Limitations to Contact Tracing And Phylogenetic Analysis in Establishing HIV Type 1 Transmission Networks in Cuba

Abstract

Sequence analysis can be used to evaluate transmission networks. We have used retrospective samples to examine two HIV-1 transmission networks established by contact tracing. Regions of the HIV-1 region representing segments of gag and env were amplified by RT-PCR from frozen plasma samples and the sequence of each PCR product was determined. Within one of the networks (composed of 38 subjects) we found only a subset of the tested sequence clusters was consistent with the reported epidemiological linkage. Of 15 presumed transmission events where sequence data were available, 9 could be rejected either by subtype mismatch or by phylogenetic tests. In the other network (composed of 89 subjects) we were able to assess sequences for 26 presumed transmission events, 18 of which were rejected based on subtype discordance. Long lags in time between the time of transmission and the time of sequence sampling (ranging from 2 to 18 years) may limit the sensitivity for the detection of sequence linkage. Also, superinfection and incomplete epidemiological information are other factors that will limit the concordance of phylogenetic reconstruction and reported epidemiological linkage.

The HIV Epidemic: High-Income Countries

“…In addition, for the first time it has become possible to investigate the dynamics of the epidemic based on such data. Although many studies of sexual behavior have shown that individuals can vary greatly in their number of sexual partners over time and this concept has underpinned many epidemiological models of HIV transmission, however, contact tracing has been shown to be poor at recovering the HIV transmission network relative to other infections (Yirrell et al 1998;Resik et al 2007). The development of the field of molecular phylodynamics, used first to estimate dates of the origin of the zoonotic transmission of HIV, provided new routes to obtain such parameter estimates, which can be applied to small-scale intensive studies of specific outbreaks, as well as to obtain global estimates relating to long-term spread.…”

HIV Type 1 Transmission Networks Among Men Having Sex with Men and Heterosexuals in Kenya

“…2,3,5,[11][12][13][14][15][16][17][18][19][20][21][22][23] To investigate MSM HIV-1 transmission networks and the level of mixing with the general population we performed a molecular phylogenetic study with HIV-1 pol sequences. Sequences were selected from a cohort study among MSM and female sex workers (FSW) in coastal Kenya and MSM sex workers in Nairobi, and from female and male patients who participated in antiretroviral drug resistance monitoring studies in hospital-based clinics in the same geographic areas.…”

Modelling the Effects of Mass Drug Administration on the Molecular Epidemiology of Schistosomes

“…HIV transmission in a dental practise (Ou et al, 1992) as well as theoretical pathogen models using evolutionary trees resulting from different evolutionary processes (Nee et al, 1994). In microparasites with rapid in-host evolution sensitivity of phylogenetic based networks may be reduced (Resik et al, 2007). Similar lack of contact tracing exists for indirectly transmitted pathogens such as STHs and schistosomes and microparasite models incorporating similar genomic data may be developed for more complex indirect transmission networks (Gupta et al, 1996) and may be highly dependent on host immunological factors (Anderson et al, 1989).…”