Laboratory diagnosis and surveillance of human respiratory viruses by PCR in Victoria, Australia, 2002-2003

ArticleinJournal of Medical Virology 75(1):122-9 · February 2005with23 Reads
Impact Factor: 2.35 · DOI: 10.1002/jmv.20246 · Source: PubMed

Respiratory viruses were identified by the polymerase chain reaction (PCR) in more than 4,200 specimens collected during 2002 and 2003 in Victoria, Australia from patients admitted to hospitals or participating in an influenza surveillance program. Influenza viruses and picornaviruses were important causes of morbidity in both years. Additional testing of picornavirus-positive samples suggested that rhinoviruses but not enteroviruses were more likely to be associated with respiratory symptoms, irrespective of the season in which they circulated. Detection of influenza viruses was strongly associated with the clinical symptoms of cough, fever, and fatigue; but each of the other respiratory viruses occasionally caused these symptoms or was responsible for symptoms severe enough to require hospitalization. Human coronaviruses HCoV-OC43 and HCoV-229E circulated at low levels throughout the study period with peak activity in winter, but overall did not circulate as widely as has often been reported for these agents. Evidence for the human metapneumovirus (hMPV) was only sought in the second year of the study and revealed low-level circulation of this virus, mainly in the cooler months among the very young and adult populations. The detection rate of all viruses declined with increasing age of the patient, particularly in hospital patients. Infection with more than one respiratory virus occurred in a small number of patients; picornaviruses were most commonly implicated in these dual infections.

    • "Influenza-like illness, a common respiratory syndrome, poses a great threat to worldwide economy as well as public health, which leads to substantial morbidity and mortality each year (LagunaTorres et al., 2009; Silva et al., 2014; Ng and Gordon, 2015). A wide range of respiratory viruses may cause influenza-like illness, such as influenza viruses, respiratory syncytial viruses and parainfluenza viruses (Coiras et al., 2003; Druce et al., 2005; Peng et al., 2012). Numerous studies have confirmed that short-and long-term exposures to ambient air pollutants are associated with a wide range of adverse health outcomes, such as higher mortality rates, greater hospital admissions and increased outpatient visits (Dockery et al., 1993; Bremner et al., 1999; Kan and Chen, 2003). "
    [Show abstract] [Hide abstract] ABSTRACT: Influenza-like illness causes substantial morbidity and mortality. Air pollution has already been linked to many health issues, and increasing evidence in recent years supports an association between air pollution and respiratory infections. It is a pioneer study in China to quantify the effects of air pollution on influenza-like illness. This study used wavelet coherence analysis and generalized additive models to explore the potential association between air pollution (including particulate matter with aerodynamic diameter ≦2.5 μm (PM2.5), particulate matter with aerodynamic diameter ≦10 μm (PM10) and nitrogen dioxide (NO2)) and influenza-like illness (a total of 59860 cases) in Nanjing, China from January 1, 2013 to December 31, 2013. The average concentrations of PM2.5, PM10 and NO2 were 77.37 μg/m3, 135.20 μg/m3 and 55.80 μg/m3. An interquartile range increase in PM2.5 concentration was associated with a 2.99% (95% confidence interval (CI): 1.64%, 4.36%) increase in daily influenza-like cases on the same day, while the corresponding increase in NO2 was associated with a 3.77% (95% CI: 2.01%, 5.56%) increase in daily cases. People aged 0–4 were proved to be significantly susceptible to PM10 and NO2; 5–14 ages were significantly susceptible to PM2.5 and PM10; and 15–24 ages were significantly susceptible to all the analyzed air pollutants. Air pollution effects tended to be null or negative for patients aged over 25, which might be due to the small number of influenza-like cases in this age group. This study can be useful for understanding the adverse health effects of air pollution and the cause of influenza-like illness.
    Full-text · Article · Mar 2016 · Chemosphere
    Lei Huang Lei Huang Lian Zhou Lian Zhou Jin Chen Jin Chen +3 more authors... Kai Chen Kai Chen
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    • "The differences could be due to true differences in the overall burden, to differences among study populations, or to detection methods that differed from among studies. It is difficult to compare the results, as the reported data were obtained with different detection methods or PCR primers [21, 25]. Future comparative studies to evaluate the sensitivity and specificity of these detection methods should clarify this issue. "
    [Show abstract] [Hide abstract] ABSTRACT: Clinical and etiological characteristics of influenza-like illness (ILI) in outpatients is poorly understood in the southern temperate region of China. We conducted laboratory-based surveillance of viral etiology for ILI outpatients in Shanghai from January 2011 to December 2013. Clinical and epidemiological data from ILI outpatients, both children and adults, were collected. A total of 1970 nasopharyngeal swabs were collected and tested for 12 respiratory viruses using multiplex RT-PCR, and the data were analyzed anonymously. All 12 respiratory viruses were detected in the specimens. At least one virus was detected in 32.4% of 1970 specimens analyzed, with 1.1% showing co-infections. The most frequently detected agents were influenza A (11.7%), influenza B (9.6%), and rhinoviruses (3.1%).Other viruses were present at a frequency less than 3.0%. We observed a winter peak in the detection rate in ILI patients during 3 years of surveillance and a summer peak in 2012. HCoV, HADV, and HMPV were detected more frequently in children than in adults. Patients infected with influenza virus experienced higher temperatures, more coughs, running noses, headaches and fatigue than patients infected with other viruses and virus-free patients (p<0.001). The spectrum, seasonality, age distribution and clinical associations of respiratory virus infections in children and adults with influenza-like illness were analyzed in this study for the first time. To a certain extent, the findings can provide baseline data for evaluating the burden of respiratory virus infection in children and adults in Shanghai. It will also provide clinicians with helpful information about the etiological patterns of outpatients presenting with complaints of acute respiratory syndrome, but further studies should be conducted, and longer-term laboratory-based surveillance would give a better picture of the etiology of ILI.
    Full-text · Article · Mar 2015 · PLoS ONE
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    • "Some clusterspecific markers of amino acid changes were noted among partial S and N protein sequences from the HCoV-OC43 isolates. Though viral isolation is the ''gold standard'' for laboratory diagnosis of virus infection, the great difficulty of HCoV isolation and the time-consuming nature of its culture led numerous researchers to prefer molecular detection methods, such as RT- PCR, to screen for HCoV-OC43 infection131415163031323334353640]. The analytic sensitivity of primers specific for different targets has been described previously [33,35]. "
    [Show abstract] [Hide abstract] ABSTRACT: To determine the prevalence, epidemiology and genetic diversity of human coronavirus OC43 (HCoV-OC43) among adult patients with acute respiratory infections (ARI) in Beijing,five hundred and fifty-nine nasopharyngeal swab samples were collected from adult patients with ARI in Beijing. The prevalence of HCoV-OC43 infection among these patients was assessed using two different OneStep reverse transcription polymerase chain reaction (RT-PCR) assays. The epidemiological profiles of the patients with HCoV-OC43 infection were described. Partial S and N genes of HCoV-OC43 circulating strains were sequenced followed by phylogenetic analysis and amino acid alignment. Our results showed that the prevalence of HCoV-OC43 infection was 12.52% (95% CI: 9.78-15.26%), and the epidemic peak occurred in autumn. Fifty partial S and 40 partial N fragments were obtained from these patients. Phylogenetic analysis based on neighbour-joining method showed that at least three distinct clusters (A, B, C/D) of HCoV-OC43 strains were circulating among adult patients with ARI in Beijing. In addition, some novel unique clusters (UNT) of HCoV-OC43 were found in the S- and N-based phylogenetic trees. Furthermore, consensus amino acids substitutes for each cluster were also found after alignment of partial S or N sequence coding region in this study. In conclusion, we herein describe the prevalence of HCoV-OC43 among adult patients and provide substantial evidence for the genetic diversity of HCoV-OC43 circulating in Beijing.
    Full-text · Article · Jul 2014 · PLoS ONE
    Qin Hu Qin Hu Roujian Lu Roujian Lu Kun Peng Kun Peng +5 more authors... Xijie Duan Xijie Duan
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