Increased mutations in Env and Pol suggest greater HIV-1 replication in sputum-derived viruses compared with blood-derived viruses

Abstract

Objective: Low-level HIV-1 replication may occur during antiretroviral therapy (ART) that suppresses plasma HIV-1 RNA to less than 50 copies/ml (suppressive ART). Antiretroviral drugs appear less effective in macrophages and monocytes compared with lymphocytes, both in vitro and as implied in vivo by greater viral evolution observed during suppressive ART. Our objective was to examine sputum, which is rich in macrophages, for evidence of increased HIV-1 replication compared with that in the blood during suppressive ART.

Design: A cross-sectional study during suppressive ART was performed, and HIV-1 DNA sequences derived from induced sputa and peripheral blood mononuclear cells were compared.

Methods: Multiple sequences encoding HIV-1 reverse transcriptase, protease, and envelope were generated using single-genome sequencing. Reverse transcriptase and protease sequences were analyzed for genotypic drug resistance. The evolutionary distances of env sequences from the inferred most recent common ancestor of infection were calculated, and CXCR4 usage was predicted.

Results: Nine hundred seventy bidirectional sequences from 11 individuals were analyzed. HIV-1 env and pol derived from sputa had greater frequency of drug-resistance mutations (P = 0.05), evolutionary divergence (P = 0.004), and tendency for CXCR4 usage (P = 0.1) compared with viruses derived from peripheral blood mononuclear cells.

Conclusion: The greater frequency of HIV-1 drug-resistance mutations and divergence of HIV-1 env in sputa-derived viruses compared with peripheral blood mononuclear cell-derived viruses suggests greater HIV-1 replication in the respiratory tract compared with the blood. Characterization of viral evolution over time and by cell-type could identify cells that provide a sanctuary for low-level viral replication in the respiratory tract during suppressive ART.

Fig. 1

HIV-1 sequences derived from induced sputa compared to those from peripheral blood mononuclear cells (PBMC). The mean value for each participant’s sequences is represented by a symbol (see key to right). Plots show (a) HIV-1 mean env divergence from the ancestor of infection, and (b) frequency of RT sequences with ≥1 drug resistance mutation. Values from each participant’s sputum and PBMC are connected with a line. The mean of all participants’ values is shown for each parameter (bold hashes connected by dashed line). P values refer to the differences between sputum and PBMC values using Wilcoxon Two-sided Ranked-Sign Test to compare the paired mean values from each individual. Values corresponding to 0% on panel B are splayed slightly for better visualization.