Table 1.
Distribution of isolates based on neighbor-joining phylogenetic analysis
| Genome subtype | No. | Protease |
RT |
Description of recombination in protease or RT | ||
|---|---|---|---|---|---|---|
| Subtype | No. | Subtype | No. | |||
| A | 10 | A | 10 | A | 10 | — |
| B | 29 | B | 29 | B | 29 | — |
| C | 15 | C | 15 | C | 15 | — |
| D | 6 | D | 6 | D | 6 | — |
| F | 6 | F | 6 | F | 6 | — |
| G | 4 | G | 4 | G | 4 | — |
| H | 3 | H | 3 | H | 3 | — |
| J | 2 | J | 2 | J | 2 | — |
| K | 2 | K | 2 | K | 2 | — |
| CRF01_AE | 11 | A | 11 | A | 11 | No evidence of recombination in protease or RT. |
| CRF02_AG | 6 | G | 6 | G | 6 | For all 6 isolates, protease is closest to subtype G. First 300 codons of RT are closest to subtype G but contain small mosaic region closer to subtype A; rest of RT is closest to subtype A [23]. |
| CRF03_AB | 2 | A | 2 | B | 2 | For both isolates, protease and about first 50 codons of RT are closest to subtype A; rest of RT is closest to subtype B [24]. |
| CRF05_DF | 2 | D | 2 | F | 2 | For both isolates, protease is closest to subtype D; RT is closest to subtype F [25]. |
| BF | 1 | B | 1 | B | 1 | No evidence of recombination in protease or RT. |
| AC | 3 | A C A |
1 1 1 |
A C C |
1 1 1 |
One isolate is closest to subtype A in both protease and RT (AC_SE9488; GenBank accession no. AF071474), 1 to subtype C in both protease and RT (AC_21301; GenBank AF067156), and 1 isolate (AC_RW009; GenBank U88823) is closest to subtype A in protease and in first 100 codons of RT but is closest to subtype C in rest of RT [26]. |
| AD | 1 | D | 1 | D | 1 | No evidence of recombination in protease or RT. |
NOTE. Subtype of complete genome of isolates is based on previously published analyses, compared with subtype indicated by clustering within protease and reverse-transcriptase (RT) neighbor-joining trees, respectively. Rows with recombinant isolates, on the basis of complete genome analysis, also contain short comment. CRF04_cpx and CRF06_cpx were omitted because of complexity.