Table 1.
Sample Origin and Recombination Analysis Summary of Thirteen HIV-1 Sequences Isolated in Africa
| Sample ID | Year | Country | Viral load (log copies/mL) | REGA |
jpHMM | Simplot | BLAST |
RAxML | Final | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Classification | Bootstrap strength | Classification | Identity | ||||||||
| 260-27 | 2005 | CM | 5.32 | NA | NA | A1/G/01/U | 01/G/A | NA | 90% | CRF01_AE | URF_A1/G/01 |
| 890-05 | 2006 | CM | 5.05 | NA | NA | A1/G | A1/G | CRF02_AG | 93% | CRF02_AG | CRF02_AG |
| A1188 | 2002 | CM | 4.25 | NA | NA | CRF01/A1/G | CRF01/A1/G | CRF01_AE | 92% | CRF01_AE | URF_01/A1/G |
| A1152 | 2002 | CM | 4.22 | CRF02_AG | 100 | A1/G | A1/G | CRF02_AG | 93% | CRF02_AG | CRF02_AG |
| A1549 | 2002 | CM | 4.11 | NA | NA | A1/G/F2/01 | CRF01/A1/F/G/U | URF_0222 | 89% | CRF01_AE | URF_01/02/F/U |
| CG-0422-02V | 2002 | DRC | NA | NA | NA | A1/D/01 | A1/D/01 | NA | 90% | D | URF_A1/D/01 |
| CG-0427a-02V | 2002 | DRC | NA | NA | NA | F1/G/01/U | F/G/01 | F1 | 90% | F1 | URF_F/G/01 |
| CG-0070-01 | 2001 | DRC | NA | NA | NA | F1/G/01/U | F/G/01 | F1 | 89% | F1 | URF_F/G/01 |
| CG-0077-01 | 2003 | DRC | NA | CRF27_cpx | 100 | G/H/C/J/01/A1/B | G/H/J/C/01/A1 | CRF27_cpx | 90% | CRF27_cpx | CRF27_cpx |
| U7957 | 2003 | CM | NA | CRF01_AE | 100 | CRF01_AE | CRF01_AEa | CRF01_AE | 92% | CRF01_AE | CRF01_AE |
| U8216 | 2003 | CM | NA | CRF01_AE | 100 | CRF01_AE | CRF01_AEa | CRF01_AE | 93% | CRF01_AE | CRF01_AE |
| 234-40 | 2005 | CM | 4.14 | CRF01_AE | 100 | CRF01_AE | CRF01_AEa | CRF01_AE | 92% | CRF01_AE | CRF01_AE |
| 1002-28 | 2006 | CM | 4.81 | CRF01_AE | 100 | CRF01_AE | CRF01_AEa | CRF01_AE | 92% | CRF01_AE | CRF01_AE |
a
Reference sequences for the Simplot analyses are described in Supplementary Table S2.
01, CRF01_AE; BLAST, Basic Local Alignment Search Tool; CM, Cameroon; CRF, circulating recombinant form; DRC, Democratic Republic of the Congo; jpHMM, jumping profile Hidden Markov Model; NA, not assigned; RAxML, Randomized Axelerated Maximum Likelihood; REGA, software from Rega Institute in Central Belgium; URF, unique recombinant form.