F and HN nucleotide sequences were separately aligned using MegaAlign software (DNAStar, 5.01) and analyzed for recombination using the split decomposition method in seven local statistical recombination tools (RDP4, GeneConv, BootScan/RecScan, MaxChi, Chimera, LARD) integrated in the RDP4 program version 4 (44). These tools were used to estimate any recombination event, recombination hotspot, recombination rate plots, etc., and to detect any putative recombination breakpoint. These methods were applied using the following parameters: window size = 20, highest acceptable p-value < 0.001, and Bonferroni correction. For reliable results, any four putative recombination events were detected and translated into corresponding amino acid sequences.

F and HN sequences of the isolates analyzed in this study were all retrieved from the GenBank database with indicated accession numbers including three waterfowl isolates reported by Wanyana et al. (36) with accession numbers LT549451–53. These included NDV/WF/UG/MU138/2011 representing the 22 isolates with identical sequences, NDV/WF/UG/MU150/2011 and NDV/WF/UG/MU186/2011 provided in Table 1. Others were the 27 F gene waterfowl isolates characterized for fusion cleavage sites and were not deposited in the GenBank database.

The College of Veterinary Medicine Animal Resources and Biosecurity Higher Degrees Research Committee and the Uganda National Council of Science and Technology (approval #HS 776) approved this study.

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