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Abstract
Sensitive, rapid detection of respiratory viruses is needed for surveillance and for investigation of epidemiologically linked cases. The utility of rapid antigen-based methods for detection of common respiratory viruses and to confirm the cause of outbreaks is well established. However, nucleic acid amplification tests (NATs) offer some benefits above antigen or culture-based procedures, with the main advantages being sensitivity and range of pathogens detectable. It is important to understand how changes in our testing methodology alter respiratory virus detection and information for epidemiological studies. For viruses such as influenza A, influenza B and respiratory syncytial virus, NATs offer enhanced sensitivity above antigen assays but still identify the seasonal peaks important for predicting disease and managing time-sensitive prophylaxis. For other viruses, such as rhinoviruses, coronaviruses, human bocavirus and parainfluenza virus type 4, culture and antigen-based procedures are not available and/or lack sensitivity. Thus such targets would be missed if NATs were not included in testing for surveillance and outbreak investigation. As more respiratory viruses are identified there is a need to expand surveillance and further evaluate new technologies and automation beyond currently-available diagnostics to address detection of a broad range of potential pathogens.
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Affiliation(s)
- Julie D Fox
- Provincial Laboratory for Public Health (Microbiology), University of Calgary, Calgary, Alberta, Canada.
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Sloots TP, Whiley DM, Lambert SB, Nissen MD. Emerging respiratory agents: new viruses for old diseases? J Clin Virol 2008; 42:233-43. [PMID: 18406664 PMCID: PMC7108325 DOI: 10.1016/j.jcv.2008.03.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 03/03/2008] [Indexed: 01/28/2023]
Abstract
The recent advances in molecular technology have enabled the detection of several new viral agents in specimens collected from the human respiratory tract. Human metapneumovirus was first described in 2001, and is a significant respiratory pathogen, particularly of children. Following the identification of severe acute respiratory syndrome (SARS) associated coronavirus, two other newly detected coronaviruses, NL63 and HKU1, have been linked to respiratory disease in humans. However, identifying a new virus as the causative agent of a specific disease is difficult, and ideally would involve satisfying Koch's postulates. The recently described human bocavirus and polyomaviruses KI and WU have been detected in samples collected from humans with acute respiratory infection, but as yet, have not been conclusively proven to be agents of human disease. We review the new viral agents that have been detected in respiratory samples since 2001, and examine their contribution as agents of human disease.
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Affiliation(s)
- T P Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Queensland, Australia.
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McErlean P, Shackelton LA, Andrews E, Webster DR, Lambert SB, Nissen MD, Sloots TP, Mackay IM. Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C). PLoS One 2008; 3:e1847. [PMID: 18382652 PMCID: PMC2268738 DOI: 10.1371/journal.pone.0001847] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 02/21/2008] [Indexed: 11/26/2022] Open
Abstract
Background Human rhinoviruses (HRVs) are the most frequently detected pathogens in acute respiratory tract infections (ARTIs) and yet little is known about the prevalence, recurrence, structure and clinical impact of individual members. During 2007, the complete coding sequences of six previously unknown and highly divergent HRV strains were reported. To catalogue the molecular and clinical features distinguishing the divergent HRV strains, we undertook, for the first time, in silico analyses of all available polyprotein sequences and performed retrospective reviews of the medical records of cases in which variants of the prototype strain, HRV-QPM, had been detected. Methodology/Principle Findings Genomic analyses revealed that the six divergent strains, residing within a clade we previously called HRV A2, had the shortest polyprotein of all picornaviruses investigated. Structure-based amino acid alignments identified conserved motifs shared among members of the genus Rhinovirus as well as substantive deletions and insertions unique to the divergent strains. Deletions mostly affected regions encoding proteins traditionally involved in antigenicity and serving as HRV and HEV receptor footprints. Because the HRV A2 strains cannot yet be cultured, we created homology models of predicted HRV-QPM structural proteins. In silico comparisons confirmed that HRV-QPM was most closely related to the major group HRVs. HRV-QPM was most frequently detected in infants with expiratory wheezing or persistent cough who had been admitted to hospital and required supplemental oxygen. It was the only virus detected in 65% of positive individuals. These observations contributed to an objective clinical impact ranging from mild to severe. Conclusions The divergent strains did not meet classification requirements for any existing species of the genus Rhinovirus or Enterovirus. HRV A2 strains should be partitioned into at least one new species, putatively called Human rhinovirus C, populated by members detected with high frequency, from individuals with respiratory symptoms requiring hospital admission.
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Affiliation(s)
- Peter McErlean
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Laura A. Shackelton
- Mueller Laboratory, Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Emily Andrews
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Dale R. Webster
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, California, United States of America
- Howard Hughes Medical Institute, University of California, San Francisco, California, United States of America
| | - Stephen B. Lambert
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Michael D. Nissen
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
- Division of Microbiology, Queensland Health Pathology Service, Royal Brisbane Hospitals Campus, Brisbane, Queensland, Australia
- Department of Paediatrics and Child Health, Royal Children's Hospitals, Brisbane, Queensland, Australia
| | - Theo P. Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
- Division of Microbiology, Queensland Health Pathology Service, Royal Brisbane Hospitals Campus, Brisbane, Queensland, Australia
- Department of Paediatrics and Child Health, Royal Children's Hospitals, Brisbane, Queensland, Australia
| | - Ian M. Mackay
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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Heikkinen T, Osterback R, Peltola V, Jartti T, Vainionpää R. Human metapneumovirus infections in children. Emerg Infect Dis 2008; 14:101-6. [PMID: 18258088 PMCID: PMC2600144 DOI: 10.3201/eid1401.070251] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Age-related incidence and effects of these infections are highest among children <2 years of age. Human metapneumovirus (hMPV) is an important cause of lower respiratory tract infections in hospitalized children, but the age-related incidence and effect of hMPV in unselected children in the community have not been evaluated. We studied a cohort of 1,338 children <13 years of age throughout 1 respiratory season in Finland during 2000–2001. We examined children and obtained a nasal swab for viral detection at any sign of respiratory infection. hMPV was detected in 47 (3.5%) of the 1,338 children. The age-related incidence of hMPV infection was highest (7.6%) in children <2 years of age, in whom hMPV accounted for 1.7% of all infections during the season. During the epidemic peak, hMPV caused 7.1% of all respiratory infections in the cohort. Acute otitis media developed in 61% of hMPV-infected children <3 years of age. Our findings demonstrate that the effect of hMPV in the community is greatest in children <2 years of age.
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Affiliation(s)
- Terho Heikkinen
- Department of Pediatrics, Turku University Hospital, Turku, Finland.
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Loo LH, Tan BH, Ng LM, Tee NWS, Lin RTP, Sugrue RJ. Human metapneumovirus in children, Singapore. Emerg Infect Dis 2008; 13:1396-8. [PMID: 18252120 PMCID: PMC2857288 DOI: 10.3201/eid1309.070220] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Four hundred specimens were collected from pediatric patients hospitalized in Singapore; 21 of these specimens tested positive for human metapneumovirus (HMPV), with the A2 genotype predominating. A 5% infection rate was estimated, suggesting that HMPV is a significant cause of morbidity among the pediatric population of Singapore.
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Affiliation(s)
- Liat Hui Loo
- Nanyang Technological University, Kandang Kerbau Women's and Children's Hospital, Singapore, Singapore
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