HIV reservoir cells that circulate in blood have been well characterized, but little is known about the dissemination of HIV-1-infected cells across multiple anatomical tissues, especially the central nervous system (CNS). Here, we performed single-genome near-full-length proviral sequencing to evaluate the proviral landscape in multiple tissues from 2 ART-treated patients.
Frozen tissues derived from 2 ART-treated individuals, were sampled during autopsy. Genomic DNA was extracted, and HIV-1 DNA levels were initially quantified using the intact proviral DNA assay (IPDA), followed by single-genome near-full-length proviral sequencing.
In patient 1, 577 HIV-1 sequences were detected in 14 different tissues from 754.77 million cells. Most of these proviruses were defective, and only a small fraction (4.5%, n=26) were intact, located in lymph node (n=18), spleen (n=3), colon (n=2), and kidney (n=3). The number of HIV copies varied from 0.02 to 6.24/million cells. The frequency of HIV sequences was highest in lymph node (6.24 total copies/million cells; 0.62 intact proviruses/million cells), followed by colon, spleen, and kidney. Four different sections of CNS were analyzed (occipital cortex, frontal cortex, basal ganglia and thalamus), but only 9 defective HIV sequences and no intact sequences were retrieved from 162.85 million cells. Two clones of intact proviruses were observed, one exclusively located in lymph node and the other disseminated across lymph node, spleen, and kidney. Ten large clones of defective proviruses were also noticed, which were broadly distributed across lymph node, spleen, the CNS, the genitourinary system, and the gastrointestinal system. In patient 2, 5 different CNS sections were analyzed, with isolation of a total of 36 HIV sequences from 147.49 million cells. Only 1 intact sequence was detected in the basal ganglia. The number of HIV copies varied from 0.10 to 0.47/million cells. Basal ganglia had the highest frequencies of HIV sequences, relative to frontal cortex, ventricle, occipital cortex and thalamus. Three clones of defective proviruses were observed across multiple CNS sections.
Lymph node represents a tissue hotspot for viral persistence, while the CNS does not seem to be a major site for persistence of intact proviruses. Multi-compartment dissemination of clonal intact and defective proviruses occurred across multiple anatomical tissues, arguing against compartmentalization of HIV reservoir cells in specific tissue types.