Olani, A. | bioRxiv Science

bioRxiv2022

A Very virulent infectious bursal disease virus closely related to New York strain isolated from vaccinated small-scale broiler poultry farm in Addis Ababa, Ethiopia

Infectious bursal disease virus (IBDV) was initially identified in the USA. The first IBD case in Ethiopia was reported in 2002 and since then vaccination was employed to control the disease. However, IBD outbreaks continued to occur despite the routine vaccination. The present study investigated IBD outbreak that had occurred in a vaccinated small-scale broiler poultry farm. Eight samples (four Bursa and four spleen) were collected and all were confirmed to be IBDV positive using reverse transcription-polymerase chain reaction (RT-PCR) targeting the hypervariable region of virus protein 2 (hVP2). All the IBDV isolates of this study were identified to be very virulent IBDV (vvIBDV) strains. For the four IBDV isolates the nucleotide and deduced amino acid sequence for hVP2 was determined. The nucleotide sequence identity of the VP2 gene of the present outbreak isolates (which showed 100% homology among themselves) with the previous 19 vvIBDV characterized isolates from Ethiopia ranged from 90.8% to 96.9% but greater than 96% identity was recorded with only six isolates. The deduced amino acid (aa) sequence of the present outbreak isolates contained aa residues commonly found in vvIBDV strains: A222, I242, I256, I294 and S299 suggesting the strains belong to genogroup three (G3). The phylogenetic analysis of the isolates showed that all isolates clustered separately from classical virulent, vaccine and variant strains and also distantly related to UK661 (UK) and DV86 (Netherlands) very virulent strains but unexpectedly closely related to the New York, USA strain. In conclusion, the present study reported vvIBDV strains (G3) isolated from a vaccinated broiler flock. Further research is needed to characterize the molecular epidemiology and pathogenicity of the vvIBDV strains and evaluate protective efficacy of the current IBD vaccine used for routine vaccination.

microbiology↗

bioRxiv2020

Population structure and transmission of Mycobacterium bovis in Ethiopia

Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis (M. bovis), which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole genome sequencing (WGS) to examine the population structure of M. bovis in Ethiopia. A total of 134 M. bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis, based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.

genomics↗