COVID-19 and Influenza A/B Diagnostic Guidelines

Patient Selection and Specimen Collection

The Centers for Disease Control and Prevention recommends testing symptomatic individuals with at least one common symptom of COVID-19 or influenza within 5 days of symptom onset for optimal performance 1, 2, 3
Anterior nasal swabs, midturbinate swabs, or nasopharyngeal swabs are acceptable specimen types for the BTNX lateral flow assay 1, 2, 4
The World Health Organization suggests that nasopharyngeal specimens may provide superior pathogen detection compared to throat swabs, although this is based on a study from Praxis Medical Insights, an alternative source indicates similar findings 5

The Infectious Diseases Society of America recommends performing testing within 5 days of symptom onset to optimize sensitivity 1, 2, 3, 4
Testing performed late in the course of infection has significantly reduced sensitivity 1, 2

A positive BTNX lateral flow assay has high specificity and can guide treatment and isolation decisions without confirmation, according to the Clinical Infectious Diseases guidelines 1, 2
Negative antigen results must be confirmed with standard NAAT if clinical suspicion for COVID-19 or influenza remains moderate or high, as per the Centers for Disease Control and Prevention recommendations 1, 2, 3, 4

Limited data exist regarding analytical performance in children, immunocompromised patients, and vaccinated individuals, and the American Academy of Pediatrics suggests exercising increased caution when interpreting results in these populations 1, 2

Never assume a negative antigen test rules out infection in symptomatic patients with high clinical suspicion—always confirm with NAAT, as recommended by the Infectious Diseases Society of America 1, 2, 3

Rapid molecular tests show the highest accuracy with pooled sensitivity of 96% (95% CI: 91-98%) and specificity of 100% (95% CI: 98-100%) in symptomatic individuals, making them suitable for immediate clinical decisions when used appropriately 6
In symptomatic individuals, antigen tests demonstrate 73% average sensitivity (95% CI: 69.3-76.4%) with 99.1% specificity, according to the Centers for Disease Control and Prevention (CDC) guidelines 7
The American College of Physicians recommends that rapid molecular tests can replace laboratory testing when immediate results are needed, with essentially equivalent accuracy 6

Sensitivity is highest in the first week after symptom onset at 80.9% (95% CI: 76.9-84.4%) for antigen tests, as stated by the World Health Organization (WHO) 7
The Infectious Diseases Society of America (IDSA) notes that sensitivity drops dramatically to 53.8% (95% CI: 48.0-59.6%) in the second week of symptoms 7

The CDC recommends that nasopharyngeal, anterior nasal, midturbinate, oropharyngeal, and saliva specimens all show acceptable sensitivity ranging from 78-92% compared to nasopharyngeal reference for molecular testing 8
Anterior nasal and oropharyngeal swabs have slightly lower sensitivity (81%) but are less invasive and suitable for self-collection, according to the American Academy of Family Physicians (AAFP) 8

The American College of Emergency Physicians (ACEP) recommends using rapid molecular tests as direct replacements for laboratory PCR when immediate treatment decisions are required 6
The WHO suggests using high-performing antigen tests in symptomatic patients within 5 days of symptom onset for triage or when PCR is unavailable 7