Mol Biol Evol 2007 Vol 24:

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

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

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

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.

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)

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.

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).

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.

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.

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.

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.

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

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.

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

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.