Diagnostic accuracy of digital RNA quantification versus real-time PCR for the detection of respiratory syncytial virus in nasopharyngeal aspirates from children with acute respiratory infection

Author(s):Show less -

Bouzas, Maiara L. ^[1] ; Oliveira, Juliana R. ^[1] ; Queiroz, Artur ^[2] ; Fukutani, Kiyoshi F. ^{[1, 3]} ; Barral, Aldina ^{[2, 1, 4]} ; Rector, Annabel ^[5] ; Wollants, Elke ^[5] ; Keyaertse, Els ^{[5, 6]} ; Van der Gucht, Winke ^[5] ; Van Ranst, Marc ^{[5, 6]} ; Beuselinck, Kurt ^[6] ; de Oliveira, I, Camila ; Van Weyenbergh, Johan ^[5] ; Nascimento-Carvalho, Cristiana M. ^{[7, 8]} ; Grp, Acute Resp Infect Wheeze Study

Affiliation

^[1] Univ Fed Bahia, Sch Med, Postgrad Program Hlth Sci, Salvador, BA - Brazil

^[2] I, Fundacao Oswaldo Cruz FIOCRUZ, Ctr Pesquisas Goncalo Moniz CPqGM, Salvador, BA - Brazil

^[3] Univ Sao Paulo, Ribeirao Preto Med Sch, Dept Biochem Immunol & Cell Biol, Ribeirao Preto - Brazil

^[4] Univ Fed Bahia, Sch Med, Dept Pathol, Salvador, BA - Brazil

^[5] Katholieke Univ Leuven, Rega Inst Med Res, Lab Clin & Epidemiol Virol, Dept Microbiol & Immunol, Leuven - Belgium

^[6] Univ Hosp Leuven, Dept Lab Med, Leuven - Belgium

^[7] de Oliveira, Camila, I, Univ Fed Bahia, Sch Med, Postgrad Program Hlth Sci, Salvador, BA - Brazil

^[8] Univ Fed Bahia, Sch Med, Dept Pediat, Salvador, BA - Brazil

• Document type: Journal article
• Source: Journal of Clinical Virology; v. 106, p. 34-40, SEP 2018.
• Web of Science Citations: 3

Abstract

Background: Virus-specific molecular assays such as real-time polymerase chain reaction (RT-PCR) are regularly used as the gold standard to diagnose viral respiratory tract infections, but simultaneous detection of multiple different pathogens is often challenging. A multiplex digital method of RNA quantification, nCounter (NanoString Technologies), can overcome this disadvantage and identify, in a single reaction, the presence of different respiratory viruses. Objectives: To evaluate the accuracy of nCounter to identify and quantify RSV-A and RSV-B in nasopharyngeal aspirates (NPA) of children (6-23-months-old) with acute respiratory infection. Study design: NPA was collected at enrolment in a prospective cross-sectional study conducted in Salvador, Brazil. A quantitative RT-PCR with a subgroup-specific primer and probeset for RSV-A and RSV-B was performed in parallel with a customized nCounter probeset containing viral targets in NPA. Results: Of 559 NPA tested, RSV was detected by RT-PCR in 139 (24.9%), by nCounter in 122 (21.8%) and by any method in 158 (28.3%) cases. Compared to the gold standard of qRT-PCR, sensitivity of nCounter was 74.3% (95%CI:63.3%-82.9% RSV-A) and 77.6% (95%CI:66.3%-85.9% RSV-B); specificity was 98.4% (95%CI:96.8%-99.2% RSV-A) and 97.8% (95%CI:96.0%-98.8% RSV-B); positive predictive value was 87.3% (95%CI:76.9%-93.4% RSV-A) and 82.5% (95%CI:71.4%-90.0% RSV-B) and negative predictive value was 96.1% (95%CI:94.1%-97.5% RSV-A), and 96.9% (95%CI:95.1%-98.2% RSV-B). Accuracy was 95.2% (95%CI:93.1%-96.7%) for RSV-A and 95.3% (95%CI:93.3%-96.9%) for RSV-B, while both methods significantly correlated for RSV-A (r = 0.44, p = 8 x 10(-5)) and RSV-B (r = 0.73, p = 3 x 10(-12)) quantification. Conclusions: nCounter is highly accurate in detecting RSV-A/B in NPA. Robustness and high-throughput multiplexing indicate its use in large-scale epidemiological studies. (AU)

• FAPESP's process: 17/03491-6 - RIDCs: Research, Innovation and Dissemination Centers
• Grantee: Kiyoshi Ferreira Fukutani
• Support Opportunities: Scholarships in Brazil - Post-Doctoral