Genetic diversity of: uncovering novel genotypes in Iranian poultry farms.

Abstract

The circulating serotypes/genotypes of avian infectious coryza (AIC) in Iran have not been fully characterized, and disease control in layer and breeder flocks largely relies on imported vaccines. Given the correlation between genotypes and serotypes based on the previously proposed genotyping method, this study aimed to determine the genotypes of 28 Iranianisolates collected over a 7-year period (2018-2025), using sequences of region 1 and the hypervariable region (HVR) of thegene. PCR amplification of both regions was performed, and the resulting sequences were analysed alongside reference strains retrieved from GenBank. Two datasets were generated: one based on region 1 (aligned with the Page serotyping scheme) and the other based on concatenated sequences (corresponding to the Kume scheme). Phylogenetic analysis identified five previously known genotypes (I, II, VI, VIII, and IX), corresponding to serovars A-1, A-2, C-4, C-3, and an undetermined Kume serovar, in 24 isolates. Notably, two isolates (AP-20 and AP-28) formed distinct, well-supported phylogenetic clusters and were designated as novel genotypes XV and XVI, respectively. TheHVR could not be amplified in two additional isolates (AP-17 and AP-18); however, analysis of their region 1 sequences indicated a close relationship to United States non-pathogenic strains. These findings suggest that the currently proposed genotyping scheme may be inadequate for classifying non-pathogenic strains. The circulation of multiple genotypes in Iran underscores the need for continued surveillance and re-evaluation of currently used vaccines, as effective control of AIC requires serotype-specific bacterins in vaccination programmes.