Figure 1.
Phylogenetic analysis of field HRVs of ARINET and SLRI based on the VP4/VP2 and the 5′ NCR sequences.
The phylogenetic trees were constructed using the Neighbor-Joining method in the program MEGA 4 and HEV-D 68 (accession no. AY426531) was designated as outgroup [35]. The distances of trees were computed using the Maximum Composite Likelihood method [42], and the units are the number of base substitutions per site. The intraspecies recombination strains of HRV-A, interspecies recombination strains of HRV-A, intraspecies recombination strains of HRV-C and interspecies recombination strains of HRV-C are labeled using white circles, black circles, white squares and black squares, respectively.
Figure 2.
Analysis of recombination events in the 5′ NCR–VP2 sequences of HRV field isolates.
The diagrams show the results of bootscan analysis in RDP. (A) KA08-3505 is a representative intraspecies recombinant of HRV-A which consists of the 5′ NCR sequence of HRV-A 78 and the VP sequence of HRV-A 12. (B) KA08-4374 is a representative interspecies recombination strain of HRV-A. The recombination event occurred between two different parent viruses: the 5′ NCR sequence of HRV-C subtype 35 and the VP sequence of HRV-A 41. (C) KL0809-374 was identified as an intraspecies recombination strain of HRV-C combining HRV-A 46 and HRV-C strain CL-170085. (D) KA08-4189 has undergone an interspecies recombination between two HRV-C viruses: the 5′ NCR sequence of HRV-C isolate LZ508 and the VP sequence of HRV-C isolate LZY101.
Figure 3.
Prediction of the recombination breakpoints.
Recombination breakpoints located in SL5 of the IRES (nt 472–554) were identified using RDP. The conserved nucleotides of each field strain are indicated by stars, and gray boxes show the recombination sites of each strain. The breakpoints were mainly scattered in a conserved region of SL5 (nt 515–554).