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Special Issue "Newly Identified Respiratory Viruses"

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A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Animal Viruses".

Deadline for manuscript submissions: closed (30 September 2009)

Special Issue Editor

Guest Editor
Dr. Ian M. Mackay

Public and Environmental Health - Virology, Forensic and Scientific Services, Health Support Queensland, Department of Health, Queensland, Australia, and Faculty of Health, Queensland University of Technology, Queensland, Australia
E-Mail
Phone: +61 7 3636 1619
Fax: +61 7 3636 1401
Interests: human respiratory viruses; human enteroviruses; human rhinoviruses; virus discovery; paediatric virology; diagnostic PCR

Published Papers (10 papers)

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Research

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Open AccessArticle A Novel Duplex Real-Time Reverse-Transcription PCR Assay for the Detection of Influenza A and the Novel Influenza A(H1N1) Strain
Viruses 2009, 1(3), 1204-1208; doi:10.3390/v1031204
Received: 13 October 2009 / Revised: 28 November 2009 / Accepted: 4 December 2009 / Published: 9 December 2009
Cited by 3 | PDF Full-text (85 KB) | HTML Full-text | XML Full-text
Abstract
Timely implementation of antiviral treatment and other public health based responses are dependent on accurate and rapid diagnosis of the novel pandemic influenza A(H1N1) strain. In this study we developed a duplex real-time PCR (RT-PCR) (dFLU-TM) assay for the simultaneous detection of a
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Timely implementation of antiviral treatment and other public health based responses are dependent on accurate and rapid diagnosis of the novel pandemic influenza A(H1N1) strain. In this study we developed a duplex real-time PCR (RT-PCR) (dFLU-TM) assay for the simultaneous detection of a broad range of influenza A subtypes and specific detection of the novel H1N1 2009 pandemic strain. The assay was compared to the combined results of two previously described monoplex RT-PCR assays using 183 clinical samples and 10 seasonal influenza A isolates. Overall, the results showed that the dFLU-TM RT-PCR method is suitable for detection of influenza A, including the novel H1N1 pandemic strain, in clinical samples. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)
Open AccessCommunication All Known Human Rhinovirus Species Are Present in Sputum Specimens of Military Recruits During Respiratory Infection
Viruses 2009, 1(3), 1178-1189; doi:10.3390/v1031178
Received: 1 September 2009 / Revised: 8 November 2009 / Accepted: 2 December 2009 / Published: 4 December 2009
Cited by 19 | PDF Full-text (153 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Human rhinoviruses (HRV) are known to cause common cold as well as more complicated respiratory infections. HRV species -A, -B and -C have all been associated with lower respiratory infections and exacerbations of asthma. However, the type distribution of strains connected to different
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Human rhinoviruses (HRV) are known to cause common cold as well as more complicated respiratory infections. HRV species -A, -B and -C have all been associated with lower respiratory infections and exacerbations of asthma. However, the type distribution of strains connected to different kinds of lower respiratory conditions is not clearly known. We have analysed the presence of HRV in sputum specimens derived from military recruits with and without pre-diagnosed asthma at times of acute respiratory infection (CIAS Study, 2004-2005). The analysis was performed with HRV and HEV real-time RT-PCR assays. Subsequently we studied type distribution of HRV strains by genetic typing in the VP4/VP2 genomic region. In total 146 (38.8%) specimens were HRV-positive and 36 (9.3%) HEV-positive. No difference was found in HRV detection between the asthmatic vs. non-asthmatic patients. Most of the genetically typed strains, 18 (62.1%), belonged to HRV-A, while HRV-B strains constituted five (17.2%) of the HRV-positive strains. HRV-C strain was typed four times from the HRV-positive cases and a HEV-D strain twice. We further typed six HEV positive strains in the partial VP1 region. Three of these belonged to HRV-A and three to HEV-D. HRV-A strains were discovered throughout the study period, while HRV-C strains originated from winter and spring specimens. Interestingly, four out of five typed HRV-B strains originated from the summer season specimens. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)
Open AccessCommunication Seroconversion to HCoV-NL63 in Rhesus Macaques
Viruses 2009, 1(3), 647-656; doi:10.3390/v1030647
Received: 26 August 2009 / Revised: 28 October 2009 / Accepted: 30 October 2009 / Published: 30 October 2009
Cited by 7 | PDF Full-text (234 KB) | HTML Full-text | XML Full-text
Abstract
HCoV-NL63 is a recently identified respiratory virus. Its pathogenesis has not been fully unraveled because an animal model is currently lacking. Here we examined whether rhesus macaques encounter HCoV-NL63 infections during life, by examining the levels of antibodies to HCoV-NL63 in time. The
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HCoV-NL63 is a recently identified respiratory virus. Its pathogenesis has not been fully unraveled because an animal model is currently lacking. Here we examined whether rhesus macaques encounter HCoV-NL63 infections during life, by examining the levels of antibodies to HCoV-NL63 in time. The animals were followed for 7 up till 19 years, and in three animals we observed a steep rise in antibodies during follow up, indicative of a natural infection with HCoV-NL63. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)
Open AccessArticle Molecular Characterization of Viruses from Clinical Respiratory Samples Producing Unidentified Cytopathic Effects in Cell Culture
Viruses 2009, 1(2), 84-90; doi:10.3390/v1020084
Received: 1 July 2009 / Revised: 14 July 2009 / Accepted: 16 July 2009 / Published: 17 July 2009
Cited by 4 | PDF Full-text (42 KB) | HTML Full-text | XML Full-text
Abstract
The sequence-independent single primer amplification (SISPA) method was performed to identify a virus in 17 clinical respiratory samples producing uncharacterized cytopathic effects in LLC-MK2 cells. Sequence analysis of 600-1600 bp amplicons allowed the identification of six viruses (one influenza C, two parechovirus-3 and
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The sequence-independent single primer amplification (SISPA) method was performed to identify a virus in 17 clinical respiratory samples producing uncharacterized cytopathic effects in LLC-MK2 cells. Sequence analysis of 600-1600 bp amplicons allowed the identification of six viruses (one influenza C, two parechovirus-3 and three cardioviruses). Genomic sequences of the cardioviruses showed similarities with those of the recently-described Saffold virus strain although significant variation was present in the viral surface EF and CD loops. These results demonstrate the usefulness of SISPA for identifying emerging viruses and also known viruses not easily identified by standard virological methods. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)
Open AccessArticle Introduction of a Novel Swine-Origin Influenza A (H1N1) Virus into Milwaukee, Wisconsin in 2009
Viruses 2009, 1(1), 72-83; doi:10.3390/v1010072
Received: 4 June 2009 / Revised: 11 June 2009 / Accepted: 11 June 2009 / Published: 11 June 2009
Cited by 15 | PDF Full-text (205 KB) | HTML Full-text | XML Full-text
Abstract
On 17 April 2009, novel swine origin influenza A virus (S-OIV) cases appeared within the United States. Most influenza A diagnostic assays currently utilized in local clinical laboratories do not allow definitive subtype determination. Detailed subtype analysis of influenza A positive samples in
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On 17 April 2009, novel swine origin influenza A virus (S-OIV) cases appeared within the United States. Most influenza A diagnostic assays currently utilized in local clinical laboratories do not allow definitive subtype determination. Detailed subtype analysis of influenza A positive samples in our laboratory allowed early confirmation of a large outbreak of S-OIV in southeastern Wisconsin (SEW). The initial case of S-OIV in SEW was detected on 28 April 2009. All influenza A samples obtained during the 16 week period prior to 28 April 2009, and the first four weeks of the subsequent epidemic were sub typed. Four different multiplex assays were employed, utilizing real time PCR and end point PCR to fully subtype human and animal influenza viral components. Specific detection of S-OIV was developed within days. Data regarding patient demographics and other concurrently circulating viruses were analyzed. During the first four weeks of the epidemic, 679 of 3726 (18.2%) adults and children tested for influenza A were identified with S-OIV infection. Thirteen patients (0.34%) tested positive for seasonal human subtypes of influenza A during the first two weeks and none in the subsequent 2 weeks of the epidemic. Parainfluenza viruses were the most prevalent seasonal viral agents circulating during the epidemic (of those tested), with detection rates of 12% followed by influenza B and RSV at 1.9% and 0.9% respectively. S-OIV was confirmed on day 2 of instituting subtype testing and within 4 days of report of national cases of S-OIV. Novel surge capacity diagnostic infrastructure exists in many specialty and research laboratories around the world. The capacity for broader influenza A sub typing at the local laboratory level allows timely and accurate detection of novel strains as they emerge in the community, despite the presence of other circulating viruses producing identical illness. This is likely to become increasingly important given the need for appropriate subtype driven anti-viral therapy and the potential shortage of such medications in a large epidemic. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)
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Figure 1

Open AccessArticle An Economical Tandem Multiplex Real-Time PCR Technique for the Detection of a Comprehensive Range of Respiratory Pathogens
Viruses 2009, 1(1), 42-56; doi:10.3390/v1010042
Received: 5 May 2009 / Revised: 2 June 2009 / Accepted: 5 June 2009 / Published: 8 June 2009
Cited by 18 | PDF Full-text (169 KB) | HTML Full-text | XML Full-text
Abstract
This study used real-time PCR assays to screen small sample volumes for a comprehensive range of 35 respiratory pathogens. Initial thermocycling was limited to 20 cycles to avoid competition for reagents, followed by a secondary real-time multiplex PCR. Supplementary semi-nested human metapneumovirus and
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This study used real-time PCR assays to screen small sample volumes for a comprehensive range of 35 respiratory pathogens. Initial thermocycling was limited to 20 cycles to avoid competition for reagents, followed by a secondary real-time multiplex PCR. Supplementary semi-nested human metapneumovirus and picornavirus PCR assays were required to complete the acute respiratory pathogen profile. Potential pathogens were detected in 85 (70%) of pernasal aspirates collected from 121 children with acute respiratory symptoms. Multiple pathogens were detected in 29 (24%) of those samples. The tandem multiplex real-time PCR was an efficient method for the rapid detection of multiple pathogens. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)
Open AccessArticle The Complete Sequence of a Human Parainfluenzavirus 4 Genome
Viruses 2009, 1(1), 26-41; doi:10.3390/v1010026
Received: 6 April 2009 / Revised: 22 May 2009 / Accepted: 26 May 2009 / Published: 2 June 2009
Cited by 7 | PDF Full-text (1268 KB) | HTML Full-text | XML Full-text
Abstract
Although the human parainfluenza virus 4 (HPIV4) has been known for a long time, its genome, alone among the human paramyxoviruses, has not been completely sequenced to date. In this study we obtained the first complete genomic sequence of HPIV4 from a clinical
[...] Read more.
Although the human parainfluenza virus 4 (HPIV4) has been known for a long time, its genome, alone among the human paramyxoviruses, has not been completely sequenced to date. In this study we obtained the first complete genomic sequence of HPIV4 from a clinical isolate named SKPIV4 obtained at the Hospital for Sick Children in Toronto (Ontario, Canada). The coding regions for the N, P/V, M, F and HN proteins show very high identities (95% to 97%) with previously available partial sequences for HPIV4B. The sequence for the L protein and the non-coding regions represent new information. A surprising feature of the genome is its length, more than 17 kb, making it the longest genome within the genus Rubulavirus, although the length is well within the known range of 15 kb to 19 kb for the subfamily Paramyxovirinae. The availability of a complete genomic sequence will facilitate investigations on a respiratory virus that is still not completely characterized. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)

Review

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Open AccessReview WU Polyomavirus (WUPyV): A Recently Detected Virus Causing Respiratory Disease?
Viruses 2009, 1(3), 678-688; doi:10.3390/v1030678
Received: 20 August 2009 / Revised: 19 October 2009 / Accepted: 4 November 2009 / Published: 4 November 2009
PDF Full-text (49 KB) | HTML Full-text | XML Full-text
Abstract
The WU polyomavirus (WUPyV) is a novel member of the family Polyomaviridae recently detected in respiratory tract specimens by shotgun sequencing. Intriguingly, viral genome has been detected in 0.4% to 11.5% of respiratory tract specimens from children with respiratory disease. The levels
[...] Read more.
The WU polyomavirus (WUPyV) is a novel member of the family Polyomaviridae recently detected in respiratory tract specimens by shotgun sequencing. Intriguingly, viral genome has been detected in 0.4% to 11.5% of respiratory tract specimens from children with respiratory disease. The levels of co-infection with established respiratory viruses were in the range between 30.8% and 91.7%. Moreover, some studies report detection of WUPyV in stool or serum. So far, WUPyV infections can not be distinguished from other viral infections by means of clinical symptoms. Respiratory tract disease like pneumonia or bronchitis is frequently observed in patients harbouring WUPyV. Detection of viremia suggests systemic infections. However, the available data do not prove WUPyV to be a human pathogen. Further investigations are necessary. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)
Open AccessReview More and More Coronaviruses: Human Coronavirus HKU1
Viruses 2009, 1(1), 57-71; doi:10.3390/v1010057
Received: 7 May 2009 / Revised: 6 June 2009 / Accepted: 11 June 2009 / Published: 11 June 2009
Cited by 18 | PDF Full-text (311 KB) | HTML Full-text | XML Full-text
Abstract
After human coronaviruses OC43, 229E and NL63, human coronavirus HKU1 (HCoV-HKU1) is the fourth human coronavirus discovered. HCoV-HKU1 is a group 2a coronavirus that is still not cultivable. The G + C contents of HCoV-HKU1 genomes are 32%, the lowest among all known
[...] Read more.
After human coronaviruses OC43, 229E and NL63, human coronavirus HKU1 (HCoV-HKU1) is the fourth human coronavirus discovered. HCoV-HKU1 is a group 2a coronavirus that is still not cultivable. The G + C contents of HCoV-HKU1 genomes are 32%, the lowest among all known coronaviruses with complete genome sequences available. Among all coronaviruses, HCoV-HKU1 shows the most extreme codon usage bias, attributed most importantly to severe cytosine deamination. All HCoV-HKU1 genomes contain unique tandem copies of a 30-base acidic tandem repeat of unknown function at the N-terminus of nsp3 inside the acidic domain upstream of papain-like protease 1. Three genotypes, A, B and C, of HCoV-HKU1 and homologous recombination among their genomes, are observed. The incidence of HCoV-HKU1 infections is the highest in winter. Similar to other human coronaviruses, HCoV-HKU1 infections have been reported globally, with a median (range) incidence of 0.9 (0 – 4.4) %. HCoV-HKU1 is associated with both upper and lower respiratory tract infections that are mostly self-limiting. The most common method for diagnosing HCoV-HKU1 infection is RT-PCR or real-time RT-PCR using RNA extracted from respiratory tract samples such as nasopharyngeal aspirates (NPA). Both the pol and nucleocapsid genes have been used as the targets for amplification. Monoclonal antibodies have been generated for direct antigen detection in NPA. For antibody detection, Escherichia coli BL21 and baculovirus-expressed recombinant nucleocapsid of HCoV-HKU1 have been used for IgG and IgM detection in sera of patients and normal individuals, using Western blot and enzyme-linked immunoassay. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)
Open AccessReview Human Bocavirus – Insights into a Newly Identified Respiratory Virus
Viruses 2009, 1(1), 3-12; doi:10.3390/v1010003
Received: 2 April 2009 / Revised: 16 April 2009 / Accepted: 20 April 2009 / Published: 21 April 2009
Cited by 7 | PDF Full-text (164 KB) | HTML Full-text | XML Full-text
Abstract
Human Bocavirus (HBoV) was discovered in 2005 using a molecular virus screening technique. It is often found in respiratory samples and is a likely cause for respiratory diseases in children. HBoV is distributed worldwide and has been found not only in respiratory samples,
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Human Bocavirus (HBoV) was discovered in 2005 using a molecular virus screening technique. It is often found in respiratory samples and is a likely cause for respiratory diseases in children. HBoV is distributed worldwide and has been found not only in respiratory samples, but also in feces, urine and serum. HBoV infections are mostly found in young children and coinfections with other respiratory viruses are often found, exacerbating the efforts to link HBoV to specific symptoms. The purpose of this review is to give an overview of recent HBoV research, highlighting some recent findings. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)

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