key: cord-0685900-riiwb6ia
authors: Gosert, Rainer; Naegele, Klaudia; Hirsch, Hans H.
title: Comparing the Cobas Liat Influenza A/B and respiratory syncytial virus assay with multiplex nucleic acid testing
date: 2018-11-13
journal: J Med Virol
DOI: 10.1002/jmv.25344
sha: 50ca0f1de477a68ad2e62202b32a4c84125836cc
doc_id: 685900
cord_uid: riiwb6ia

Influenza virus and respiratory syncytial virus (RSV) detection with short turn‐around‐time (TAT) is pivotal for rapid decisions regarding treatment and infection control. However, negative rapid testing results may come from poor assay sensitivity or from influenza‐like illnesses caused by other community‐acquired respiratory viruses (CARVs). We prospectively compared the performance of Cobas Liat Influenza A/B and RSV assay (LIAT) with our routine multiplexNAT‐1 (xTAG Respiratory Pathogen Panel; Luminex) and multiplexNAT‐2 (ePlex‐RPP; GenMark Diagnostics) using 194 consecutive nasopharyngeal swabs from patients with influenza‐like illness during winter 2017/2018. Discordant results were reanalyzed by specific in‐house quantitative nucleic acid amplification testing (NAT). LIAT was positive for influenza virus‐A, ‐B, and RSV in 18 (9.3%), 13 (6.7%), and 55 (28.4%) samples, and negative in 108 samples. Other CARVs were detected by multiplexNAT in 66 (34.0%) samples. Concordant results for influenza and RSV were seen in 190 (97.9%), discordant results in 4 (2.1%), which showed low‐level RSV (<40 000 copies/mL). Sensitivity and specificity of LIAT for influenza‐A, ‐B, and RSV were 100%, 100% and 100%, and 100%, 99.5% and 100%, respectively. The average TAT of LIAT was 20 minutes compared to 6 hours and 2 hours for the multiplexNAT‐1 and ‐2, respectively. Thus, LIAT demonstrated excellent sensitivity and specificity for influenza and RSV, which together with the simple sample processing and short TAT renders this assay suitable for near‐patient testing.

Influenza virus and respiratory syncytial virus (RSV) detection with short turn-around-time (TAT) is pivotal for rapid decisions regarding treatment and infection control. 1, 2 Current diagnostics for the detection of influenza virus and RSV include direct antigen detection (DAD), virus isolation by cell culture (VIC), and nucleic acid amplification testing (NAT). DAD is rapid, but had been shown to be of limited sensitivity compared to VIC. 3, 4 In the past, VIC has been the gold standard for sensitive and specific identification of community-acquired respiratory viruses (CARVs) including influenza viruse and RSV. However, VIC requires skilled technicians, dedicated cell culture equipments, and a TAT of several days, which limits the use of this technique to specialized laboratories. 5 By contrast, NAT has the advantage of a shorter TAT of approximately 6 to 8 hours, and the detection of multiple pathogens by parallel testing in a semiquantitative format and as multiplexNAT. More recently, NAT platforms became available for detecting influenza viruse as point-ofcare tests (POCTs). 3, 6, 7 Besides short TAT of less than 2 hours, cartridge-based POCTs are simple to operate, which permit their use in near-patient settings without extensive laboratory training.

However, negative results are difficult to interpret since POCT J Med Virol. 2019;91:582-587. wileyonlinelibrary.com/journal/jmv may have a limited sensitivity or the influenza-like illnesses in question may be due to other CARVs not covered by the POCT. For this reason, comparison with a multiplexNAT assay is of considerable advantage. 3 In fact, a number of centres are exploring deepsequencing to detect other CARVs. 8 The Cobas Liat Influenza A/B and RSV real-time assay (LIAT) is of interest, since both influenza virus-A, -B as well as the RSV-A and -B are targeted, all of which cause significant morbidity in younger children and older adults during the cold season, and can therefore guide initial decisions regarding antiviral therapy as well as infection control measures. 9-12

In a first phase, eight external quality assurance samples covering influenza virus-A, -B, and RSV were tested by the LIAT and by our inhouse tests. 4, 13 Then, the limit of detection was estimated by using twofold serial dilutions in virus transport medium (VTM) of patient samples that had tested positive for either influenza or RSV in our inhouse quantitative nucleic acid amplification (QNAT) assays. 4, 13 For a prospective parallel study, 194 consecutive nasopharyngeal swabs had been submitted for routine testing between November 2017 and January 2018. The swabs were compared using the LIAT and two Food and Drug Administration (FDA)-cleared multiplex-NATs. Discordant results between the LIAT and the multiplexNATs were resolved by in-house real-time QNAT. Briefly, nasopharyngeal samples were collected using Copan swabs for adults or for infants and submersed in 2 mL VTM. For the LIAT, 200 µL of respiratory specimen was transferred into the single-use, disposable assay tube using a sterile transfer pipette. The tube was capped and directly inserted into the LIAT analyzer. 15, 16 In-house QNATs for influenza viruse and RSV were performed as previously described. 3, 4, 13, 14 Briefly, after reverse transcription, influenza virus-A was identified by amplifying specific sequences of the matrix protein M1, whereas specific hemagglutinin sequences were targeted for identifying influenza virus-B. RSV-A and -B were detected by a duplex QNAT amplifying specific sequences of the nonstructural protein 1 C. QNAT reactions were incubated at 50°C for 10 minutes and at 95°C for 5 minutes, followed by 45 cycles of 95°C for 30 seconds and 60°C for 1 minute. The reaction mix had a total volume of 25 μL after adding 5 μL extracted nucleic acids for one-step reverse transcription and amplification. All samples were tested in duplicates. An additional replicate was spiked with 1000 copies of the respective plasmid to detect amplification inhibition.

The viral load of patient samples was determined by our in-house QNAT. For quantification, a plasmid that contains the corresponding region of the pathogen genome is used in triplicate at 1e6, 1e4, and 1e2 copies to generate a standard curve. External quality assurance programs testing different types at different dilutions of influenza and RSV are used for validation. 

The eight external quality assurance samples correctly identified Taken together, the LIAT showed a sensitivity and specificity for influenza virus-A of 100% and 100%, for influenza virus-B 100% and 99.5%, and for RSV 100% and 100%, respectively. The positive predictive value, negative predictive value, and κ values (interobserver agreement) were high for all three pathogens ( Table 2 ).

The multiplexNAT detected 77 additional pathogens (Figure 1 ), which were present either alone in 43 cases, or as coinfections in 23 cases (Table 3) . Single infections included adenovirus (3), human bocavirus (4), coronaviruses (5), human metapneumovirus (6), parainfluenza viruses (6), and rhinovirus/enterovirus (19 9 years) and thus a strong trend was seen for male gender but did not reach statistical significance, P = 0.056. This observation is solely based on the demographics, and would require dedicated clinicaldiagnostic studies. However, it has been reported by others that children of male gender may be more susceptible for severe respiratory disease manifestations. [17] [18] [19] [20] In 17 of 23 (73.9%) coinfections, RSV (13), and influenza virus-A (4) were found together with other pathogens, but influenza virus-B was not found in coinfections ( Table 3) (Table 2) . For the influenza virus-B case, the sample was negative by multiplexNAT-1 and tested twice negative by in-house QNAT. 13 Repeat testing by LIAT was not possible due to lack of sample material.

For the RSV cases, the LIAT scored three samples positive that tested negative by multiplexNAT (multiplexNAT-1: two samples, multiplexNAT-2: one sample). These discordant results were resolved by our in-house QNAT with viral loads of 6000, 30 800, and 34 600 copies/mL of VTM, respectively. This suggested a limited sensitivity of the multiplexNAT possibly due to multiplexing or target sequence issues. 21 The detection of 6000 copies/mL of VTM by QNAT in one LIAT RSV-positive sample is in line with the results from our where 5000 copies/mL of VTM of RSV were detectable. The sensitivities for influenza virus-A (2500 copies/mL of VTM) and influenza virus-B (1250 copies /mL of VTM) were in a similar range, thereby permitting detection of acutely ill patients having typically much higher viral loads. 4, 13 In previous studies, the LIAT was compared to other commercial NAT. 6, 7, 22, 23 The results of these studies suggest that LIAT has superior sensitivity compared to other POCT. However, the samples Age range 2 wk-87 y were mostly obtained from adult patients, which is now complemented by our study, where the majority was symptomatic children (Table 1) . 

The following limitations should be noted. First, batch testing of patient samples is not possible and at the peak season of influenza and RSV, the sequential testing may result in the loss of the TAT advantage (3 samples per hour, 24 per 8 hours, 72 per 24 hours) .

However, it can be partly compensated for by direct and parallel testing on more than one LIAT instrument. Second, LIAT lacks the identification of influenza virus-A subtypes. Detection of influenza virus-A subtypes may influence isolation procedures in hospital settings. In addition, in immunocompromised patients may be at risk for dual infections, which is rare and usually one pathogen is dominant. In such cases, subsequent multiplexNAT or QNAT provide semiquantitative results that are helpful to identify the main driver of the infection. Because the LIAT is easy to handle, the testing system may be attractive for being used by personnel not trained as professional laboratory analysts. However, in our practice, a qualification program with corresponding documentation and requalification every 1 or 2 years need to be performed in accordance with laboratory regulations, and not only when failing internal and external quality assurance programs.

In conclusion, the LIAT can reduce the TAT compared to conventional multiplexNAT or QNAT. In this study, the sensitivity of the LIAT seemed to be equivalent or slightly increased over current multiplexNAT and comparable to specific QNAT. The specificity was similar to the multiplexNAT. Thus, LIAT seems useful for rapid testing and management decisions regarding infection control and therapy, and could be followed by QNAT to document viral replication and clearance if needed, and/or by multiplexNAT to detect other respiratory pathogens.

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seasonal-influenza-annual-epidemiological-report-2017-18-season How to cite this article: Gosert R, Naegele K, Hirsch HH. Comparing the Cobas Liat Influenza A/B and respiratory syncytial virus assay with multiplex nucleic acid testing

The authors thank the members of the Division Infection Diagnostics for dedicated technical assistance, and Professors Ulrich Heininger, MD, and Urs Frey, MD, and the team at the University Children's

Hospital Basel for the excellent collaboration. The manufacturer of the LIAT (Roche, Rothkreuz, Switzerland) provided two instruments and the used tests free of charge

The authors declare that there are no conflicts of interest.

http://orcid.org/0000-0002-8440-8550Hans H. Hirsch http://orcid.org/0000-0003-0883-0423