ARS | Publication request: Bioinformatic analysis of variability of Newcastle disease virus diagnostic primers and probes and the potential for false negative detection

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: May 16, 2011
Publication Date: May 16, 2011
Citation: Suarez, D.L., Afonso, C.L. 2011. Bioinformatic analysis of variability of Newcastle disease virus diagnostic primers and probes and the potential for false negative detection [abstract]. 1st International Respiratory Disease Converence, May 15-18, 2011, Athens, Georgia. p. 13.

Technical Abstract: The use of reverse transcriptase polymerase chain reaction (RT-PCR) or other molecular diagnostic methods is commonly used for the primary diagnosis of Newcastle disease virus (NDV). However, NDV in nature has a range of virulence, and the low virulence viruses must be differentiated from virulent forms of the virus. Two approaches have been used including a RT-PCR pan-NDV test designed to identify all NDV viruses and then a reflex test designed to differentiate virulent from non-virulent viruses. Alternatively, a single test that can simultaneously identify and differentiate virulent from non-virulent NDV viruses has been developed. Several genes have been used to target all NDV viruses, but the fusion gene cleavage site is the only target available that will differentiate viruses based on virulence. Using several bioinformatics approaches, including single nucleotide polymorphism (SNP) analysis and Blast analysis, primers and probes from several published tests were compared for sequence variability to the homologous regions in viruses from GenBank. From this bioinformatic analysis, selected comparisons on common variants were tested in the laboratory to evaluate how this variability affects sensitivity of the test. Because of the wide sequence variation that exists among Newcastle disease (ND) viruses, analysis of all the primers and probes show enough sequence mismatches so that some variants are likely to be missed with any of the available diagnostic tests. Understanding the limitations of each test will provide strategies that will allow detection of all important ND viruses.