In March 2003, a novel coronavirus (SARS-CoV) was discovered in association with cases of severe acute respiratory syndrome (SARS). The sequence of the complete genome of SARS-CoV was determined, and ...the initial characterization of the viral genome is presented in this report. The genome of SARS-CoV is 29,727 nucleotides in length and has 11 open reading frames, and its genome organization is similar to that of other coronaviruses. Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closely related to any of the previously characterized coronaviruses.
Screening pneumonia patients for mimivirus Dare, Ryan K; Chittaganpitch, Malinee; Erdman, Dean D
Emerging infectious diseases,
03/2008, Letnik:
14, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Acanthamoeba polyphaga mimivirus (APM), a virus of free-living amebae, has reportedly caused human respiratory disease. Using 2 newly developed real-time PCR assays, we screened 496 respiratory ...specimens from 9 pneumonia-patient populations for APM. This virus was not detected in any specimen, which suggests it is not a common respiratory pathogen.
Abstract Background Multipathogen reverse transcription real-time PCR (RT-qPCR) platforms have proven useful in surveillance for acute respiratory illness (ARI) and study of respiratory outbreaks of ...unknown etiology. The TaqMan® Array Card (TAC, Life Technologies™), can simultaneously test 7 clinical specimens for up to 21 individual pathogens (depending on arrangement of controls and use of duplicate wells) by arrayed singleplex RT-qPCR on a single assay card, using minimal amounts of clinical specimens. A previous study described the development of TAC for the detection of respiratory viral and bacterial pathogens; the assay was evaluated against well-characterized analytical materials and a limited collection of human clinical specimens. Objectives We wished to compare TAC assay performance against standard individual RT-qPCR assays for respiratory viral detection, focusing on 10 viruses (adenovirus, human metapneumovirus, human parainfluenza viruses 1–4, influenza viruses A and B, respiratory syncytial virus, and rhinovirus) from a larger collection of human specimens. Study design We used specimens from 942 children with ARI enrolled systematically in a population-based, ARI surveillance study (New Vaccine Surveillance Network, NVSN). Results Compared with standard individual RT-qPCR assays, the sensitivity of TAC for the targeted viruses ranged from 54% to 95% (54%, 56%, and 75% for adenovirus, human parainfluenza viruses-1 and -2, respectively, and 82%–95% for the other viruses). Assay specificity was 99%, and coefficients of variation for virus controls ranged from 1.5% to 4.5%. Conclusion The TAC assay should prove useful for multipathogen studies and rapid outbreak response.
Human adenoviruses (HAdVs) were previously detected at high prevalence by real‐time reverse transcription‐polymerase chain reaction (rRT‐PCR) in the upper respiratory tract of residents of two Kenyan ...refugee camps under surveillance for acute respiratory infection (ARI) between October 2006 and April 2008. We sought to confirm this finding and characterize the HAdVs detected. Of 2148 respiratory specimens originally tested, 511 (23.8%) screened positive for HAdV and 510 were available for retesting. Of these, 421 (82.4%) were confirmed positive by repeat rRT‐PCR or PCR and sequencing. Other respiratory viruses were codetected in 55.8% of confirmed HAdV‐positive specimens. Species B and C viruses predominated at 82.8%, and HAdV‐C1, ‐C2, and ‐B3 were the most commonly identified types. Species A, D, and F HAdVs, which are rarely associated with ARI, comprised the remainder. Viral loads were highest among species B HAdVs, particularly HAdV‐B3. Species C showed the widest range of viral loads, and species A, D, and F were most often present at low loads and more often with codetections. These findings suggest that many HAdV detections were incidental and not a primary cause of ARI among camp patients. Species/type, codetections, and viral load determinations may permit more accurate HAdV disease burden estimates in these populations.
A high prevalence of human adenovirus (HAdV) detections were confirmed from the respiratory tract of refugees in Kenya presenting with acute respiratory infection (ARI).
HAdV species B and C predominated, although other HAdV species not commonly associated with ARI were also detected.
A high proportion of HAdV positive respiratory specimens had low virus loads and co-detections with other respiratory virus pathogens were common.
Many HAdV detections in this refugee population were likely incidental and not associated with ARI.
Background. Health care workers continued to contract severe acute respiratory syndrome (SARS), even after barrier precautions were widely implemented. Methods. We explored the possible contribution ...of contaminated hospital surfaces to SARS transmission by swabbing surfaces in 2 hospitals and testing the swab samples by reverse-transcriptase polymerase chain reaction (RT-PCR) and viral culture. Results. Twenty-six of 94 swab samples tested positive for viral RNA. Swab samples of respiratory secretions from each of the 4 patients examined tested positive by RT-PCR, as were 12 of 43 swabs from patient rooms and 10 of 47 swabs from other parts of the hospital, including the computer mouses at 2 nursing stations and the handrail of the public elevator. Specimens from areas with patients with SARS in the most infectious phase of illness (days 5–15 after onset) were more likely to be RNA positive than were swab specimens from elsewhere (24 of 63 samples vs. 2 of 31 samples; P = .001). All cultures showed no growth. Conclusions. Although the viruses identified may have been noninfectious, health care workers should be aware that SARS coronavirus can contaminate environmental surfaces in the hospital, and fomites should be considered to be a possible mode of transmission of SARS.
BACKGROUND:Few comprehensive data exist on the etiology of severe acute respiratory illness (SARI) among African children.
METHODS:From March 1, 2007 to February 28, 2010, we collected blood for ...culture and nasopharyngeal and oropharyngeal swabs for real-time quantitative polymerase chain reaction for 10 viruses and 3 atypical bacteria among children aged <5 years with SARI, defined as World Health Organization–classified severe or very severe pneumonia or oxygen saturation <90%, who visited a clinic in rural western Kenya. We collected swabs from controls without febrile or respiratory symptoms. We calculated odds ratios for infection among cases, adjusting for age and season in logistic regression. We calculated SARI incidence, adjusting for healthcare seeking for SARI in the community.
RESULTS:Two thousand nine hundred seventy-three SARI cases were identified (54% inpatient, 46% outpatient), yielding an adjusted incidence of 56 cases per 100 person-years. A pathogen was detected in 3.3% of noncontaminated blood cultures; non-typhi Salmonella (1.9%) and Streptococcus pneumoniae (0.7%) predominated. A pathogen was detected in 84% of nasopharyngeal/oropharyngeal specimens, the most common being rhino/enterovirus (50%), respiratory syncytial virus (RSV, 22%), adenovirus (16%) and influenza viruses (8%). Only RSV and influenza viruses were found more commonly among cases than controls (odds ratio 2.9, 95% confidence interval1.3–6.7 and odds ratio 4.8, 95% confidence interval1.1–21, respectively). Incidence of RSV, influenza viruses and S. pneumoniae were 7.1, 5.8 and 0.04 cases per 100 person-years, respectively.
CONCLUSIONS:Among Kenyan children with SARI, RSV and influenza virus are the most likely viral causes and pneumococcus the most likely bacterial cause. Contemporaneous controls are important for interpreting upper respiratory tract specimens.
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