Rapid Detection of SARS-CoV-2 Variants of Concern, Including B.1.1.28/P.1, British Columbia, Canada.

To screen all severe acute respiratory syndrome coronavirus 2-positive samples in Vancouver, British Columbia, Canada, and determine whether they represented variants of concern, we implemented a real-time reverse transcription PCR-based algorithm. We rapidly identified 77 samples with variants: 57 with B.1.1.7, 7 with B.1.351, and an epidemiologic cluster of 13 with B.1.1.28/P.1.

Practical challenges to the clinical implementation of saliva for SARS-CoV-2 detection.

Due to global shortages of flocked nasopharyngeal swabs and appropriate viral transport media during the COVID-19 pandemic, alternate diagnostic specimens for SARS-CoV-2 detection are sought. The accuracy and feasibility of saliva samples collected and transported without specialized collection devices or media were evaluated. Saliva demonstrated good concordance with paired nasopharyngeal swabs for SARS-CoV-2 detection in 67/74 cases (90.5%), though barriers to saliva collection were observed in long-term care residents and outbreak settings. SARS-CoV-2 RNA was stable in human saliva at room temperature for up to 48 h after initial specimen collection, informing appropriate transport time and conditions.

Suboptimal Biological Sampling as a Probable Cause of False-Negative COVID-19 Diagnostic Test Results.

False-negative severe acute respiratory syndrome coronavirus 2 test results can negatively impact the clinical and public health response to coronavirus disease 2019 (COVID-19). We used droplet digital polymerase chain reaction (ddPCR) to demonstrate that human DNA levels, a stable molecular marker of sampling quality, were significantly lower in samples from 40 confirmed or suspected COVID-19 cases that yielded negative diagnostic test results (ie, suspected false-negative test results) compared with a representative pool of 87 specimens submitted for COVID-19 testing. Our results support suboptimal biological sampling as a contributor to false-negative COVID-19 test results and underscore the importance of proper training and technique in the collection of nasopharyngeal specimens.

Phenotypic and Genotypic Correlates of Penicillin Susceptibility in Nontoxigenic Corynebacterium diphtheriae, British Columbia, Canada, 2015-2018.

In 2015, the Clinical and Laboratory Standards Institute (CLSI) updated its breakpoints for penicillin susceptibility in Corynebacterium species from <1 mg/L to <0.12 mg/L. We assessed the effect of this change on C. diphtheriae susceptibility reported at an inner city, tertiary care center in Vancouver, British Columbia, Canada, during 2015-2018 and performed whole-genome sequencing to investigate phenotypic and genotypic resistance to penicillin. We identified 44/45 isolates that were intermediately susceptible to penicillin by the 2015 breakpoint, despite meeting previous CLSI criteria for susceptibility. Sequencing did not reveal ß-lactam resistance genes. Multilocus sequence typing revealed a notable predominance of sequence type 76. Overall, we saw no evidence of penicillin nonsusceptibility at the phenotypic or genotypic level in C. diphtheriae isolates from our institution. The 2015 CLSI breakpoint change could cause misclassification of penicillin susceptibility in C. diphtheriae isolates, potentially leading to suboptimal antimicrobial treatment selection.

Whole-Genome Sequencing of Corynebacterium diphtheriae Isolates Recovered from an Inner-City Population Demonstrates the Predominance of a Single Molecular Strain.

In some parts of the world, Corynebacterium diphtheriae has reemerged as a pathogen, especially as a cause of infections among impoverished and marginalized populations. We performed whole-genome sequencing (WGS) on all cutaneous C. diphtheriae isolates (n = 56) from Vancouver's inner-city population over a 3-year time period (2015 to 2018). All isolates with complete genome assembly were toxin negative, contained a common set of 22 virulence factors, and shared a highly conserved accessory genome. One of our isolates harbored a novel plasmid conferring macrolide and lincosamide resistance. Fifty-two out of 56 isolates were multilocus sequence type 76, and single nucleotide variants (SNV) and core-genome multilocus sequence typing (cgMLST) analysis demonstrated tight clustering of our isolates relative to all publicly available C. diphtheriae genomes. All sequence type 76 (ST76) study isolates were within a median of 22 SNVs and 13 cgMLST alleles of each other, while NCBI genomes were within a median of 17,436 SNVs and 1,552 cgMLST alleles of each other (both P < 2.2 × 10-16). A single strain of C. diphtheriae appears to be causing cutaneous infections in the low-income population of Vancouver. Further research is needed to elucidate transmission networks in our study population and standardize C. diphtheriae epidemiological typing when whole genomes are sequenced.

Relevance of reviewing endpoint analysis for negative results on the Xpert Xpress Flu/RSV.

After the implementation of the Xpert Xpress Flu/respiratory syncytial virus (RSV) assay for rapid respiratory molecular testing, we investigated the significance of reported endpoint values for influenza A, influenza B, and RSV). This study prospectively analyzed nasopharyngeal swabs submitted to our virology laboratory in the 2018/19 influenza season. Initial testing was performed on the Xpress Flu/RSV assay. Samples were further tested on a laboratory-developed multiplex polymerase chain reaction (laboratory-developed multiplex respiratory test [LDT]) if the sample was reported as negative by the Xpress Flu/RSV but had an elevated endpoint value ≥5 for any respiratory virus target. There were 1040 negative results on the Xpress Flu/RSV; thirty-one had at least one endpoint value ≥5 [influenza A (25), influenza B (1), RSV (2), influenza A/RSV (1), and influenza A/B/RSV (2)]. Five samples (5/31, 16.1%) were positive on the LDT for influenza A or RSV. In contrast, the positivity rate on the LDT for negative Xpress Flu/RSV samples with endpoint values less than 5 was 0.35% (P < .0001). A threshold for endpoint values could not reliably be established to differentiate a potential influenza A positive result from a negative result on the LDT. Routine evaluation ofendpoint values should be a consideration for laboratories implementing Xpress Flu/RSV, in addition to supplementary respiratory virus testing for clinically relevant situations.

Transitioning cytomegalovirus viral load testing from a laboratory developed test to the cobas® CMV quantitative nucleic acid assay.

Commutability between human cytomegalovirus (CMV) viral load assays (VLA) is poor, despite the development of a WHO CMV International Standard (CMV IS). We evaluated a new CMV VLA, cobas® CMV, as compared to our current laboratory developed CMV VLA (LDT), for clinical use. Both the LDT and cobas® CMV were run in parallel for 109 patient samples. In addition, 104 replicates, over 8 dilutions, of the CMV IS were tested. Conversion factors and correlation between the two assays were calculated. The correlation coefficient between the LDT and cobas® CMV was 0.91 for patient samples. The Bland-Altman graph displayed a systematic bias of +0.31 log10 for the cobas® CMV as compared to the LDT. The bias was greater for lower CMV viral loads. This increase in CMV viral loads was not seen with testing of the CMV IS dilutions by both the LDT and cobas® CMV. CMV VLA inter-assay commutability continues to be an issue when switching CMV testing platforms and requires communication between the laboratory and clinicians during the transition period to prevent misinterpretation of results.

Testing the limits of multiplex respiratory virus assays for SARS-CoV-2 at high cycle threshold values: Comparative performance of cobas 6800/8800 SARS-CoV-2 & Influenza A/B, Xpert Xpress SARS-CoV-2/Flu/RSV, and cobas Liat SARS-CoV-2 & Influenza A/B.

Background: Multiplex real-time RT-PCR assays for respiratory pathogens are valuable tools to optimize laboratory workflow and turnaround time. At a time when resurgence of influenza and respiratory syncytial virus (RSV) cases have been widely observed along with continued transmission of SARS-CoV-2, timely identification of all circulating respiratory viruses is crucial. This study evaluates the detection of low viral loads of SARS-CoV-2 by four multiplex molecular assays: Roche cobas 6800/8800 SARS-CoV-2 & Influenza A/B Test, Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV, cobas Liat SARS-CoV-2 & Influenza A/B, and a laboratory-developed test (LDT). Methods: Retrospective upper respiratory tract specimens positive for various respiratory viruses at a range of cycle threshold (Ct) values (18-40) were tested by four multiplex assays. Positive and negative percent agreement (PPA and NPA) with validated RT-PCR assays were calculated. Results: A total of 82 samples were assessed, with discordant results observed in a portion of the samples (10/82, 12.2%) where Ct values were >33. The majority of the discordant results (6/10, 60%) were false negatives. Overall, PPA was 100% (58/58) for cobas 6800, 97.4% (38/39) for GeneXpert, 100% (17/17) for Liat, and 90.5% (57/63) for the LDT. PPA for the LDT increased to 92.1% after manual review of amplification curves. Conclusions: Commercial multiplex respiratory virus assays have good performance for samples with medium to high viral loads (Ct values <33). Laboratories should consider appropriate test result review and confirmation protocols to optimize sensitivity, and may consider reporting samples with additional interpretive comments when low viral loads are detected.

Historique: Les dosages multiplex par RT-PCR en temps réel (amplification en chaîne par polymérase avec transcription inverse en temps réel) des agents pathogènes respiratoires sont des outils précieux pour optimiser le flux de travail et le temps de traitement en laboratoire. Alors qu'on observe une résurgence générale des cas d'influenza et du virus respiratoire syncytial (VRS) et une transmission continue du SRAS-CoV-2, il est crucial de détecter rapidement tous les virus respiratoires en circulation. Dans la présente étude, les chercheurs ont évalué la détection des faibles charges virales du SRAS-CoV-2 à l'aide de quatre dosages moléculaires multiplex : le test cobas 6800/8800 SRAS-CoV-2 et influenza A/B de Roche, le test Xpress SRAS-CoV-2/influenza/VRS de Cepheid Xpert, le test cobas SRAS-CoV-2 et influenza A/B de Liat et un test créé par le laboratoire (TCL). Méthodologie: Les chercheurs ont procédé au dépistage rétrospectif d'échantillons ayant obtenu un résultat positif à divers virus respiratoires à une série de valeurs de cycle seuil (Ct) (18­40) à l'aide de quatre dosages multiplex. Ils ont calculé le pourcentage de concordance positif (PCP) et négatif (PCN) avec les dosages par RT-PCR validés. Résultats: Au total, les chercheurs ont évalué 82 échantillons et observé des résultats discordants dans une partie des échantillons (dix sur 82, 12,2 %), pour lesquels les valeurs Ct étaient supérieures à 33. La majorité de ces résultats discordants (six sur dix, 60 %) étaient faussement négatifs. Dans l'ensemble, le PCP atteignait 100 % (58 sur 58) selon le test cobas 6800, 97,4 % (38 sur 39) selon le test GeneXpert, 100 % (17 sur 17) selon le test Liat et 90,5 % (57 sur 63) selon le TCL. Le PCP du TCL est passé à 92,1 % après l'examen manuel des courbes d'amplification. Conclusions: Les dosages multiplex commerciaux des virus respiratoires donnent un bon rendement pour les échantillons contenant une charge virale modérée à élevée (valeurs Ct inférieures à 33). Les laboratoires devraient envisager de procéder à une analyse des résultats du dépistage et à des protocoles de confirmation appropriés pour en optimiser la sensibilité et pourraient également envisager d'ajouter des commentaires interprétatifs aux résultats des échantillons lorsque la charge virale décelée est faible.

Stability of BK polyomavirus DNA in urine over time and analytical evaluation of an automated BKV quantitative nucleic acid test.

Introduction. BK polyomavirus (BKPyV) quantitative testing is an important screening tool post-transplantation, although interpretation can be challenging due to lack of standardization, assay heterogeneity and variability of BKPyV DNA over time (in urine).Methods. Remnant clinical EDTA plasma and urine samples were tested by the cobas BKV test and a validated laboratory-developed test (LDT). Accuracy [positive and negative percent agreement (PPA and NPA), Pearson's correlation, Bland-Altman analysis] and reproducibility were evaluated. To assess BKPyV DNA stability in urine, prospective urine samples were maintained at two different storage temperatures and tested in triplicate over 7 days.Results. Overall PPA was 95.6 % (43/45) and NPA was 94.4 % (170/180). For plasma, Pearson's correlation (0.950) and Bland-Altman analysis (0.113±0.22 log10 IU ml-1) showed high agreement. For neat urine, Pearson's correlation (0.842) and Bland-Altman analysis (0.326±0.80 log10 IU ml-1) showed somewhat higher variability. Reproducibility was high for the cobas BKV versus the LDT. BKPyV DNA levels in neat urine remained relatively stable over 7 days at both storage temperatures, although outlier results were intermittently detected.Conclusion. The cobas BKV test showed high agreement and reproducibility compared to the reference LDT. BKPyV viral load testing in urine has known limitations, but neat urine can be processed by the cobas BKV.

Melting curve analysis reveals false-positive norovirus detection in a molecular syndromic panel.

BACKGROUND: Molecular syndromic panels can improve rapidity of results and ease clinical laboratory workflow, although caution has been raised for potential false-positive results. Upon implementation of a new panel for infectious diarrhea (BioFire® FilmArray® Gastrointestinal [GI] Panel, bioMérieux) in our clinical laboratory, a higher than expected number of stool samples with norovirus were detected. OBJECTIVES: The goal of this study was to investigate positive percent agreement and the false-positive rate of norovirus detected by the multiplex BioFire GI panel compared to a singleplex commercial assay. STUDY DESIGN: From October 2023 to January 2024, all prospective stool samples with a positive norovirus result by BioFire had melting curves reviewed manually using the BioFire FilmArray Torch System. Stool samples further underwent testing by a supplementary real-time RT-PCR assay (Xpert® Norovirus, Cepheid) for comparative analysis. RESULTS: Of the 50 stool samples with norovirus detected by BioFire, 18 (36 %) tested negative by Xpert (deemed "false-positives"). Furthermore, melting curve analysis revealed nearly all of these samples had atypical melting curve morphologies for the "Noro-1" target on BioFire (16/18, 89 %), which was statistically significant (Odds Ratio 173.2, 95 % CI [22.2, 5326.9], p < 0.0001). Stool samples with multiple pathogens detected by BioFire including norovirus were not more likely to produce false-positive norovirus results (Odds Ratio 1, 95 % CI [0.3, 3.3], p = 1). CONCLUSIONS: Although not described in the manufacturer's Instructions for Use, we propose routine manual review of melting curves for the BioFire GI panel prior to reporting, to mitigate potential false-positive norovirus results.

Effects of COVID-19 mRNA vaccination on HIV viremia and reservoir size.

OBJECTIVE: The immunogenic nature of coronavirus disease 2019 (COVID-19) mRNA vaccines led to some initial concern that these could stimulate the HIV reservoir. We analyzed changes in plasma HIV loads (pVL) and reservoir size following COVID-19 mRNA vaccination in 62 people with HIV (PWH) receiving antiretroviral therapy (ART), and analyzed province-wide trends in pVL before and after the mass vaccination campaign. DESIGN: Longitudinal observational cohort and province-wide analysis. METHODS: Sixty-two participants were sampled prevaccination, and one month after their first and second COVID-19 immunizations. Vaccine-induced anti-SARS-CoV-2-Spike antibodies in serum were measured using the Roche Elecsys Anti-S assay. HIV reservoirs were quantified using the intact proviral DNA assay; pVL were measured using the cobas 6800 (lower limit of quantification: 20 copies/ml). The province-wide analysis included all 290 401 pVL performed in British Columbia, Canada between 2012 and 2022. RESULTS: Prevaccination, the median intact reservoir size was 77 [interquartile range (IQR): 20-204] HIV copies/million CD4 + T-cells, compared to 74 (IQR: 27-212) and 65 (IQR: 22-174) postfirst and -second dose, respectively (all comparisons P > 0.07). Prevaccination, 82% of participants had pVL <20 copies/ml (max: 110 copies/ml), compared to 79% postfirst dose (max: 183 copies/ml) and 85% postsecond dose (max: 79 copies/ml) ( P  > 0.4). There was no evidence that the magnitude of the vaccine-elicited anti-SARS-CoV-2-Spike immune response influenced pVL nor changes in reservoir size ( P  > 0.6). We found no evidence linking the COVID-19 mass vaccination campaign to population-level increases in detectable pVL frequency among all PWH in the province, nor among those who maintained pVL suppression on ART. CONCLUSION: We found no evidence that COVID-19 mRNA vaccines induced changes in HIV reservoir size nor plasma viremia.

Effects of COVID-19 mRNA vaccination on HIV viremia and reservoir size.

Objective: The immunogenic nature of COVID-19 mRNA vaccines led to some initial concern that these could stimulate the HIV reservoir. We analyzed changes in plasma HIV loads (pVL) and reservoir size following COVID-19 mRNA vaccination in 62 people with HIV (PWH) receiving antiretroviral therapy (ART), and analyzed province-wide trends in pVL before and after the mass vaccination campaign. Design: Longitudinal observational cohort and province-wide analysis. Methods: 62 participants were sampled pre-vaccination, and one month after their first and second COVID-19 immunizations. Vaccine-induced anti-SARS-CoV-2-Spike antibodies in serum were measured using the Roche Elecsys Anti-S assay. HIV reservoirs were quantified using the Intact Proviral DNA Assay; pVL were measured using the cobas 6800 (LLOQ:20 copies/mL). The province-wide analysis included all 290,401 pVL performed in British Columbia, Canada between 2012-2022. Results: Pre-vaccination, the median intact reservoir size was 77 (IQR:20-204) HIV copies/million CD4+ T-cells, compared to 74 (IQR:27-212) and 65 (IQR:22-174) post-first and -second dose, respectively (all comparisons p>0.07). Pre-vaccination, 82% of participants had pVL<20 copies/mL (max:110 copies/mL), compared to 79% post-first dose (max:183 copies/mL) and 85% post-second dose (max:79 copies/mL) (p>0.4). The magnitude of the vaccine-elicited anti-SARS-CoV-2-Spike antibody response did not correlate with changes in reservoir size nor detectable pVL frequency (p>0.6). We found no evidence linking the COVID-19 mass vaccination campaign to population-level increases in detectable pVL frequency among all PWH in the province, nor among those who maintained pVL suppression on ART. Conclusion: We found no evidence that COVID-19 mRNA vaccines induced changes in HIV reservoir size nor plasma viremia.

Next-generation sequencing for cytomegalovirus antiviral resistance genotyping in a clinical virology laboratory.

INTRODUCTION: The identification of CMV antiviral drug resistance (AVDR) is a critical diagnostic test for immunocompromised patients with CMV infection and a failure of virologic response on optimal antiviral treatment. We developed a next-generation sequencing (NGS) assay for CMV AVDR testing and compared the AVDR mutations identified by NGS to Sanger sequencing. METHODS: Retrospective review of CMV AVDR testing requests for UL97 and UL54 at our laboratory from 2014 to 2019 was conducted. NGS was performed on the MinION and compared to Sanger sequencing performed at the national reference laboratory. Analysis of the sequences was completed with a novel cloud bioinformatics platform (BugSeq). RESULTS: Twenty patient samples previously characterized were included for study on the MinION. NGS captured all of the CMV AVDR mutations identified by Sanger, and identified additional mutations in UL97 and/or UL54 in 8/13 (62%) of the samples. An analysis of the depth of coverage at which we no longer detected minority single nucleotide variants (SNVs) detected in the original data was conducted, estimating a recall of 95% at 1800 fold coverage. CONCLUSION: NGS utilizing MinION technology for the detection of CMV AVDR mutations identified additional minority variants in UL97 and UL54 as compared with Sanger sequencing. Through the application of a bioinformatics pipeline available online, our NGS process eliminates barriers associated with the use of the MinION and NGS in clinical laboratories.

Automated molecular testing of saliva for SARS-CoV-2 detection.

With surging global demand for SARS-CoV-2 testing capacity, laboratories seek automated, high-throughput molecular solutions, particularly for specimens not requiring specialized collection devices or viral transport media. Saliva specimens submitted from patients under investigation for COVID-19 from March to July 2020 were processed in the laboratory with sterile phosphate-buffered saline in a 1:2 dilution and tested using manual extraction and a commercial assay for detection of the SARS-CoV-2 E gene (LightMix®) in comparison to the Roche cobas® SARS-CoV-2 Test on the cobas® 6800 instrument. 34.4% (22/64) of saliva samples were positive for SARS-CoV-2. Positive and negative concordance between the LightMix® and cobas® assays were 100%. The overall invalid rate for saliva on the cobas® 6800 (1/128, 0.78%) was similar to the baseline invalid rate observed for nasopharyngeal swabs/viral transport media. Saliva is a feasible specimen type for SARS-CoV-2 testing on the cobas® 6800 platform, with potential to improve turnaround time and enhance testing capacity.

SARS-CoV-2 RNA Quantification Using Droplet Digital RT-PCR.

Quantitative viral load assays have transformed our understanding of viral diseases. They hold similar potential to advance COVID-19 control and prevention, but SARS-CoV-2 viral load tests are not yet widely available. SARS-CoV-2 molecular diagnostic tests, which typically employ real-time RT-PCR, yield semiquantitative results only. Droplet digital RT-PCR (RT-ddPCR) offers an attractive platform for SARS-CoV-2 RNA quantification. Eight primer/probe sets originally developed for real-time RT-PCR-based SARS-CoV-2 diagnostic tests were evaluated for use in RT-ddPCR; three were identified as the most efficient, precise, and sensitive for RT-ddPCR-based SARS-CoV-2 RNA quantification. For example, the analytical efficiency for the E-Sarbeco primer/probe set was approximately 83%, whereas assay precision, measured as the coefficient of variation, was approximately 2% at 1000 input copies/reaction. Lower limits of quantification and detection for this primer/probe set were 18.6 and 4.4 input SARS-CoV-2 RNA copies/reaction, respectively. SARS-CoV-2 RNA viral loads in a convenience panel of 48 COVID-19-positive diagnostic specimens spanned a 6.2log10 range, confirming substantial viral load variation in vivo. RT-ddPCR-derived SARS-CoV-2 E gene copy numbers were further calibrated against cycle threshold values from a commercial real-time RT-PCR diagnostic platform. This log-linear relationship can be used to mathematically derive SARS-CoV-2 RNA copy numbers from cycle threshold values, allowing the wealth of available diagnostic test data to be harnessed to address foundational questions in SARS-CoV-2 biology.

Detection of low levels of SARS-CoV-2 RNA from nasopharyngeal swabs using three commercial molecular assays.

In response to the COVID-19 pandemic, commercial molecular assays for SARS-CoV-2 testing have been rapidly developed and broadly deployed in laboratories worldwide. Although these assays have been reported to correlate well, we sought to compare the Xpert® Xpress SARS-CoV-2 to the cobas® SARS-CoV-2 or the Lightmix® Modular SARS and Wuhan CoV E-gene assay for nasopharyngeal (NP) swabs with low levels of SARS-CoV-2 RNA. Thirty-seven NP swabs were studied, including 10 samples with a moderate cycle threshold (Ct) between 30-33.9, and 22 with Ct≥34, and 5 negative for SARS-CoV-2. Overall concordance on initial comparison was 86.5 % (32/37), which was 100 % concordance for samples with Ct values ranging between 30-33.9. Discordance amongst samples showing a Ct ≥34 was 22.7 % (5/22). Endpoint value analysis on the Xpress SARS-CoV-2 within the discordant samples noted two with an endpoint value >5, which were detected by the cobas® or Lightmix®. Testing of SARS-CoV-2 on the three commercial assays was comparable for NP swabs with moderate Ct values, while high Ct values were less concordant. Importantly, analysis of Xpert® endpoint values improved interpretation of discrepant results.

Utility of Rapid Influenza Molecular Testing in an Outpatient Hemodialysis Unit: A Prospective Cohort Study.

BACKGROUND: Early initiation of antiviral therapy for individuals at risk for severe influenza infection is important for improving patient outcomes. Current guidelines recommend empiric antiviral therapy for patients with end-stage kidney disease presenting with suspected influenza infection. Rapid molecular influenza assays may reduce diagnostic uncertainty and improve patient outcomes by providing faster diagnostics compared to traditional batched polymerase chain reaction (PCR) testing. OBJECTIVE: To determine the utility of implementing a rapid influenza PCR assay compared to the standard of care in a hemodialysis unit. DESIGN: This is a prospective cohort study. SETTING: A hospital-based dialysis unit in a tertiary care hospital. PATIENTS: Adult patients with end-stage kidney disease on intermittent hemodialysis. MEASUREMENTS: Patient characteristics, influenza PCR swab results, antibiotic prescriptions, antiviral prescriptions, emergency room visits and hospitalizations. METHODS: From November 1, 2017 to March 31, 2018, we assigned samples collected from a single center, hemodialysis unit to be processed using a rapid influenza PCR (cobas® Influenza A/B & respiratory syncytial virus assay) or the standard of care (in-house developed multiplex PCR). Samples were assigned to the rapid PCR if the patient received dialysis treatment in the morning dialysis shift, while the remainder were processed as per standard of care. Study outcomes included the time from collection to result of nasopharyngeal swab, prescription of influenza antiviral therapy, time to receiving prescription, and the need for emergency department visit or hospitalization within 2 weeks of presentation. RESULTS: During the study period, 44 patients were assessed (14 with the rapid PCR and 30 with the standard of care assay). Compared to conventional testing, the time to result was shorter using rapid PCR compared to conventional testing (2.3 vs 22.6 hours, P < .0001). Individuals who were tested using the rapid PCR had a tendency to shorter time to receiving antiviral prescriptions (0.7 days vs 2.1 days, P = .11), and fewer emergency department visits (7.1% vs 30%, P = .13) but no difference in hospitalizations (14.3% vs 30%, P = .46) within 2 weeks of testing. LIMITATIONS: This is a single center non-randomized study with a relatively small sample size. Patients who were tested using the standard of care assay experienced a delay in the prescription of antiviral therapy which deviates from recommended clinical practice. CONCLUSIONS: Rapid influenza molecular testing in the hemodialysis unit was associated with a shorter time to a reportable result and with a tendency to reduced time to prescription of antiviral therapy. Rapid molecular testing should be compared with standard of care (empiric therapy) in terms of economic costs, adverse events, and influenza-related outcomes.

CONTEXTE: L'initiation précoce d'un traitement antiviral est essentielle pour améliorer les résultats de santé des personnes exposées à un grand risque d'infection grippale. Chez les patients atteints d'insuffisance rénale terminale (IRT) suspectés d'une infection grippale, les recommandations actuelles préconisent une approche empirique de traitement antiviral. Les tests moléculaires de dépistage rapide du virus influenza peuvent réduire l'incertitude diagnostique et améliorer les résultats pour les patients en posant un diagnostic plus rapidement que les tests PCR en lots traditionnellement utilisés. OBJECTIF: Mesurer l'intérêt de mettre en place un test PCR de dépistage rapide de la grippe comparativement à la norme de soins d'une unité d'hémodialyse. TYPE D'ÉTUDE: Étude de cohorte prospective. CADRE: Une unité de dialyze hospitalière de soins tertiaires. SUJETS: Des adultes atteints d'IRT et traités par hémodialyse intermittente. MESURES: Les caractéristiques des patients, les résultats de dépistage du virus influenza, les prescriptions d'antibiotiques et d'antiviraux, les visites à l'urgence et les hospitalisations. MÉTHODOLOGIE: Entre le 1er novembre 2017 et le 31 mars 2018, les échantillons prélevés à l'unité d'hémodialyse du center ont été répartis pour être analysés soit par la méthode PCR de dépistage rapide (cobas®Essai Influenza A/B & VRS), soit par la méthode traditionnellement utilisée (PCR multiplex mises au point à l'interne). Les prélèvements des patients dialysés pendant le quart de travail du matin ont été assignés à la méthode rapide, les autres ont été testés par la méthode traditionnelle. Les résultats incluaient le délai entre le prélèvement et le résultat de l'écouvillonnage naso-pharyngé, la prescription d'un traitement antiviral, le temps requis pour obtenir la prescription et la nécessité de se rendre à l'urgence ou d'être hospitalisé dans les deux semaines suivant la présentation des symptômes. RÉSULTATS: Au cours de l'étude, 44 patients ont été diagnostiqués avec la méthode rapide par PCR (n=14) ou la méthode traditionnelle (n=30). Comparativement à la méthode traditionnelle, la méthode rapide par PCR a permis de réduire le temps d'obtention du résultat (2,3 h contre 22,6 h pour la méthode traditionnelle; P < .0001). Les patients diagnostiqués avec la méthode rapide par PCR tendaient à obtenir une ordonnance d'antiviraux plus rapidement (0,7 jour contre 2,1 pour la méthode traditionnelle; P = .11) et à avoir visité l'urgence moins souvent (7,1 % contre 30 % pour la méthode traditionnelle, P = .13), mais ne présentaient aucune différence significative dans le nombre d'hospitalisations (14,3 % contre 30 % pour la méthode traditionnelle; P = .46) dans les deux semaines de suivi. LIMITES: Il s'agit d'une étude non répartie aléatoirement, qui s'est tenue dans un seul center et sur un échantillon relativement restreint. Les patients diagnostiqués avec la méthode traditionnelle ont subi un retard dans la prescription du traitement antiviral, ce qui s'écarte de la pratique clinique recommandée. CONCLUSION: Chez les patients d'une unité d'hémodialyse, le dépistage moléculaire rapide du virus influenza a été associé à un diagnostic plus rapide et à une tendance à une réduction du délai de prescription du traitement antiviral. Il serait pertinent de comparer le dépistage moléculaire rapide avec la norme standard de soin (traitement empirique) en ce qui concerne les coûts, les événements indésirables et les issues de santé liées à la grippe.

Evaluation of Nasopharyngeal Swab Collection Techniques for Nucleic Acid Recovery and Participant Experience: Recommendations for COVID-19 Diagnostics.

Nasopharyngeal swabs are critical to the diagnosis of respiratory infections including coronavirus disease 2019, but collection techniques vary. We compared 2 recommended nasopharyngeal swab collection techniques in adult volunteers and found that swab rotation following nasopharyngeal contact did not recover additional nucleic acid (as measured by human DNA/RNA copy number). Rotation was also less tolerable for participants. Notably, both discomfort and nucleic acid recovery were significantly higher in Asian participants, consistent with nasal anatomy differences. Our results suggest that it is unnecessary to rotate the swab in place following contact with the nasopharynx and reveal that procedural discomfort levels can differ by ethnicity.