Significance of plasma and peripheral blood mononuclear cell derived HIV-1 sequences in establishing epidemiologic linkage between two individuals multiply exposed to HIV-1

Establishing epidemiologic linkage in individuals multiply exposed to HIV can be a difficult task. To date, only peripheral blood mononuclear cell (PBMC)-derived sequences have been used in studying HIV-1 transmission between individuals. So far, the combined utility of plasma and PBMC-derived HIV-1 sequences has not been assessed in establishing epidemiologic linkage in people involved in transmission of HIV. In this study, both PBMC (DNA) and plasma (RNA) derived viral quasispecies was used in establishing epidemiologic linkage between two infected individuals (B-90 and B-69) multiply exposed to HIV-1 via injecting drug use. A detailed sequence, and phylogenetic analyses of HIV-1V3 region quasispecies derived from these two compartments clearly demonstrated compartmentalization of viral quasispecies between PBMC and plasma. More importantly, these data also demonstrate that in order to establish epidemiologic linkage between individuals multiply exposed to HIV-1, analyses of viral strains from both plasma and PBMC compartments may be necessary. The PBMC compartment alone may not provide sufficient information on epidemiologic linkage, overall diversification of viral quasispecies, replacement of older strains and the emergence of new viral recombinant strains in vivo. These are the first analyses that demonstrate the incremental value of plasma derived sequences, when used in conjunction with PBMC-derived sequences, in establishing the epidemiologic linkage between individuals multiply exposed to HIV parenterally. Further, the plasma derived HIV-1 sequences may prove to be invaluable in predicting a recent transmission between two epidemiologically-linked individuals.