Background: Recently, we reported the case of an HIV-infected patient diagnosed with T-cell lymphoma who subsequently underwent allogeneic stem-cell transplantation (alloSCT) from a CCR5 delta32 homozygously mutated donor. In this case HIV replication could not be controlled by the immune system and the patient died after a relapse of the T-cell lymphoma. So far, the evolutionary pathways of the HIV tropism in this patient has remained unclear.
Methods: The tropism of HIV was analyzed from viral RNA and proviral DNA using the Illumina MiSeq platform for deep sequencing of gp120 V3. Samples were taken before (-287d: RNA, -103d: RNA/DNA) and after alloSCT (+20d: RNA, +280d: DNA, +373d: RNA). Viral tropism was predicted by using geno2pheno[coreceptor] indicating the probability of classifying a R5-tropic virus falsely as a CXCR4-capable virus (FPR).
Results: Several distinct virus populations could be observed before and after alloSCT, which harbored specific mutational patterns (I14L, A19V, G24-, H34Y). Before alloSCT two virus populations were dominantly found in viral RNA and DNA only distinguished by mutation (R18K) with FPR of 10.5 (R18wt) and 8.5 (R18K), respectively. Apart from these two virus populations several minority variants could be detected carrying additional amino acid substitutions (N7S, K10R, H13T, R18W, Q32K, H34F) resulting in FPR from 7.8 to 4.2. These minority variants were especially detected in proviral DNA (-103d). One HIV variant detected in proviral DNA (4.4%) before alloSCT (-103d) had a unique mutational pattern (S11A, H13T, I14L, A19V, F20Y, T21K, Q32K) classified as clearly X4-capable (FPR 0.4). This sequence was identical to the sequence of the dominant HIV variant replicating in the patient after alloSCT. Overall, the viral variability was limited in sequences obtained after alloSCT from viral RNA and proviral DNA. Only a small fraction of the virus population displayed further unique amino acid substitutions marginally influencing the FPR (FPR 0.2: H13A, I26T and I26V, respectively; FPR 0.5: A19I; FPR 0.7: G28E).
Conclusions: The selective pressure exerted by the transplantation of allogeneic stem-cells homozygous for the CCR5 delta32 mutation resulted in the selection of already preexisting X4 capable HIV. Even the presence of only a minor X4 variant before alloSCT prevented the control of HIV in the absence functional CCR5 receptor.