Single phylogenetic reconstruction method is insufficient to clarify relationships between patient isolates in HIV-1 transmission case

Factors influencing HIV-1 phylogenetic clustering

PURPOSE OF REVIEW

A major goal of public health in relation to HIV/AIDS is to prevent new transmissions in communities. Phylogenetic techniques have improved our understanding of the structure and dynamics of HIV transmissions. However, there is still no consensus about phylogenetic methodology, sampling coverage, gene target and/or minimum fragment size.

RECENT FINDINGS

Several studies use a combined methodology, which includes both a genetic or patristic distance cut-off and a branching support threshold to identify phylogenetic clusters. However, the choice about these thresholds remains an inherently subjective process, which affects the results of these studies. There is still a lack of consensus about the genomic region and the size of fragments that should be used, although there seems to be emerging a consensus that using longer segments, allied with the use of a realistic model of evolution and a codon alignment, increases the likelihood of inferring true transmission clusters. The pol gene is still the most used genomic region, but recent studies have suggested that whole genomes and/or sequences from nef and gp41 are also good targets for cluster reconstruction.

SUMMARY

The development and application of standard methodologies for phylogenetic clustering analysis will advance our understanding of factors associated with HIV transmission. This will lead to the design of more precise public health interventions.

Molecular epidemiology of HIV-1 infection in a small Brazilian county: usefulness of envelope and polymerase sequences to epidemiologic studies

OBJECTIVE

The AIDS epidemic in Brazil is spreading from the large urban centers to small counties and the innermost parts of the country; however, data on the features of HIV-1 infection in these places are scarce. To study the routes of HIV-1 spread and assess the existence of transmission networks in such a setting, we performed a genetic analysis of viral sequences from the small county of Miracema, Rio de Janeiro State.

METHODS

HIV-1 envelope and polymerase sequences recovered from 63 adult patients (from a cohort of 78 patients) were phylogenetically analyzed.

RESULTS

A polyphyletic pattern ensued. Six clusters of sequences sharing close genetic relatedness were also recovered from 29 (46%) patients. Envelope and polymerase phylogenies yielded essentially the same results.

CONCLUSIONS

The polyphyletic pattern suggests multiple viral introductions in the region. Intracluster cases, including those with no known direct epidemiologic link, probably took part in the same chain of viral transmission. Such a pattern suggests the existence of sexual networks and the emergence of multiple new infections within a relatively short period, a potential molecular marker of high incidence.