What Do Clusters of Similar HIV Genetic Sequences Tell Us About HIV Risks in Africa?

Abstract

Better knowledge about how HIV transmits in sub-Saharan Africa can guide more effective HIV prevention efforts. Studies that look for similarities among HIV sequences can provide insights into patterns of HIV transmission.
This review found seven studies that sampled HIV from communities in Africa, systematically identified at least some sexual partners, sequenced HIV, and looked for similarities pointing to transmission links. Across these seven studies, 0-19% (median 9.3%) of sequences were similar to (clustered with) sequences from known sexual partners. Because the HIV source for the first person infected in a sex-linked cluster is unknown, these studies provide a sexual explanation for 0-10% (median 4.6%) of HIV infections. More sequences were in clusters with no known sexual link.
Although most sex partners are in or close to home, genetic diversity showed much less geographic structure in the three studies that looked at the issue.
Evidence from these studies does not support the common view that sex accounts for most HIV infections in Africa. Studies did not do what they could to elucidate risks: no study traced and tested sexual partners not already in the sample or reported blood-borne risks.

Keywords: HIV, Africa, sequencing, phylogenetic analysis, sexual transmission, blood-borne transmission