The combination of phylogenetic analysis with epidemiological and serological data to track HIV-1 transmission in a sexual transmission case

Abstract

Objective: To investigate the linkage of HIV transmission from a man to a woman through unprotected sexual contact without disclosing his HIV-positive status.

Methods: Combined with epidemiological information and serological tests, phylogenetic analysis was used to test the a priori hypothesis of HIV transmission from the man to the woman. Control subjects, infected with HIV through heterosexual intercourse, from the same location were also sampled. Phylogenetic analyses were performed using the consensus gag, pol and env sequences obtained from blood samples of the man, the woman and the local control subjects. The env quasispecies of the man, the woman, and two controls were also obtained using single genome amplification and sequencing (SGA/S) to explore the paraphyletic relationship by phylogenetic analysis.

Results: Epidemiological information and serological tests indicated that the man was infected with HIV-1 earlier than the woman. Phylogenetic analyses of the consensus sequences showed a monophyletic cluster for the man and woman in all three genomic regions. Furthermore, gag sequences of the man and woman shared a unique recombination pattern from subtype B and C, which was different from those of CRF07_BC or CRF08_BC observed in the local samples. These indicated that the viral sequences from the two subjects display a high level of similarity. Further, viral quasispecies from the man exhibited a paraphyletic relationship with those from the woman in the Bayesian and maximum-likelihood (ML) phylogenetic trees of the env region, which supported the transmission direction from the man to the woman.

Conclusions: In the context of epidemiological and serological evidence, the results of phylogenetic analyses support the transmission from the man to the woman.

Fig 1. Neighbor-joining phylogenetic tree of consensus sequences from the man, the woman and local controls.

A, Neighbor-joining phylogenetic tree for consensus gag sequences and reference sequences. The scale bar indicates 5% nucleotide sequence divergence. B, Neighbor-joining phylogenetic tree for consensus pol sequences and relative reference sequences. The scale bar indicates 5% nucleotide sequence divergence. C, Neighbor-joining phylogenetic tree for consensus env sequences and relative reference sequences. The scale bar indicates 10% nucleotide sequence divergence. Values on the branches represent the percentage of 1000 bootstrap replicates and bootstrap values over 70% are shown in the tree. Red triangle: the sequence from the male source; Green triangle: the sequences from the female recipient.

Fig 2. Bootscanning analysis of possible intertype mosaicism.

Window: 80 bp, step: 10 bp, GapStrip: on, reps: 100, Kinura (2-parameter), T/t: 2.0. The reference sequences are shown at the bottom right of the figure.

Fig 3. Maximum clade credibility (MCC) tree for env quasispecies from the subjects.

The MCC trees were obtained by Bayesian MCMC analysis based on partial env gene (HXB2: 7002–7541) implemented in BEAST. The uncorrelated exponential relaxed molecular clock method was used in combination with the Bayesian Skyline coalescent tree prior under GTR+I+G4 nucleotide substitution model. Red taxon: the viral quasispecies from the man; Green taxon: the viral quasispecies from the woman. The posterior probabilities of the key nodes are indicated. The most recent common ancestor of sequences from the man is shown by a filled circle. The scale bar indicates 5% nucleotide sequence divergence.