Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: Identification of a candidate etiologic agent

Kistler, Amy L; Gancz, Ady; Clubb, Susan; Skewes-Cox, Peter; Fischer, Kael; Sorber, Katherine; Chiu, Charles Y; Lublin, Avishai; Mechani, Sara; Farnoushi, Yigal; Greninger, Alexander; Wen, Christopher C; Karlene, Scott B; Ganem, Don; DeRisi, Joseph L

As our initial PCR results suggested, the bornavirus genome sequence we recovered is quite diverged from all known BDV genomes, including the BDV isolate No/98, a divergent isolate sharing only 81% sequence identity with all other BDV genomes [20] . Overall, this newly recovered bornavirus genome sequence shares only 64% sequence identity at the nucleotide level to each of the complete BDV genomes. Scanning pairwise sequence identity analysis indicates this genetic divergence exists across the entire genome ( Figure 2A , Sequence identity shared with BDV genomes track). Given this divergence, we re-examined the depth and distribution of the 322,790 reads from this specimen that passed the host filter to determine if we had missed reads derived from the recovered ABV in our initial screen against all BDV sequences. Not surprisingly, this retrospective BLAST analysis revealed an additional 2600 reads from across the recovered bornavirus genome that were missed in the initial BLAST analyses due to the lack of sequence conservation between the ABV sequence and the available BDV sequences (Figure 2A , Solexa reads track). In total, approximately 1% of all the high throughput shotgun reads could be mapped to the recovered bornavirus genome.