Evaluating the impact of organic matter and sample processing techniques on RNA detection using environmental samples

Abstract

This study evaluated sample processing methods and the presence of organic matter on detection of porcine epidemic diarrhea virus (PEDV) from environmental samples using real-time reverse transcriptase-polymerase chain reaction (qRT-PCR). Steel coupons were inoculated with PEDV and different types of organic material contamination. Surface samples were collected and processed in one of four ways: none, centrifugation, syringe filtration, or combination of centrifugation and syringe filtration, then submitted for PEDV qRT-PCR. There was a surface inoculation type by processing method interaction (P < .001) that impacted the sample cycle threshold value. Centrifugation resulted in the most consistent detection of PEDV RNA.

Development and optimization of sampling techniques for environmental samples from African swine fever virus-contaminated surfaces with no organic contaminants

“…In contrast, low speed centrifugation of the environmental samples had no impact on ASFV DNA detection. These results were consistent with the previous findings in which centrifugation at low speed had no impact on diagnostic sensitivity for porcine epidemic diarrhea virus, but the reduced sensitivity was found after filtration ( 25 ). In this study, the effect of centrifugation and filtration on environmental samples containing organic matters was not evaluated, but it would improve our understanding of ASFV diagnostics for environmental samples which mimic the real-world situation where organic matters are present.…”