The SnoB study: frequency of baseline raltegravir resistance mutations prevalence in different non-B subtypes

Abstract

The SnoB study analysed the variability of the integrase (IN) gene of non-B viruses from treatment-naïve patients to determine whether non-B subtypes carry natural resistance mutations to raltegravir (RAL). Plasma viral RNA from 427 patients was gained, and IN sequences were subtyped and screened for subtype-specific highly-variable residues. Seven viruses of different subtypes were phenotypically tested for RAL susceptibility; 359/427 samples could be sequenced. One hundred and seventy samples (47%) were classified as non-B subtypes. No primary RAL resistance-associated mutations (RRAMs) were detected. Certain secondary mutations were found, mostly related to specific non-B subtypes. L74 M was significantly more prevalent in subtype 02_AG, T97A in A and 06_cpx, V151I in 06_cpx, and G163R in 12_BF. Various additional mutations were also detected and could be associated with the subtype too. While K156 N and S230 N were correlated with B subtype, V72I, L74I, T112I, T125A, V201I and T206S were more frequent in certain non-B subtypes. The resistance factors (RF) of 7 viral strains of different subtypes ranged from 1.0 to 1.9. No primary or secondary but subtype-associated additional RRAMs were present. No correlation between RF and additional RRAMs was found. The prevalence of RRAMs was higher in non-B samples. However, the RFs for the analysed non-B subtypes showed lower values to those reported relevant to clinical failure. As the role of baseline secondary and additional mutations on RAL therapy failure is actually not known, baseline IN screening is necessary.

Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors

“…Our analyses could confirm and considerably extend previously published results based on INSTI-naïve [ 26 , 31 – 35 ] or ART-naïve [ 35 – 40 ] study populations that either focused on HIV-1 subtype B [ 31 , 36 , 38 ] or included various HIV-1 group M subtypes [ 26 , 32 – 35 , 37 , 39 , 40 ]. We restricted our analyses to HIV-1 subtype B strains because these are predominant in Germany [ 43 – 45 ] and because different HIV-1 subtypes have different consensus amino acids at some sites, which can bias the degree of variability when compared to consensus B [ 33 , 35 ].…”

HIV-1 Genetic Variability and Clinical Implications

“…The residues associated with primary resistance seem to be highly conserved across subtypes, but polymorphisms at the sites of secondary resistance mutations are more common in non-B subtypes [147, 198–200]. …”

“…The additional INI-resistance associated mutations K156N and S230N mutations were more frequent in B subtype while V72I, L74I, T125A, V201I, and T206S were more frequent in certain non-B subtypes [200, 205]. No differences in phenotypic raltegravir resistance were found in several non-B isolates tested [196].…”

“…It showed a higher genetic barrier to resistance and retains activity against viruses with resistance to raltegravir or elvitegravir. Interestingly, among the mutations associated with in vitro resistance to dolutegravir, the mutations L101I and T124A were polymorphic and significantly more prevalent in patients with non-B subtypes [200]. In addition, mutation R263K seems to be preferentially selected in subtype B under dolutegravir pressure (Table 1) [206].…”

Mutagenesis of Lysines 156 and 159 in Human Immunodeficiency Virus Type 1 Integrase (IN) Reveals Differential Interactions between these Residues and Different IN Inhibitors

“…Taken together, these inhibitor attributes suggest that STI and L-CA have different mechanisms of action. We chose to test predicted roles of K156 and K159 in inhibitor action for several reasons: 1) in the only reported HIV IN-inhibitor co-crystal structure [41] both K156 and K159 are proximal to the DKA analog, 5-CITEP; 2) K156 and K159 are implicated in both STI and L-CA binding suggesting that these two lysines are involved in an overlapping mechanism of inhibitor action; and 3) K156 and K159 cross-link to the viral DNA 3'-end containing the conserved 5'-CpA-OH motif [42][43][44][45] and the PFV IN ortholog to K159 (PFV IN K228) is shown bound directly to the phosphate backbone in the 5'-CpA-OH motif [7,46] suggesting that K156 and K159 are directly involved in orienting the viral DNA donor strand during catalysis; and 4) polymorphisms at residue 156 are associated with resistance to RGV [47] and are found within multiple clades of HIV [47][48][49][50]. We substituted K156 and K159 with increasingly non-conservative arginine, alanine, and aspartate residues and predicted that these mutations would confer increasing resistance to a spectrum of IN inhibitors, perhaps to the detriment of enzyme activity.…”