Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing.

Rapid influenza diagnostic tests (RIDT) demonstrate varying sensitivities, often necessitating reverse transcriptase polymerase chain reaction (RT-PCR) to confirm results. The two methods generally require separate specimens. Using the same anterior nasal swab for both RIDT and molecular confirmation would reduce cost and waste and increase patient comfort. The aim of this study was to determine if RIDT residual nasal swab (rNS) specimens are adequate for RT-PCR and whole genome sequencing (WGS). We performed RT-PCR and WGS on paired rNS and nasopharyngeal or oropharyngeal (NP/OP) swab specimens that were collected from primary care patients across all ages. We randomly selected 199 and 40 paired specimens for RT-PCR and WGS, respectively, from the 962 paired surveillance specimens collected during the 2014-2015 influenza season. Sensitivity and specificity for rNS specimens were 81.3% and 96.7%, respectively, as compared to NP/OP specimens. The mean cycle threshold (Ct) value for the NP/OP specimen was significantly lower when the paired specimens were both positive than when the NP/OP swab was positive and the nasal swab was negative (25.5 vs 29.5; p<0.001). Genomic information was extracted from all 40 rNS specimens and 37 of the 40 NP/OP specimens. Complete WGS reads were available for 67.5% (14 influenza A; 13 influenza B) of the rNS specimens and 59.5% (14 influenza A; 8 influenza B) of the NP/OP specimens. It is feasible to use a single anterior nasal swab for RIDT followed by RT-PCR and/or WGS. This approach may be appropriate in situations where training and supplies are limited. Additional studies are needed to determine if residual nasal swabs from other rapid diagnostic tests produce similar results.

The Influence of Rapid Influenza Diagnostic Testing on Clinician Decision-Making for Patients With Acute Respiratory Infection in Urgent Care.

BACKGROUND: The potential benefits of using rapid influenza diagnostic tests (RIDTs) in urgent care facilities for clinical care and prescribing practices are understudied. We compared antiviral and antibiotic prescribing, imaging, and laboratory ordering in clinical encounters with and without RIDT results. METHODS: We compared patients with acute respiratory infection (ARI) symptoms who received an RIDT and patients who did not at 2 urgent care facilities. Primary analysis using 1-to-1 exact matching resulted in 1145 matched pairs to which McNemar 2 × 2 tests were used to assess the association between the likelihood of prescribing, imaging/laboratory ordering, and RIDT use. Secondary analysis compared the same outcomes using logistic regression among the RIDT-tested population between participants who tested negative (RIDT(-)) and positive (RIDT(+)). RESULTS: Primary analysis revealed that compared to the non-RIDT-tested population, RIDT(+) patients were more likely to be prescribed antivirals (OR, 10.23; 95% CI, 5.78-19.72) and less likely to be prescribed antibiotics (OR, 0.15; 95% CI, .08-.27). Comparing RIDT-tested to non-RIDT-tested participants, RIDT use increased antiviral prescribing odds (OR, 3.07; 95% CI, 2.25-4.26) and reduced antibiotic prescribing odds (OR, 0.52; 95% CI, .43-.63). Secondary analysis identified increased odds of prescribing antivirals (OR, 28.21; 95% CI, 18.15-43.86) and decreased odds of prescribing antibiotics (OR, 0.20; 95% CI, .13-.30) for RIDT(+) participants compared with RIDT(-). CONCLUSIONS: Use of RIDTs in patients presenting with ARI symptoms influences clinician diagnostic and treatment decision-making, which could lead to improved patient outcomes, population-level reductions in influenza burden, and a decreased threat of antibiotic resistance.

New Method for Real Time Influenza Surveillance in Primary Care: A Wisconsin Research and Education Network (WREN) Supported Study.

INTRODUCTION: The goal of public health infectious disease surveillance systems is to provide accurate laboratory results in near-real time. When it comes to influenza surveillance, most current systems are encumbered with inherent delays encountered in the real-life chaos of medical practice. To combat this, we implemented and tested near-real-time surveillance using a rapid influenza detection test (RIDT) coupled with immediate, wireless transmission of results to public health entities. METHODS: A network of 19 primary care clinics across Wisconsin were recruited, including 4 sites already involved in ongoing influenza surveillance and 15 sites that were new to surveillance activities. Each site was provided with a Quidel Sofia Influenza A+B RIDT analyzer attached to a wireless router. Influenza test results, along with patient age, were transmitted immediately to a cloud-based server, automatically compiled, and forwarded to the surveillance team daily. Weekly counts of positive influenza A and B cases were compared with positive polymerase chain reaction (PCR) detections from an independent surveillance system within the state. RESULTS: Following Institutional Review Board (IRB) and institutional approvals, we recruited 19 surveillance sites, installed equipment, and trained staff within 4 months. Of the 1119 cases tested between September 15, 2013 and June 28, 2014, 316 were positive for influenza. The system provided early detection of the influenza outbreak in Wisconsin. The influenza peak between January 12 and 25, 2014, as well as the epidemic curve, closely matched that derived from the established PCR laboratory network (r = 0.927; P < .001). CONCLUSIONS: A network of influenza RIDTs with wireless transmission of results approximated the long-sought-after goal of real-time influenza surveillance. Results from the initial year strongly support this approach to highly accurate and timely influenza surveillance.

Synchronicity of influenza activity within Phoenix, AZ during the 2015-2016 seasonal epidemic.

BACKGROUND: Variability in the timing of influenza epidemics has been observed across global and regional scales, but this variability has not been studied extensively at finer spatial scales. As such, the aim of this study was to test whether influenza cases were synchronized across sites and/or age-groups within a major city. METHODS: We used influenza cases identified by rapid influenza tests from a network of clinics across Phoenix, AZ during the 2015-2016 influenza A season. We used a combination of KS tests and a bootstrapping approach to evaluate whether the temporal distribution of cases varied by site and/or age group. RESULTS: Our analysis indicates that the timing of influenza cases during the 2015-2016 seasonal influenza epidemic were generally synchronized across sites and age groups. That said, we did observe some statistically significant differences in the timing of cases across some sites, and by site and age group. We found no evidence that influenza activity consistently begins or peaks earlier in children than in adults. CONCLUSIONS: To our knowledge, this is the first study to investigate differences in the intra-urban timing of influenza using influenza-specific case data. We were able to show evidence that influenza cases are not entirely synchronized across an urban area, but the differences we observed were relatively minor. It is important to understand the geographic scale at which influenza is synchronized in order to gain a better understanding of local transmission dynamics, and to determine the appropriate geographic scale that influenza surveillance data should be aggregated for prediction and warning systems.

Detection of influenza A and B viruses with the Sofia analyzer: a novel, rapid immunofluorescence-based in vitro diagnostic device.

This report describes the clinical evaluation of a novel fluorescent immunoassay (FIA), Sofia Influenza A+B FIA (Quidel, San Diego, CA), for the rapid detection and differentiation of influenza A and B viruses. A total of 2,047 subjects provided nasal swabs and nasopharyngeal swabs or aspirates. The overall sensitivity and specificity for influenza A virus vs virus culture were 94% and 95%, respectively, and for influenza B virus were 89% and 96%, respectively. Fourteen hundred and sixty-one specimens were available for testing with reverse transcriptase-polymerase chain reaction (RT-PCR). The sensitivity of the Sofia Influenza A+B FIA for detecting influenza A and B viruses compared with the RT-PCR method was 78% and 86%, respectively. A high percentage of the positive specimens had low cycle threshold values, and almost all of these were positive with the Sofia test. This high level of sensitivity demonstrates that the Sofia influenza A+B FIA could improve the usefulness of rapid influenza virus testing.

Comparison of the MChip to viral culture, reverse transcription-PCR, and the QuickVue influenza A+B test for rapid diagnosis of influenza.

The performance of a diagnostic microarray (the MChip assay) for influenza was compared in a blind study to that of viral culture, reverse transcription (RT)-PCR, and the QuickVue Influenza A+B test. The patient sample data set was composed of 102 respiratory secretion specimens collected between 29 December 2005 and 2 February 2006 at Scott & White Hospital and Clinic in Temple, Texas. Samples were collected from a wide range of age groups by using direct collection, nasal/nasopharyngeal swabs, or nasopharyngeal aspiration. Viral culture and the QuickVue assay were performed at the Texas site at the time of collection. Aliquots for each sample, identified only by study numbers, were provided to the University of Colorado and Vanderbilt University teams for blinded analysis. When referenced to viral culture, the MChip exhibited a clinical sensitivity of 98% and a clinical specificity of 98%. When referenced to RT-PCR, the MChip assay exhibited a clinical sensitivity of 92% and a clinical specificity of 98%. While the MChip assay currently requires 7 to 8 h to complete the analysis, a significant advantage of the test for influenza virus-positive samples is simultaneous detection and full subtype identification for the two subtypes currently circulating in humans (A/H3N2 and A/H1N1) and avian (A/H5N1) viruses.