| Literature DB >> 19864468 |
Marcos Pérez-Losada1, David V Jobes, Faruk Sinangil, Keith A Crandall, David Posada, Phillip W Berman.
Abstract
In 2003, a phase III placebo-controlled trial (VAX004) of a candidate HIV-1 vaccine (AIDSVAX B/B) was completed in 5,403 volunteers at high risk for HIV-1 infection from North America and the Netherlands. A total of 368 individuals became infected with HIV-1 during the trial. The envelope glycoprotein gene (gp120) from the HIV-1 subtype B viruses infecting 349 patients was sequenced from clinical samples taken as close as possible to the time of diagnosis, rendering a final data set of 1,047 sequences (1,032 from North America and 15 from the Netherlands). Here, we used these data in combination with other sequences available in public databases to assess HIV-1 variation as a function of vaccination treatment, geographic region, race, risk behavior, and viral load. Viral samples did not show any phylogenetic structure for any of these factors, but individuals with different viral loads showed significant differences (P = 0.009) in genetic diversity. The estimated time of emergence of HIV-1 subtype B was 1966-1970. Despite the fact that the number of AIDS cases has decreased in North America since the early 90s, HIV-1 genetic diversity seems to have remained almost constant over time. This study represents one of the largest molecular epidemiologic surveys of viruses responsible for new HIV-1 infections in North America and could help the selection of epidemiologically representative vaccine antigens to include in the next generation of candidate HIV-1 vaccines.Entities:
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Year: 2009 PMID: 19864468 PMCID: PMC2806245 DOI: 10.1093/molbev/msp254
Source DB: PubMed Journal: Mol Biol Evol ISSN: 0737-4038 Impact factor: 16.240
Mean intrapatient genetic diversity (θ), population recombination rate (ρ), and selection (ω) estimates.
| HIV-1 subtype B | |||
| Treatment | |||
| Placebo (122) | 0.0046 | 5.53 | 1.06 |
| Vaccine (228) | 0.0042 | 4.55 | 0.90 |
| Race | |||
| Asian (5) | 0.0030 | 5.2 | 0.72 |
| Black (12) | 0.0052 | 2.15 | 1.45 |
| Hispanic (22) | 0.0046 | 3.61 | 0.73 |
| Other (15) | 0.0041 | 2.57 | 1.20 |
| White (291) | 0.0043 | 5.22 | 0.95 |
| North American region | |||
| Midwest (44) | 0.0039 | 6.26 | 1.06 |
| Northeast (82) | 0.0038 | 4.90 | 0.85 |
| South (63) | 0.0049 | 3.91 | 0.89 |
| Southwest (66) | 0.0046 | 4.97 | 1.11 |
| West Coast (90) | 0.0044 | 4.85 | 0.93 |
| Risk | |||
| Low (43) | 0.0045 | 8.54 | 0.99 |
| Medium (267) | 0.0044 | 4.23 | 0.98 |
| High (58) | 0.0038 | 5.60 | 0.90 |
| Viral load categories (virions/ml) | |||
| 1: | 0.0034 | 2.81 | 0.86 |
| 2: 0.1 | 0.0031 | 6.82 | 0.81 |
| 3: 0.5 | 0.0038 | 5.40 | 0.94 |
| 4: 1 | 0.0046 | 4.31 | 0.82 |
| 5: 5 | 0.0040 | 4.71 | 0.90 |
| 6: 10 | 0.0054 | 4.05 | 1.06 |
| 7: 50 | 0.0043 | 4.27 | 1.43 |
| 8: | 0.0048 | 4.28 | 0.85 |
NOTE.—Individuals analyzed are indicated between parentheses.
Selection estimates were taken from Pérez-Losada et al. (2009).
FCharacterization of gp120 sequence data set with respect to viral load and estimated time after infection. Line indicates the mean viral load as a function of time. Plasma used for viral load testing was collected as soon as possible following diagnostic tests confirming HIV-1 infection. The date of infection was defined as the midpoint between the last seronegative specimen and the first seropositive specimen.
FMaximum likelihood phylogenetic inference of North American HIV-1 subtype B population structure based on the VAX004NA data set. Branch lengths are shown proportional to the amount of change along the branches. Clades supported by bootstrap proportions ≥70% or posterior probabilities ≥0.95 in the Bayesian tree are shown in bold. Only one clone per patient is represented for simplicity.
FBayesian skyline plots of the past population dynamics of HIV-1 subtype B in North America. Solid lines show the median estimate and dashed lines the 95% highest posterior density limits. Number of AIDS cases (×1000) since 1980–2006 are indicated in red.