1. Mol Biol Evol 2007 Vol 24:1853-1860

2. Which adaptations to human characterize the transfer from SIVcpz to HIV-1?

3. Method 1.Reconstruct ancestral amino acid sequences of HIV-1 M, N, and O subtypes. 2.Analyze 19 sequences: 12 SIVcpzPtt 4 SIVcpzPts 3 HIV-1 ancestral sequences Pts = P. t. schweinfurthii

4. 3.Search for sites which are relatively conserved in SIVcpz -> the same character in at least 9 of the 12 SIVcpzPtt. Among these sites, search for those in which the AA in HIV-1 is the same for all HIV-1 ancestors but differ from the consensus character of SIVcpzPtt Method A L T L L T T L L L L L L L

5. Specificity determinants Sites that are found are called “specificity determinants” as it is expected that these sites are responsible for adaptation of the SIVcpzPtt to it (new) human host.

6. Results 7 sites were found. For example, Ser in position 46 of Nef is found in the ancestor of all 3 HIV-1 subtypes. But in 11 of the 12 genomes analyzed, Arg is found in SIVcpzPtt. However, for this site, still some of the amino acids (Ser) are common to HIV-1 and SIVcpzPtt (in bold)

7. HIV-1 vs. SIVcpzPtt vs. SIVcpzPts For 6 sites, there are shared AA between all 3 groups. Only site Gag-30 is clearly different among these groups.

8. Position 30 of Gag is a specificity determinant M and L are chemically similar (Grantham distance = 15). M and R are not similar (Grantham distance = 91).

9. Gag 30 in SIVgor The most parsimonious reconstruction for the character state at the root is M. Three independent M->R replacements. L M R R R M M M M SIVgor also codes for M in position 30.

10. HIV-1 after passage in chimps for > 10 years There are two clones of HIV-1 viruses that were introduced to chimps for vaccine based research. It was later found that chimps are not a viable animal model for HIV-1. Yet, these viruses “evolved” to fit chimps.

11. HIV-1 after passage in chimps for > 10 years For Gag-30, when HIV-1 were reintroduced to chimps for 10 years – the AA reverted to Met. Note that it was reverted from Lys rather than from Arg, since the virus used to infect the chimps was known.

12. HIV-1 after passage in chimps for > 10 years For Gag-224, when HIV-1 were reintroduced to chimps for 10 years – the AA reverted to Ala. However, Ala is very common in type M subtype B and hence this may not reflect a real adaptation to chimpanzee hosts.

13. Mutagenesis experiments (Gag-30) For the 2 clones that were introduced to chimps, the M was reverted to L and the replication of the virus in CD4+ lymphocytes was measured, both in human and in chimp cells. RED = LYS MET = BLUE

14. Gag 30 among HIV-1 subtypes In all subtypes there is either L or R. Only in subtype C there is M – as in chimps. Subtype C is not considered basal, and the meaning of the reversion to M in subtype C is unknown.

15. Gag 30 in HIV-2 Some code for M, some for R. In SIVsm M is found.

16. Gag-30 – cellular function Gag-30 is part of the N-terminal of the gag- encoded matrix protein p17. p17 is critical for Gag precursor targeting to the plasma membrane during assembly. PI(4,5)P 2, TIP47, and AP-3 are cellular components known to bind Gag. Gag-30 is not currently known to be part of the binding sites of these components.