Complete Genome Sequencing of an Embryonated Chicken Egg-Adapted Duck atadenovirus A.

Egg drop syndrome (EDS) is prevalent in industrial poultry globally. This disease is caused by Duck atadenovirus A or EDS virus (EDSV), a member of the genus Atadenovirus under the family Adenoviridae. The disease is attributed to significant economic losses in the poultry industry worldwide due to a drop in egg production, reduction in egg quality, and failure to reach maximum egg production. Oil-adjuvant inactivated vaccines, which are widely used in the poultry industry, provide good protection for immunized chickens against EDS. This study aimed to genetically and phylogenetically analyze the full-length genome of an embryonated chicken egg-adapted EDSV strain 127. After extraction of viral DNA from the allantoic fluid, overlapping fragments of the viral genome sequence were generated by polymerase chain reaction (PCR) using 25 pairs of primers. Purified PCR products were subjected to complete genome sequencing by the next-generation sequencing (NGS) approach. The nucleotide homology observed between genomes of the studied strain and that of the original strain 127 (NC_001813) of laying chickens was 99.9%. Its genome was 33,213 bp in length, with a G + C content of 43.01%. A comparison of the genome sequence of the egg-adapted virus with strain 127 revealed only three non-synonymous single-nucleotide polymorphisms (SNPs) between these viral genome sequences. Two mutations of S320G and I62K out of these SNPs were found within the coding regions of fiber and hypothetical proteins which may play a role in the adaptation of EDSV in the embryonated chicken eggs. The full genome sequencing of EDSV using NGS techniques provides insights into the discovery of genetic variants. Moreover, the genome sequence information of the EDSV provides valuable data for vaccine development in near future.

Characterization and full genome sequencing of a velogenic Newcastle disease virus (NDV) strain Ck/IR/Beh/2011 belonging to subgenotype VII(L).

Avian avulavirus 1, better known as Newcastle disease virus (NDV), causes substantial loss to the poultry industry in many developing countries. In this study we have characterized and fully sequenced the genome of a velogenic NDV strain named Beh (Ck/IR/Beh/2011) that has been used in our lab for a number of challenge and immunological studies over the last few years. This strain was isolated from poultry in the city of Behshahr, Mazandaran Province, Iran after an outbreak reported in the region in 2011. The intracerebral pathogenicity index (ICPI) was 1.8 in one-day-old chicks, characteristic of a velogenic NDV strain. Later, the virus was purified using a sucrose gradient centrifugation and used for next-generation sequencing (NGS). The results showed that the genome length was 15192 bp, similar to those of class II velogenic strains. In addition, the phylogenetic analysis based on the complete F gene showed that the NDV strain Beh has an F protein cleavage site 112RRQKR↓ F117 and belongs to the newly identified subgenotype VII(L). Based on the biological and genetic characterization, NDV strain Beh is now the best documented reference isolate representing the novel subgenotype VII(L) in Iran. Keywords: NDV; NGS; velogenic strain, subgenotype VII(L); phylogenetic analysis.