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High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR
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Optimizing sample collection methods for detection of respiratory viruses in poultry housing environments
Jongseo Mo1, Christopher B Stephens1, Brian Jordan2,3
1Southeast Poultry Research Laboratory, United States Department of Agriculture, US National Poultry Research Center, Agricultural Research Service, Athens, Georgia.
Transboundary and Emerging Diseases
|April 2, 2022
Summary
Pre-moistened cotton gauze is the best device for collecting poultry respiratory virus samples. The tops of drinker lines within pens yielded the highest viral RNA loads, crucial for effective environmental sampling.
Area of Science:
- Veterinary Virology
- Poultry Health Management
- Environmental Monitoring
Background:
- Viral respiratory diseases cause significant economic losses in the poultry industry.
- Environmental sampling is critical for virus eradication and restocking after outbreaks.
Purpose of the Study:
- To identify optimal sample collection devices for poultry respiratory viruses.
- To determine the most effective locations for environmental virus sampling in poultry housing.
Main Methods:
- Evaluated five sample collection devices (foam swabs, cellulose sponges, polyester swabs, dry cotton gauze, pre-moistened cotton gauze) for viral RNA recovery.
- Compared virus detection in 10 locations within two types of poultry housing (curtain-sided wood-framed and cement block).
- Used infectious bronchitis virus as a model for enveloped poultry respiratory viruses.
Main Results:
- Cotton gauze pre-moistened with viral transport media demonstrated the highest sensitivity for viral RNA recovery.
- The highest viral RNA loads were consistently recovered from the tops of drinker lines within pens.
- Direct contact surfaces (feeder rims) and high-traffic areas (hallway floors) also showed higher viral RNA levels.
Conclusions:
- Pre-moistened cotton gauze is recommended for efficient environmental sampling of poultry respiratory viruses.
- Targeting specific locations like drinker lines and high-contact areas improves sampling efficacy.
- Optimized sampling procedures are essential for effective disease control and biosecurity in poultry farms.

