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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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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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3
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Hamza IA, Abd-Elmaksoud S. Applicability of crAssphage as a performance indicator for viral reduction during activated sludge wastewater treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:50723-50731. [PMID: 36800087 PMCID: PMC10104927 DOI: 10.1007/s11356-023-25824-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/05/2023] [Indexed: 04/16/2023]
Abstract
A major threat to water quality is the discharge of human-derived wastewater, which can cause waterborne illnesses associated with enteric viruses. A poor association exists between fecal indicator bacteria and virus fate in the environment, especially during wastewater treatment. In the current study, the potential of using a novel human gut bacteriophage crAssphage as a wastewater treatment process indicator was evaluated. Using qPCR, influent and effluent wastewater samples of two wastewater treatment plants were analyzed for crAssphage and human viruses including human bocavirus (HBoV), human adenovirus (HAdV), and human polyomavirus (HPyV). All samples were positive for crAssphage. The annual crAssphage concentrations varied between 1.45E + 04 and 2.39E + 08 gc/l in influent samples and from 1.25E + 04 to 7.88E + 06 gc/l in effluent samples. Human viruses concentrations were some orders of magnitude lower than that of crAssphage. Data demonstrated a significant correlation between crAssphage, HAdV, and HPyV during the wastewater treatment process, suggesting that crAssphage and human viral pathogens have similar removal mechanisms. Ultimately, this work concludes that crAssphage could be a performance indicator for viral reduction in the wastewater treatment process.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, 33 El Buhouth St., Giza, 12622, Dokki, Egypt.
| | - Sherif Abd-Elmaksoud
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, 33 El Buhouth St., Giza, 12622, Dokki, Egypt
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Randhawa MS, Randhawa TS, Angurana SK, Ratho RK. Acute encephalopathy with biphasic seizures and late restricted diffusion temporally associated with human bocavirus infection. BMJ Case Rep 2022; 15:e251019. [PMID: 35817489 PMCID: PMC9274515 DOI: 10.1136/bcr-2022-251019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2022] [Indexed: 11/03/2022] Open
Abstract
Acute encephalitis is a syndromic diagnosis. In the last two decades, a unique clinico-radiological entity, named acute encephalopathy with biphasic seizures and late restricted diffusion (AESD), has been reported in children from Asia. It is characterised by an acute febrile illness with seizures and encephalopathy, with some initial improvement followed by a second flurry of seizures and deep encephalopathy, 3-4 days later. MRI may show a pattern of 'bright tree appearance'. An aetiological agent may not always be identified but an infectious trigger is proposed. Immunomodulatory therapy has been tried with variable results. The prognosis is variable, and children are usually left with neurological sequelae including epilepsy and cognitive impairment. We describe a female infant who presented with the typical clinico-radiological syndrome of AESD and human bocavirus was identified in the stool. She received steroids and antiepileptic drugs. She has persistent cognitive impairment at follow-up but remained seizure free.
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Affiliation(s)
- Manjinder Singh Randhawa
- Division of Pediatric Critical Care, Department of Paediatrics, Advanced Paediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Suresh Kumar Angurana
- Division of Pediatric Critical Care, Department of Paediatrics, Advanced Paediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Radha Kanta Ratho
- Department of Virology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Karaaslan A, Çetin C, Tekol S, Yükselmiş U, Köle M, Akin Y. Human bocavirus infection in children hospitalized with lower respiratory tract infections: Does viral load affect disease course? ASIAN PAC J TROP MED 2022. [DOI: 10.4103/1995-7645.354421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Zhang XA, Zhao RQ, Chen JJ, Yuan Y, Tang X, Zhou ZW, Ren L, Lu QB, Wang YN, Zhang HY, Zhang PH, Fang LQ, Zhou HS, Liu EM, Xu HM, Liu W. The Identification and Genetic Characterization of Parechovirus Infection Among Pediatric Patients With Wide Clinical Spectrum in Chongqing, China. Front Microbiol 2021; 12:709849. [PMID: 34594310 PMCID: PMC8477803 DOI: 10.3389/fmicb.2021.709849] [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: 05/14/2021] [Accepted: 08/05/2021] [Indexed: 12/03/2022] Open
Abstract
Human parechoviruses (HPeVs) are important causes of infection in children. However, without a comprehensive and persistent surveillance, the epidemiology and clinical features of HPeV infection remain ambiguous. We performed a hospital-based surveillance study among three groups of pediatric patients with acute respiratory infection (Group 1), acute diarrhea (Group 2), and hand, foot and mouth disease (Group 3) in Chongqing, China, from 2009 to 2015. Among 10,212 tested patients, 707 (6.92%) were positive for HPeV, with the positive rates differing significantly among three groups (Group 1, 3.43%; Group 2, 14.94%; Group 3, 3.55%; P < 0.001). The co-infection with other pathogens was detected in 75.2% (531/707) of HPeV-positive patients. Significant negative interaction between HPeV and Parainfluenza virus (PIV) (P = 0.046, OR = 0.59, 95% CI = 0.34–0.98) and positive interactions between HPeV and Enterovirus (EV) (P = 0.015, OR = 2.28, 95% CI = 1.23–4.73) were identified. Among 707 HPeV-positive patients, 592 (83.73%) were successfully sequenced, and 10 genotypes were identified, with HPeV1 (n = 396), HPeV4 (n = 86), and HPeV3 (n = 46) as the most frequently seen. The proportion of genotypes differed among three groups (P < 0.001), with HPeV1 and HPeV4 overrepresented in Group 2 and HPeV6 overrepresented in Group 3. The spatial patterns of HPeV genotypes disclosed more close clustering of the currently sequenced strains than those from other countries/regions, although they were indeed mixed. Three main genotypes (HPeV1, HPeV3, and HPeV4) had shown distinct seasonal peaks, highlighting a bi-annual cycle of all HpeV and two genotypes (HPeV 1 and HPeV 4) with peaks in odd-numbered years and with peaks in even-numbered years HPeV3. Significantly higher HPeV1 viral loads were associated with severe diarrhea in Group 2 (P = 0.044), while associated with HPeV single infection than HPeV-EV coinfection among HFMD patients (P = 0.001). It’s concluded that HPeV infection was correlated with wide clinical spectrum in pediatric patients with a high variety of genotypes determined. Still no clinical significance can be confirmed, which warranted more molecular surveillance in the future.
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Affiliation(s)
- Xiao-Ai Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Rui-Qiu Zhao
- Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jin-Jin Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yang Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiang Tang
- Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zi-Wei Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Luo Ren
- Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Qin-Bin Lu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, China
| | - Yu-Na Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hai-Yang Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Pan-He Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Li-Qun Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hai-Sheng Zhou
- Key Laboratory of Dermatology, Anhui Medical University, Hefei, China.,Department of Biochemistry and Molecular Biology, Anhui Medical University, Hefei, China
| | - En-Mei Liu
- Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Hong-Mei Xu
- Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Beijing, China
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7
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González N, Marquès M, Domingo JL. Respiratory viruses in foods and their potential transmission through the diet: A review of the literature. ENVIRONMENTAL RESEARCH 2021; 195:110826. [PMID: 33529649 PMCID: PMC7963685 DOI: 10.1016/j.envres.2021.110826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 05/04/2023]
Abstract
Respiratory viruses are the main agents causing respiratory tract diseases. Nowadays, coronaviruses - and specifically, SARS-CoV-1, MERS-CoV and SARS-CoV-2 - are the principal responsible for the major epidemic outbreaks of the 21st century. The major routes of transmission for respiratory viruses - including coronaviruses - are via direct and indirect contacts. However, transmission through contaminated foods has not been extensively assessed. The present paper was aimed at reviewing scientific data on the transmission of respiratory viruses through potentially contaminated foods. While the current data seem to suggest that this route of transmission is not likely to occur, in order to increase the knowledge on this issue further investigations are still clearly necessary for a more complete prevention of the risks. Studies should include fresh produce and cooked foods. Anyway, prevention measures and good hygienic practices for both consumers and workers are mandatory when handling and cooking foods.
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Affiliation(s)
- Neus González
- Laboratory of Toxicology and Environmental Health, School of Medicine, Universitat Rovira I Virgili, Sant Llorenç 21, 43201, Reus, Catalonia, Spain.
| | - Montse Marquès
- Laboratory of Toxicology and Environmental Health, School of Medicine, Universitat Rovira I Virgili, Sant Llorenç 21, 43201, Reus, Catalonia, Spain
| | - José L Domingo
- Laboratory of Toxicology and Environmental Health, School of Medicine, Universitat Rovira I Virgili, Sant Llorenç 21, 43201, Reus, Catalonia, Spain
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8
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Koonin EV, Dolja VV, Krupovic M. The healthy human virome: from virus-host symbiosis to disease. Curr Opin Virol 2021; 47:86-94. [PMID: 33652230 DOI: 10.1016/j.coviro.2021.02.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 02/07/2023]
Abstract
Viruses are ubiquitous, essential components of any ecosystem, and of multicellular organism holobionts. Numerous viruses cause acute infection, killing the host or being cleared by immune system. In many other cases, viruses coexist with the host as symbionts, either temporarily or for the duration of the host's life. Apparently, virus-host relationships span the entire range from aggressive parasitism to mutualism. Here we attempt to delineate the healthy human virome, that is, the entirety of viruses that are present in a healthy human body. The bulk of the healthy virome consists of bacteriophages infecting bacteria in the intestine and other locations. However, a variety of viruses, such as anelloviruses and herpesviruses, and the numerous endogenous retroviruses, persist by replicating in human cells, and these are our primary focus. Crucially, the boundary between symbiotic and pathogenic viruses is fluid such that members of the healthy virome can become pathogens under changing conditions.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
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9
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Tarim EA, Karakuzu B, Oksuz C, Sarigil O, Kizilkaya M, Al-Ruweidi MKAA, Yalcin HC, Ozcivici E, Tekin HC. Microfluidic-based virus detection methods for respiratory diseases. EMERGENT MATERIALS 2021; 4:143-168. [PMID: 33786415 PMCID: PMC7992628 DOI: 10.1007/s42247-021-00169-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
With the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid-based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.
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Affiliation(s)
- E. Alperay Tarim
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Betul Karakuzu
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Cemre Oksuz
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Oyku Sarigil
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Melike Kizilkaya
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | | | | | - Engin Ozcivici
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - H. Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
- METU MEMS Center, Ankara, Turkey
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10
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Sharif N, Parvez AK, Haque A, Talukder AA, Ushijima H, Dey SK. Molecular and epidemiological trends of human bocavirus and adenovirus in children with acute gastroenteritis in Bangladesh during 2015 to 2019. J Med Virol 2020; 92:3194-3201. [PMID: 32237149 DOI: 10.1002/jmv.25812] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/05/2020] [Accepted: 03/27/2020] [Indexed: 01/11/2023]
Abstract
Virus associated diarrhea remains one of the leading causes of children morbidity and mortality in Bangladesh. Human bocavirus (HBoV) has been reported as a potential pathogen of children's diarrhea worldwide. However, due to its frequent association with other gastroenteric pathogens, its role as diarrhea causative agent remains to be defined. This study focuses to detect the incidence of HBoV and adenovirus (AdV) and to determine the molecular and epidemiological characteristics of HBoV and AdV. Between January 2015 to January 2019, 290 fecal specimens were collected from diarrheal children in Bangladesh. All fecal specimens were tested for HBoV and AdV by conventional polymerase chain reaction and sequencing methods. HBoV was detected in 7.24% (21 of 290) of the stool samples, as a sole virus in 71.42% (15 of 21) of the positive samples. AdV was detected in 4.82% (14 of 290) of the samples. The most common clinical symptoms of HBoV infected patients were diarrhea (100%) and vomiting (57%). All of the isolates of HBoV were from HBoV1 and AdV were from AdV41, AdV5, AdV7, and AdV8. To the best of our knowledge, this is the first epidemiological and molecular analysis report of HBoV from clinical specimens in Bangladesh. In the future, more studies are needed to clarify the role of HBoV as diarrheal pathogens.
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Affiliation(s)
- Nadim Sharif
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
| | | | - Aynul Haque
- Department of Physiology, Pabna Medical College, Pabna, Bangladesh
| | - Ali Azam Talukder
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University, Tokyo, Japan
| | - Shuvra Kanti Dey
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
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Kwiyolecha E, Groendahl B, Okamo B, Kayange N, Manyama F, Kidenya BR, Mahamba DC, Msanga DR, Gehring S, Majigo M, Mshana SE, Mirambo MM. Patterns of viral pathogens causing upper respiratory tract infections among symptomatic children in Mwanza, Tanzania. Sci Rep 2020; 10:18490. [PMID: 33116166 PMCID: PMC7595034 DOI: 10.1038/s41598-020-74555-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/05/2020] [Indexed: 11/29/2022] Open
Abstract
Upper-respiratory tract infections (URTI) are the leading causes of childhood morbidities. This study investigated etiologies and patterns of URTI among children in Mwanza, Tanzania. A cross-sectional study involving 339 children was conducted between October-2017 and February-2018. Children with features suggestive of URTI such as nasal congestion, dry cough, painful swallowing and nasal discharge with/without fever were enrolled. Pathogens were detected from nasopharyngeal and ear-swabs by multiplex-PCR and culture respectively. Full blood count and C-reactive protein analysis were also done. The median age was 16 (IQR: 8-34) months. Majority (82.3%) had fever and nasal-congestion (65.5%). Rhinitis (55.9%) was the commonest diagnosis followed by pharyngitis (19.5%). Viruses were isolated in 46% of children, the commonest being Rhinoviruses (23.9%). Nineteen percent of children had more than 2 viruses; Rhinovirus and Enterovirus being the commonest combination. The commonest bacteria isolated from ears were Staphylococcus aureus and Pseudomonas aeruginosa. Children with viral pathogens had significantly right shift of lymphocytes (73%-sensitivity). Majority (257/339) of children were symptoms free on eighth day. Viruses are the commonest cause of URTI with Rhinitis being the common diagnosis. Rapid diagnostic assays for URTI pathogens are urgently needed in low-income countries to reduce unnecessary antibiotic prescriptions which is associated with antibiotic resistance.
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Affiliation(s)
- Elizabeth Kwiyolecha
- Department of Pediatrics & Child Health, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
| | - Britta Groendahl
- Department of Pediatrics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Bernard Okamo
- Department of Biochemistry and Molecular Biology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
| | - Neema Kayange
- Department of Pediatrics & Child Health, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
| | - Festo Manyama
- Department of Pediatrics & Child Health, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
| | - Benson R Kidenya
- Department of Biochemistry and Molecular Biology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
| | - Dina C Mahamba
- Department of Pediatrics & Child Health, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
| | - Delfina R Msanga
- Department of Pediatrics & Child Health, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
| | - Stephan Gehring
- Department of Pediatrics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Mtebe Majigo
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
| | - Mariam M Mirambo
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania.
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12
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Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients. Clin Microbiol Rev 2020; 33:33/4/e00027-20. [PMID: 32847820 DOI: 10.1128/cmr.00027-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.
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13
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Lee HN, Koo HJ, Kim SH, Choi SH, Sung H, Do KH. Human Bocavirus Infection in Adults: Clinical Features and Radiological Findings. Korean J Radiol 2020; 20:1226-1235. [PMID: 31270986 PMCID: PMC6609429 DOI: 10.3348/kjr.2018.0634] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 04/07/2019] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Human bocavirus (HBoV) is a newly identified pathogen that can cause upper and lower respiratory infections usually in children; however, its clinical characteristics and significance in respiratory infections in adults have not been well known. Our objective was to evaluate the clinical features of respiratory HBoV infection and to describe the CT findings of HBoV pneumonia in adults. MATERIALS AND METHODS A total of 185 adult patients diagnosed with HBoV infection at a tertiary referral center between January 2010 and December 2017 were retrospectively evaluated with respect to the clinical characteristics of HBoV infection and its risk factors for pneumonia. Chest CT findings for 34 patients with HBoV pneumonia without co-infection were analyzed and compared between immunocompetent (n = 18) and immunocompromised (n = 16) patients. RESULTS HBoV infections were predominantly noted between February and June. Among the 185 patients with HBoV infection, 119 (64.3%) had community-acquired infections and 110 (59.5%) had pneumonia. In multivariable analysis, older age (odds ratio [OR], 1.02; 95% confidence interval [CI], 1.00-1.04; p = 0.045) and nosocomial infection (OR, 2.07; 95% CI, 1.05-4.10; p = 0.037) were associated with HBoV pneumonia. The main CT findings were bilateral consolidation (70.6%) and/or ground-glass opacities (64.7%); centrilobular nodules (14.7%) were found less frequently. The pattern of CT findings were not significantly different between immunocompetent and immunocompromised patients (all, p > 0.05). CONCLUSION HBoV infection can be a potential respiratory tract infection in adults. The most frequent CT findings of HBoV pneumonia were bilateral consolidation and/or ground-glass opacities.
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Affiliation(s)
- Han Na Lee
- Department of Radiology, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Hyun Jung Koo
- Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Soo Hyun Kim
- Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Ho Choi
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung Hyun Do
- Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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14
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Bian J, Liang M, Ding S, Wang L, Ni W, Xiong S, Li W, Bao X, Gao X, Wang R. iTRAQ-based high-throughput proteomics analysis reveals alterations of plasma proteins in patients infected with human bocavirus. PLoS One 2019; 14:e0225261. [PMID: 31751365 PMCID: PMC6872134 DOI: 10.1371/journal.pone.0225261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/31/2019] [Indexed: 12/18/2022] Open
Abstract
Human bocavirus (HBoV) is a member of the genus Bocavirus, family Parvoviridae, and subfamily Parvovirus and was first identified in nasopharyngeal aspirates of Swedish children with acute respiratory tract infection (ARTI) in 2005. It is the causative agent of nasopharyngeal aspirate disease and death in children. The HboV genomic structure is a linear single-stranded DNA (ssDNA). Its clinical pathogenic characteristics have been extensively studied, however, at present the molecular mechanism underlying the pathogenesis of HBoV infection is not completely clear. In this study, a total of 293 differentially expressed proteins (DEPs) between ARTI cases and healthy plasma samples were characterized using isobaric tags for relative and absolute quantitation (iTRAQ)-coupled bioinformatics analysis, among which 148 were up-regulated and 135 were down-regulated. Gene Ontology (GO) and Cluster of Orthologous Groups of proteins (COG) annotated an enrichment of DEPs in complement activation and biological processes like immunity, inflammation, signal transduction, substance synthesis, and metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis enriched DEPs mainly in the Wnt signaling pathway (ko04310), PPAR signaling pathway (ko03320), intestinal immune network for IgA production (ko04672), complement and coagulation cascades (ko04610), Toll-like receptor signaling pathway (ko04620) and B cell receptor signaling pathway (ko04662). Further, expression levels of three candidate proteins (upregulated PPP2R1A and CUL1, and downregulated CETP) were validated using western blotting. Our investigation is the first analysis of the proteomic profile of HBoV-infected ARTI cases using the iTRAQ approach, providing a foundation for a better molecular understanding of the pathogenesis of ARTI in children.
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Affiliation(s)
- Junmei Bian
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Min Liang
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Shuxian Ding
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Liyan Wang
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Wenchang Ni
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Shisi Xiong
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Wan Li
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Xingxing Bao
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Xue Gao
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Rong Wang
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
- * E-mail:
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15
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Chaves A, Ibarra-Cerdeña CN, López-Pérez AM, Monge O, Avendaño R, Ureña-Saborio H, Chavarría M, Zaldaña K, Sánchez L, Ortíz-Malavassi E, Suzan G, Foley J, Gutiérrez-Espeleta GA. Bocaparvovirus, Erythroparvovirus and Tetraparvovirus in New World Primates from Central America. Transbound Emerg Dis 2019; 67:377-387. [PMID: 31529612 DOI: 10.1111/tbed.13357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 09/02/2019] [Accepted: 09/07/2019] [Indexed: 12/20/2022]
Abstract
Parvoviruses in the genera Bocaparvovirus (HBoV), Erythroparvovirus (B19) and Tetraparvovirus (PARV4) are the only autonomous parvoviruses known to be associated with human and non-human primates based on studies and clinical cases in humans worldwide and non-human primates in Asia and Africa. Here, the presence of these agents with pathogenic potential was assessed by PCR in blood and faeces from 55 howler monkeys, 112 white-face monkeys, 3 squirrel monkeys and 127 spider monkeys in Costa Rica and El Salvador. Overall, 3.7% (11/297) of the monkeys had HboV DNA, 0.67% (2/297) had B19 DNA, and 14.1% (42/297) had PARV4 DNA, representing the first detection of these viruses in New World Primates (NWP). Sex was significantly associated with the presence of HBoV, males having greater risk up to nine times compared with females. Captivity was associated with increased prevalence for PARV4 and when all viruses were analysed together. This study provides compelling molecular evidence of parvoviruses in NWPs and underscores the importance of future research aimed at understanding how these viruses behave in natural environments of the Neotropics and what variables may favour their presence and transmission.
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Affiliation(s)
- Andrea Chaves
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA.,Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Carlos N Ibarra-Cerdeña
- Departamento de Ecología Humana, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), Unidad Mérida, Mérida, México
| | - Andrés M López-Pérez
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA.,Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F, México
| | - Otto Monge
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Hilary Ureña-Saborio
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica.,Escuela de Química & CIPRONA, Universidad de Costa Rica, San José, Costa Rica
| | - Karla Zaldaña
- Asociación Territorios Vivos El Salvador, San Salvador, El Salvador
| | - Lucía Sánchez
- Asociación Territorios Vivos El Salvador, San Salvador, El Salvador
| | - Edgar Ortíz-Malavassi
- Escuela de Ingienería Forestal, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Gerardo Suzan
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F, México
| | - Janet Foley
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
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Mohammadi M, Yavarian J, Karbasizade V, Moghim S, Esfahani BN, Hosseini NS. Phylogenetic analysis of human bocavirus in children with acute respiratory infections in Iran. Acta Microbiol Immunol Hung 2019; 66:485-497. [PMID: 31146533 DOI: 10.1556/030.66.2019.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Human bocavirus (HBoV) was first characterized in nasopharyngeal aspirates from young children with acute respiratory infections. It is prevalent among children with acute wheezing. This study was carried out in order to analyze the infection frequency and coinfection rates of HBoV with respiratory syncytial virus (RSV) and to perform phylogenetic analysis of HBoV in samples of children with acute respiratory infection in Isfahan, Iran. During the time period 2016-2017, altogether 75 respiratory samples from children hospitalized with acute respiratory infection were collected. The samples were first screened for RSV by direct immunofluorescence method and then subjected to detect HBoV DNA by PCR. Genotyping of HBoV-positive samples was conducted by direct sequencing of PCR products using NP and VP1/VP2 genes. Out of 75 respiratory samples, 20 (26.7%) and 10 (13.3%) were positive for RSV and HBoV, respectively. The coinfection rate was 40% (p = 0.048). Considering the seasonal distribution, winter has the highest extent outbreak (p = 0.036). Sequence analysis of positive samples exhibits that all of the isolated HBoV were related to genotype 1 (HBoV-1) with minimal sequence variations. Increasing frequency of HBoV suggests that the virus is related to acute respiratory infection in children. A single genetic lineage of HBoV1 seems to be the major genotype in Iran.
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Affiliation(s)
- Mehrdad Mohammadi
- 1 Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jila Yavarian
- 2 Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Vajihe Karbasizade
- 1 Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sharareh Moghim
- 1 Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahram Nasr Esfahani
- 1 Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, Iran
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17
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Pochon C, Voigt S. Respiratory Virus Infections in Hematopoietic Cell Transplant Recipients. Front Microbiol 2019; 9:3294. [PMID: 30687278 PMCID: PMC6333648 DOI: 10.3389/fmicb.2018.03294] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/18/2018] [Indexed: 12/13/2022] Open
Abstract
Highly immunocompromised pediatric and adult hematopoietic cell transplant (HCT) recipients frequently experience respiratory infections caused by viruses that are less virulent in immunocompetent individuals. Most of these infections, with the exception of rhinovirus as well as adenovirus and parainfluenza virus in tropical areas, are seasonal variable and occur before and after HCT. Infectious disease management includes sampling of respiratory specimens from nasopharyngeal washes or swabs as well as sputum and tracheal or tracheobronchial lavages. These are subjected to improved diagnostic tools including multiplex PCR assays that are routinely used allowing for expedient detection of all respiratory viruses. Disease progression along with high mortality is frequently associated with respiratory syncytial virus, parainfluenza virus, influenza virus, and metapneumovirus infections. In this review, we discuss clinical findings and the appropriate use of diagnostic measures. Additionally, we also discuss treatment options and suggest new drug formulations that might prove useful in treating respiratory viral infections. Finally, we shed light on the role of the state of immune reconstitution and on the use of immunosuppressive drugs on the outcome of infection.
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Affiliation(s)
- Cécile Pochon
- Allogeneic Hematopoietic Stem Cell Transplantation Unit, Department of Pediatric Oncohematology, Nancy University Hospital, Vandœuvre-lès-Nancy, France
| | - Sebastian Voigt
- Department of Pediatric Oncology/Hematology/Stem Cell Transplantation, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
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18
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Appak Ö, Duman M, Belet N, Sayiner AA. Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients. J Med Virol 2019; 91:731-737. [PMID: 30570759 PMCID: PMC7167103 DOI: 10.1002/jmv.25379] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/16/2018] [Indexed: 12/22/2022]
Abstract
Syndromic diagnosis by multiplex nucleic acid amplification tests is the most practical approach to respiratory tract infections since the symptoms are rarely agent‐specific. The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. A total of 3162 respiratory samples collected from children between April 2011 and April 2018 tested by a multiplex real‐time PCR assay. Two different commercial assays were used during the study period, "AusDiagnostics/Respiratory Pathogens 12 (AusDiagnostics)" used between April 2011 and December 2015, which changed to "Fast Track Diagnostics/Respiratory Pathogens 21 (Fast Track Diagnostics)" after January 2016 to cover more viruses. Nucleic acid extraction was done by EZ1 Advanced XL platform (QIAGEN). Respiratory pathogens detected in 1857 of the 3162 (58.7%) samples. The most prevalent viruses during the 8‐year period were rhinovirus/enterovirus (RV/EV; 36.2%), respiratory syncytial virus (RSV; 19%), and influenza virus A/B (14.7%). Rhinovirus was the main contributor to the RV/EV group as shown by the assay used during the 2016‐2018 period. RV/EV and adenoviruses detected throughout the year. Influenza virus was most frequently detected during January to March when both RSV and metapneumovirus were also in circulation. The coinfection percentage was 10.2%. Rhinovirus was the most common virus in coinfections while RSV plus rhinovirus/enterovirus were the most frequent combination. RSV and metapneumovirus showed a similar seasonal distribution to the influenza virus, which made it necessary to use a virological diagnostic assay during the influenza season.
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Affiliation(s)
- Özgür Appak
- Department of Medical Microbiology, Division of Medical Virology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Murat Duman
- Department of Pediatrics, Division of Pediatric Emergency Care, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Nurşen Belet
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Ayça Arzu Sayiner
- Department of Medical Microbiology, Division of Medical Virology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
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19
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Sun H, Sun J, Ji W, Hao C, Yan Y, Chen Z, Wang Y. Impact of RSV Coinfection on Human Bocavirus in Children with Acute Respiratory Infections. J Trop Pediatr 2018; 65:342-351. [PMID: 30202992 PMCID: PMC7107312 DOI: 10.1093/tropej/fmy057] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
OBJECTIVE The objective of this study was to assess epidemiological and clinical features of human bocavirus (HBoV) coinfection with other viruses. METHOD Children coinfected with HBoV between January 2012 and December 2014 were enrolled and retrospectively reviewed. RESULT A total of 984 patients were stratified into five groups: HBoV infection alone (n = 249), respiratory syncytial virus (RSV) infection alone (n = 649), HBoV coinfection with RSV (n = 28), with human rhinovirus (HRV) (n = 39) and with other virus (n = 19). Length of hospitalization was longer in HBoV coinfection with RSV group than HBoV (9.0 days vs. 7.0 days, p = 0.001), RSV (9.0 days vs. 8.0 days, p = 0.016) infection alone group. Pneumonia was more common in the HBoV coinfection with RSV group compared with the HBoV, RSV infection alone group, respectively (75.0% vs. 44.2%, 31.3%, p < 0.001). HBoV DNA copy numbers (383 000 copies/ml) were positively correlated with the length of hospitalization (r = 0.334, p < 0.001). CONCLUSION HBoV coinfection with RSV increases HBoV infection severity.
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Affiliation(s)
- Huiming Sun
- Attending, Department of Respiratory Medicine, Children’s Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jiyang Sun
- Attending, Department of Respiratory Medicine, Children’s Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Wei Ji
- Chief Physician, Department of Respiratory Medicine, Children’s Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chuangli Hao
- Director, Department of Respiratory Medicine, Children’s Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yongdong Yan
- Vice Director, Department of Respiratory Medicine, Children’s Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Zhengrong Chen
- Vice Director, Department of Respiratory Medicine, Children’s Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yuqing Wang
- Vice Director, Department of Respiratory Medicine, Children’s Hospital of Soochow University, Suzhou, Jiangsu, China,Correspondence: Yuqing Wang, Department of Respiratory Medicine, Children’s Hospital of Soochow University, No. 303 Jing De Road, Suzhou, Jiangsu, China. Tel: +86 051267788313; Fax: +8651267786316. E-mail <>
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20
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Garcia-Nuñez M, Gallego M, Monton C, Capilla S, Millares L, Pomares X, Espasa M, Ferrari R, Moya A, Monsó E, Perez-Brocal V. The respiratory virome in chronic obstructive pulmonary disease. Future Virol 2018. [DOI: 10.2217/fvl-2018-0027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aim: To characterize the respiratory virome in moderate/severe chronic obstructive pulmonary disease (COPD) patients using metagenomics, with healthy subjects as the reference. Patients & Methods: Sputum COPD samples were collected during stability and exacerbations with negative usual-care microbiologic analysis. Results: Eukaryotic viruses from the Anelloviridae, Herpesviridae and Retroviridae families and phages from the Shiphoviridae family were commonly found in COPD, and the respiratory virome in stability and noninfectious exacerbations showed a substantial similarity. DNA viruses with the highest relative abundance in COPD are Anelloviridae. Conclusion: These results support a colonizing role for eukaryotic viruses in COPD and highlight the importance of analyzing both DNA and RNA viruses when focusing on the respiratory virome.
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Affiliation(s)
- Marian Garcia-Nuñez
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Fundació Insitut d'Investigació GermansTrias i Pujol, Badalona, Spain
| | - Miguel Gallego
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - Concepción Monton
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
| | - Silvia Capilla
- Department of Microbiology, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
| | - Laura Millares
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Fundació Insitut d'Investigació GermansTrias i Pujol, Badalona, Spain
| | - Xavier Pomares
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - Mateu Espasa
- Department of Microbiology, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
| | - Rafaella Ferrari
- Genomics & Health Area, Centro Superior de Investigación en Salud Pública – Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain
| | - Andres Moya
- Genomics & Health Area, Centro Superior de Investigación en Salud Pública – Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain
- Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, València, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Eduard Monsó
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - Vicente Perez-Brocal
- Genomics & Health Area, Centro Superior de Investigación en Salud Pública – Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain
- Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, València, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
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21
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Identification of Human Bocavirus type 4 in a child asymptomatic for respiratory tract infection and acute gastroenteritis - Goiânia, Goiás, Brazil. Braz J Infect Dis 2017; 21:472-476. [PMID: 28500864 PMCID: PMC9427974 DOI: 10.1016/j.bjid.2017.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/24/2017] [Accepted: 03/17/2017] [Indexed: 01/15/2023] Open
Abstract
Human Bocavirus (HBoV) has been identified from feces and respiratory samples from cases of both acute gastroenteritis and respiratory illness as well as in asymptomatic individuals. The aim of this study was to detect and characterize HBoV from fecal samples collected from hospitalized children aged less than five years old with no symptoms of respiratory tract infection (RTI) or acute gastroenteritis (AGE). The study involved 119 children and one fecal sample was collected from each participant between 2014 and 2015. HBoV was detected using Nested-PCR, and the viral type identified by genomic sequencing. HBoV-4 was identified from one sample obtained from a hospitalized child with soft tissue tumor of the submandibular region. This is the first report of HBoV-4 identification in Brazil, but we consider that this type may be circulating in the country similar to the other types and new investigations are necessary.
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22
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A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach. Arch Virol 2017; 162:2003-2012. [PMID: 28424887 PMCID: PMC7087367 DOI: 10.1007/s00705-017-3367-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/09/2017] [Indexed: 12/14/2022]
Abstract
Metagenomic approaches to detect viral genomes and variants in clinical samples have various challenges, including low viral titers and bacterial and human genome contamination. To address these limitations, we examined a next-generation sequencing (NGS) and iterative mapping approach for virus detection in clinical samples. We analyzed 40 clinical specimens from hospitalized children diagnosed with acute bronchiolitis, croup, or respiratory tract infections in which virus identification by viral culture or polymerase chain reaction (PCR) was unsuccessful. For our NGS data analysis pipeline, clinical samples were pooled into two NGS groups to reduce sequencing costs, and the depth and coverage of assembled contigs were effectively increased using an iterative mapping approach. PCR was individually performed for each specimen according to the NGS-predicted viral type. We successfully detected previously unidentified respiratory viruses in 26 of 40 specimens using our proposed NGS pipeline. Two dominant populations within the detected viruses were human rhinoviruses (HRVs; n = 14) and human coronavirus NL63 (n = 8), followed by human parainfluenza virus (HPIV), human parechovirus, influenza A virus, respiratory syncytial virus (RSV), and human metapneumovirus. This is the first study reporting the complete genome sequences of HRV-A101, HRV-C3, HPIV-4a, and RSV, as well as an analysis of their genetic variants, in Taiwan. These results demonstrate that this NGS pipeline allows to detect viruses which were not identified by routine diagnostic assays, directly from clinical samples.
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Annamalay A, Le Souëf P. Viral-Bacterial Interactions in Childhood Respiratory Tract Infections. VIRAL INFECTIONS IN CHILDREN, VOLUME I 2017. [PMCID: PMC7122469 DOI: 10.1007/978-3-319-54033-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Windisch W, Pieper M, Ziemele I, Rockstroh J, Brockmann M, Schildgen O, Schildgen V. Latent infection of human bocavirus accompanied by flare of chronic cough, fatigue and episodes of viral replication in an immunocompetent adult patient, Cologne, Germany. JMM Case Rep 2016; 3:e005052. [PMID: 28348774 PMCID: PMC5330242 DOI: 10.1099/jmmcr.0.005052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 06/03/2016] [Indexed: 02/05/2023] Open
Abstract
Introduction: The human bocavirus (HBoV) is a parvovirus and is associated with mild to life-threatening acute or persisting respiratory infections, frequently accompanied by further pathogens. So far, there is limited knowledge on the mechanisms of persistence, and no reports on chronic infections or latency have been published so far. Case presentation: An immunocompetent male patient suffers from a chronic HBoV1 infection, i.e. viral DNA was detected in both serum and bronchoalveolar lavage (BAL) for >5 months without co-infections and with respiratory symptoms resolved spontaneously while receiving symptomatic treatment with montelukast and corticosteroids. Following the symptomatic medication of a chronic infection with HBoV1 viraemia indicating active viral replication lasting over 5 months, the patient cleared the viraemia and no further viral DNA was detectable in the BAL. However, by fluorescence in situ hybridization analyses of mucosal biopsies, it was shown that the virus genome still persisted in the absence of viral shedding but in a more compact manner possibly representing a supercoiled episomal form of this otherwise linear single-stranded DNA genome. This indicated the entry into a latency phase. Moreover, the cytokine profile and the IP-10/TARC ratio, a marker for fibrotization, seem to have been altered by HBoV1 replication. Although specific IgG antibodies were detectable during the whole observation period, they showed an apparently insufficient neutralising activity. Conclusion: On the one hand, these findings suggest that the symptomatic medication may have led to clearance of the virus from blood and airways and, moreover, that the viral DNA persists in the tissue as an altered episomal form favoured by lacking neutralising antibodies. This appears to be important in order to reduce possible long-term effects such as lung fibrosis.
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Affiliation(s)
- Wolfram Windisch
- Department of Pneumology, Kliniken der Stadt Köln gGmbH, University of Witten/Herdecke, Cologne, Germany
| | - Monika Pieper
- Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Cologne , Germany
| | - Inga Ziemele
- Virology, University of Helsinki, Helsinki, Finland; Riga Stradiņš University, Riga, Latvia
| | - Jürgen Rockstroh
- Universitätsklinikum Bonn, Immunologische Ambulanz , Bonn , Germany
| | - Michael Brockmann
- Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Cologne , Germany
| | - Oliver Schildgen
- Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Cologne , Germany
| | - Verena Schildgen
- Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Cologne , Germany
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Abstract
BACKGROUND Although human bocavirus type 1 (HBoV1) is a respiratory pathogen, presence of HBoV-DNA in secretions of asymptomatic children raised the question on the significance of HBoV-positive results. METHODS Archived specimens from a prospective, longitudinal study were tested for HBoV. A total of 94 children (aged 6-36 months) were HBoV(+) during 172 upper respiratory tract infection (URI) and/or acute otitis media (AOM) episodes. We used pyrosequencing of NP1, VP1 and VP2 genes to type HBoV and subtype HBoV1 in these specimens. RESULTS Of the specimens tested, HBoV-DNA were successfully sequenced in 128 (74%) samples from 70 children; all were HBoV type 1. Subtypes identified (n = 108) were LWK/TW (63%), LWK/BJ (20%), Bonn/BJ (16%) and LWK/KU3 (1%). Of 46 children for whom shedding pattern could be determined, viral clearance within 30 days (13-29 days) occurred in 28%; another 22% of children had no recurrence after 32-267 days. Prolonged virus presence of >30 days (34-181 days+) occurred in 22%; intermittent detection (61+ to 170+ days) in 20%. Infection with the same HBoV1 subtype after 4-5 negative samples (244 and 265 days interval) occurred in 4%. Infection with 2 different HBoV1 subtypes (29 and 87 days apart) occurred in only 4%. Newly acquired HBoV1-URI resulted in AOM in 53% of cases. CONCLUSIONS Children with HBoV1 infection commonly shed for a prolonged period leading to repeated viral DNA detection. Recurrence after 8-9 months suggests possible persistence and reactivation. Infections with 2 different HBoV1 subtypes within 1-year period are uncommon. Newly acquired HBoV1-URI is often complicated by AOM.
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Khalfaoui S, Eichhorn V, Karagiannidis C, Bayh I, Brockmann M, Pieper M, Windisch W, Schildgen O, Schildgen V. Lung Infection by Human Bocavirus Induces the Release of Profibrotic Mediator Cytokines In Vivo and In Vitro. PLoS One 2016; 11:e0147010. [PMID: 26807786 PMCID: PMC4726461 DOI: 10.1371/journal.pone.0147010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/28/2015] [Indexed: 12/12/2022] Open
Abstract
Human Bocavirus subtype 1 (HBoV1) is associated with respiratory diseases and may contribute to chronic lung diseases by persisting in the infected host. Here the question was addressed if HBoV infections could contribute to fibrogenesis processes as suggested by previously published clinical observations. Cytokine profiles induced by HBoV infection in CuFi-8 air-liquid interphase cell cultures and in bronchoalveolar lavage fluid (BALF) of 20 HBoV-positive and 12 HBoV-negative patients were analysed by semi-quantitative Western spot blot analyses. Although lots of cytokines were regulated independently of HBoV status, several cytokines associated with lung fibrosis and tumour development, e.g., EGF, VEGF, TARC (CCL17), TNF-α, TNF-β, TIMP-1, were clearly upregulated in the HBoV-positive cohort. These findings suggest that the development of lung fibrosis might be triggered by HBoV induced cytokine expression.
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Affiliation(s)
- Soumaya Khalfaoui
- Kliniken der Stadt Köln gGmbH, University Hospital Witten/Herdecke, Cologne-Merheim, Ostmerheimer Strasse 200, Institute for Pathology, D-51109 Cologne, Germany
| | - Vivien Eichhorn
- Kliniken der Stadt Köln gGmbH, University Hospital Witten/Herdecke, Cologne-Merheim, Ostmerheimer Strasse 200, Institute for Pathology, D-51109 Cologne, Germany
| | - Christian Karagiannidis
- Kliniken der Stadt Köln gGmbH, University Hospital Witten/Herdecke, Cologne-Merheim, Ostmerheimer Strasse 200, Department of Pneumology and Critical Care Medicine, D-51109 Cologne, Germany
| | - Inga Bayh
- Institute for Medical Biometry and Epidemiology, Faculty of Health, Alfred-Herrhausen-Str. 50, Witten/Herdecke University, Witten, Germany
| | - Michael Brockmann
- Kliniken der Stadt Köln gGmbH, University Hospital Witten/Herdecke, Cologne-Merheim, Ostmerheimer Strasse 200, Institute for Pathology, D-51109 Cologne, Germany
| | - Monika Pieper
- Kliniken der Stadt Köln gGmbH, University Hospital Witten/Herdecke, Cologne-Merheim, Ostmerheimer Strasse 200, Institute for Pathology, D-51109 Cologne, Germany
| | - Wolfram Windisch
- Kliniken der Stadt Köln gGmbH, University Hospital Witten/Herdecke, Cologne-Merheim, Ostmerheimer Strasse 200, Department of Pneumology and Critical Care Medicine, D-51109 Cologne, Germany
| | - Oliver Schildgen
- Kliniken der Stadt Köln gGmbH, University Hospital Witten/Herdecke, Cologne-Merheim, Ostmerheimer Strasse 200, Institute for Pathology, D-51109 Cologne, Germany
| | - Verena Schildgen
- Kliniken der Stadt Köln gGmbH, University Hospital Witten/Herdecke, Cologne-Merheim, Ostmerheimer Strasse 200, Institute for Pathology, D-51109 Cologne, Germany
- * E-mail: ;
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A novel primer set for improved direct gene sequencing of human bocavirus genotype-1 from clinical samples. J Virol Methods 2015; 228:108-13. [PMID: 26658621 DOI: 10.1016/j.jviromet.2015.11.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/27/2015] [Accepted: 11/29/2015] [Indexed: 02/07/2023]
Abstract
Human bocavirus genotype (HBoV-1) is a parvovirus associated with respiratory tract infections in children with different degrees of severity. The current study intended to improve the direct gene sequencing of the HBoV-1 using a newly developed primer set. Screening the presence of human bocavirus infection among in-patients children suffering from lower respiratory tract infections was another aim of the current study. Nasopharyngeal swab samples from in-patients children suffering from lower respiratory tract infections were examined. The real-time polymerase chain reaction was used for the initial screening as a highly sensitive method to detect the HBoV. Genotyping of real-time positive samples was attempted by direct sequencing of PCR amplicons using NP, VP1/2 and the newly developed VP/NC primers. HBoV-1 was present in 56.8% of the examined children. The newly developed primer set successfully amplified all real-time PCR positive samples, however, the other primer pairs did not reliably detect real-time PCR positive samples. The gene sequences of the detected HBoV-1 showed conserved sequences to each other with a low rate of discrepancies. The high rate of infection and the similarity between the detected strains strongly suggest nosocomial infections.
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Saekhow P, Ikeda H. Prevalence and genomic characterization of porcine parvoviruses detected in Chiangmai area of Thailand in 2011. Microbiol Immunol 2015; 59:82-8. [PMID: 25431024 DOI: 10.1111/1348-0421.12218] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 11/17/2014] [Accepted: 11/24/2014] [Indexed: 12/23/2022]
Abstract
Porcine parvovirus (PPV) causes reproductive failure in sows and has spread worldwide. Several new types of porcine parvoviruses have recently been identified in pig herds. The prevalence of five porcine parvoviruses in the Chiangmai area of Thailand was studied. The prevalence in 80 pigs was 53% for PPV (PPV-Kr or -NADL2 being the new abbreviations), 83% for PPV2 (CnP-PARV4), 73% for PPV3 (P-PARV4), 44% for PPV4 (PPV4), and 18% for PBo-likeV (PBoV7). Over 60% of the pigs carried more than three of the five porcine parvoviruses and occurrence together of the two pairs of viral genes, PPV1/PPV3 and PPV2/PBo-likeV were observed. Phylogenetic analyses for PPV2 and PPV3 indicated the existence of only two major clades of PPV2 and one major clade of PPV3.
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Affiliation(s)
- Prayuth Saekhow
- Laboratory of Veterinary Hygiene, Graduate School of Veterinary Medicine and Life Science, Nippon Veterinary and Life Science University, 1-7-1, Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan; Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Mae Hia, Muang, Chiang Mai, 50100, Thailand
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Identification of new respiratory viruses in the new millennium. Viruses 2015; 7:996-1019. [PMID: 25757061 PMCID: PMC4379558 DOI: 10.3390/v7030996] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/23/2015] [Accepted: 02/26/2015] [Indexed: 12/13/2022] Open
Abstract
The rapid advancement of molecular tools in the past 15 years has allowed for the retrospective discovery of several new respiratory viruses as well as the characterization of novel emergent strains. The inability to characterize the etiological origins of respiratory conditions, particularly in children, led several researchers to pursue the discovery of the underlying etiology of disease. In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Human bocavirus, with its four separate lineages, discovered in 2005, has been linked to acute respiratory tract infections and gastrointestinal complications. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. This review will detail the most current clinical and epidemiological findings to all respiratory viruses discovered since 2001.
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Goka EA, Vallely PJ, Mutton KJ, Klapper PE. Single and multiple respiratory virus infections and severity of respiratory disease: a systematic review. Paediatr Respir Rev 2014; 15:363-70. [PMID: 24361079 PMCID: PMC7106320 DOI: 10.1016/j.prrv.2013.11.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/30/2013] [Accepted: 11/01/2013] [Indexed: 12/20/2022]
Abstract
INTRODUCTION There are suggestions that virus co-infections may influence the clinical outcome of respiratory virus illness. We performed a systematic review of the literature to summarise the evidence. METHODS MEDLINE, EMBASE, Ovid and WEB of Science databases, major organisation websites and reference lists of published studies were searched. The quality of studies was assessed using the STROBE tool (von Elm et al., 1) Individual study data was analyzed using odds ratios and 95% confidence intervals as a measure of association between exposure (co-infection), patient outcome and results summarised using forest plots and tables RESULTS Nineteen (19) studies from all over the world were identified and included in the review. Most of the studies 73.7% (14/19) recruited children ≤ 6 years old. Evidence on the role of co-infection in increasing disease severity was inconclusive. In five out of eight studies, co-infection significantly increased risk of admission to general ward (OR: 2.4, 95% CI: 1.3 - 4.4, p = 0.005; OR: 2.4, 95% CI: 1.1 - 7.7, P = 0.04; OR: 3.1, 95% CI: 2.0 - 5.1, p = <0.001; OR: 2.4, 95% CI: 1.7-3.4, p = <0.0001 and OR: 2.3, 95% CI: 1.1 - 5.1, p = 0.34), one found it did not (OR: 0.59, 95% CI: 0.4 - 0.9, p = 0.02) and the other 2 had insignificant results. Similarly on risk of admission to ICU, some studies found that co-infection significantly increased risk of admission to ICU (OR: 2.9, 95% CI: 1.4 - 5.9, p = 0.004 and OR: 3.0, 95% CI: 1.7 - 5.6, p = <0.0001), whereas others did not (OR: 0.18, 95% CI: 0.05 - 0.75, p = 0.02 and OR: 0.3, 95% CI: 0.2 - 0.6, p = <0.0001). There was no evidence for or against respiratory virus co-infections and risk of bronchiolitis or pneumonia. CONCLUSION The influence of co-infections on severe viral respiratory disease is still unclear. The observed conflict in outcomes could be because they were conducted in different seasons and covered different years and periods. It could also be due to bias towards the null, especially in studies where only crude analysis was conducted. Future studies should employ stratified analysis.
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Affiliation(s)
- Edward Anthony Goka
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester.
| | - Pamela J. Vallely
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester
| | - Kenneth J. Mutton
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester,Department of Clinical Virology, Central Manchester Universities NHS Trust
| | - Paul E. Klapper
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester,Department of Clinical Virology, Central Manchester Universities NHS Trust
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Ghietto LM, Majul D, Ferreyra Soaje P, Baumeister E, Avaro M, Insfrán C, Mosca L, Cámara A, Moreno LB, Adamo MP. Comorbidity and high viral load linked to clinical presentation of respiratory human bocavirus infection. Arch Virol 2014; 160:117-27. [PMID: 25269520 DOI: 10.1007/s00705-014-2238-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 09/19/2014] [Indexed: 12/21/2022]
Abstract
Human bocavirus (HBoV) is a new parvovirus associated with acute respiratory tract infection (ARTI). In order to evaluate HBoV significance as an agent of acute respiratory disease, we screened 1,135 respiratory samples from children and adults with and without symptoms during two complete calendar years. HBoV1 prevalence in patients with ARTI was 6.33 % in 2011 and 11.64 % in 2012, including neonatal and adult patients. HBoV1 was also detected in 3.77 % of asymptomatic individuals. The co-detection rate was 78.1 %. Among children, 87 % were clinically diagnosed with lower respiratory infection (no significant differences between patients with and without coinfection), and 31 % exhibited comorbidities. Pediatric patients with comorbidities were significantly older than patients without comorbidities. Patients with ARTI had either high or low viral load, while controls had only low viral load, but there were no clinical differences between patients with high or low viral load. In conclusion, we present evidence of the pathogenic potential of HBoV1 in young children with ARTI. Since patients with HBoV1-single infection are not significantly different from those with coinfection with respect to clinical features, the virus can be as pathogenic by itself as other respiratory agents are. Furthermore, an association between high HBoV1 load and disease could not be demonstrated in this study, but all asymptomatic individuals had low viral loads. Also, children with comorbidities are susceptible to HBoV1 infection at older ages than previously healthy children. Thus, the clinical presentation of infection may occur depending on both viral load and the particular interaction between the HBoV1 and the host.
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Affiliation(s)
- Lucía María Ghietto
- Facultad de Ciencias Médicas, Instituto de Virología "Dr. J. M. Vanella", Universidad Nacional de Córdoba, Calle Enf. Grodillo Gómez S/N, Ciudad Universitaria, CP 5016, Córdoba, Argentina
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Cotton M, Innes S, Jaspan H, Madide A, Rabie H. Management of upper respiratory tract infections in children. S Afr Fam Pract (2004) 2014; 50:6-12. [PMID: 21603094 DOI: 10.1080/20786204.2008.10873685] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Upper respiratory tract infection (URTI) occurs commonly in both children and adults and is a major cause of mild morbidity. It has a high cost to society, being responsible for absenteeism from school and work and unnecessary medical care, and is occasionally associated with serious sequelae. URTIs are usually caused by several families of virus; these are the rhinovirus, coronavirus, parainfluenza, respiratory syncytial virus (RSV), adenovirus, human metapneumovirus, influenza, enterovirus and the recently discovered bocavirus. This review will mainly focus on the rhinovirus, where significant advances have been made in understanding the epidemiology, natural history and relationship with other pathogens.
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Affiliation(s)
- Mf Cotton
- Paediatric Infectious Diseases Unit, Department of Paediatrics and Child Health, Stellenbosch University
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Zhou L, Zheng S, Xiao Q, Ren L, Xie X, Luo J, Wang L, Huang A, Liu W, Liu E. Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children. BMC Infect Dis 2014; 14:424. [PMID: 25078257 PMCID: PMC4125703 DOI: 10.1186/1471-2334-14-424] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/15/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Human bocavirus is a newly discovered parvovirus. Multiple studies have confirmed the presence of human bocavirus1 (HBoV1) in respiratory tract samples of children. The viral load, presentation of single detection and its role as a causative agent of severe respiratory tract infections have not been thoroughly elucidated. METHODS We investigated the presence of HBoV1 by quantitative polymerase chain reaction (PCR) of nasopharyngeal aspirate specimens from 1229 children hospitalized for respiratory tract infections. The samples were analyzed for 15 respiratory viruses by PCR and 7 respiratory viruses by viral culture. RESULTS At least one virus was detected in 652 (53.1%) of 1229 children, and two or more viruses were detected in 266 (21.6%) children. HBoV1 was detected in 127 children (10.3%), in which 66/127 (52%) of the cases were the only HBoV1 virus detected. Seasonal variation was observed with a high HBoV1 infection rate in summer. A cutoff value of 107 copies/mL was used to distinguish high and low HBoV1 viral loads in the nasopharyngeal aspirates. High viral loads of HBoV1 were noted predominantly in the absence of other viral agents (28/39, 71.8%) whereas there was primarily co-detection in cases of low HBoV1 viral loads (50/88, 56.8%). There were no differences in the clinical symptoms and severity between HBoV1 single detection and co-detection. In cases of HBoV1 single detection, the high viral load group was more prevalent among children with dyspnea and wheezing than was the low viral load group (42.9% vs. 23.7%, P = 0.036; 60.7% vs. 31.6%, P = 0.018). In clinical severity, a significant difference was recorded (25.0% vs. 5.3%, P = 0.003) between high viral load and low viral load groups. Of the HBoV1 positive patients associated with severe respiratory tract infections, 10/18 (55.6%) patients belonged to the HBoV1 high viral load group, and 7/10 (70%) patients had cases of HBoV1 single detection. CONCLUSIONS HBoV1 at a high viral load is not frequently found in co-detection with other respiratory viruses, and a single detection with a high viral load could be an etiological agent of severe respiratory tract infections.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Enmei Liu
- Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, P, R, China.
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Lu QB, Wo Y, Wang HY, Huang DD, Zhao J, Zhang XA, Zhang YY, Liu EM, Liu W, Cao WC. Epidemic and molecular evolution of human bocavirus in hospitalized children with acute respiratory tract infection. Eur J Clin Microbiol Infect Dis 2014; 34:75-81. [PMID: 25070494 PMCID: PMC7087953 DOI: 10.1007/s10096-014-2215-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 07/14/2014] [Indexed: 12/13/2022]
Abstract
Human bocavirus (HBoV) is a novel parvovirus, often associated with respiratory tract diseases in children. This study explored the epidemiological characteristics and molecular evolution of HBoV-1 in southeastern China. Nasopharyngeal aspirates were collected from children admitted to hospital with acute respiratory tract infections. HBoV-1 was detected using real-time reverse transcription polymerase chain reaction and further characterized by complete genome sequences analysis. Among the 3,022 recruited children, 386 (12.77 %) were HBoV-1-positive and 300 (77.72 %) had co-detection with other respiratory viruses. Seasonal prevalence peaked in summer. HBoV-1 presence was significantly associated with asthma attack [odds ratio = 1.74; 95 % confidence interval: 1.30, 2.31; p < 0.001]. Similar results were obtained when either single detection or co-detection of HBoV-1 was considered, demonstrating the minor impact of co-detection on the clinical characteristics or epidemic pattern. Phylogenetic analysis based on the complete genome sequences showed that all the HBoV-1 sequences clustered together and no branch was formed that was supported by bootstrap value ≥750. The overall evolutionary rate of the complete genome of HBoV-1 was estimated at 1.08 × 10−4 nucleotide substitutions per site per year (s/s/y) [95 % highest probability density: (0.40–1.86) × 10−4 s/s/y]. Selective pressure analysis showed that all the ω-values were less than 1, suggesting that HBoV-1 was under negative selective pressure. Site-by-site analysis identified the codon site 40 of the VP1 gene under positive selection. In conclusion, our study disclosed the epidemiological and genetic dynamics of HBoV-1 epidemics in southeastern China in the most recent 3 years, the information of which might help to further improve our understanding of HBoV-1 infection and guide better surveillance and control strategies in the future.
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Affiliation(s)
- Q-B Lu
- School of Public Health, Peking University, Beijing, 100191, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Y Wo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - H-Y Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - D-D Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - J Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - X-A Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Y-Y Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - E-M Liu
- Children's Hospital, Chongqing Medical University, Chongqing, 400014, China
| | - W Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China.
| | - W-C Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China.
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Li H, He M, Zeng P, Gao Z, Bian G, Yang C, Li W. The genomic and seroprevalence of human bocavirus in healthy Chinese plasma donors and plasma derivatives. Transfusion 2014; 55:154-63. [PMID: 25052026 DOI: 10.1111/trf.12785] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/18/2014] [Accepted: 05/27/2014] [Indexed: 12/16/2022]
Abstract
BACKGROUND Human bocavirus (HBoV) is a novel parvovirus identified in 2005. It has mostly been detected in respiratory and enteric infections and has not been studied large scale in blood products in relation to transfusion. STUDY DESIGN AND METHODS An in-house quantitative polymerase chain reaction (Q-PCR) was developed to test HBoV DNA in plasma and plasma derivatives. Plasma samples (n = 6096) collected from healthy donors, 241 plasma pools, and 326 plasma derivatives were screened for HBoV DNA by Q-PCR. Positive samples were confirmed by nested PCR and further amplified for sequence analysis and phylogenetic studies. The prevalence of immunoglobulin (Ig)G and IgM specific to HBoV structural proteins was measured by enzyme-linked immunosorbent assay in 209 samples grouped according to virus load (Group 1, HBoV DNA >10(4) copies/mL; Group 2, HBoV DNA >5 × 10(2) copies/mL but below 10(4) copies/mL; Group 3,HBoV DNA negative). RESULTS The genomic prevalence of HBoV in the plasma donors was 9.06%, ranging from 5.01 × 10(2) to 3.02 × 10(6) copies/mL. HBoV-specific IgG and IgM were detected at 20.00 and 7.50% in Group 1, at 20.29 and 2.90% in Group 2, and at 13.00 and 4.0% in Group 3, respectively. Phylogenetic analyses proved that HBoV Genotype 1 was the prevalent genotype in Chinese plasma donors. CONCLUSION Low levels of HBoV DNA were detectable at high prevalence in Chinese plasma donors and plasma derivatives. Further study is needed to determine whether HBoV screening is necessary.
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Affiliation(s)
- Hongxue Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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36
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Levican J, Navas E, Orizola J, Avendaño LF, Gaggero A. Human bocavirus in children with acute gastroenteritis, Chile, 1985-2010. Emerg Infect Dis 2014; 19:1877-80. [PMID: 24209884 PMCID: PMC3837656 DOI: 10.3201/eid1911.130601] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We detected human bocavirus in 89 (19.3%) of 462 fecal samples collected during 3 periods from 1985 through 2010 from children <5 years of age in Chile who were hospitalized with acute gastroenteritis. Our findings confirm the long-term circulation of human bocavirus in Chile.
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37
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Thomas AO, Lemanske RF, Jackson DJ. Infections and their role in childhood asthma inception. Pediatr Allergy Immunol 2014; 25:122-8. [PMID: 24236893 PMCID: PMC3977202 DOI: 10.1111/pai.12147] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/10/2013] [Indexed: 02/02/2023]
Abstract
The association of early-onset wheezing with common viral and bacterial infections has raised significant interest in the role of infections in childhood asthma inception. This article serves to review these relationships among infections, host factors, and asthma inception in childhood.
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Affiliation(s)
- Amy O Thomas
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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38
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Human Bocavirus. Emerg Infect Dis 2014. [PMCID: PMC7173585 DOI: 10.1016/b978-0-12-416975-3.00015-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Human bocavirus 1 (HBoV1), family Parvoviridae, subfamily Parvovirinae, genus Bocavirus, is a recently described respiratory virus with a worldwide distribution. It is recognized as one of the most frequently detected respiratory viruses in hospitalized children below 5 years of age and mainly detected in children between 6 and 24 months of age. The severe clinical course of HBoV1 infection can be seen in prematurely born children or children, but rarely adults, with other underlying medical conditions. The seroepidemiological studies show that most of the children are infected with HBoV1 by the age of 6 and that the IgG antibodies remain for life. The routine laboratory diagnostics of HBoV1 infections is almost exclusively based on detection of HBoV1 DNA in respiratory samples by PCR. Due to frequent coinfections with other respiratory viruses, PCR of plasma samples and detection of specific IgM might aid in determining the etiology of infection.
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39
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PROENCA-MODENA JL, MARTINEZ M, AMARILLA AA, ESPÍNOLA EE, GALEANO ME, FARIÑA N, RUSSOMANDO G, AQUINO VH, PARRA GI, ARRUDA E. Viral load of human bocavirus-1 in stools from children with viral diarrhoea in Paraguay. Epidemiol Infect 2013; 141:2576-80. [PMID: 23425775 PMCID: PMC9151358 DOI: 10.1017/s095026881300023x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/12/2013] [Accepted: 01/19/2012] [Indexed: 01/04/2023] Open
Abstract
Since their discovery, four species of human bocavirus (HBoV) have been described in patients with respiratory and gastrointestinal diseases. However, a clear causal association between HBoV-1 and gastroenteritis has not been demonstrated. In this study, we describe the detection and quantification of HBoV-1 in stools from children with acute non-bacterial gastroenteritis using quantitative polymerase chain reaction. HBoV-1 genome was detected in 10.6% of stools with frequent association with rotavirus and norovirus. The median of HBoV-1 viral load was 1.88 × 104 genome/ml, lower than previously shown in secretions of patients with respiratory infections, without any obvious association between high viral load and presence of HBoV as single agent. Thus, although HBoV-1 was frequently detected in these patients, there is no clear causal association of this agent with diarrhoea. Indeed, HBoV-1 DNA in stools of patients with gastroenteritis without respiratory symptoms may be a remnant of previous infections or associated with prolonged shedding of virus in the respiratory or digestive tracts.
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Affiliation(s)
- J. L. PROENCA-MODENA
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - M. MARTINEZ
- Departamento de Biología Molecular y Genética, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
| | - A. A. AMARILLA
- Departamento de Biología Molecular y Genética, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - E. E. ESPÍNOLA
- Departamento de Biología Molecular y Genética, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
| | - M. E. GALEANO
- Departamento de Biología Molecular y Genética, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
| | - N. FARIÑA
- Departamento de Análisis Clínicos y Microbiología, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
| | - G. RUSSOMANDO
- Departamento de Biología Molecular y Genética, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
| | - V. H. AQUINO
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - G. I. PARRA
- Departamento de Biología Molecular y Genética, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
| | - E. ARRUDA
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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Popgeorgiev N, Temmam S, Raoult D, Desnues C. Describing the silent human virome with an emphasis on giant viruses. Intervirology 2013; 56:395-412. [PMID: 24157886 DOI: 10.1159/000354561] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Viruses are the most abundant obligate intracellular entities in our body. Until recently, they were only considered to be pathogens that caused a broad array of pathologies, ranging from mild disease to deaths in the most severe cases. However, recent advances in unbiased mass sequencing techniques as well as increasing epidemiological evidence have indicated that the human body is home to diverse viral species under non-pathological conditions. Despite these studies, the description of the presumably healthy viral flora, i.e. the normal human virome, is still in its infancy regarding viral composition and dynamics. This review summarizes our current knowledge of the human virome under non-pathological conditions.
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Affiliation(s)
- Nikolay Popgeorgiev
- URMITE UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France
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41
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Structure of the NS1 protein N-terminal origin recognition/nickase domain from the emerging human bocavirus. J Virol 2013; 87:11487-93. [PMID: 23966383 DOI: 10.1128/jvi.01770-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human bocavirus is a newly identified, globally prevalent, parvovirus that is associated with respiratory infection in infants and young children. Parvoviruses encode a large nonstructural protein 1 (NS1) that is essential for replication of the viral single-stranded DNA genome and DNA packaging and may play versatile roles in virus-host interactions. Here, we report the structure of the human bocavirus NS1 N-terminal domain, the first for any autonomous parvovirus. The structure shows an overall fold that is canonical to the histidine-hydrophobic-histidine superfamily of nucleases, which integrates two distinct DNA-binding sites: (i) a positively charged region mediated by a surface hairpin (residues 190 to 198) that is responsible for recognition of the viral origin of replication of the double-stranded DNA nature and (ii) the nickase active site that binds to the single-stranded DNA substrate for site-specific cleavage. The structure reveals an acidic-residue-rich subdomain that is present in bocavirus NS1 proteins but not in the NS1 orthologs in erythrovirus or dependovirus, which may mediate bocavirus-specific interaction with DNA or potential host factors. These results provide insights into recognition of the origin of replication and nicking of DNA during bocavirus genome replication. Mapping of variable amino acid residues of NS1s from four human bocavirus species onto the structure shows a scattered pattern, but the origin recognition site and the nuclease active site are invariable, suggesting potential targets for antivirals against this clade of highly diverse human viruses.
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Abstract
Viral pathogens are commonly isolated from children with community-acquired pneumonia (CAP). Viruses like respiratory syncytial virus, human rhinovirus, human metapneumovirus, parainfluenza viruses, and influenza may act as sole pathogens or may predispose to bacterial pneumonia by a variety of mechanisms. New, emerging, or reemerging viral pathogens occasionally cause outbreaks of severe respiratory tract infection in children. The 2009–2010 H1N1 influenza virus pandemic resulted in increased rates of influenza-related hospitalizations and deaths in children. Rapid viral diagnostic tests based on antigen detection or nucleic acid amplification are increasingly available for clinical use and confirm the importance of viral infection in children hospitalized with CAP. Recently published guidelines for the management of CAP in children note that positive viral test results can modify clinical decision making in children with suspected pneumonia by allowing antibacterial therapy to be withheld in the absence of clinical, laboratory, or radiographic findings that suggest bacterial coinfection.
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Affiliation(s)
- Charles R Woods
- Pediatric Infectious Diseases, University of Louisville School of Medicine, 571 South Floyd Street, Suite 321, Louisville, KY, 40202, USA,
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43
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Khamrin P, Okitsu S, Ushijima H, Maneekarn N. Complete genome sequence analysis of novel human bocavirus reveals genetic recombination between human bocavirus 2 and human bocavirus 4. INFECTION GENETICS AND EVOLUTION 2013; 17:132-6. [PMID: 23579236 DOI: 10.1016/j.meegid.2013.03.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/21/2013] [Accepted: 03/23/2013] [Indexed: 12/20/2022]
Abstract
Epidemiological surveillance of human bocavirus (HBoV) was conducted on fecal specimens collected from hospitalized children with diarrhea in Chiang Mai, Thailand in 2011. By partial sequence analysis of VP1 gene, an unusual strain of HBoV (CMH-S011-11), was initially identified as HBoV4. The complete genome sequence of CMH-S011-11 was performed and analyzed further to clarify whether it was a recombinant strain or a new HBoV variant. Analysis of complete genome sequence revealed that the coding sequence starting from NS1, NP1 to VP1/VP2 was 4795 nucleotides long. Interestingly, the nucleotide sequence of NS1 gene of CMH-S011-11 was most closely related to the HBoV2 reference strains detected in Pakistan, which contradicted to the initial genotyping result of the partial VP1 region in the previous study. In addition, comparison of NP1 nucleotide sequence of CMH-S011-11 with those of other HBoV1-4 reference strains also revealed a high level of sequence identity with HBoV2. On the other hand, nucleotide sequence of VP1/VP2 gene of CMH-S011-11 was most closely related to those of HBoV4 reference strains detected in Nigeria. The overall full-length sequence analysis revealed that this CMH-S011-11 was grouped within HBoV4 species, but located in a separate branch from other HBoV4 prototype strains. Recombination analysis revealed that CMH-S011-11 was the result of recombination between HBoV2 and HBoV4 strains with the break point located near the start codon of VP2.
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Affiliation(s)
- Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
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44
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Sun B, Cai Y, Li Y, Li J, Liu K, Li Y, Yang Y. The nonstructural protein NP1 of human bocavirus 1 induces cell cycle arrest and apoptosis in Hela cells. Virology 2013; 440:75-83. [PMID: 23507451 DOI: 10.1016/j.virol.2013.02.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/09/2013] [Accepted: 02/13/2013] [Indexed: 12/27/2022]
Abstract
Human bocavirus type 1 (HBoV1) is a newly identified pathogen associated with human respiratory tract illnesses. Previous studies demonstrated that proteins of HBoV1 failed to cause cell death, which is considered as a possible common feature of bocaviruses. However, our work showed that the NP1 of HBoV1 induced apoptotic cell death in Hela cells in the absence of viral genome replication and expression of other viral proteins. Mitochondria apoptotic pathway was involved in the NP1-induced apoptosis that was confirmed by apoptotic characteristics including morphological changes, DNA fragmentation and caspase activation. We also demonstrated that the cell cycle of NP1-transfected Hela cells was transiently arrested at G2/M phase followed by rapid appearance of apoptosis and that the N terminal domain of NP1 was critical to its nuclear localization and function in apoptosis induction in Hela cells. These findings might provide alternative information for further study of mechanism of HBoV1 pathogenesis.
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Affiliation(s)
- Bin Sun
- College of Life Science, Central China Normal University, Wuhan 430079, Hubei, China
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45
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Curtis N, Finn A, Pollard AJ. Elucidation and clinical role of emerging viral respiratory tract infections in children. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 764:191-204. [PMID: 23654068 PMCID: PMC7123406 DOI: 10.1007/978-1-4614-4726-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/29/2024]
Abstract
Acute respiratory viral infections (ARVI's) are the most common infectious disease in humans. With the appearance of molecular techniques the recovery of viruses has dramatically increased. Nowadays virologists can quickly discriminate virological families and related viruses from emerging viruses and consequently identify novel viruses. Many new respiratory viruses have been identified in children in the past 15 years. In this review we shortly discuss novel respiratory viruses and their pathogenic role in pediatric respiratory disease. Advantages and drawbacks of the technique and our current knowledge will be discussed. We will conclude this review with a general discussion on the future role of molecular diagnostic virology in the clinic.
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Affiliation(s)
- Nigel Curtis
- Royal Children's Hospital, Dept. Pediatrics, University of Melbourne, Flemington Road, Parkville, 3052 Victoria Australia
| | - Adam Finn
- Institute of Child Life and Health, UBHT Education Centre, University of Bristol, Upper Maudlin Street, Bristol, BS28AE UK
| | - Andrew J. Pollard
- University of Oxford, Level 4,John Radcliffe Hospital, Oxford, OX3 9DU UK
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46
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Pavia AT. What is the role of respiratory viruses in community-acquired pneumonia?: What is the best therapy for influenza and other viral causes of community-acquired pneumonia? Infect Dis Clin North Am 2012; 27:157-75. [PMID: 23398872 PMCID: PMC3572787 DOI: 10.1016/j.idc.2012.11.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Andrew T Pavia
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Utah, Salt Lake City, UT 84108, USA.
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47
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Colvin JM, Muenzer JT, Jaffe DM, Smason A, Deych E, Shannon WD, Arens MQ, Buller RS, Lee WM, Weinstock EJS, Weinstock GM, Storch GA. Detection of viruses in young children with fever without an apparent source. Pediatrics 2012; 130:e1455-62. [PMID: 23129086 PMCID: PMC3507256 DOI: 10.1542/peds.2012-1391] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE Fever without an apparent source is common in young children. Currently in the United States, serious bacterial infection is unusual. Our objective was to determine specific viruses that might be responsible. METHODS We enrolled children aged 2 to 36 months with temperature of 38°C or greater without an apparent source or with definite or probable bacterial infection being evaluated in the St Louis Children's Hospital Emergency Department and afebrile children having ambulatory surgery. Blood and nasopharyngeal swab samples were tested with an extensive battery of virus-specific polymerase chain reaction assays. RESULTS One or more viruses were detected in 76% of 75 children with fever without an apparent source, 40% of 15 children with fever and a definite or probable bacterial infection, and 35% of 116 afebrile children (P < .001). Four viruses (adenovirus, human herpesvirus 6, enterovirus, and parechovirus) were predominant, being detected in 57% of children with fever without a source, 13% of children with fever and definite or probable bacterial infection, and 7% of afebrile children (P < .001). Thirty-four percent of 146 viral infections were detected only by polymerase chain reaction performed on blood. Fifty-one percent of children with viral infections and no evidence of bacterial infection were treated with antibiotics. CONCLUSIONS Viral infections are frequent in children with fever without an apparent source. Testing of blood in addition to nasopharyngeal secretions expanded the range of viruses detected. Future studies should explore the utility of testing for the implicated viruses. Better recognition of viruses that cause undifferentiated fever in young children may help limit unnecessary antibiotic use.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - George M. Weinstock
- the Genome Institute, Washington University School of Medicine, St Louis, Missouri; and
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Characterization of the nonstructural proteins of the bocavirus minute virus of canines. J Virol 2012; 87:1098-104. [PMID: 23135724 DOI: 10.1128/jvi.02627-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present a detailed characterization of a single-cycle infection of the bocavirus minute virus of canines (MVC) in canine WRD cells. This has allowed identification of an additional smaller NS protein that derives from an mRNA spliced within the NS gene that had not been previously reported. In addition, we have identified a role for the viral NP1 protein during infection. NP1 is required for read-through of the MVC internal polyadenylation site and, thus, access of the capsid gene by MVC mRNAs. Although the mechanism of NP1's action has not yet been fully elucidated, it represents the first parvovirus protein to be implicated directly in viral RNA processing.
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Acute diarrhea in West African children: diverse enteric viruses and a novel parvovirus genus. J Virol 2012; 86:11024-30. [PMID: 22855485 DOI: 10.1128/jvi.01427-12] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Parvoviruses cause a variety of mild to severe symptoms or asymptomatic infections in humans and animals. During a viral metagenomic analysis of feces from children with acute diarrhea in Burkina Faso, we identified in decreasing prevalence nucleic acids from anelloviruses, dependoviruses, sapoviruses, enteroviruses, bocaviruses, noroviruses, adenoviruses, parechoviruses, rotaviruses, cosavirus, astroviruses, and hepatitis B virus. Sequences from a highly divergent parvovirus, provisionally called bufavirus, were also detected whose NS1 and VP1 proteins showed <39% and <31% identities to those of previously known parvoviruses. Four percent of the fecal samples were PCR positive for this new parvovirus, including a related bufavirus species showing only 72% identity in VP1. The high degree of genetic divergence of these related genomes from those of other parvoviruses indicates the presence of a proposed new Parvoviridae genus containing at least two species. Studies of the tropism and pathogenicity of these novel parvoviruses will be facilitated by the availability of their genome sequences.
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Abstract
Canine minute virus (CnMV) is a member of the Bocavirus genus, together with Bovine parvovirus (BPV), which emerged as a new pathogen of dogs in 1967. The genus Bocavirus gained more recognition after the recent identification of Human bocavirus in pooled specimens from the respiratory tract of children. The cell culture host range of CnMV appears to be restricted to the Walter Reed canine cell (WRCC) line, although there is a report that indicates susceptibility of the Madin-Darby canine kidney (MDCK) cell line. In order to study the susceptibility of different cell lines to CnMV, the replication in cell cultures of canine, bovine, and human origin and the interaction of the virus with freshly isolated canine peripheral blood mononuclear cells were evaluated. The in vitro host range was unexpectedly wide. As shown by indirect fluorescent antibody and polymerase chain reaction assays, CnMV replicates efficiently in the A72 and MDCK canine cell lines. Bovine and human cell lines support the replication of CnMV less efficiently. In contrast, canine mononuclear blood cells are permissive to replication of CnMV in vitro. The present study revealed the ability of CnMV to replicate in continuous cell lines of different origin and, partially, in canine mononuclear cells.
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Affiliation(s)
- Annamaria Pratelli
- Department of Public Health and Animal Sciences, Strada per Casamassima km 3, 70010 Valenzano, Bari, Italy.
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