Influenza A virus drift variants reduced the detection sensitivity of a commercial multiplex nucleic acid amplification assay in the season 2014/15

Abstract

The influenza season 2014/15 was dominated by drift variants of influenza A(H3N2), which resulted in a reduced vaccine effectiveness. It was not clear if the performance of commercial nucleic-acid-based amplification (NAT) assays for the detection of influenza was affected. The purpose of this study was to perform a real-life evaluation of two commercial NAT assays. During January-April 2015, we tested a total of 665 samples from patients with influenza-like illness using the Fast Track Diagnostics Respiratory pathogens 21, a commercial multiplex kit, (cohorts 1 and 2, n = 563 patients) and the Xpert Flu/RSV XC assay (cohort 3, n = 102 patients), a single-use cartridge system. An in-house influenza real-time RT-PCR (cohort 1) and the RealStar Influenza RT-PCR 1.0 Kit (cohort 2 and 3) served as reference tests. Compared to the reference assay, an overall agreement of 95.9 % (cohort 1), 95 % (cohort 2), and 98 % (cohort 3) was achieved. A total of 24 false-negative results were observed using the Fast Track Diagnostics Respiratory pathogens 21 kit. No false-negative results occurred using the Xpert Flu/RSV XC assay. The Fast Track Diagnostics Respiratory pathogens 21 kit and the Xpert Flu/RSV XC assay had sensitivities of 90.7 % and 100 % and specificities of 100 % and 94.1 %, respectively, compared to the RealStar 1.0 kit. Upon modification of the Fast Track Diagnostics Respiratory pathogens 21 kit, the sensitivity increased to 97.3 %. Influenza virus strains circulating during the 2014/15 season reduced the detection sensitivity of a commercial NAT assay, and continuous monitoring of test performance is therefore necessary.

Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples

“…We retrieved 40 left-over NA preparations of respiratory samples from 2019 representing a variety of non-SARS-CoV-2 viruses from our local biobank in Freiburg and set up MP. We tested four MP using the same RT-PCR as for individual patient testing as described (3). To exclude possible unspecific reactions of the MP procedure these MP were also tested using the SARS-CoV-2 specific real-time RT-PCR as described below.…”

Recent advances in the detection of respiratory virus infection in humans

“…This kit has sensitivity of 90.7% and specificity of 100% compared to the RealStar 1.0 kit. In addition, upon modification of the FTD21 kit, the sensitivity increased to 97.3% 76 …”

Diagnosing Viral and Atypical Pathogens in the Setting of Community-Acquired Pneumonia

“…Unlike bacterial pathogens, the constant genomic shifts in influenza A do affect the performance of assays and they need to be revalidated constantly as new strains appear. 53 A variety of point-of-care platforms have been developed for detecting influenza, of which the GeneXpert system (Cepheid, Sunnyvale, CA) is perhaps so far the best studied. 54 GeneXpert is an "all-in-one" platform requiring minimal technical expertise, and is a potential point-of-care platform for diagnosing influenza.…”