotenv.2019.135491] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/31/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Brucellosis has always been one of the major public health problems in China. Investigating the influencing factors of brucellosis is conducive to its prevention and control. The incidence trend of brucellosis shows an obvious seasonality, suggesting that there may be a correlation between brucellosis and meteorological factors, but related studies were few. We aimed to use the autoregressive integrated moving average (ARIMA) model to analyze the relationship between meteorological factors and brucellosis. METHODS The data of monthly incidence of brucellosis and meteorological factors in Hebei province from January 2004 to December 2015 were collected from the Chinese Public Health Science Data Center and Chinese meteorological data website. An ARIMA model incorporated with covariables was conducted to estimate the effects of meteorological variables on brucellosis. RESULTS There was a highest peak from May to July every year and an upward trend during the study period. Atmospheric pressure, wind speed, mean temperature, and relative humidity had significant effects on brucellosis. The ARIMA(1,0,0)(1,1,0)12 model with the covariates of atmospheric pressure, wind speed and mean temperature was the optimal model. The results showed that the atmospheric pressure with a 2-month lag (β = -0.004, p = 0.037), the wind speed with a 1-month lag (β = 0.030, p = 0.035), and the mean temperature with a 2-month lag (β = -0.003, p = 0.034) were significant predictors. CONCLUSION Our study suggests that atmospheric pressure, wind speed, mean temperature, and relative humidity have a significant impact on brucellosis. Further understanding of its mechanism would help facilitate the monitoring and early warning of brucellosis.
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Affiliation(s)
- Long-Ting Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230036, China
| | - Hong-Hui Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230036, China
| | - Juan Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230036, China
| | - Xiao-Dong Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230036, China
| | - Yu Duan
- Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, Hefei, Anhui 230036, China
| | - Jing Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230036, China.
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Zou W, Xiong M, Deng X, Engelhardt JF, Yan Z, Qiu J. A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium. Viruses 2019; 11:v11010033. [PMID: 30621044 PMCID: PMC6357044 DOI: 10.3390/v11010033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/30/2018] [Accepted: 01/02/2019] [Indexed: 02/07/2023] Open
Abstract
Human bocavirus 1 (HBoV1) infects well-differentiated (polarized) human airway epithelium (HAE) cultured at an air-liquid interface (ALI). In the present study, we applied next-generation RNA sequencing to investigate the genome-wide transcription profile of HBoV1, including viral mRNA and small RNA transcripts, in HBoV1-infected HAE cells. We identified novel transcription start and termination sites and confirmed the previously identified splicing events. Importantly, an additional proximal polyadenylation site (pA)p2 and a new distal polyadenylation site (pA)dREH lying on the right-hand hairpin (REH) of the HBoV1 genome were identified in processing viral pre-mRNA. Of note, all viral nonstructural proteins-encoding mRNA transcripts use both the proximal polyadenylation sites [(pA)p1 and (pA)p2] and distal polyadenylation sites [(pA)d1 and (pA)dREH] for termination. However, capsid proteins-encoding transcripts only use the distal polyadenylation sites. While the (pA)p1 and (pA)p2 sites were utilized at roughly equal efficiency for proximal polyadenylation of HBoV1 mRNA transcripts, the (pA)d1 site was more preferred for distal polyadenylation. Additionally, small RNA-seq analysis confirmed there is only one viral noncoding RNA (BocaSR) transcribed from nt 5199⁻5340 of the HBoV1 genome. Thus, our study provides a systematic and unbiased transcription profile, including both mRNA and small RNA transcripts, of HBoV1 in HBoV1-infected HAE-ALI cultures.
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Affiliation(s)
- Wei Zou
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Min Xiong
- The Children's Mercy Hospital, School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA.
| | - Xuefeng Deng
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - John F Engelhardt
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Ziying Yan
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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