The latent HIV reservoir: current advances in genetic sequencing approaches

Abstract

Multiple cellular HIV reservoirs in diverse anatomical sites can undergo clonal expansion and persist for years despite suppressive antiretroviral therapy, posing a major barrier toward an HIV cure. Commonly adopted assays to assess HIV reservoir size mainly consist of PCR-based measures of cell-associated total proviral DNA, intact proviruses and transcriptionally competent provirus (viral RNA), flow cytometry and microscopy-based methods to measure translationally competent provirus (viral protein), and quantitative viral outgrowth assay, the gold standard to measure replication-competent provirus; yet no assay alone can provide a comprehensive view of the total HIV reservoir or its dynamics. Furthermore, the detection of extant provirus by these measures does not preclude defects affecting replication competence. An accurate measure of the latent reservoir is essential for evaluating the efficacy of HIV cure strategies. Recent approaches have been developed, which generate proviral sequence data to create a more detailed profile of the latent reservoir. These sequencing approaches are valuable tools to understand the complex multicellular processes in a diverse range of tissues and cell types and have provided insights into the mechanisms of HIV establishment and persistence. These advancements over previous sequencing methods have allowed multiplexing and new assays have emerged, which can document transcriptional activity, chromosome accessibility, and in-depth cellular phenotypes harboring latent HIV, enabling the characterization of rare infected cells across restrictive sites such as the brain. In this manuscript, we provide a review of HIV sequencing-based assays adopted to address challenges in quantifying and characterizing the latent HIV reservoir.

Macrophages: Key Cellular Players in HIV Infection and Pathogenesis

“…However, additional investigations seeking to elucidate the specific role of macrophages in HIV-1 transmission, particularly in mucosal tissues, are needed to shed light on the early events that contribute to the establishment of an infection. Finally, infected macrophages are not susceptible to the virus-induced cytopathic effect, and can thus participate, together with latently infected CD4+ T cells, in the early establishment and persistence of virus reservoirs in numerous host tissues (for recent reviews, see [ 2 , 10 ]). As recently shown [ 3 ], these virus reservoirs in myeloid cells can be detected over several years in patients on cART.…”

Peripheral B Lymphocyte Serves as A Reservoir for The Persistently Covert Infection of MandarinfishSiniperca chuatsiRanavirus

“…White blood cell (WBC), a pivotal role in the immune system, serves as dormant or latent carriers for numerous viruses. For instance, the human immunodeficiency virus (HIV) specifically targets T cells as its latent host cells, while the human T-cell leukemia virus (HTLV) can establish residence in both B and T cells(23, 24). Similarly, the herpesvirus can conceal itself within B lymphocytes in both human and animal(25-29).…”