Genome sequencing and characterization of an avian orthoavulavirus 1 VG/GA-like isolate with a unique fusion cleavage site motif

Authors: KARIITHI, HENRY - Orise Fellow; Suarez, David; DAVIS, JAMES - Georgia Poultry Laboratory Network; DUFOUR-ZAVALA, LOUISE - (NCE, CECR)networks Of Centres Of Exellence Of Canada, Centres Of Excellence For Commercilization A; Olivier, Timothy; Williams Coplin, Tina; Bakre, Abhijeet; Lee, Chang

Submitted to: Avian Diseases
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2022
Publication Date: 3/7/2023
Citation: Kariithi, H.M., Suarez, D.L., Davis, J.F., Dufour-Zavala, L., Olivier, T.L., Williams Coplin, T.D., Bakre, A.A., Lee, C.W. 2023. Genome sequencing and characterization of an avian orthoavulavirus 1 VG/GA-like isolate with a unique fusion cleavage site motif. Avian Diseases. 67(1):33-41. https://doi.org/10.1637/aviandiseases-D-22-00064.
DOI: https://doi.org/10.1637/aviandiseases-D-22-00064

Interpretive Summary: Newcastle disease is one of the most important infectious diseases of poultry because of its potential for devastating loses. Not all avian orthoavulavirus-1 (AOAV-1) cause Newcastle disease but the virus has ability to change their genetic makeup and become more virulent while adapting to new hosts and environments. In this study, we identified a low virulent AOAV-1 isolate with a unique amino acid signature that is found in virulent viruses. Although our animal study confirmed that the virus is low virulent, it is important to monitor if viruses with similar genetic makeup is circulating in poultry and any additional changes are occurring toward more virulent form. It is also important to note that the new virus was detected by official diagnostic test that specifically detect virulent AOAV-1. Thus, in addition to concern for potential pathogenic shift of the virus through additional change, our finding warrants the reevaluation of current diagnostic test for virulent AOAV-1 detection.

Technical Abstract: A complete genome sequence of a VG/GA -like strain of avian orthoavulavirus 1 (AOAV-1) was identified by nontargeted next-generation sequencing of an oropharyngeal swab sample collected from a carcass of a 12-mo-old backyard chicken. The isolate has a fusion (F) protein cleavage site motif consistent with a low virulent AOAV-1, but it has a unique motif with phenylalanine at position 117 (112G-R-Q-G-R'F117), which is typical for virulent AOAV-1 strains. The one nucleotide difference at the cleavage site compared to other low-virulence viruses made the isolate detectable by F-gene–specific real-time reverse transcription-PCR (rRT-PCR) developed as a diagnostic test to specifically detect virulent strains. The mean death time determined in eggs and intracerebral pathogenicity index determined in chickens classified the isolate as lentogenic. This is the first report of a lentogenic VG/GA-like virus with a phenylalanine residue at position 117 of the F protein cleavage site in the United States. In addition to concern for potential pathogenic shift of the virus through additional changes at the cleavage site, our finding warrants increased awareness of diagnosticians of potential false positive F-gene rRT-PCR tests.