Ethical issues associated with HIV phylogenetics in HIV transmission dynamics research: A review of the literature using the Emanuel Framework (original) (raw)
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Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052
Clinical Infectious Diseases, 2020
Background Phylogenetic analysis can be used to assess HIV transmission in populations. We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction. Methods Complete next generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 trial (up to two samples/person). Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion. The bioinformatics method, phyloscanner, was used to infer transmission direction. Analyses were performed using samples from individual sample pairs, samples from all couples (one sample/person; group analysis) and all available samples (multi-sample group analysis). Analysis was also performed using NGS data from defined regions of the HIV genome (gag, pol, env). Results Using whole-genome NGS data,...
Assessment of phylogenetic sensitivity for reconstructing HIV-1 epidemiological relationships
Virus research, 2012
Phylogenetic analysis has been extensively used as a tool for the reconstruction of epidemiological relations for research or for forensic purposes. It was our objective to assess the sensitivity of different phylogenetic methods and various phylogenetic programs to reconstruct epidemiological links among HIV-1 infected patients that is the probability to reveal a true transmission relationship. Multiple datasets (90) were prepared consisting of HIV-1 sequences in protease (PR) and partial reverse transcriptase (RT) sampled from patients with documented epidemiological relationship (target population), and from unrelated individuals (control population) belonging to the same HIV-1 subtype as the target population. Each dataset varied regarding the number, the geographic origin and the transmission risk groups of the sequences among the control population. Phylogenetic trees were inferred by neighbor-joining (NJ), maximum likelihood heuristics (hML) and Bayesian methods. All clusters of sequences belonging to the target population were correctly reconstructed by NJ and Bayesian methods receiving high bootstrap and posterior probability (PP) support, respectively. On the other hand, TreePuzzle failed to reconstruct or provide significant support for several clusters; high puzzling step support was associated with the inclusion of control sequences from the same geographic area as the target population. In contrary, all clusters were correctly reconstructed by hML as implemented in PhyML 3.0 receiving high bootstrap support. We report that under the conditions of our study, hML using PhyML, NJ and Bayesian methods were the most sensitive for the reconstruction of epidemiological links mostly from sexually infected individuals.
Genetic and phylogenetic analyses of HIV1 corroborate the transmission link hypothesis
Journal of Clinical Virology, 2004
Background: Phylogenetic and genetic analyses have proven a valuable tool to infer epidemiological links between human immunodeficiency virus type-1 (HIV-1) isolates. These methods were applied in the present report for studying the genetic relatedness of the viral strains involved in two episodes of suspected HIV-1 transmission. Objectives: Provide any evidence that may help establish or refute the transmission link. Study design: In the first case, a leukemic patient became HIV-1 positive following the transfusion of platelets from a donor who was subsequently found to have tested false HIV-seronegative and to be sexual partner to an infected woman. In the second, a wife claimed to have acquired the infection from her husband who had concealed his infected status. Results and conclusions: The viral pairs detected in each of the suspected transmission cases exhibited common amino acid signatures and low genetic distances and segregated together in phylogenetic trees, thus showing a level of genetic relatedness similar to reference pairs known with certainty to be epidemiologically linked. These findings corroborated the existence of a direct transmission link in both the episodes with a high level of confidence.
Phylogenetic Analysis of HIV-1 Using Dataset of gag gene Sequences
"Objective: Insecure mating between individuals who are both infected with HIV-1 can direct the exposure to their partner's virus and potentially to superinfection. Epidemiological studies of virus help out to scrutinize the genetic divergence, worldwide spread of HIV, and its paths of infection. The infected individuals with HIV-1 hold a vigorously evolving population of closely related genomes. Phylogenetic and genetic analyses have verified a valuable tool to conclude epidemiological links between HIV-1 isolates. Present study was conducted to investigate the epidemiological profiling and molecular diversity of HIV-1 on the bases of gag gene sequences. Methods: Maximum Parsimony, Maximum Likelihood methods were used for the phylogenetic analysis of gag gene sequences. Results: The clades (A,B,C) revealed possible viral spread through phylogenetic approach. HIV-1 gag gene sequence variations among the different strains isolated from different locations resulted in the spread of virus by means of physical carriers. Conclusion: Nucleotide sequences based phylogenetic studies of viral genomes may disclose the mode of spreading and time span as viral genomes keep on changing themselves and their evolutionary rate is the key to calculate the time window of such dispersal."
Phylogenetic analysis -the study of the genetic relatedness between HIV strains -has recently been used in criminal prosecutions as evidence of responsibility for HIV transmission. In these trials, the expert opinion of virologists has been of critical importance.