0A06-01. Multiplicity of infection by HIV-1 in injection drug users, men who have sex with men and heterosexuals
Bibliographic record
Abstract
We have recently shown that transmitted/founder virus(es) can be identified unambiguously using single genome amplification (SGA) (Keele, PNAS, 2008; Salazar, JEM, 2009) and that in heterosexual transmissions approximately 80% of patients are infected by a single virus or infected cell (Keele, PNAS, 2008; Haaland, PLoS Pathogens, 2009; Abrahams, JVirol, 2009). Here we explore the characteristics of virus transmission in men who have sex with men (MSM) and injection drug users (IDU). Full-length env sequences were derived by SGA from plasma vRNA from 30 acutely infected MSM and 11 IDU from North America. Modes of infection were determined by self-report. Uncloned amplicons were sequenced, aligned, and analyzed by neighbor-joining phylogenies and the Highlighter tool. Maximum within-patient diversity ranged from 0.08–7.12%. In the MSM group, 19 of 30 (63%) acutely infected subjects had evidence of a single transmitted/founder (t/f) virus and 11 of the 30 had evidence of transmission by a minimum of 2–10 viruses. In the IDU group, 4 of the 11(36%) had evidence of a single t/f virus, while the remaining 7 demonstrated transmission by a minimum of 3–19 variants. In the subjects with multiple transmissions, the median number of t/f variants was 3 for MSM and 5 for IDU. Differences in single versus multiple virus transmissions among HSX, MSM and IDU were statistically significant (p < 0.006). The HIV-1 transmission event is different in HSX, MSM and IDU. We see single variant transmission in approximately 80% of HSX, 60% of MSM and 40% of IDU. When multiple transmissions occur, they tend to have a higher number of variants in IDU than in MSM or HSX. These findings indicate that risk of HIV-1 acquisition correlates with numbers of transmitted viruses. This, along with the phenotypic properties of these viruses (especially Env), may be important in vaccine design and assessment.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.070 | 0.008 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".