BACKGROUND:Avian avulavirus-1 (AAvV-1, previously Newcastle Disease Virus) is responsible for poultry and wild birds' disease outbreaks. Numerous whole genome sequencing methods were reported for this virus. These methods included cloning, specific primers amplification, shotgun PCR approaches, Sequence Independent Single Primer Amplification and next generation sequencing platform kits.METHODS:Three methods were used to sequence 173 Israeli Avian avulavirus-1 field isolates and one vaccine strain (VH). The sequencing was performed on Proton and Ion Torrent Personal Genome Machine and to a lesser extent, Illumina MiSeq and NextSeq sequencers. Target specific primers (SP) and Sequence Independent Single Primer Amplification (SISPA) products sequenced via the Ion torrent sequencer had a high error rate and truncated genomes. All the next generation sequencing platform sequencing kits generated high sequence accuracy and near-complete genomic size.RESULTS:A high level of mutations was observed in the intergenic regions between the avian avulavirus-1 genes. Within genes, multiple regions are more mutated than the Fusion region currently used for typing.CONCLUSIONS:Our findings suggest that the whole genome sequencing by the Ion torrent sequencing kit is sufficient. However, when higher fidelity is desired, the Illumina NextSeq and Proton torrent sequencing kits were found to be preferable.

•Three class II genotype VII sub-genotypes from different origin were present in parallel in Israel between 2007 and 2016.•Israeli class II genotype VI Isolates form a new sub-genotype.•Diverse infection distance was observed. The various VII sub-genotypes were isolated from all poultry sectors and regions.•The mean clock rate for sub-genotypes VIIb, VIId and VIIi was 2.72 x 10-3, 2.61 x 10-3 and 2.15 x 10-3 respectively.

Due to the ongoing need to protect poultry from virulent Newcastle disease virus, all commercial poultry flocks in Israel are vaccinated according to a defined programme using a combination of live and inactivated vaccines. The vaccination protocol for broilers during the years of the study comprised a live vaccine administered by spray on the day of hatching, inactivated vaccine by subcutaneous injection at 10-12 days of age, and another live vaccine given by aerosol at 17-21 days of age. A cross-sectional study was designed in order to examine the influence of herd immunity on the risk of Newcastle disease outbreak in broiler flocks. The study was based on the extensive field data kept in the Poultry Health Laboratories database. The results of serology tests employing haemagglutination inhibition for Newcastle disease virus were analysed and crossed with the list of flocks that had been diagnosed with ND in the years 2007-2014. At the peak of induced immunization (fifth week of growth), 87.5% of the tested flocks had achieved herd immunity (85% of birds in the flock with an HI titre 4). Based on a logistic regression model, the odds ratio for ND in flocks without herd immunity was 3.7 (95% CI 1.8-7.3, P-value<0.001). The higher the percentage of birds with low HI titres the higher the risk of ND outbreak. Under field conditions, herd immunity is an important indicator for the risk of ND outbreak.

Our aim was to characterize the A/ck/Israeli/1055/2008 (H5N1) avian influenza virus that was isolated at the beginning of 2008, and to establish the phylogenetic relationship of this isolate to other H5N1 viruses that were recently isolated in adjacent countries. In light of a study of complete nucleotide sequences of all the genes we found that the isolate (year 2008) was closely related to the H5N1 viruses isolated in Egypt, Israel and Gaza in 2006. The Israeli isolate had the hemagglutinin-connecting peptide with a polybasic amino acid insertion. The most host-restriction sites of the 2008 isolate were typical of avian hosts, with one exception: K627 at the PB2 protein. As compared with previous local H5N1 isolates, a high mutation rate was found at the HA gene, which antigenic sites were under positive selection pressure.

During March 2006, an outbreak of highly pathogenic avian influenza (H5N1) occurred in multiple poultry farms in Israel. The epidemiologic investigation and review of outbreak mitigation efforts uncovered gaps in planning for and containing the outbreak, thus affording valuable lessons applicable to other countries in similar settings.