Table 3 Representative sample matrices, pretreatment protocols, and compatible detection modalities for avian influenza virus detection128,129
From: Multimodal sensing technologies for HPAI biosurveillance in poultry production systems
Sample matrix/source | Typical collection method | Common pretreatment or processing | Suitable detection modalities | Notes/applications |
|---|---|---|---|---|
Oropharyngeal/cloacal swabs | Sterile polyester or nylon flocked swabs; stored in viral transport medium (VTM) | Vortexing → low-speed centrifugation → RNA extraction | RT-qPCR, RT-LAMP, CRISPR–Cas12a, electrochemical biosensors | Standard diagnostic sample; high viral load during acute infection |
Blood/serum | Venipuncture or post-mortem collection | Centrifugation (3000×g, 10 min) → serum separation | Serological assays (HI, ELISA), SPR biosensors | Detects antibodies or antigenemia; used for surveillance or confirmation |
Aerosol/airborne dust | Cyclone sampler, gelatin filter, or impinger | Filtration or condensation → buffer elution → centrifugal concentration | Capacitive/impedance biosensors, SERS | Enables non-invasive environmental monitoring; humidity affects signal stability |
Water/brine (drinking troughs, wetlands) | Sterile bottle sampling (250–500 mL) | Pre-filtration (0.45 µm) → ultrafiltration or PEG precipitation → RNA extraction | RT-qPCR, RT-LAMP, CRISPR–Cas12a, Electrochemical | Low viral titers; concentration step critical for sensitivity |
Feces/litter | Fresh droppings collected with a sterile spatula | Homogenization (10% w/v) → clarification → RNA extraction | RT-qPCR, electrochemical, SPR | Suitable for flock-level surveillance; inhibitors may require dilution |
Feed/surface swabs (Fomites) | Sterile gauze or sponge moistened in PBS | Elution → filtration → RNA extraction | RT-qPCR, CRISPR–Cas12a, electrochemical | Detects environmental contamination from handling or equipment |
