Title : Molecular detection and characterization of Avian Paramyxovirus type-1 strain genetic lineages from chickens in mid-Rift Valley and central part of Ethiopia
Abstract:
Newcastle disease (ND) is a highly infectious chicken disease that causes major economic losses worldwide. A study was conducted from February 2020 to October 2020 to detect and characterize Avian Paramyxovirus type-1 (APMV-1) strain genetic lineages from chickens in mid-Rift Valley and central parts of Ethiopia. For this purpose, a total of 98 samples: 78 (tracheal and cloacal) swabs from chicken pools of five and 20 tissue samples were collected. To detect APMV-1 strain, conserved region of the virus Matrix (M) gene was amplified by qRT-PCR. To characterize APMV-1 strain genetic lineages, M-gene positive samples were specifically re-amplified by conventional PCR targeting the Fusion (F) gene and sequenced by Sanger method. Accordingly, 13.26% of tested samples were positive for APMV-1 strain in the study area with statistically significant difference (P<0.05) among the study sites. Further characterization of the F genes from APMV-1 strain isolates by phylogenic analysis indicated that one field isolate clustered with lineage 5 (genotype VIIg) whereas three of the isolates clustered to the genotype of lineages 1, 2, and 3 (genotype I, II, and III). The isolate of the current APMV-1 strain vaccine in use in the study area clustered with lineage 2 (genotype II) strains. The current study indicates the existence of different lineage of APMV-1 strain from the vaccine strain currently in use. 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 APMV-1 strain lineages and vaccine strain lineages currently in-use against ND in the country.
Keywords: APMV-1 strain lineages, F gene, Mid Rift Valley, Phylogenetic tree, qRT-PCR
