Table 4. Blast results of VP4/VP2 and 5′ NCR regions.
| Samples | VP4/VP2 Blast Results | 5′NCR Blast Results | Classification of recombination |
|---|---|---|---|
| Nearest strain (% a) | Nearest strain (%) | ||
| KA08-3505 | HRV-A 78 (92) | HRV-A 12 (98) | Intraspecies recombination of HRV-A |
| KA08-4418 | HRV-A 56 (92) | HRV-C 26 (99)b | |
| KA09-446 | HRV-A 85 (91) | HRV-A 78 (96) | |
| KA09-560 | HRV-A 12 (94) | HRV-A 9 (97) | |
| KA09-822 | HRV-A 45 (92) | HRV-A 21 (97) | |
| KA08-3539 | HRV-A 43 (91) | HRV-C isolate LZ508 (95) | Interspecies recombination of HRV-A |
| KA08-4374 | HRV-A isolate LZY172(98), HRV-A 41 (88)c | HRV-C isolate Resp_4817/07 (99), HRV-C subtype 35 (93)c | |
| KA09-864 | HRV-A strain HRV-A21_p1177_sR3307_2010 (96) | HRV-C isolate Resp_5153/07 (99), HRV-C strain HRV-C36_p1093_sR548_2008 (83)c | |
| KA08-4189 | HRV-C isolate LZY101 (99) b | HRV-C isolate LZ508 (95) | Intraspecies recombination of HRV-C |
| KA09-101 | HRV-C 26 (98)b | HRV-C isolate N10 (99) | |
| KA09-756 | HRV-C isolate LZ269 (97) b | HRV-C isolate Resp_4817/07 (99), HRV-C subtype 35 (93)c | |
| KA09-893 | HRV-C strain CL-170085 (96) b | HRV-C isolate Resp_5789/07 (97), HRV-C strain HRV-C36_p1093_sR548_2008 (84)c | |
| KA08-4010 | HRV-C PHL TTa425s (98), HRV-C isolate N46 (96)b,c | HRV-C strain HRV-C43_p1154_sR1124_2009 (98)b | Interspecies recombination of HRV-C |
| KA08-4631 | HRV-C isolate Resp_4122(98)HRV-C isolate N10 (96)c | HRV-C 26 (99)b | |
| KA09-218 | HRV-C isolate LZY79 (99) b | HRV-C 26 (99)b | |
| KA09-495 | HRV-C isolate N36 (93)b | HRV-A 40 (98) | |
| KA09-806 | HRV-C strain CU136(98), HRV-C sub-type 35 (82)c | HRV-A 53 (99) | |
| KA09-917 | HRV-C strain NY-074 (98) b | HRV-A 53 (96) | |
| KL0809-374 | HRV-C strain Ca09-0309-U (98), HRV-C strain CL-170085 (94) b,c | HRV-A 46 (98) |
The amplified sequences of VP4/VP2 and 5′NCR were identified by megablast program. 11 strains of HRV-C recombination events were identified compared to 8 strains of HRV-A recombination events. Interestingly, the recombinant viruses were mainly found in ARINET samples (94.7%: 18 of 19 strains).
a Identity
b
These reference strains clustered with HRV-A in the 5′NCR phylogenetic tree in this study and previous report [10,25].
c The parent genomes, that contained 5′NCR and VP4/VP2 region, of low identity for confirming recombination events