Characterization of full genome sequences of chicken anemia viruses circulating in Egypt reveals distinct genetic diversity and evidence of recombination

• Published in: Virus research Vol. 251; pp. 78 - 85
• Main Authors: Erfan, Ahmed M., Selim, Abdullah A., Naguib, Mahmoud M.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 02-06-2018
• Subjects: Amino Acid Substitution; Animals; Chicken anemia virus; Chicken anemia virus - classification; Chicken anemia virus - genetics; Chicken anemia virus - isolation & purification; Chickens; Circoviridae Infections - epidemiology; Circoviridae Infections - mortality; Circoviridae Infections - veterinary; Circoviridae Infections - virology; Egypt; Egypt - epidemiology; Evolution, Molecular; Full genome; Genetic Variation; Genome, Viral; Genotype; Phylogeography; Poultry Diseases - epidemiology; Poultry Diseases - mortality; Poultry Diseases - virology; Poultry production; Recombination event; Recombination, Genetic; Sequence Analysis, DNA; Chicken anemia virus; Full genome; Egypt; Poultry production; Recombination event
• ISSN: 0168-1702; 1872-7492; 1872-7492
• DOI: 10.1016/j.virusres.2018.05.008

•Detection and full genomic characterization of chicken anemia virus (CAV) circulating in Egypt.•Segregation of the Egyptian CAVs into four phylogroups was detected.•Evidence of recombination among the viral genome of CAV in Egypt.
Chicken anemia virus (CAV) is one of the commercially important diseases of poultry worldwide. In Egypt, CAV has been reported to be a potential threat to the commercial poultry sectors. Hence, this study was aimed at isolation and full genomic analysis of CAVs circulating in chicken populations in different geographical location in Egypt. A total of 42 samples were collected from broiler chicken flocks in 9 governorates in Egypt from 12 to 42 days of age. The mortality rate observed among chickens was ranging from 3% to 22%. Nineteen out of 42 farms were found positive for the CAV genome by polymerase chain reaction (PCR).
Full genome sequencing was conducted for 18 positive samples. Genetic analysis revealed a high similarity of >99% in 11 viruses with the vaccine strain Del-Ros; while the other seven samples shared close similarity to CAV field strains isolated from China, Taiwan, and Brazil. The data also indicated Q139 and Q144 amino acids substitutions among the VP1 of Egyptian field strains, which are known to be important in virus replication and spread. Phylogenetic analysis of the sequenced viruses (n = 18) based on either the full gene nucleotide sequence or VP1 coding sequence, suggested the circulation of four distinct genotypes in Egypt designated as group A, B, C and D. Moreover, evidence of recombination was detected among four Egyptian CAVs located within group A. The findings of this study succeeded to elucidate the epidemiological and genetic features of CAVs circulating in Egypt, and underscores the important of CAVs surveillance.