HIV-1 Genetic Diversity in Antenatal Cohort, Canada
Bibliographic record
Abstract
We studied HIV genetic diversity in a cohort of 127 pregnant, HIV-infected women who received prenatal care at Sainte-Justine Hospital in Montreal, Canada, between 1999 and 2003.Clade assignments were derived by phylogenetic analysis of amplified pol sequences.Genotyping was successful in 103 of 127 women, 59 (57.3%) of whom were infected with clade B HIV-1, and 44 (42.7%) with nonclade B viruses, including subtypes A, C, D, F, G, and H. Four sequences remained unassigned.Forty-three of 44 women infected with non-clade B viruses were newcomers from sub-Saharan Africa, and subtype identity was consistent with those circulating in their countries of origin.These results highlight the epidemiologic importance of non-B HIV-1 in antenatal populations in a large North American urban center, underscore the influence of population movements on clade intermixing, and identify a group of patients who could be targeted for surveillance and drug therapy followup. H IV-1 exhibits considerable genetic diversity resultingfrom the high mutation rate of reverse transcriptase, high viral turnover, viral genomic recombination, and immune and therapeutic selection pressures (1-3).This diversity is a challenge for viral load determination, drug resistance testing, and AIDS vaccine development (1,4-6).Three phylogenetic groups of HIV-1, main (M), outlier (O), non-M, non-O (N), are recognized (2,7).Most HIV-1 infections are caused by group M viruses that comprise 9 clades (A-D, F-H, J, and K) and >13 intersubtype recombinants known as circulating recombinant forms (CRFs) (8).Clade B is most common in North America, Europe, and Australia.However, in the last decade, prevalence of infection with nonclade B viruses has increased in France, Belgium, Spain, and Switzerland (9-12), in large part after migration from or international travel into HIV-endemic areas (13).Nonclade B viruses also circulate in Cuba ( 14) and the United States (15,16).We measured HIV-1 subtype diversity in a multiethnic cohort of pregnant, HIV-infected women to determine whether nonclade B HIV-1 is emerging in Canada after population movement, and whether antenatal cohorts are suitable sentinel sites to monitor the introduction of nonclade B viruses into Canada. Patients and Methods PatientsOne hundred twenty-seven HIV-infected women receiving prenatal care at Centre Maternel et Infantile sur le SIDA, Sainte-Justine Hospital, Montreal, from October 1999 to September 2003 were included in the study.Inclusion criteria were 1) age ≥18 years, 2) a request for prenatal care, 3) positive HIV-1 serologic results, and 4) informed consent.Standardized clinical followup, including antiretroviral (ARV) prophylaxis and treatment, was provided to all women and their children.This cohort study was conducted according to the guidelines of the Ethics Review Board of Sainte-Justine Hospital.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
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".