Rozera Gabriella, Abbate Isabella, Giombini Emanuela, Castagna Antonella, De Luca Andrea, Ceccherini-Silberstein Francesca, Cozzi Lepri Alessandro, Cassola Giovanni, Torti Carlo, d'Arminio Monforte Antonella, Ippolito Giuseppe, Capobianchi Maria R
National Institute for Infectious Diseases L. Spallanzani, Rome, Italy.
National Institute for Infectious Diseases L. Spallanzani, Rome, Italy
J Antimicrob Chemother. 2014 Nov;69(11):3085-94. doi: 10.1093/jac/dku255. Epub 2014 Jul 10.
Tropism evolution of HIV-1 quasispecies was analysed by ultra-deep pyrosequencing (UDPS) in patients on first-line combination antiretroviral therapy (cART) always suppressed or experiencing virological failure episodes.
Among ICONA patients, two groups of 20 patients on cART for ≥5 years, matched for baseline viraemia and therapy duration, were analysed [Group I, patients always suppressed; and Group II, patients experiencing episode(s) of virological failure]. Viral tropism was assessed by V3 UDPS on plasma RNA before therapy (T0) and on peripheral blood mononuclear cell proviral DNA before-after therapy (T0-T1), using geno2pheno false positive rate (FPR) (threshold for X4: 5.75). For each sample, quasispecies tropism was assigned according to X4 variant frequency: R5, <0.3% X4; minority X4, 0.3%-19.9% X4; and X4, ≥20% X4. An R5-X4 switch was defined as a change from R5/minority X4 in plasma/proviral genomes at T0 to X4 in provirus at T1.
At baseline, mean FPR and %X4 of viral RNA were positively correlated with those of proviral DNA. After therapy, proviral DNA load significantly decreased in Group I; mean FPR of proviral quasispecies significantly decreased and %X4 increased in Group II. An R5-X4 switch was observed in five patients (two in Group I and three in Group II), all harbouring minority X4 variants at T0.
UDPS analysis reveals that the tropism switch is not an 'on-off' phenomenon, but may result from a profound re-shaping of viral quasispecies, even under suppressive cART. However, episodes of virological failure seem to prevent reduction of proviral DNA and to accelerate viral evolution, as suggested by decreased FPR and increased %X4 at T1 in Group II patients.
采用超深度焦磷酸测序（UDPS）分析一线联合抗逆转录病毒疗法（cART）治疗下病毒载量始终被抑制或经历病毒学失败期的患者中HIV-1准种的嗜性演变。
在ICONA研究的患者中，分析了两组接受cART治疗≥5年的20例患者[第一组，病毒载量始终被抑制的患者；第二组，经历病毒学失败期的患者]，两组患者的基线病毒血症和治疗持续时间相匹配。在治疗前（T0）对血浆RNA以及治疗前后（T0-T1）对外周血单个核细胞前病毒DNA进行V3 UDPS分析以评估病毒嗜性，使用基因2表型假阳性率（FPR）（X4的阈值为5.75）。对于每个样本，根据X4变异频率确定准种嗜性：R5，X4变异频率<0.3%；少数X4，X4变异频率为0.3%-19.9%；X4，X4变异频率≥20%。R5-X4转换定义为从T0时血浆/前病毒基因组中的R5/少数X4变为T1时前病毒中的X4。
基线时，病毒RNA的平均FPR和%X4与前病毒DNA的平均FPR和%X4呈正相关。治疗后，第一组患者的前病毒DNA载量显著下降；第二组患者前病毒准种的平均FPR显著下降，%X4增加。在5例患者中观察到R5-X4转换（第一组2例，第二组3例），所有患者在T0时均携带少数X4变异。
UDPS分析显示，嗜性转换不是一种“开-关”现象，而是可能源于病毒准种的深刻重塑，即使在抑制性cART治疗下也是如此。然而，病毒学失败期似乎会阻止前病毒DNA的减少并加速病毒进化，如第二组患者在T1时FPR降低和%X4增加所提示的那样。
