Prospective, clinical comparison of self-collected throat-bilateral nares swabs and saline gargle compared to health care provider collected nasopharyngeal swabs among symptomatic outpatients with potential SARS-CoV-2 infection

Background

In British Columbia (BC), self-collected saline gargle (SG) is the only alternative to health care provider (HCP)-collected nasopharyngeal (NP) swabs to detect SARS-CoV-2 in an outpatient setting by polymerase chain reaction (PCR). However, some individuals cannot perform a SG. Our study aimed to assess combined throat-bilateral nares (TN) swabbing as a swab-based alternative.

Methods

Symptomatic individuals greater than 12 years of age seeking a COVID-19 PCR test at one of two COVID-19 collection centres in Metro Vancouver were asked to participate in this study. Participants provided a HCP-collected NP sample and a self-collected SG and TN sample for PCR testing, which were either HCP observed or unobserved.

Results

Three-hundred and eleven individuals underwent all three collections. Compared against HCP-NP, SG was 99% sensitive and 98% specific (kappa 0.97) and TN was 99% sensitive and 99% specific (kappa 0.98). Using the final clinical test interpretation as the reference standard, NP was 98% sensitive and 100% specific (kappa 0.98), and both SG and TN were 99% sensitive and 100% specific (both kappa 0.99). Mean cycle threshold values for each viral target were higher in SG specimens compared to the other sample types; however, this did not significantly impact the clinical performance, because the positivity rates were similar. The clinical performance of all specimen types was comparable within the first 7 days of symptom onset, regardless of the observation method. SG self-collections were rated the most acceptable, followed by TN.

Conclusions

TN provides another less invasive self-collection modality for symptomatic outpatient SARS-CoV-2 PCR testing.

Two-phase Bayesian latent class analysis to assess diagnostic test performance in the absence of a gold standard: COVID-19 serological assays as a proof of concept

BACKGROUND AND OBJECTIVES

In this proof-of-concept study, which included blood donor samples, we aimed to demonstrate how Bayesian latent class models (BLCMs) could be used to estimate SARS-CoV-2 seroprevalence in the absence of a gold standard assay under a two-phase sampling design.

MATERIALS AND METHODS

To this end, 6810 plasma samples from blood donors who resided in Québec (Canada) were collected from May to July 2020 and tested for anti-SARS-CoV-2 antibodies using seven serological assays (five commercial and two non-commercial).

RESULTS

SARS-CoV-2 seroprevalence was estimated at 0.71% (95% credible interval [CrI] = 0.53%-0.92%). The cPass assay had the lowest sensitivity estimate (88.7%; 95% CrI = 80.6%-94.7%), while the Héma-Québec assay had the highest (98.7%; 95% CrI = 97.0%-99.6%).

CONCLUSION

The estimated low seroprevalence (which indicates a relatively limited spread of SARS-CoV-2 in Quebec) might change rapidly-and this tool, developed using blood donors, could enable a rapid update of the prevalence estimate in the absence of a gold standard. Further, the present analysis illustrates how a two-stage BLCM sampling design, along with blood donor samples, can be used to estimate the performance of new diagnostic tests and inform public health decisions regarding a new or emerging disease for which a perfect reference standard does not exist.

Uptake of SARS-CoV-2 vaccination among structurally-marginalized people who use drugs in Vancouver, Canada

We sought to evaluate the rates and predictors of SARS-CoV-2 vaccination among members of a structurally-marginalized population of people who use drugs (PWUD) during a targeted, community-wide, vaccination campaign in Vancouver, Canada. Interviewer-administered data were collected from study participants between June 2021 and March 2022. Generalized estimating equation analysis was used to identify factors associated with SARS-CoV-2 vaccine uptake, ascertained through a province-wide vaccine registry. Among 223 PWUD, 107 (48.0%) reported receipt of at least two SARS-CoV-2 vaccine doses at baseline and this increased to 151 (67.7%) by the end of the study period. Using social media as a source of vaccine information was negatively associated with SARS-CoV-2 vaccine uptake (Adjusted odds ratio [AOR] 0.27, 95% confidence interval [CI] 0.09-0.81) and HIV seropositivity (AOR 2.68, 95% CI 1.12-6.39) and older age (AOR 1.27, 95% CI 1.07-1.51) were positively associated with SARS-CoV-2 vaccine uptake. These findings suggest that the targeted vaccination campaign in Vancouver may be an effective model to promote SARS-CoV-2 vaccination in other jurisdictions. However, using social media as a source of vaccine information likely reduced SARS-CoV-2 vaccine uptake in PWUD arguing for further efforts to promote accessible and evidence-based vaccine information among marginalized populations.

Mapping SARS-CoV-2 antigenic relationships and serological responses

During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, multiple variants escaping preexisting immunity emerged, causing reinfections of previously exposed individuals. Here, we used antigenic cartography to analyze patterns of cross-reactivity among 21 variants and 15 groups of human sera obtained after primary infection with 10 different variants or after messenger RNA (mRNA)-1273 or mRNA-1273.351 vaccination. We found antigenic differences among pre-Omicron variants caused by substitutions at spike-protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and >3 months after a second dose. We found changes in immunodominance of different spike regions, depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine-strain selection.

Mapping SARS-CoV-2 antigenic relationships and serological responses

During the SARS-CoV-2 pandemic, multiple variants escaping pre-existing immunity emerged, causing concerns about continued protection. Here, we use antigenic cartography to analyze patterns of cross-reactivity among a panel of 21 variants and 15 groups of human sera obtained following primary infection with 10 different variants or after mRNA-1273 or mRNA-1273.351 vaccination. We find antigenic differences among pre-Omicron variants caused by substitutions at spike protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and >3 months post-2nd dose. We find changes in immunodominance of different spike regions depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine strain selection.

Spike Mutation Profiles Associated With SARS-CoV-2 Breakthrough Infections in Delta Emerging and Predominant Time Periods in British Columbia, Canada

Background

COVID-19 vaccination is a key public health measure in the pandemic response. The rapid evolution of SARS-CoV-2 variants introduce new groups of spike protein mutations. These new mutations are thought to aid in the evasion of vaccine-induced immunity and render vaccines less effective. However, not all spike mutations contribute equally to vaccine escape. Previous studies associate mutations with vaccine breakthrough infections (BTI), but information at the population level remains scarce. We aimed to identify spike mutations associated with SARS-CoV-2 vaccine BTI in a community setting during the emergence and predominance of the Delta-variant.

Methods

This case-control study used both genomic, and epidemiological data from a provincial COVID-19 surveillance program. Analyses were stratified into two periods approximating the emergence and predominance of the Delta-variant, and restricted to primary SARS-CoV-2 infections from either unvaccinated individuals, or those infected ≥14 days after their second vaccination dose in a community setting. Each sample's spike mutations were concatenated into a unique spike mutation profile (SMP). Penalized logistic regression was used to identify spike mutations and SMPs associated with SARS-CoV-2 vaccine BTI in both time periods.

Results and Discussion

This study reports population level relative risk estimates, between 2 and 4-folds, of spike mutation profiles associated with BTI during the emergence and predominance of the Delta-variant, which comprised 19,624 and 17,331 observations, respectively. The identified mutations cover multiple spike domains including the N-terminal domain (NTD), receptor binding domain (RBD), S1/S2 cleavage region, fusion peptide and heptad regions. Mutations in these different regions imply various mechanisms contribute to vaccine escape. Our profiling method identifies naturally occurring spike mutations associated with BTI, and can be applied to emerging SARS-CoV-2 variants with novel groups of spike mutations.

Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents

The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagnostic testing. Magnetic bead-based nucleic acid extraction protocols using 96-well plates on open liquid handlers are readily amenable to meet this need. Here, one such approach is rigorously optimized to minimize cross-well contamination while maintaining sensitivity.

Comparison of longitudinal SARS-CoV-2 nasopharyngeal specimens reveals the transcriptomic COVIDome

Introduction/Objective

SARS-Cov-2 is well established to introduce a cytokine-like storm among select individuals that results in multisystem failure and death. Comorbidities, age, oxygen status, and real-time appraisal of inflammatory markers in the blood have been used to risk stratify patients, however, these clinical markers do not comprehensively characterize the at-risk population or disease course. To understand the molecular underpinnings of the primary site of SARS-CoV-2 infection, here, we interrogated the transcriptomic profile of the nasopharyngeal tissue among paired SARS-CoV-2 specimens.

Methods/Case Report

We performed ribosomal depletion RNAseq on 24 primary samples, including 16 paired samples from 8 unique patients who converted between SARS-CoV-2 negative and positive status via clinical diagnostic qRT-PCR. Additional targeted qRT-PCR was performed for ACE2 and TMPRSS2 in an extension sample of 54 paired specimens from 27 unique patients who converted in their SARS-CoV-2 status on the basis of the qRT- PCR test. Differential gene expression, differential correlative expression with ACE2, and correlative expression with viral load was used to identify genes, which were integral to SARS-CoV-2 pathogenesis, so termed the COVIDome. Gene ontologies, pathways, and reactive infiltrate was assessed between specimens and compared with measures of clinical outcome using regression with appropriate correction for multiple hypotheses.

Results (if a Case Study enter NA)

We observed significant enrichment for ontologies of lymphocyte activation, specifically interferon gamma signaling; (P<1E-20) and platelet activation (P<1E-5). Genes specifically enriched across all three modules included: ADAMDEC1, EPSTI1, GRIP2, IRF7, KLHDC7B, OAS3, OASL, PIK3R4, RSAD2, and XAF1. Using CIBERSORT to approximate immune cell populations from bulk RNA, we observed and enrichment for CD4 immune cells, which was associated with viral status (P<0.01) while high-risk gene signatures were associated with measures of clinical outcome (P<0.05).

Conclusion

We characterized the pathogenesis of SARS-CoV-2 in longitudinal nasopharyngeal samples of COVID- 19 patients and related these molecular manifestations with measures of clinical outcome. As proof of principal, our findings suggest additional study in a large, longitudinal extension sample is warranted to validate and assess molecular features of clinical outcome associated with SARS-CoV-2 infection.

Evaluation of the clinical and analytical performance of the Seegene allplex™ SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI)

Background

High-throughput assays for the detection of SARS-CoV-2 variants of concern (VOC) and interest (VOI) are a diagnostic alternative when whole genome sequencing (WGS) is unavailable or limited.

Objective

This study evaluated the clinical and analytical performance of the Seegene Allplex™ SARS-CoV-2 Variants I assay, which detects the HV69/70 deletion, N501Y and E484K mutations of the S gene.

Methods

Genotyping was evaluated on -871 SARS-CoV-2 RNA positive specimens, 408 nasopharyngeal (NP) swabs and 463 saline gargle (SG) specimens, with WGS used as the reference standard. Analytical performance was assessed including stability, reproducibility, limit of detection (LOD), cross-reactivity and interference with various respiratory microorganisms.

Results

The clinical study revealed sensitivity of 100% (95% CI 99.27%–100%) and specificity of 100% (95% CI 98.99%–100%) for HV69/70 deletion, sensitivity of 100% (95% CI 99.55%–100%) and specificity of 100% (95% CI 93.73% – 100%) for N501Y, and sensitivity of 100% (95% CI 98.94% – 100%) and specificity of 98.10% (95% CI 96.53% – 99.08%) for E484K mutation. The E484Q mutation was detected in 10 specimens of the Kappa variant (B.1.627.1). Analytical performance demonstrated stability and reproducibility over 7 days, and LOD was calculated at 698 cp/mL for NP swab specimens, and 968 cp/mL for SG specimens. No interference or cross-reactivity with other microorganisms was noted.

Conclusion

The Allplex™ SARS-CoV-2 Variants I assay is acceptable for clinical use for the detection of variant of concern and variant of interest.

Prenatal hepatitis C screening, diagnoses, and follow-up testing in British Columbia, 2008-2019

OBJECTIVE

Current guidelines in British Columbia recommend prenatal screening for hepatitis C antibodies (anti-HCV) if risk factors are present. We aimed to estimate frequency of prenatal anti-HCV testing, new diagnoses, repeated and follow-up testing among BC women.

METHODS

BC Centre for Disease Control Public Health Laboratory data estimated the number of BC women (assigned female at birth or unknown sex) aged 13-49 who received routine prenatal serological screening (HIV, hepatitis B, syphilis and rubella) from 2008-2019. Anti-HCV tests ordered the same day as routine prenatal screens were considered prenatal anti-HCV tests. Assessment of follow-up was based on HCV RNA and/or genotype testing within one year of new prenatal anti-HCV diagnoses.

RESULTS

In 2019, 55,202 routine prenatal screens were carried out for 50,392 BC women. Prenatal anti-HCV tests increased significantly, from 19.6% (9,704/49,515) in 2008 to 54.6% (27,516/50,392) in 2019 (p<0.001). New prenatal anti-HCV diagnoses (HCV positive diagnoses at first test or seroconversions) declined from 14.3% in 2008 to 10.1% in 2019. The proportion of women with new prenatal anti-HCV diagnoses that were a result of a first HCV test declined from 0.3% (29/9,701) in 2008 to 0.03% (8/27,500) in 2019. For women known to be anti-HCV positive at the time of prenatal screening, the proportion who had a prenatal anti-HCV test increased from 35.6% in 2008 to 50.8% in 2019.

CONCLUSION

Prenatal anti-HCV testing increased substantially over the study period. However, new HCV diagnoses remained relatively stable, suggesting that a considerable proportion of BC women with low or no risk are being screened as part of prenatal care. The vast majority of women with new HCV diagnoses receive appropriate follow-up HCV RNA and genotype testing, which may indicate interest in HCV treatment. These findings contribute to the discussion around potential for prenatal anti-HCV screening in an effort to eliminate HCV.

Influenza Vaccine Does Not Increase the Risk of Coronavirus or Other Noninfluenza Respiratory Viruses: Retrospective Analysis From Canada, 2010-2011 to 2016-2017

Influenza vaccine effectiveness against influenza and noninfluenza respiratory viruses (NIRVs) was assessed by test-negative design using historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network, spanning 2010-2011 to 2016-2017. Vaccine significantly reduced the risk of influenza illness by >40% with no effect on coronaviruses or other NIRV risk.

Interim estimates of 2019/20 vaccine effectiveness during early-season co-circulation of influenza A and B viruses, Canada, February 2020

Interim results from Canada's Sentinel Practitioner Surveillance Network show that during a season characterised by early co-circulation of influenza A and B viruses, the 2019/20 influenza vaccine has provided substantial protection against medically-attended influenza illness. Adjusted VE overall was 58% (95% confidence interval (CI): 47 to 66): 44% (95% CI: 26 to 58) for A(H1N1)pdm09, 62% (95% CI: 37 to 77) for A(H3N2) and 69% (95% CI: 57 to 77) for influenza B viruses, predominantly B/Victoria lineage.

Vaccine Effectiveness Against Lineage-matched and -mismatched Influenza B Viruses Across 8 Seasons in Canada, 2010-2011 to 2017-2018

Vaccine effectiveness (VE) against influenza B was derived separately for Victoria and Yamagata lineages across 8 seasons (2010–2011 to 2017–2018) in Canada when trivalent influenza vaccine was predominantly used. VE was ≥50% regardless of lineage match to circulating viruses, except when the vaccine strain was unchanged from the prior season.

Children under 10 years of age were more affected by the 2018/19 influenza A(H1N1)pdm09 epidemic in Canada: ‎possible cohort effect following the 2009 influenza pandemic

Introduction

Findings from the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN) suggest children were more affected by the 2018/19 influenza A(H1N1)pdm09 epidemic.

Aim

To compare the age distribution of A(H1N1)pdm09 cases in 2018/19 to prior seasonal influenza epidemics in Canada.

Methods

The age distribution of unvaccinated influenza A(H1N1)pdm09 cases and test-negative controls were compared across A(H1N1)pdm09-dominant epidemics in 2018/19, 2015/16 and 2013/14 and with the general population of SPSN provinces. Similar comparisons were undertaken for influenza A(H3N2)-dominant epidemics.

Results

In 2018/19, more influenza A(H1N1)pdm09 cases were under 10 years old than controls (29% vs 16%; p < 0.001). In particular, children aged 5–9 years comprised 14% of cases, greater than their contribution to controls (4%) or the general population (5%) and at least twice their contribution in 2015/16 (7%; p < 0.001) or 2013/14 (5%; p < 0.001). Conversely, children aged 10–19 years (11% of the population) were under-represented among A(H1N1)pdm09 cases versus controls in 2018/19 (7% vs 12%; p < 0.001), 2015/16 (7% vs 13%; p < 0.001) and 2013/14 (9% vs 12%; p = 0.12).

Conclusion

Children under 10 years old contributed more to outpatient A(H1N1)pdm09 medical visits in 2018/19 than prior seasonal epidemics in Canada. In 2018/19, all children under 10 years old were born after the 2009 A(H1N1)pdm09 pandemic and therefore lacked pandemic-induced immunity. In addition, more than half those born after 2009 now attend school (i.e. 5–9-year-olds), a socio-behavioural context that may enhance transmission and did not apply during prior A(H1N1)pdm09 epidemics.

Extraction and Detection of Avian Influenza Virus From Wetland Sediment Using Enrichment-Based Targeted Resequencing

Early virus detection and characterization is key to successful avian influenza virus (AIV) surveillance for the health of humans as well as domestic poultry. We explored a novel sampling approach and molecular strategy using sediment from wetlands and outdoor waterbodies on poultry farms as a population-level proxy of AIV activity in waterfowls. RNA was extracted using the MoBio RNA PowerSoil Total RNA isolation kit with additional chloroform extraction steps to reduce PCR inhibition. AIV matrix protein (MP) gene was detected in 42/345 (12.2%) samples by RT-qPCR; an additional 64 (18.6%) samples showed evidence of amplification below the threshold and were categorized as “suspect positive.” Enrichment-based targeted resequencing (TR) identified AIV sequences in 79/345 (22.9%) samples. TR probes were designed for MP, hemagglutinin (HA), and neuraminidase (NA), however PB2 and PA were also identified. Although RT-qPCR and TR only had fair-moderate agreement, RT-qPCR positivity was predictive of TR-positivity both when using only strictly positive RT-qPCR samples (OR = 11.29) and when coding suspect positives as positive (OR = 7.56). This indicates that RT-qPCR could be used as a screening tool to select samples for virus characterization by TR and that future studies should consider RT-qPCR suspect positives to be positive samples for subsequent resequencing when avoiding false negatives is the priority, for instance in a diagnostic test, and to consider suspect positives to be negative samples when cost efficiency over a large number of samples is the priority, for instance in a surveillance program. A total of 13 HA (H1-7, H9-13, H16) and 9 NA (N1-9) subtypes were identified, with a maximum of 8 HA and 8 NA subtypes detected in a single sample. The optimized RNA extraction and targeted resequencing methods provided increased virus detection and subtyping characterization that could be implemented in an AIV surveillance system.

Influenza vaccine effectiveness by A(H3N2) phylogenetic sub-cluster and prior vaccination history: 2016-17 and 2017-18 epidemics in Canada

Background

The influenza A(H3N2) vaccine was updated from clade 3C.3a in 2015–2016 to 3C.2a for 2016–2017 and 2017–2018. Circulating 3C.2a viruses showed considerable hemagglutinin glycoprotein diversification and the egg-adapted vaccine also bore mutations.

Methods

Vaccine effectiveness (VE) in 2016–2017 and 2017–2018 was assessed by test-negative design, explored by A(H3N2) phylogenetic subcluster and prior season’s vaccination history.

Results

In 2016–2017, A(H3N2) VE was 36% (95% confidence interval [CI], 18%–50%), comparable with (43%; 95% CI, 24%–58%) or without (33%; 95% CI, −21% to 62%) prior season’s vaccination. In 2017–2018, VE was 14% (95% CI, −8% to 31%), lower with (9%; 95% CI, −18% to 30%) versus without (45%; 95% CI, −7% to 71%) prior season’s vaccination. In 2016–2017, VE against predominant clade 3C.2a1 viruses was 33% (95% CI, 11%–50%): 18% (95% CI, −40% to 52%) for 3C.2a1a defined by a pivotal T135K loss of glycosylation; 60% (95% CI, 19%–81%) for 3C.2a1b (without T135K); and 31% (95% CI, 2%–51%) for other 3C.2a1 variants (with/without T135K). VE against 3C.2a2 viruses was 45% (95% CI, 2%–70%) in 2016–2017 but 15% (95% CI, −7% to 33%) in 2017–2018 when 3C.2a2 predominated. VE against 3C.2a1b in 2017–2018 was 37% (95% CI, −57% to 75%), lower at 12% (95% CI, −129% to 67%) for a new 3C.2a1b subcluster (n = 28) also bearing T135K.

Conclusions

Exploring VE by phylogenetic subcluster and prior vaccination history reveals informative heterogeneity. Pivotal mutations affecting glycosylation sites, and repeat vaccination using unchanged antigen, may reduce VE.

Influenza Classification Suite: An automated Galaxy workflow for rapid influenza sequence analysis

Influenza viruses continually evolve to evade population immunity, and the different lineages are assigned into clades based on shared mutations. We have developed a publicly available computational workflow, the Influenza Classification Suite, for rapid clade mapping of sequenced influenza viruses. This suite provides a user‐friendly workflow implemented in Galaxy to automate clade calling and antigenic site extraction. Workflow input includes clade definition and amino acid index array files, which can be customized to identify any clades of interest. The Influenza Classification Suite provides rapid, high‐resolution understanding of circulating influenza strain evolution to inform influenza vaccine effectiveness and the need for potential vaccine reformulation.

Paradoxical clade- and age-specific vaccine effectiveness during the 2018/19 influenza A(H3N2) epidemic in Canada: potential imprint-regulated effect of vaccine (I-REV)

IntroductionThe Canadian Sentinel Practitioner Surveillance Network reports vaccine effectiveness (VE) for the 2018/19 influenza A(H3N2) epidemic.AimTo explain a paradoxical signal of increased clade 3C.3a risk among 35-54-year-old vaccinees, we hypothesise childhood immunological imprinting and a cohort effect following the 1968 influenza A(H3N2) pandemic.MethodsWe assessed VE by test-negative design for influenza A(H3N2) overall and for co-circulating clades 3C.2a1b and 3C.3a. VE variation by age in 2018/19 was compared with amino acid variation in the haemagglutinin glycoprotein by year since 1968.ResultsInfluenza A(H3N2) VE was 17% (95% CI: -13 to 39) overall: 27% (95% CI: -7 to 50) for 3C.2a1b and -32% (95% CI: -119 to 21) for 3C.3a. Among 20-64-year-olds, VE was -7% (95% CI: -56 to 26): 6% (95% CI: -49 to 41) for 3C.2a1b and -96% (95% CI: -277 to -2) for 3C.3a. Clade 3C.3a VE showed a pronounced negative dip among 35-54-year-olds in whom the odds of medically attended illness were > 4-fold increased for vaccinated vs unvaccinated participants (p < 0.005). This age group was primed in childhood to influenza A(H3N2) viruses that for two decades following the 1968 pandemic bore a serine at haemagglutinin position 159, in common with contemporary 3C.3a viruses but mismatched to 3C.2a vaccine strains instead bearing tyrosine.DiscussionImprinting by the first childhood influenza infection is known to confer long-lasting immunity focused toward priming epitopes. Our findings suggest vaccine mismatch may negatively interact with imprinted immunity. The immunological mechanisms for imprint-regulated effect of vaccine (I-REV) warrant investigation.

FilmArray respiratory panel assay: An effective method for detecting viral and atypical bacterial pathogens in bronchoscopy specimens

The BioFire FilmArray Respiratory Panel (FA RP) is a rapid multiplexed molecular assay approved for detection of viral and atypical bacterial pathogens in nasopharyngeal specimens. This study aimed to evaluate the performance of the BioFire FilmArray Respiratory Panel v1.7 on bronchoscopy specimens. We tested 133 bronchial specimens (87 archived and 46 prospectively collected) with the FA RP and compared the results to the Luminex NxTAG Respiratory Pathogen Panel (NxTAG RPP). After discordant analysis, 123 specimens gave concordant results using the FA RP and the NxTAG RPP for an overall agreement of 93.9% (kappa = 0.88 [95% CI 0.80–0.96]), a positive percent agreement of 93.7% (95% CI 83.7–97.7) and a negative percent agreement of 94.1% (95% CI 84.9–98.1). In conclusion, the BioFire FilmArray RP performed reliably to detect a broad range of respiratory pathogens in bronchoscopy specimens.

Should Sex Be Considered an Effect Modifier in the Evaluation of Influenza Vaccine Effectiveness?

We investigated sex as a potential modifier of influenza vaccine effectiveness (VE) between 2010–2011 and 2016–2017 in Canada. Overall VE was 49% (95% confidence interval [CI], 43% to 55%) for females and 38% (95% CI, 28% to 46%) for males (absolute difference [AD], 11%; P = .03). Sex differences were greatest for influenza A(H3N2) (AD, 17%; P = .07) and B(Victoria) (AD, 20%; P = .08) compared with A(H1N1)pdm09 (AD, 10%; P = .19) or B(Yamagata) (AD, –3%; P = .68). They were also more pronounced in older adults ≥50 years (AD, 19%; P = .03) compared with those <20 years (AD, 4%; P = .74) or 20–49 years (AD, –1%; P = .90) but with variation by subtype/lineage. More definitive investigations of VE by sex and age are warranted to elucidate these potential interactions.

HIV serology signal-to-cutoff ratio as a rapid method to predict confirmation of HIV infection

Early and rapid detection of patients with HIV is a key to preventing further transmission. The purpose of this study was to assess the ability of signal-to-cutoff (S/CO) ratio from initial screening fourth-generation HIV serology to predict subsequent confirmation of HIV. Patients with a first-time positive HIV serology (S/CO ratio ≥ 1) from 2012 to 2016 were included. Ratios were compared to the results of confirmatory testing. Predictive probabilities (PPs) of a positive confirmatory result were calculated based on a logistic regression model. A total of 45,138 HIV serology tests were performed; 250 patients met inclusion criteria, comprising 84 (34%) HIV negative patients, 136 (54%) chronic infections, and 30 (12%) acute infections. The PP of a confirmed positive result increased with higher S/CO ratios, with a PP of 100% for a S/CO of 55 (95% CI 95-100). This study enables a more informed discussion of the probability of HIV infection, based on HIV serology S/CO thresholds, prior to a confirmatory result.

BioFire FilmArray Decreases Infection Control Isolation Times by 4 days in ICU, BMT and Respiratory Wards

Background

Novel, rapid, syndromic testing of patients presenting with respiratory infections has the potential to improve patient access and care by decreasing time to diagnosis. BioFire FilmArray (BioFire Diagnostics, bioMerieux) is a cartridge-based, multiplex PCR platform capable of detecting 17 viral and 3 bacterial targets in one hour. This study assessed the impact of implementing this technology on the duration of infection control isolation.

Methods

A randomized control trial in a 900-bed tertiary-care academic hospital was conducted between December 2016 and January 2017. Fifty consecutive samples of patients with respiratory infections on our ICU, BMT and Respiratory wards to received either BioFire FilmArray Respiratory Panel (BF) diagnostic testing or our routine diagnostic testing (RO) consisting of an influenza A/B/RSV PCR (in-house) followed by Luminex NxTag Respiratory Pathogen Panel that was batched at a reference lab. Five patient charts with missing data were excluded from analysis. Statistical analysis was completed using RStudio Version 1.0.136 – © 2009–2016 RStudio, Inc.

Results

Patients randomized to the BF arm remained on respiratory isolation precautions on average (42.3 ± 72.9 hours) over 100 hours less than patients randomized to the routine arm (151.3 ± 151.8 hours) (95% CI: 35.6–184.4 hours, P = 0.0052).

Conclusion

Implementing the BioFire FilmArray Respiratory Panel decreased infection control isolation time by approximately 4 days compared with routine testing; further study is warranted to determine the impact of this technology on patient outcomes and cost benefit.

Disclosures

T. Wong, bioMerieux: Investigator, Research grant A. Stefanovic, bioMerieux: Investigator, Research grant E. Bryce, bioMerieux: Investigator, Research grant J. M. Grant, bioMerieux: Investigator, Research grant D. Roscoe, bioMerieux: Investigator, Research grant

Interim estimates of 2016/17 vaccine effectiveness against influenza A(H3N2), Canada, January 2017

Using a test-negative design, the Canadian Sentinel Practitioner Surveillance Network (SPSN) assessed interim 2016/17 influenza vaccine effectiveness (VE) against dominant influenza A(H3N2) viruses considered antigenically matched to the clade 3C.2a vaccine strain. Sequence analysis revealed substantial heterogeneity in emerging 3C.2a1 variants by province and over time. Adjusted VE was 42% (95% confidence interval: 18-59%) overall, with variation by province. Interim virological and VE findings reported here warrant further investigation to inform potential vaccine reformulation.