The fifth virus identified by all RDP3 methods, DQ485230, was a genotype VII isolate that contained a small region within the HN gene contributed by genotype III. In addition, a region spanning 1479 to 3751 in P and M appeared to be derived from a different genotype VII virus. Inter-genotype recombination was also detected by fewer than five of the RDP3 methods in DQ486859(GM/China), DQ485231(Guangxi11/China/2003) and AF309418(Fowl/B1/USA/1947). Genotype VII isolate DQ659677(NA-1/China) contained a 640 bp region within L contributed from genotype VI. The origin of the putative recombinant fragment spanning the M and F genes of EF065682(rAnhinga/USA) could not be determined. These data provide compelling evidence that genotypes II and VII are most commonly associated with recombinant viruses and that both intra-and intergenic recombination events can be detected using full genome sequence analysis.