Article Figures & Data
Figures
- FIG. 1.
Real-time HIV-1 transmission history as identified by contact tracing. The open arrows denote the transmission events; the width of the arrows represents the time interval for transmission. The arrow representing the transmission event between patient A and patient B is dashed because the time and direction of transmission could not be determined. The patient's bars filled with gray indicate an HIV-1-infected status with (superimposed) the therapy history. The therapy history is either monotherapy (Mono), bitherapy (Bi), or HAART. †, patient is deceased. The bent black arrows indicate available samples, including date of isolation.
- FIG. 2.
Maximum likelihood phylogenetic reconstruction for the HIV-1 transmission chain patients and unrelated controls based on the pol gene region. The sequences sampled from the transmission chain patients are represented in bold. Subtype C sequences retrieved from a local database are labeled “LC.” The tree is rooted at its midpoint. The upper numbers at the nodes indicate the percentage of neighbor-joining bootstrap samples, based on 1,000 replicates, in which the node is supported (only values of >80% are shown). The lower numbers at the nodes represent approximate posterior probabilities obtained from a posterior sample of trees (only values of >80% are shown).
- FIG. 3.
Phylogenetic trees inferred for the pol and env gp41 gene regions. Maximum likelihood and Bayesian methods resulted in the same topology for each gene region. Both trees are represented on the same scale and rooted at the position that does not distinguish between patient A and patient B as the original donor for this transmission chain. The most likely host transmission scheme is superimposed onto the viral evolutionary history: hosts are separated arbitrarily along the branch between donor and recipient. For isolates C99pop, D99pop, and I99pop320, not enough sample was left to perform env gp41 sequencing. The upper numbers at the nodes indicate the percentage of bootstrap samples, based on 1,000 replicates, in which the node is supported. The lower numbers at the nodes represent approximate posterior probabilities obtained from a posterior sample of trees. The arrow in gray indicates the branch swapping that would make the pol phylogeny topologically congruent with the known transmission history. The branch set tested to be under positive selective pressure is indicated in gray in the env gp41 tree; the branch tested to have a higher nucleotide substitution rate is indicated with the horizontal bracket.
- FIG. 4.
Phylogenetic trees reconstructed using synonymous (dS) and nonsynonymous (dN) distances for pol. Both trees are represented as rooted at the position that does not distinguish between patient A and patient B as the original donor for this transmission chain. The most likely host transmission scheme is superimposed onto the viral evolutionary history. The arrow in gray indicates the branch swapping that would make the dN phylogeny topologically congruent with the known transmission history.
Tables
- TABLE 1.
P values for the tree incongruence tests
Dataa P value for treeb: pol env gp41 KH SH KH SH pol Best ML tree Best ML tree 0.324 0.166 env gp41 <0.001 <0.001 Best ML tree Best ML tree polenv 0.033 0.024 Best ML tree Best ML tree pol-RT 0.822 0.388 Best ML tree Best ML tree ↵ a polenv represents the concatenated pol and env gp41 alignment, and pol-RT represents the pol alignment after exclusion of the positions associated with drug resistance in the RT.
↵ b The results for the Kishino-Hasegawa (KH) and Shimodaira-Hasegawa (SH) tests are listed for the Hasegawa-Kishino-Yano model of evolution with gamma-distributed rate heterogeneity among sites; the tests for other models of evolution are consistent with these results (data not shown).
- TABLE 2.
Drug resistance-associated mutations
Patient and sample Pro mutation(s)a RT mutation(s) A A96pop M36L M41L, D67DN, K70KR, L210LW, T215Y A00pop L101, L33F, M41L, E44D, D67N, V118X, M184V, M36L, G48V G190AG, L210W, T215HY, K219N, 154A, V82A F227FL B B90pop M36L B96 M36L M41L, E44DE, V118IV, L2190W, T215Y C C94pop M36L C99pop M36L C02pop M36L D D99pop M36L D01pop M36L D02pop M36L E E01pop M36L V75IV F F02pop K20M, M36L G G02pop K20M, M36L H H98pop M36L M184V I I99pop320 M36L V118X, M184V, T215Y I99pop506 M36L M184V, T215Y ↵ a Drug resistance-associated mutations in protease (Pro) and RT were identified according to the criteria of the International AIDS Society—USA (14). Protease mutations in bold represent major mutations. The ubiquitous M36L mutation has been shown to confer cross-resistance to atazanavir in combination with other known protease inhibitor resistance mutations, although it has not been selected for by atazanavir either in vitro or in vivo (3). However, no patient in this transmission chain has been treated with this drug. Also the K20M mutation is only important in combination with other protease inhibitor resistance mutations and should here be considered as natural polymorphism.
- TABLE 3.
Parameter estimates for the codon substitution models applied to the pol data
Model pa Log Ld Estimates of parametersb Positively selected sitesc M0 (1 ratio) 1 −2,137.255821 ω̂ = 0.3918 None Branch specific (2 ratios) 2 −2,129.700900 ω̂0 = 0.2495, ω̂1 = 1.6230 NA Site-specific M1, neutral (K = 2) 1 −2,118.947877 p̂ 0 = 0.68985 (p̂1 = 0.31015) Not allowed M2, selection (K = 3) 3 −2,107.074525 p̂ 0 = 0.67099, p̂1 = 0.32597 (p̂2 = 0.00304), ω̂2 = 52.92262 RT, 215 (P > 99) M3, discrete (K = 2) 3 −2,112.026513 p̂ 0 = 0.93249, (p̂1 = 0.06751) ω0 = 0.17437, ω̂1 = 4.26134 Pro, 12, 54, 72 (at 0.5 < P < 0.95), 37 (at P > 99) RT, 41, 174, 177, 245 (at 0.5 < P < 0.95), 36, 135, 184, 210, 211, 215 (at P > 99) M3, discrete (K = 3) 5 −2,104.838467 p̂ 0 = 0.89797, p̂1 = 0.09907, (p̂2 = 0.00297) PRO, 10, 12, 16, 18, 38, 72, 82, (at 0.5 < P < 0.95), 37, 54, (at P > 95) ω̂0 = 0.14630, ω̂1 = 2.75117, ω̂2 = 60.67074 RT, 41, 174, 177, 204 (at 0.5 < P < 0.95), 210, 211, 215T*, 245, 36, 135, 184 (at P > 95) M7, beta 2 −2,118.943419 p̂ = 0.04111, q̂ = 0.11138 Not allowed M8, beta & ω 4 −2,112.028167 p̂ 0 = 0.93293, p̂ = 21.08181, q̂ = 99.00000 (p̂1 = 0.06707), ω̂ = 4.27569 Same as M3 (K = 2) Branch site A 3 −2,113.535572 p̂ 0 = 0.64620, p̂1 = 0.18545, (p̂2 + p̂3 = 0.16835) ω2 = 4.73987 Sites for foreground: PRO, 10, 13, 33, 37, 38, 41, 48, 62, 82, 89 (at 0.5 < P < 0.95), 54 (at P > 95) RT, 20, 44, 48, 67, 201, 208, 215, 219, 223 (at 0.5 < P < 0.95) B 5 −2,108.351559 p̂ 0 = 0.77144, p̂1 = 0.04723 (p̂2 + p̂3 = 0.18132) Sites for background: Pro, 12, 37 (at 0.5 < P < 0.95) RT, 36, 41, 135, 174, 177, 184, 204, 210, 211, 215, 245 at (0.5 < P < 0.95) ω̂0 = 0.10933, ω̂1 = 4.34176, ω̂2 = 2.91030 Sites for foreground: Pro, 10, 13, 33, 38, 41, 48, 54, 62, 72, 82, 89 (at 0.5 < P < 0.95) RT, 20, 44, 48, 67, 201, 208, 219, 223 (at 0.5 < P < 0.95) ↵ a p is the number of free parameters for the ω ratios.
↵ b Parameters indicating positive selection are presented in bold type. Those in parentheses are presented for clarity only but are not free parameters.
↵ c An asterisk indicates the site belonging to the class with p̂2 and ω̂2 in model M3 (K = 3). Underlined sites refer to positions associated with drug resistance. NA, not applicable.
↵ d Log L, log likelihood.
- TABLE 4.
Molecular clock results
Model Data pa Log Lc Evolutionary rate (nucleotide substitutions/site/yr) Different rates pol 30 −2,148.63 NAb env gp41 28 −2,294.18 Single rate pol 19 −2,186.81 NA env gp41 18 −2,320.77 Single rate dated tips pol 20 −2,172.89 1.21E-03 env gp41 19 −2,308.45 2.11E-03 Local clock dated tips pol 21 −2,162.15 Background, 0.973E-03 Foreground, 6.16E-03 env gp41 20 −2,308.36 Background, 2.06E-03 Foreground, 2.45E-03
Supplemental material
Files in this Data Supplement:
- Supplemental file 1 -
Fig. S1. Deduced amino acid alignment of the pol sequences obtained from the known transmission chain.
Fig. S2. Phylogenetic tree reconstructed based on a 591-bp region in the RT gene.
PDF document, 285K.
- Supplemental file 1 -
Fig. S1. Deduced amino acid alignment of the pol sequences obtained from the known transmission chain.
