Syndromic diagnosis of upper respiratory infections in patients presenting with a suspicion of COVID-19 in Madagascar: contribution of the Biofire Film Array respiratory panel 2.1

Abstract

Acute respiratory infections (ARIs) are challenging to diagnose due to overlapping symptoms among pathogens. During the COVID-19 pandemic in Antananarivo (2020–2022), 19% of SARS-CoV-2-negative symptomatic patients tested positive for other respiratory viruses by RT-PCR. Automated multiplex assays such as FilmArray® Biofire RP2.1 (Biofire FA-RP2.1) enable simultaneous pathogen detection and improve ARIs surveillance. This study aimed to i) estimate the diagnostic gain in terms of etiology for a sequential strategy combining targeted RT-PCR followed by multiplex testing, (ii) evaluate the ability of Biofire FA-RP2.1 to identify non-SARS-CoV-2 respiratory agents, (iii) describe the discrepancies in SARS-CoV-2 detection between simplex RT-PCR and multiplex testing, (iv) explore the performance of symptom-based models for determining etiology. A total of 384 nasopharyngeal samples from symptomatic patients with suspected COVID-19 collected in Antananarivo (March 2021–August 2022) were tested by simplex RT-PCR for SARS-CoV-2 and the Biofire FA-RP2.1. Discordant SARS-CoV-2 results were investigated using targeted next-generation sequencing (tNGS). Statistical analyses included Fisher’s exact Student’s t-test, risk ratio estimation, logistic regression, and ROC analysis. RT-PCR and Biofire FA-RP2.1 detected 163 and 141 SARS-CoV-2–positive cases, respectively. Biofire FA-RP2.1 detected 192 mono-infections and 20 co-infections. The most frequent mono-infections were SARS-CoV-2 ( n = 129) and rhinovirus ( n = 48). Sixty-one SARS-CoV-2 detection discrepancies were identified: 39 (64%) were positive on RT-PCR but negative on Biofire FA-RP2.1, and 22 (36%) showed the opposite pattern. Discordance was associated with high Ct values (mean Ct 30.9 vs. 27.4; p = 0.003) and co-infections (RR = 2.1, 95% CI: 1.36–3.30). Among the 23 discordant samples tested by tNGS, 22 were confirmed positive for SARS-CoV-2. Arthralgia and cough were associated with SARS-CoV-2 positivity (OR = 3.22 and 1.77, respectively); dyspnea was associated with negative results. Symptom-based models showed moderate performance (AUC ≈ 0.72–0.74). Biofire FA-RP2.1 is a useful tool for ARIs surveillance despite a 16% discordance with simplex RT-PCR for SARS-CoV-2 detection, mainly observed in samples with higher Ct values or co-infection. tNGS provided complementary insights into these discrepancies. Clinical features were insufficient for etiological differentiation, highlighting the added value of multiplex approaches for syndromic surveillance of ARIs.