Evolution of HIV-1 V3 envelope sequences from residual lymph node RNA from patients on potent antiretroviral therapy with undetectable plasma viraemia for up to 2 years
ABSTRACT: Background: HIV RNA persists at low levels in lymph nodes (LN) from patients on potent antiretroviral therapy with undetectable plasma viraemia (<50 copies/mL) for up to 2 years. It is not known whether such residual RNA represents continuous replenishment by chronically infected cells or whether it represents trapped virus from the time of initiation of therapy. We studied evolution of V3 env sequences derived from residual LN RNA from patients with different levels of viral suppression.
Methods: LN biopsies from six patients from the San Diego Cohort of the Merck 035 study were obtained at year 1 (n=3) and at year 2 (n=6) after initiation of therapy. Evolution of V3 sequences was examined by comparing pairwise distances between baseline plasma and year 1 and 2 LN sequences. Seven to 18 clones obtained from RT and quadruplicate nested PCR from plasma and LN RNA extracts were bi-directionally sequenced by 'Big Dye' didieoxynucleotide terminator cycle sequencing. HIV RNA quantification from plasma [including calculation of the area-under-the-curve (AUC) from the plot of RNA concentration over time] and LN and DNA quantification from LN were performed and correlated with pairwise evolutionary distances.
Results: From the patient with the fastest RNA decay and subsequent undetectable plasma viraemia (<50 copies/mL) no evolution between baseline plasma RNA and LN sequences from year 1 and 2 was detectable. In patients with slower RNA decay and/or intermittent low level plasma viraemia, significant evolution of the V3 loop in lymphatic tissue was seen. AUC of plasma RNA and concentration of HIV RNA in LN tissue were positively correlated with V3 evolution.
Conclusions: In a subset of patients with rapid initial RNA decay and undetectable plasma viraemia for up to 2 years, no evolution of the V3 env region was detectable in sequential RNA extracts from lymphatic tissue suggesting that such residual RNA represents trapped virus rather than the product of ongoing replications. However, in patients with slower RNA decay and intermittent low level plasma viraemia, viral evolution in the LN can be detected and correlates with the magnitude of viral replication
