Molecular Characterization of Infectious Laryngotracheitis Virus Circulating in Egypt during 2023

Since its discovery in Egypt in 1983, the infectious laryngotracheitis virus (ILTV) has continued to spread, leading to substantial losses for poultry farms. This study aimed to identify and molecularly characterize the ILTV currently in circulation in Egypt in 2023. Fifteen pooled trachea and lung samples were collected from affected vaccinated and non-vaccinated layer farms (Shiver, Lohhman, Brown layer, and Aviagel) aged from 10-30 weeks old spread throughout eight governorates in Egypt. A real-time polymerase chain reaction (PCR) is used to detect ILTV. Ten positive samples representing various governorates were chosen for partial sequencing of the ICP4 gene, and four positive samples were chosen for sequencing of the TK, gD, and gG genes. Using phylogenetic analysis, the ICP4 clusters into chicken embryo origin vaccine and vaccine-like strains (CEO) and tissue culture origin vaccine and vaccine-like strains (TCO) and wild type. The GAHV-1-Egy-WO5-2023, GAHV-1-Egy-WO7-2023, and GAHV-1-Egy-WO8-2023 strains cluster in the CEO group with the CEO vaccine and vaccine-like strains with 98.9%–100% amino acid identity (A.A.); However, the remaining strains (GAHV-1-Egy-WO1-2023, GAHV-1-Egy-WO2-2023, GAHV-1-Egy-WO3-2023, GAHV-1-Egy-WO4-2023, GAHV-1-Egy-WO6-2023, GAHV-1-Egy-WO9-2023, and GAHV-1-Egy-WO10-2023) were clustered in the TCO group with TCO vaccine strains and vaccine-like strains with 100 % A.A. By analysis of gD, gG, and Tk genes, there is no difference between the TCO and CEO groups. Compared with several reference CEO and TCO vaccine strains and vaccine-like strains, some new specific mutations (Q161H and Q182H) were recorded in the ICP4 in GAHV-1- Egy-WO8-2023. In addition, A34G, and P276L were recorded in the gD gene in the GAHV-1-Egy-WO1-2023 and GAHV-1-WO4-2023. Also, the R115I, G126A, and S163I were recorded in the TK gene in GAHV-1-Egy-WO8-2023 and A99E in GAHV-1-Egy-WO5-2023, which can affect the virulence and pathogenicity of the virus, which may be due to the reactivation of the vaccine strain by the bird-to-bird transmission or viral recombination. In conclusion, the ILTV outbreaks in poultry farms across several regions of Egypt during 2023 were induced by vaccine strains derived from TCO and CEO. Thus employing innovative vector vaccines and reassessing the current vaccination regimens is necessary.