Clinical Sampling Challenges in Diagnosing Severe Respiratory Viral Infections

Area of Science:

• Medical diagnostics
• Virology
• Respiratory medicine

Background:

• Respiratory viruses cause significant pneumonia, especially in severe acute respiratory infection (SARI) cases.
• Accurate diagnosis of SARI relies heavily on appropriate sample site selection for molecular testing.

Purpose of the Study:

• To compare the diagnostic yield and concordance of respiratory virus detection between paired upper respiratory tract (URT) and lower respiratory tract (LRT) samples in SARI patients.
• To evaluate the impact of sampling site on diagnostic accuracy for respiratory viruses in hospitalized patients.

Main Methods:

• A multicenter, retrospective study analyzed paired URT and LRT samples from SARI patients (2014-2022).
• Multiplex PCR assays were used for respiratory virus detection.
• Viral detection rates, concordance, discordance, and quantification cycle (Cq) values (viral load proxy) were compared between sample types.

Main Results:

• Of 346 paired samples, 32.1% were discordant, with viruses detected in LRT but not URT samples in 21.7% of cases.
• Influenza A virus (IAV), Rhinovirus/Enterovirus (RV/EV), and Respiratory Syncytial Virus (RSV) were most prevalent.
• Median Cq values were significantly lower in LRT samples (24.5 vs. 27.5), indicating higher viral loads, particularly in concordant pairs.

Conclusions:

• Relying solely on URT sampling may lead to missed viral diagnoses in SARI patients.
• LRT sampling enhances diagnostic sensitivity for respiratory viruses, especially in later infection stages.
• Incorporating LRT sampling into diagnostic protocols can improve clinical decision-making for SARI management.