Molecular Detection and Characterization of Newcastle Disease Virus from Chickens in Mid-Rift Valley and Central Part of Ethiopia

Background: Newcastle disease (ND) is a highly infectious poultry disease that causes major economic losses worldwide. The disease is caused by Newcastle Disease Virus (NDV) and early detection and identification of the viral strain is essential. Having knowledge of the NDV strain genotype that circulates in some regions would help in designing an effective vaccine to control the disease. In this regard, there is little information on NDV strain in chickens in mid Rift Valley and the central part of Ethiopia. Therefore, the purpose of this study was to detect and characterize NDV strain genotype from chickens in mid-Rift Valley and the central part of Ethiopia and test whether this NDV strain genotype matches the vaccine strain currently used in the study area. Methods: A total of 98 samples: 78 (tracheal and cloacal) swabs from chicken pools of five and 20 tissue samples were collected. To detect NDV strain, conserved region of the virus Matrix (M) gene was amplified by qRT-PCR. To characterize NDV strain genotypes, M-gene positive samples were specifically re-amplified by conventional PCR targeting the Fusion (F) gene region and sequenced by Sanger method. Results: 13.26% of tested samples were positive for NDV strain in the study area with statistically significant difference (P< 0.05) among the study sites. Further characterization of the F genes from NDV strain isolates by phylogenetic analysis indicated that one field isolate clustered with genotype VII whereas three of the isolates clustered to genotype I, II, and III. The isolate of the current NDV strain vaccine in use in the study area clustered with genotype II. Conclusion: The current study indicates the existence of different NDV strain genotype from that of the vaccine strain currently used. Even though large-scale characterization of several isolates is required at national level, the current study laid baseline information for the existence of variations between field NDV strain genotype and vaccine strain currently used against ND in the country. Keywords: APMV-1 strain genotype, F gene, mid rift valley, phylogenetic tree, qRT-PCR