Standard operating protocol for influenza testing, treatment and prophylaxis

Effective influenza management requires early testing to guide time-sensitive antiviral therapy, the indiscriminate use of which may promote drug resistance. Reverse transcriptase polymerase chain reaction (RT-PCR) testing is constrained by laboratory infrastructure needs and a turnaround time of several hours. Point-of-care nucleic acid amplification tests (NAATs) and digital immunoassays (DIAs), though rapid, remain costly and are not widely available in low- and middle-income countries (LMICs). This standard operating protocol provides practical guidance for managing seasonal and zoonotic (avian) influenza, primarily based on WHO recommendations. Oseltamivir is reserved for severe influenza, with empirical use permitted only if RT-PCR results are delayed beyond 24 h. For non-severe illness, Baloxavir is recommended in patients at high risk of hospitalisation, but only after a positive NAAT or DIA; however, its access and affordability remain limited in LMICs. Post-exposure prophylaxis is reserved for specific high-risk exposures.