Comparison of Six Sample-to-Answer Influenza A/B and Respiratory Syncytial Virus Nucleic Acid Amplification Assays Using Respiratory Specimens from Children

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ABSTRACT

The rapid and accurate detection of influenza A virus (FluA), influenza B virus (FluB), and respiratory syncytial virus (RSV) improves patient care. Sample-to-answer (STA) platforms based on nucleic acid amplification and detection of these viruses are simple, automated, and accurate. We compared six such platforms for the detection of FluA, FluB, and RSV: Cepheid GeneXpert Xpress Flu/RSV (Xpert), Hologic Panther Fusion Flu A/B/RSV (Fusion), Cobas influenza A/B & RSV (Liat), Luminex Aries Flu A/B & RSV (Aries), BioFire FilmArray respiratory panel (RP), and Diasorin Simplexa Flu A/B & RSV (Simplexa). Nasopharyngeal (NP) swab specimens ( n = 225) from children previously tested by RP were assessed on these platforms. The results were compared to those of the Centers for Disease Control and Prevention (CDC)-developed real-time reverse transcription-PCR (rRT-PCR) assay for influenza A/B viruses and RSV. Subtyping for FluA and FluB was performed for discrepant analysis where applicable. The percent sensitivities/specificities for FluA detection were 100/100 (Fusion), 98.6/99.3 (Xpert), 100/100 (Liat), 98.6/100 (Aries), 98.6/100 (Simplexa), and 100/100 (RP). The percent sensitivities/specificities for FluB detection were 100/100 (Fusion), 97.9/99.4 (Xpert), 97.9/98.3 (Liat), 93.7/99.4 (Aries), 85.4/99.4 (Simplexa), and 95.8/97.7 (RP); and those for RSV detection were 98.1/99.4 (Xpert), 98.1/99.4 (Liat), 96.3/100 (Fusion), 94.4/100 (Aries), 87/94.4 (Simplexa), and 94.4/100 (RP). The 75 strains confirmed to be FluA included 29 pH1N1, 39 H3N2, 4 sH1N1, and 3 untyped strains. The 48 strains confirmed to be FluB included 33 strains of the Yamagata lineage, 13 of the Victoria lineage, 1 of both the Yamagata and Victoria lineages, and 1 of an unknown lineage. All six STA platforms demonstrated >95% sensitivity for FluA detection, while three platforms (Fusion, Xpert, and Liat) demonstrated >95% sensitivity for FluB and RSV detection.

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Viral Loads and Duration of Viral Shedding in Adult Patients Hospitalized with Influenza

Nelson Lee, Paul K S Chan, David S. C. Hui … (2009)

Abstract BackgroundThe goal of this study was to characterize viral loads and factors affecting viral clearance in persons with severe influenza MethodsThis was a 1-year prospective, observational study involving consecutive adults hospitalized with influenza. Nasal and throat swabs were collected at presentation, then daily until 1 week after symptom onset. Real-time reverse-transcriptase polymerase chain reaction to determine viral RNA concentration and virus isolation were performed. Viral RNA concentration was analyzed using multiple linear or logistic regressions or mixed-effect models ResultsOne hundred forty-seven inpatients with influenza A (H3N2) infection were studied (mean age ± standard deviation, 72±16 years). Viral RNA concentration at presentation positively correlated with symptom scores and was significantly higher than that among time-matched outpatients (control subjects). Patients with major comorbidities had high viral RNA concentration even when presenting >2 days after symptom onset (mean ± standard deviation, 5.06±1.85 vs 3.62±2.13 log10 copies/mL; P=.005; β, +0.86 [95% confidence interval, +0.03 to +1.68]). Viral RNA concentration demonstrated a nonlinear decrease with time; 26% of oseltamivir-treated and 57% of untreated patients had RNA detected at 1 week after symptom onset. Oseltamivir started on or before symptom day 4 was independently associated with an accelerated decrease in viral RNA concentration (mean β [standard error], −1.19 [0.43] and −0.68 [0.33] log10 copies/mL for patients treated on day 1 and days 2–3, respectively; P<.05) and viral RNA clearance at 1 week (odds ratio, 0.10 [95% confidence interval, 0.03–0.35] and 0.30 [0.10–0.90] for patients treated on day 1–2 and day 3–4, respectively). Conversely, major comorbidities and systemic corticosteroid use for asthma or chronic obstructive pulmonary disease exacerbations were associated with slower viral clearance. Viral RNA clearance was associated with a shorter hospital stay (7.0 vs 13.5 days; P=.001) ConclusionPatients hospitalized with severe influenza have more active and prolonged viral replication. Weakened host defenses slow viral clearance, whereas antivirals started within the first 4 days of illness enhance viral clearance

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Acute respiratory tract infections are the most common illnesses in all individuals, regardless of age or gender. Epidemiologic surveys and community-based studies conducted since the beginning of the 20th century have determined the rates of illness and the pathogens involved in such infections. These studies have shown that rhinoviruses cause the great majority of these respiratory illnesses, and their findings have examined the means of transmission of respiratory illness. More recently, advances in diagnostic techniques have enabled more complete identification of the viruses involved in respiratory infections, which has aided in the ability to direct specific therapeutic agents at the causative pathogens.

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Impact of the rapid diagnosis of influenza on physician decision-making and patient management in the pediatric emergency department: results of a randomized, prospective, controlled trial.

W Monroe, Lynya I Talley, Ann Klasner … (2003)

To determine the impact of the rapid diagnosis of influenza on physician decision-making and patient management, including laboratory tests and radiographs ordered, patient charges associated with these tests, antibiotics/antivirals prescribed, and length of time to patient discharge from the emergency department. Patients aged 2 months to 21 years presenting to an urban children's teaching hospital emergency department were screened for fever and cough, coryza, myalgias, headache, and/or malaise. After obtaining informed consent, patients were randomized to 1 of 2 groups: 1) physician receives (physician aware of) the rapid influenza test result; or 2) physician does not receive (physician unaware of) the result. For patients in the physician aware group, nasopharyngeal swabs were obtained, immediately tested with the FluOIA test for influenza A and B, and the result was placed on the chart before patient evaluation by the attending physician. For the physician unaware group, nasopharyngeal swabs were obtained, stored according to manufacturer's directions, and tested within 24 hours. Results for the physician unaware group were not disclosed to the treating physicians at any time. The 2 resultant influenza-positive groups (aware and unaware) were compared for laboratory and radiograph studies and their associated patient charges, antibiotic/antiviral prescriptions, and length of stay in the emergency department. A total of 418 patients were enrolled, and 391 completed the study. Of these, 202 tested positive for influenza. Comparison of the 96 influenza-positive patients whose physician was aware of the result with the 106 influenza-positive patients whose physician was unaware of the result revealed significant reductions among the former group in: 1) numbers of complete blood counts, blood cultures, urinalyses, urine cultures, and chest radiographs performed; 2) charges associated with these tests; 3) antibiotics prescribed; and 4) length of stay in the emergency department. The number of influenza-positive patients who received prescriptions for antiviral drugs was significantly higher among those whose physician was aware of the result. Physician awareness of a rapid diagnosis of influenza in the pediatric emergency department significantly reduced the number of laboratory tests and radiographs ordered and their associated charges, decreased antibiotic use, increased antiviral use, and decreased length of time to discharge.