Computational protocol: Airborne Transmission of Highly Pathogenic Influenza Virus during Processing of Infected Poultry

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Protocol publication

[…] Each run (i.e., tested virus per bird species) was repeated at least twice for reproducibility. Chickens (10 for VN/04 and 5 for all other viruses) and ducks (5 per virus) were inoculated intranasally with 105.3–106.5 mean egg infectious dose (EID50)0.1 mL per virus and housed in negative-pressure isolators with HEPA-filtered ventilation. We moved chickens at 24 h after inoculation and ducks at 2.5 days after inoculation, which corresponded to times of peak shedding titers, to the processing enclosure while they were still asymptomatic. We anesthetized them by intramuscular injection of ketamine (10 g/kg) and xylazine (1 g/kg) and collected oral swab samples to confirm infection. The anesthetized birds were processed following 5 steps (total duration 6–7 min/bird) (): 1) manual killing by severing the right jugular vein with a scalpel blade, causing bleeding and agonal involuntary muscle contractions (1 min); 2) scalding in a covered pot (52–53°C/2 min); 3) manual defeathering (2 min); 4) evisceration and removal of head, feet, and internal organs (1.5 min); and 5) cleanup of processing area with water (0.5 min). We rubbed the ducks with detergent before the scalding step to remove preening oils and facilitate defeathering. During the processing, air samplers were used as aforementioned. After each run, we disinfected all materials and surfaces within the enclosure, as well as the units holding the infected birds, with Virkon S 2% (DuPont, Wilmington, DE, USA). We tested swab samples for viable virus in ECE and titrated aerosol samples in ECE (). The minimum detectable titer in ECE was 0.9 log10 EID50/mL. […]

Pipeline specifications

Software tools Scalpel, MUSCLE
Application Nucleotide sequence alignment
Organisms Homo sapiens, Gallus gallus, Viruses, Anas platyrhynchos, Mustela putorius furo, Human poliovirus 1 Mahoney
Diseases Infection, HIV Infections