Going Nowhere Fast: Lentivirus genetic sequence evolution does not correlate with phenotypic evolution.

Transcription

1 Going Nowhere Fast: Lentivirus genetic sequence evolution does not correlate with phenotypic evolution. Brian T. Foley, PhD HIV Genetic Sequences, Immunology, Drug Resistance and Vaccine Trials Databases

2 Structure of Lentiviruses

3 Primate Lentiviruses P. t. troglodytes x P. t. schweinfurthii 10% Van Heuverswyn, Nature 2006 Keele, Science 2006 Gao, Nature 1999 Santiago, Science 2002 Corbet, J. Virol 2000 Brian Foley, HIV databases

4 Phylogeny built from the Complete Genome Sequences of Primate Lentiviruses (Primate Immunodeficiency Viruses) ~70 years in humans vs. Millions?? of years of evolution? in simians

5 Repesentatives of all known retroviruses Primate, Bovine Leukemia Pol gene, RT, RNAse, Integrase Baboon endogenous, Mouse, Cat Leukemia Walleye Snake Lentiviruses Primate, Equine, Bovine and Feline Foamy Retroviruses Primate Lentiviruses

6

7 Dating the most recent common ancestor of the HIV pandemic 1931 ( ) Korber et al., Science 2000

8 Validation using the 1959 sequence (also the beginning of the Thai epidemic in the mid 1980 s)

9 Pattern of Influenza Evolution differs from that of HIV-1 C Ancestral

10 Evolution of FIV-Leo in free-ranging African lions is similar to patterns of evolution of HIV-1, with distinct clades and geographical correlations.

11 Evolution of FIV-puma in free-ranging Rocky Mountain cougars is similar to patterns of evolution of HIV-1, with distinct clades and geographical correlations. African Lion/Tiger and housecat FIV outgroups are not extremely distant. Pol gene, partial.

12 SIV-AGM envelope displays phylogenetic distances similar to HIV-1 M group. Millions of years vs. ~90 years of evolution?

13 Evolution of genes is complex, site-specific, and sometimes lineage-specific. LTR Gag Pol Vpu, Vpr Tat, Rev Env LTR Nef Simplot (Stuart Ray s Similarity Plot Program) of a HIV-1 subtype C/D recombinant genome vs B, C, D and E

14 Distribution of Rates of Evolution in HIV-1 M group Viruses: Most sites are in the slowly evolving rate categories

15 Distribution of Rates of Evolution in HIV-1 M group Viruses: A few sites evolve extremely rapidly

16 Sum of Rates in 20-base windows across HIV-1 genome: Env has two notable hypervariable sites Gag Pol Env Nef

17 HIV-1 M Group DNA and protein sequences exhibit invariant and hypervariable sites and regions

18 HIV-1 M Group DNA and protein sequences exhibit invariant and hypervariable sites and regions

19 HIV-1 Protease Enzyme With Bound Substrate Colored by Conservation from most conserved to most variable amino acid side chains, backbone in grey cartoon mode. Amino acid side chain atoms are colored from most conserved to most variable. Protein backbone is illustrated in cartoon mode. Phylogeny (History, shape of the phylogenetic tree) is an important factor in assessing diversity. Amino acid sitespecific rate of evolution can be calculated from a multiple sequence alignment plus a phylogenetic tree. The ConSurf Tool ( ) is one tool for exploring site-specific rates. DNA-Rates by Gary Olsen is another useful program.

20 Halpern and Bruno CodonSat and RIND Mol Biol Evol Jul;15(7): Attempting to determine which Phylogenetic Distances (calculated with DNADIST or PROTDIST, for example) are indicative of complete saturation of silent or mutable sites. FIG. 1. Comparison of pairwise distance estimates with correct distances for simulated data set described in text. In each figure, the x-axis gives the path length between pairs of sequences through the tree used in simulating the data set. The y-axis gives the pairwise distance estimate for each method. A, Pairwise distances were estimated using the maximum-likelihood model of DNADIST (Felsenstein 1993) with parameter settings corresponding to the mutational param eters used to simulate the sequences (frequencies of A, C, G, T 5 0.3, 0.2, 0.2, 0.3, respectively; transition/transversion ratio 2.0, corresponding to setting the T option of the program to ), with rates at all sites equal. B, Distances were estimated under the same model as in A, but allowing site-to-site rate variation. Positions were assigned to one of 9 rate categories by DNArates (Olsen et al. 1994), using an initial topology estimated with DNADIST (as above) and NEIGHBOR. Pairwise distances between sequences were estimated using these rate assignments using fastdnaml (Olsen et al. 1994). C, Distances were estimated with the model described here, using the same parameter values as were used to simulate the sequences. D, Distances were estimated with the model described here, with parameters estimated from the simulated data set using RIND counts (Bruno 1996), adding 0.65 pseudocounts to each category. In all cases, the line indicates the best linear fit through the origin for points with input distance #1.5.A

21 Lentivirus Pol Gene, Protease-RT-RNAseH- Integrase

22 Halpern fig 1B

23 Global Distribution of HIV-1

24

25 HIV-1 Sequences from Democratic Republic of Congo Epicenter of the HIV-1 M group epidemic.

26

27 HIV-1 M group came from MB and/or LB tribes HIV-1 N group originated in EK tribe

28

29

30 ??

31 PFAM Geminivirus Tree AL1 Rep protein PFAM ID Gemini_AL1 Maize Streak Viruses Panicum Streak Kenya Without human-readable labels, trees and other figures can be impossible to interpret. Databases most often do not supply good labels, even if the authors of the entries provided accurate taxonomy. Authors often supply incorrect taxonomy.

32 Structure of Lentiviruses

33 CTL Epitope Generation

34 C-terminal positions of epitopes bind to class I F pocket- Rare C-terminal aa tend to be small, polar or negatively charged CC-terminal

35 Can we identify lineage differences in specific antibody epitopes? gp160 ML tree, 2F5 epitope: Identify critical residues: -- Paul Parren Draw epitope relative to tree Colors indicate side-chain chemistry C subtype lineages most distinctive

36 Potential binding of 2F5 antibody to subtype C Core epitope: DKWA 72 references for 2F5 studies in the HIV Antibody database Lysine substitutions abrogate binding of 2F5 monoclonal antibody Evidence of convergent evolution indicates parallel selection pressure(s).

37 An Excel Spreadsheet is useful for annotations of the HIV-1 Genome and Proteome Gag protein Protein functional Site Web links and other information Gag- Pol fusion protein

38 Hypervariable (high immune system selection pressure?) can be mapped onto the 3D structure of the HIV-1 proteins Hypervariable alpha helix between V3 and V4 loops V3 loop In this view, sites which are more or less variable in subtype C than in subtype B viruses are highlighted.

39 ENV gp120 CdN/dS > 4 BdN/dS > 4 B,C dn/ds>4 CD4 17B monoclonal ENV without loops model from PDB entry 1G9M. Kwong et al. Structure 8 pp (2000)

40 The HIV Immunology Database does not note any Antibody binding to the hypervariable alpha helix. Alpha helix V3 Loop

41 V3 Loop Alpha helix The HIV Immunology Database notes many Helper T-cell epitopes in this region