High-level resistance to bictegravir and cabotegravir in subtype A- and D-infected HIV-1 patients failing raltegravir with multiple resistance mutations

Abstract

Objectives: The second-generation integrase strand transfer inhibitor (INSTI) bictegravir is becoming accessible in low- and middle-income countries (LMICs), and another INSTI, cabotegravir, has recently been approved as a long-acting injectable. Data on bictegravir and cabotegravir susceptibility in raltegravir-experienced HIV-1 subtype A- and D-infected patients carrying drug resistance mutations (DRMs) remain very scarce in LMICs.

Patients and methods: HIV-1 integrase (IN)-recombinant viruses from eight patients failing raltegravir-based third-line therapy in Uganda were genotypically and phenotypically tested for susceptibility to bictegravir and cabotegravir. Ability of these viruses to integrate into human genomes was assessed in MT-4 cells.

Results: HIV-1 IN-recombinant viruses harbouring single primary mutations (N155H or Y143R/S) or in combination with secondary INSTI mutations (T97A, M50I, L74IM, E157Q, G163R or V151I) were susceptible to both bictegravir and cabotegravir. However, combinations of primary INSTI-resistance mutations such as E138A/G140A/G163R/Q148R or E138K/G140A/S147G/Q148K led to decreased susceptibility to both cabotegravir (fold change in EC50 values from 429 to 1000×) and bictegravir (60 to 100×), exhibiting a high degree of cross-resistance. However, these same IN-recombinant viruses showed impaired integration capacity (14% to 48%) relative to the WT HIV-1 NL4-3 strain in the absence of drug.

Conclusions: Though not currently widely accessible in most LMICs, bictegravir and cabotegravir offer a valid alternative to HIV-infected individuals harbouring subtype A and D HIV-1 variants with reduced susceptibility to first-generation INSTIs but previous exposure to raltegravir may reduce efficacy, more so with cabotegravir.

Figure 1.

The chemical structures of different INSTIs. (a) Elvitegravir; (b) raltegravir; (c) dolutegravir; (d) cabotegravir; and (e) bictegravir. The coplanar oxygen atoms are highlighted in red; green circles highlight extended linkers, which are a common feature of all second-generation INSTIs. This figure appears in colour in the online version of JAC and in black and white in the printed version of JAC.

Figure 2.

The FC in EC₅₀ of IN-recombinant viruses. The susceptibility of IN-recombinant viruses UG537 (with mutation N155H), UG1179 (N155H), UG481 (Y143R, T97AT, G163R), UG23 (E138A, T97A, V151A), UG42 (N155H, E157Q, G163R, M50L, L74I, V151I), UG35 (Y143R, T97A, M50I, L74IM), UG1059 (E138A, G140A, Q148R, G163R) and UG206 (E138K, G140A, Q148K, S147G) to bictegravir and cabotegravir was determined using TZM-bl cells. The mean EC₅₀ (nM) values from independent experiments run in quadruplicate were used to determine FC in EC₅₀ (nM) of recombinant viruses harbouring INSTI-resistance mutations relative to subtype B, A and D references (a, b and c). The error bars represent ±SD of FC in EC₅₀ values between replicates of independent experiments. The horizontal line represents an FC of 1. This figure appears in colour in the online version of JAC and in black and white in the printed version of JAC.

Figure 3.

The susceptibility of recombinant viruses to cabotegravir and bictegravir. The susceptibility of recombinant viruses to the INSTIs bictegravir and cabotegravir was determined using a short-term infectivity assay in TZM-bl cells. Each experiment was done in quadruplicate. The change in EC₅₀ (nM) of recombinant viruses harbouring INSTI-resistance mutations was determined in reference to NL4-3 WT. (a) UG206; (b) UG1059; (c) UG537; (d) UG42; (e) UG35; and (f) UG481: drug susceptibility to bictegravir (left panel) and cabotegravir (right panel). This figure appears in colour in the online version of JAC and in black and white in the printed version of JAC.

Figure 4.

FC in EC₅₀ of recombinant viruses carrying multiple primary INSTI-resistance mutations. FC in EC₅₀ (nM) of bictegravir and cabotegravir for recombinant virus UG1059 (a) and UG206 (b). FC in EC₅₀ (nM) of recombinant viruses harbouring INSTI-resistance mutations relative to WT NL4-3 was determined in a short infection assay in TZM-bl cells. The mean EC₅₀ (nM) values for cabotegravir and bictegravir were compared using non-parametric two-tailed t-test; P = 0.005 was considered statistically significant. This figure appears in colour in the online version of JAC and in black and white in the printed version of JAC.

Figure 5.

The relative integration capacity of IN-recombinant viruses with diverse INSTI-resistance mutations. The relative integration capacity of mutant viruses compared with controls (UG14 and UG98) and WT (NL4-3) was determined in MT4 cells. The integrated HIV-1 long terminal repeat (LTR) was amplified and quantified using Alu-gag qPCR. (a) Relative integration of mutant viruses; (b) correlation between the relative integration and replicative fitness (the latter being based on our previous reports). Mean ± SD values are shown from two independent experiments carried out in triplicate for each sample. The correlation was determined by Spearman’s correlation coefficient. qPCR results were normalized relative to NL4-3 WT, arbitrarily set at 100%. This figure appears in colour in the online version of JAC and in black and white in the printed version of JAC.