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Contexte : Cette étude PRONTO a examiné le rendement clinique de la méthode diagnostique COVID-19 d’Abbott ID NOWTM (IDN) utilisé au point de service et son impact sur le délai de divulgation des résultats du test. Méthodes : Étude prospective menée de décembre 2020 à février 2021 chez des participants avec des symptômes aigus se présentant dans trois centres désignés de dépistage de la province de Québec. Résultats : Des échantillons appariés valides ont été obtenus auprès de 2 372 participants. Un résultat positif soit pour l’IDN, soit au test d’amplification des acides nucléiques standard (TAAN-S a été obtenu chez 423 participants (prévalence de 17,8 %). Les sensibilités globales de l’IDN et du TAAN-S étaient de 96,4 % (IC 95 % : 94,2–98,0 %) et 99,1 % (IC 95 % : 97,6–99,8), respectivement; les valeurs prédictives négatives étaient de 99,2 % (IC 95 % : 98,7–99,6%) et 99,8% (IC 95 % : 99,5–100 %), respectivement. Le délai d’obtention de résultats positifs était nettement plus rapide avec l’IDN. Conclusion : D’après notre expérience, l’utilisation de l’IDN chez les personnes symptomatiques dans les centres désignés de dépistage est une alternative sensible fiable au TAAN-S, sans qu’il soit nécessaire de confirmer ultérieurement les résultats négatifs. Ce déploiement peut accélérer la recherche des contacts, réduire la charge des laboratoires et améliorer l’accès aux tests.

The objective of this study was to validate the use of spring water gargle (SWG) as an alternative to oral and nasopharyngeal swab (ONPS) for SARS‐CoV‐2 detection with a laboratory‐developed test. Healthcare workers and adults from the general population, presenting to one of two COVID‐19 screening clinics in Montréal and Québec City, were prospectively recruited to provide a gargle sample in addition to the standard ONPS. The paired specimens were analyzed using thermal lysis followed by a laboratory‐developed nucleic acid amplification test (LD‐NAAT) to detect SARS‐CoV‐2, and comparative performance analysis was performed. An individual was considered infected if a positive result was obtained on either sample. A total of 1297 adult participants were recruited. Invalid results (n = 18) were excluded from the analysis. SARS‐CoV‐2 was detected in 144/1279 (11.3%) participants: 126 from both samples, 15 only from ONPS, and 3 only from SWG. Overall, the sensitivity was 97.9% (95% CI: 93.7–99.3) for ONPS and 89.6% (95% CI: 83.4–93.6; p = 0.005) for SWG. The mean ONPS cycle threshold (Ct) value was significantly lower for the concordant paired samples as compared to discordant ones (22.9 vs. 32.1; p, Highlights Using a laboratory‐developed NAAT preceded by thermal lysis, the overall percent agreement between spring water gargle (SWG) and oral combined with nasopharyngeal swab (ONPS), sampled at the same time among 1297 participants, is excellent (98.6%).Although the SARS‐CoV‐2 NAAT from SWG is globally less sensitive than from ONPS (89.6% vs. 97.9%), the difference is markedly less in individuals symptomatic for

Background Gargle samples have been proposed as a non-invasive method for detection of SARS-CoV-2 RNA. The clinical performance of gargle specimens diluted in cobas® PCR Media and in cobas® Omni Lysis Reagent was compared to oropharyngeal/nasopharyngeal swab (ONPS) for the detection of SARS-CoV-2 RNA. Study design Participants were recruited prospectively in two COVID-19 screening clinics. In addition to the ONPS, participants gargled with 5 mL of natural spring water split in the laboratory as follows: 1 mL was added to 4.3 mL of PCR Media and 400 μL was added to 200 μL of lysis buffer. Testing was performed with the cobas® SARS-CoV-2 test on the cobas® 6800 or 8800 platforms. Results Overall, 134/647 (20.7%) participants were considered infected because the ONPS or at least one gargle tests was positive. ONPS had respectively a sensitivity of 96.3% (95%CI 91.3-98.5); both gargle processing methods were slightly less but equally sensitive [90.3% (95%CI 83.9-94.3)]. When ONPS and gargle specimens were both positive, the mean cycle threshold (Ct) was significantly higher for gargles, suggesting lower viral loads. Conclusion Gargle specimens directly added in PCR Media provides a similar clinical sensitivity to chemical lysis, both having a slightly, not significantly, lower sensitivity to ONPS. This article is protected by copyright. All rights reserved.

BACKGROUND A comprehensive description of the combined effect of SARS-CoV-2 and respiratory viruses (RV) other than SARS-CoV-2 (ORV) on hospitalizations is lacking. OBJECTIVE We compared viral etiology of acute respiratory infections (ARI) hospitalizations before and during two pandemic years from a surveillance network in Quebec, Canada. METHODS We compared detection of ORV and SARS-CoV-2 during 2020-21 and 2021-22 to 8 pre-pandemic influenza seasons in patients hospitalized with ARI who were tested systematically by a multiplex PCR. RESULTS During pre-pandemic influenza seasons, overall RV detection was 92.7% (1,493) (48.3% respiratory syncytial virus (RSV)) in children and 62.8% (4,339) (40.1% influenza) in adults. Overall RV detection in 2020-21 was 58.6% (29) in children (all ORV) and 43.7% (333) in adults (3.4% ORV, 40.3% SARS-CoV2, both including coinfections). In 2021-22 overall RV detection was 91.0% (201) in children (82.8% ORV, 8.1% SARS-CoV-2, both including coinfections) and 55.5% (527) in adults (14.1% ORV, 41.4% SARS-CoV-2, both including coinfections). Virtually no influenza was detected in 2020-21 and in 2021-22 up to epi-week 2022-9 presented here; no RSV was detected in 2020-21. In 2021-22, detection of RSV was comparable to pre-pandemic years but with an unusually early season. There were significant differences in ORV and SARS-CoV-2 detection between time periods and age groups. CONCLUSIONS Significant continuous shifts in age distribution and viral etiology of ARI hospitalizations occurred during two pandemic years. This reflects evolving RV epidemiology and underscores the need for increased scrutiny of ARI hospitalization etiology to inform tailored public health recommendations.

BackgroundA comprehensive description of the combined effect of SARS-CoV-2 and respiratory viruses (RV) other than SARS-CoV-2 (ORV) on hospitalisations is lacking.AimTo compare viral etiology of acute respiratory infections (ARI) hospitalisations before and during two pandemic years from a surveillance network in Quebec, Canada.MethodWe compared detection of ORV and SARS-CoV-2 during 2020-21 and 2021-22 to 8 pre-pandemic influenza seasons in patients hospitalised with ARI who were tested systematically by a multiplex PCR.ResultsDuring pre-pandemic influenza seasons, overall RV detection was 92.7% (1,493) (48.3% respiratory syncytial virus (RSV)) in children and 62.8% (4,339) (40.1% influenza) in adults. Overall RV detection in 2020-21 was 58.6% (29) in children (all ORV) and 43.7% (333) in adults (3.4% ORV, 40.3% SARS-CoV2, both including coinfections). In 2021-22 overall RV detection was 91.0% (201) in children (82.8% ORV, 8.1% SARS-CoV-2, both including coinfections) and 55.5% (527) in adults (14.1% ORV, 41.4% SARS-CoV-2, both including coinfections).Virtually no influenza was detected in 2020-21 and in 2021-22 up to epi-week 2022-9 presented here; no RSV was detected in 2020-21. In 2021-22, detection of RSV was comparable to pre-pandemic years but with an unusually early season. There were significant differences in ORV and SARS-CoV-2 detection between time periods and age groups.ConclusionSignificant continuous shifts in age distribution and viral etiology of ARI hospitalisations occurred during two pandemic years. This reflects evolving RV epidemiology and underscores the need for increased scrutiny of ARI hospitalisation etiology to inform tailored public health recommendations.

The Abbott ID NOW™ COVID-19 assay has been shown as a reliable and sensitive alternative to reverse transcription-polymerase chain reaction (RT-PCR) testing from nasopharyngeal or nasal samples in symptomatic patients. Water gargle is an acceptable noninvasive alternative specimen for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) detection by RT-PCR. The objective of this study was to evaluate the performance of water gargle samples for the detection of SARS-CoV-2 using the ID NOW. Residual gargle samples were randomly selected among positive standard of care (SOC)-nucleic acid amplification test (NAAT) samples. For testing on ID NOW, the manufacturer's instructions were followed, except for the specimen addition step: 500 µl of the gargle specimen was added to the blue sample receiver with a pipette and gently mixed. Among the 202 positive samples by SOC-NAAT, 185 were positive by ID NOW (positive percent agreement [PPA]) = 91.6% (95% confidence interval [CI]: 86.9-95.0). For the 17 discordant samples, cycle threshold (C

The efficacy of convalescent plasma for COVID-19 is unclear. While most randomized controlled trials have shown negative results, uncontrolled studies have suggested that the antibody content may influence patient outcomes.We conducted an open-label, randomized controlled trial of convalescent plasma for adults with COVID-19 receiving oxygen within 12 days of respiratory symptom onset. Patients were allocated 2:1 to 500 mL of convalescent plasma or standard of care. The composite primary outcome was intubation or death by 30 days. The effect of convalescent plasma antibodies on the primary outcome was assessed by logistic regression.The trial was terminated at 78% of planned enrollment after meeting stopping criteria for futility. 940 patients were randomized and 921 patients were included in the intent-to-treat analysis. Intubation or death occurred in 199/614 (32.4%) in the convalescent plasma arm and 86/307 (28.0%) in the standard of care arm; relative risk (RR) 1.16 (95% confidence interval (CI) 0.94-1.43; p=0.18). Patients in the convalescent plasma arm had more serious adverse events (33.4% vs. 26.4%; RR=1.27, 95% CI 1.02-1.57, p=0.034). The antibody content significantly modulated the therapeutic effect of convalescent plasma. In multivariate analysis, each standard log increase in neutralization or antibody-dependent cellular cytotoxicity independently reduced the potential harmful effect of plasma (OR=0.74; 0.57-0.95 and OR=0.66; 0.50-0.87, respectively), while IgG against the full transmembrane Spike protein increased it (OR=1.53, 95% CI 1.14-2.05).Convalescent plasma did not reduce the risk of intubation or death at 30 days among hospitalized patients with COVID-19. Transfusion of convalescent plasma with unfavourable antibody profiles may be associated with worse clinical outcomes compared to standard care.Trial registrationCONvalescent Plasma for Hospitalized Adults With COVID-19 Respiratory Illness (CONCOR-1); NCT04348656; https://www.clinicaltrials.gov/ct2/show/NCT04348656

The efficacy of convalescent plasma for coronavirus disease 2019 (COVID-19) is unclear. Although most randomized controlled trials have shown negative results, uncontrolled studies have suggested that the antibody content could influence patient outcomes. We conducted an open-label, randomized controlled trial of convalescent plasma for adults with COVID-19 receiving oxygen within 12 d of respiratory symptom onset (NCT04348656). Patients were allocated 2:1 to 500 ml of convalescent plasma or standard of care. The composite primary outcome was intubation or death by 30 d. Exploratory analyses of the effect of convalescent plasma antibodies on the primary outcome was assessed by logistic regression. The trial was terminated at 78% of planned enrollment after meeting stopping criteria for futility. In total, 940 patients were randomized, and 921 patients were included in the intention-to-treat analysis. Intubation or death occurred in 199/614 (32.4%) patients in the convalescent plasma arm and 86/307 (28.0%) patients in the standard of care arm—relative risk (RR) = 1.16 (95% confidence interval (CI) 0.94–1.43, P = 0.18). Patients in the convalescent plasma arm had more serious adverse events (33.4% versus 26.4%; RR = 1.27, 95% CI 1.02–1.57, P = 0.034). The antibody content significantly modulated the therapeutic effect of convalescent plasma. In multivariate analysis, each standardized log increase in neutralization or antibody-dependent cellular cytotoxicity independently reduced the potential harmful effect of plasma (odds ratio (OR) = 0.74, 95% CI 0.57–0.95 and OR = 0.66, 95% CI 0.50–0.87, respectively), whereas IgG against the full transmembrane spike protein increased it (OR = 1.53, 95% CI 1.14–2.05). Convalescent plasma did not reduce the risk of intubation or death at 30 d in hospitalized patients with COVID-19. Transfusion of convalescent plasma with unfavorable antibody profiles could be associated with worse clinical outcomes compared to standard care., A randomized trial in patients hospitalized with COVID-19 showed no benefit and potentially increased harm associated with the use of convalescent plasma, with subgroup analyses suggesting that the antibody profile in donor plasma is critical in determining clinical outcomes.

The accurate laboratory detection of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a crucial element in the fight against coronavirus disease 2019 (COVID‐19). Reverse transcription‐polymerase chain reaction testing on combined oral and nasopharyngeal swab (ONPS) suffers from several limitations, including the need for qualified personnel, the discomfort caused by invasive nasopharyngeal sample collection, and the possibility of swab and transport media shortage. Testing on saliva would represent an advancement. The aim of this study was to compare the concordance between saliva samples and ONPS for the detection of SARS‐CoV‐2 on various commercial and laboratory‐developed tests (LDT). Individuals were recruited from eight institutions in Quebec, Canada, if they had SARS‐CoV‐2 RNA detected on a recently collected ONPS, and accepted to provide another ONPS, paired with saliva. Assays available in the different laboratories (Abbott RealTime SARS‐CoV‐2, Cobas® SARS‐CoV‐2, Simplexa™ COVID‐19 Direct, Allplex™ 2019‐nCoV, RIDA®GENE SARS‐CoV‐2, and an LDT preceded by three different extraction methods) were used to determine the concordance between saliva and ONPS results. Overall, 320 tests were run from a total of 125 saliva and ONPS sample pairs. All assays yielded similar sensitivity when saliva was compared to ONPS, with the exception of one LDT (67% vs. 93%). The mean difference in cycle threshold (∆C t) was generally (but not significantly) in favor of the ONPS for all nucleic acid amplification tests. The maximum mean ∆​​​​​C t was 2.0, while individual ∆C t varied importantly from −17.5 to 12.4. Saliva seems to be associated with sensitivity similar to ONPS for the detection of SARS‐CoV‐2 by various assays., Highlights Shortage of trained staff and sampling material calls for alternative, ideally non‐invasive, sampling methodsWe analysed and compared the ONPS and saliva paired specimens collected from 125 individuals who had SARS‐CoV‐2 RNA detected on another recently collected ONPS.All commercial assays yielded similar sensitivity when saliva was compared to ONPS. However, mean difference in cycle threshold was generally in favor of the ONPS for all assays, with important individual variability.Saliva sampling offers a suitable alternative to swab sampling in a context of sampling material shortage

Background Nasopharyngeal swab has long been considered the specimen of choice for the diagnosis of respiratory viral infections, including SARS-CoV-2 infection, but it suffers from several drawbacks: its discomfort limits screening acceptability, and it is vulnerable to shortages in both specialized materials and trained healthcare workers in the context of a pandemic. Methods We prospectively compared natural spring water gargle to combined oro-nasopharyngeal swab (ONPS) for the diagnosis of coronavirus disease 2019 (COVID-19) in paired clinical specimens (1005 ONPS and 1005 gargles) collected from 987 unique early symptomatic as well as asymptomatic individuals from the community. Results Using a direct RT-PCR method with the Allplex™ 2019-nCoV Assay (Seegene), the clinical sensitivity of the gargle was 95.3% (95% confidence interval [CI], 90.2 – 98.3%), similar to the sensitivity of the ONPS (93.8%; 95% CI, 88.2 – 97.3%), despite significantly lower viral RNA concentration in gargles, as reflected by higher cycle threshold values. No single specimen type detected all COVID-19 cases. SARS-CoV-2 RNA was stable in gargles at room temperature for at least 7 days. Conclusion The simplicity of this sampling method coupled with the accessibility of spring water are clear advantages in a pandemic situation where testing frequency, turnaround time and shortage of consumables and trained staff are critical elements.

Brevibacterium linens is one of the main bacteria found in the smear of surface-ripened cheeses. The genome of the industrial strain SMQ-1335 was sequenced using PacBio. It has 4,209,935 bp, a 62.6% G+C content, 3,848 open reading frames, and 61 structural RNAs. A new type I restriction-modification system was identified.

Endothelial cells are actively involved in regulating the exchanges between blood and tissues. This function is tightly dependent on actin cytoskeleton dynamics and is challenged by a wide variety of stimuli, including oxidative stress. In endothelial cells, oxidative stress quickly activates the extracellular-signal-regulated kinase (ERK) MAP kinase, which results in the phosphorylation of tropomyosin. Here, we investigated further the mechanisms of tropomyosin phosphorylation and its function in actin remodeling. We identified, for the first time, death-associated protein kinase 1 (DAP kinase 1) as the kinase that phosphorylates tropomyosin-1 in response to ERK activation by hydrogen peroxide (H2O2). We also report that the phosphorylation of tropomyosin-1 mediated by DAP kinase occurs on Ser283. Moreover, the expression of the pseudophosphorylated tropomyosin mutant Ser283Glu triggers by itself the formation of stress fibers in untreated cells, and the effect is maintained in H2O2-treated cells in which DAP kinase expression is knocked-down by siRNA. By contrast, the expression of the nonphosphorylatable tropomyosin mutant Ser283Ala is not associated with stress fibers and leads to membrane blebbing in response to H2O2. Our finding that tropomyosin-1 is phosphorylated downstream of ERK and DAP kinase and that it helps regulate the formation of stress fibers will aid understanding the role of this protein in regulating the endothelial functions associated with cytoskeletal remodeling.

Staphylococcus xylosus is a bacterial species used in meat fermentation and a commensal microorganism found on animals. We present the first complete circular genome from this species. The genome is composed of 2,757,557 bp, with a G+C content of 32.9%, and contains 2,514 genes and 79 structural RNAs.

The diagnosis of neurosyphilis (NS) is a challenge, especially in HIV-infected patients, and the criteria for deciding when to perform a lumbar puncture (LP) in HIV-infected patients with syphilis are controversial. We retrospectively reviewed demographic, clinical, and laboratory data from 122 cases of HIV-infected patients with documented early syphilis who underwent an LP to rule out NS, and we evaluated 3 laboratory-developed validated real-time PCR assays, the Treponema pallidum particle agglutination (TPPA) assay, the fluorescent treponemal antibody absorption (FTA-ABS) assay, and the line immunoassay INNO-LIA Syphilis, for the diagnosis of NS from cerebrospinal fluid (CSF) samples of these patients. NS was defined by a reactive CSF-VDRL test result and/or a CSF white blood cell (WBC) count of >20 cells/μl. Thirty of the 122 patients (24.6%) had early NS. Headache, visual symptoms, a CD4 cell count of P = P = 0.575). For the diagnosis of NS, the PCR, FTA-ABS, TPPA, and INNO-LIA assays had sensitivities of 58%, 100%, 68%, and 100%, specificities of 67%, 12%, 49%, and 13%, and negative predictive values of 85%, 100%, 84%, and 100%, respectively. Visual disturbances, headache, uncontrolled HIV-1 viremia, and a CD4 cell count of