19Laboratories are currently witnessing extraordinary demand globally for sampling devices, 20 reagents, consumables, and diagnostic instruments needed for timely diagnosis of SARS-CoV-2 21 infection. To meet diagnostic needs as the pandemic grows, the US Food and Drug 22 Administration (FDA) recently granted several commercial SARS-CoV-2 tests Emergency Use 23 Authorization (EUA), but manufacturer-independent evaluation data are scarce. We performed 24 the first manufacturer-independent evaluation of the fully automated sample-to-result two-25 target test cobas 6800 SARS-CoV-2 (cobas) (Roche Molecular Systems, Branchburg, NJ), which 26 received US FDA EUA on March 12, 2020. The comparator was a standardized 3-hour SARS-CoV-27 2 protocol, consisting of RNA extraction using an automated portable instrument, followed by a 28 two-target RT-PCR, which our laboratory has routinely used since January 2020 (Corman VM et 29 al. EuroSurveill 25(3):2000045). Cobas and the comparator showed overall agreement of 98.1% 30 and a kappa value of 0.95 on an in-house validation panel consisting of 217 well-characterized 31 retrospective samples. Immediate prospective head-to-head comparative evaluation followed 32 on 502 samples, and the diagnostic approaches showed overall percent agreement of 99.6% 33 and a kappa value of 0.98. A good correlation (r² = 0.96) between cycle threshold values for 34 SARS-CoV-2 specific targets obtained by cobas and the comparator was observed. Our results 35 showed that cobas is a reliable assay for qualitative detection of SARS-CoV-2 in nasopharyngeal 36 swab samples collected in the UTM-RT system. Under the extraordinary circumstances that 37 laboratories are facing worldwide, a safe diagnostic platform switch is feasible in only 48 hours 38 and in the midst of the COVID-19 pandemic if carefully planned and executed. 39 on June 9, 2020 by guest http://jcm.asm.org/ Downloaded from 3 40 Keywords: SARS-CoV-2, COVID-19, cobas, cobas 6800 41 on June 9, 2020 by guest http://jcm.asm.org/ Downloaded from 58 12), followed by the launch of a range of commercial SARS-CoV-2 PCR-based assays in the last 3 59 months. Despite the fact that the US Food and Drug Administration (FDA) granted several 60 commercial SARS-CoV-2 amplification assays Emergency Use Authorization (EUA), as of March 61 29, 2020 no manufacturer-independent evaluation data for any commercial SARS-CoV-2 assay 62 with US FDA EUA is available in peer-reviewed literature. 63 on June 9, 2020 by guest http://jcm.asm.org/ Downloaded from 5 Here we present the results of the first manufacturer-independent evaluation of the fully 64 automated sample-to-result two-target test cobas 6800 SARS-CoV-2 (cobas) (Roche Molecular 65 Systems, Branchburg, NJ, USA), which received US FDA EUA on March 12, 2020. The 66 performance of cobas was first evaluated on a well-characterized in-house validation panel 67 consisting of 217 samples. The comparator was a standardized 3-hour SARS-CoV-2 detection 68 protocol, consisting of RNA extraction using an automated por...
Human bocavirus is a recently described respiratory pathogen. A case of a life-threatening human bocavirus infection of a previously healthy pediatric patient is described. An initial clinical presentation of acute bronchiolitis developed into an extremely severe course of disease characterized by pneumothorax, pneumomediastinum, and acute respiratory failure with pronounced air-leak syndrome.
BackgroundAcute viral respiratory infections are an important cause of morbidity and mortality in humans worldwide. The etiological backgrounds of these infections remain unconfirmed in most clinical cases. The aim of this study was to estimate the prevalence of human coronavirus infections in a series of children hospitalized with symptoms of acute respiratory tract disease in a one-year period in Slovenia.MethodsThe 664 specimens from 592 children under six years of age hospitalized at the University Children’s Hospital in Ljubljana were sent for the routine laboratory detection of respiratory viruses. Respiratory viruses were detected with a direct immunofluorescence assay and human coronaviruses were detected with a modified real-time RT–PCR.ResultsHCoV RNA was detected in 40 (6%, 95% CI: 4.3%–8.1%) of 664 samples. Of these specimens, 21/40 (52.5%) were identified as species HKU1, 7/40 (17.5%) as OC43, 6/40 (15%) as 229E, and 6/40 (15%) as NL63. Infection with HCoV occurred as a coinfection with one or more other viruses in most samples (70%). Of the HCoV-positive children, 70.3% had lower respiratory tract infections.ConclusionThe results of our study show that HCoV are frequently detected human pathogens, often associated with other respiratory viruses and acute respiratory tract infections in hospitalized children. An association between age and the viral load was found. The highest viral load was detected in children approximately 10 months of age.
Cytomegalovirus (CMV) reactivation is a common complication in patients with inflammatory bowel diseases (IBD), particularly in those with steroid-resistant ulcerative colitis. It is usually diagnosed by histopathologic and immunohistochemical examination of the colon biopsy. The introduction of quantitative, real-time polymerase chain reaction (qPCR) has been recommended to improve the sensitivity, but there is little consensus on how to use it. We compared the two methods in samples from resected bowel of patients with IBD. Twelve patients with IBD who had undergone bowel resection were analysed for CMV, using qPCR and immunohistochemistry. In all cases, tissue samples from the base and the edge of ulcers and from uninvolved mucosa were obtained. The highest densities of CMV-positive cells were found in samples from the base of ulcers (immunohistochemistry 0-0.47 positive cells/mm(2); qPCR 10-3809 viral copies/mg) or the edge of ulcers (immunohistochemistry 0.06-0.32 positive cells/mm(2); qPCR 35-1049 viral copies/mg). In samples of uninvolved mucosa, immunohistochemistry was negative, whereas qPCR was either negative or showed very low values (0-3 viral copies/mg). We conclude that both immunohistochemistry and qPCR can be successfully used for diagnosing CMV reactivation in patients with IBD. The base and the edge of ulcers are the optimal sites for endoscopic biopsies. The density of CMV-positive cells was low and their distribution within the colon uneven. It therefore seems that the number of sampled biopsies and/or the number of investigated levels is more important that the choice of diagnostic method.
We report a rapid increase in enterovirus D68 (EV-D68) infections, with 139 cases reported from eight European countries between 31 July and 14 October 2021. This upsurge is in line with the seasonality of EV-D68 and was presumably stimulated by the widespread reopening after COVID-19 lockdown. Most cases were identified in September, but more are to be expected in the coming months. Reinforcement of clinical awareness, diagnostic capacities and surveillance of EV-D68 is urgently needed in Europe.
A prospective cohort study was conducted during the Delta and Omicron severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) epidemic waves from paired nasopharyngeal swab (NPS or NP swab) and saliva samples taken from 624 participants.The study aimed to assess if any differences among participants from both waves could be observed and if any difference in molecular diagnostic performance could be observed among the two sample types. Samples were transported immediately to the laboratory to ensure the highest possible sample quality without any freezing and thawing steps before processing. Nucleic acids from saliva and NPS were prospectively extracted and SARS-CoV-2 was detected using a real-time reverse-transcription polymerase chain reaction. All observed results were statistically analyzed. Although the results obtained with NP and saliva agreed overall, higher viral loads were observed in NP swabs regardless of the day of specimen collection in both SARS-CoV-2 epidemic waves. No significant difference could be observed between the two epidemic waves characterized by Delta or Omicron SARS-CoV-2. To note, Delta infection resulted in higher viral loads both in NP and saliva and more symptoms, including rhinorrhea, cough, and dyspnea, whereas Omicron wave patients more frequently reported sore throat. An increase in the mean log RNA of SARS-CoV-2 was observed with the number of expressed symptoms in both waves, however, the difference was not significant. Data confirmed that results from saliva were concordant with those from NP swabs, although saliva proved to be a challenging sample with frequent inhibitions that required substantial retesting.
BackgroundThe knowledge on viral respiratory infections in nursing home (NH) residents and their caregivers is limited. The purpose of the present study was to assess and compare the incidence of acute respiratory infections (ARI) in nursing home (NH) residents and staff, to identify viruses involved in ARI and to correlate viral etiology with clinical manifestations of ARI.MethodsThe prospective surveillance study was accomplished in a medium-sized NH in Slovenia (central Europe). Ninety NH residents and 42 NH staff were included. Nasopharyngeal swabs were collected from all participants at enrollment (December 5th, 2011) and at the end of the study (May 31st, 2012), and from each participant that developed ARI within this timeframe. Molecular detection of 15 respiratory viruses in nasopharyngeal swab samples was performed.ResultsThe weekly incidence rate of ARI in NH residents and NH staff correlated; however, it was higher in staff members than in residents (5.9 versus 3.8/1,000 person-days, P = 0.03), and was 2.5 (95 % CI: 1.36–4.72) times greater in residents without dementia than in residents with dementia. Staff members typically presented with upper respiratory tract involvement, whereas in residents lower respiratory tract infections predominated. Respiratory viruses were detected in 55/100 ARI episodes. In residents, influenza A virus, respiratory syncytial virus, and human metapneumovirus were detected most commonly, whereas in NH staff rhinovirus and influenza A virus prevailed. 38/100 ARI episodes (30/56 in residents, 8/44 in staff) belonged to one of three outbreaks (caused by human metapneumovirus, influenza A virus and respiratory syncytial virus, respectively). NH residents had higher chances for virus positivity within outbreak than HN staff (OR = 7.4, 95 % CI: 1.73–31.48, P < 0.01).ConclusionsARI are common among NH residents and staff, and viruses were detected in a majority of the episodes of ARI. Many ARI episodes among NH residents were outbreak cases and could be considered preventable.Trial registrationThe study was registered on the 1th of December 2011 at ClinicalTrials (NCT01486160).
Systemic capillary leak syndrome is a rare condition, characterized by hypotension, edema, hemoconcentration and hypoalbuminemia. We describe 2 episodes of systemic capillary leak syndrome, following influenza A virus infection, occurring during 2 subsequent influenza seasons, in an 8-year-old boy.
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