Genetic and phylogenetic characterization
Sequences of the F2-fragment, including the proteolytic cleavage site were used for initial phylogenic characterization (358 nt). BLAST tools indicated highest homology for isolate AR2178/2014, with Egyptian Avian avulavirus-1/168-2012 (Genbank accession: MN381174) with nt and aa identities of 99% and 99%, respectively, clustering in phylogenetic analysis with genotype 2.VII.1.1 viruses (supplementary Fig 1.). In contrast, virulent NDV clones from 2011 (R1954/2011-cl 6; R1973/2011-cl 4) showed highest identities to EG-14/90 (Genbank accession: DQ096604) and chicken/Nigeria/2006 (Genbank accession: MH092825) respectively The lentogenic clone R1954/2011-cl 1 matched 100 % with vaccine strain LaSota (Genbank accession: AF077761), while R1973/2011-cl 2 matched with vaccine strain Hitchner B1 (Genbank accession: JN872151). When sequence collection of the genotyping group (Dimitrov et al. 2019) were used to create a first phylogenetic analysis (S1), viruses grouped to genotype 2.VII.1.1 (AR2178/2014), 2.XXI (R1954/2011-cl 6; R1973/2011-cl 4) and 2.II (R1954/2011-cl 1; R1973/2011-cl 2). While genotype 2.VII.1.1 viruses are circulating in Egypt from 2012 up to 2019 (Fig. S1), no further sequences for NDV genotype 2.XXI have been reported for chickens after 2011. However subsequent viruses from genotype 2.XXI belong to sub-genotype 2. XXI.1.1 and are derived from pigeons.