Eight studies reported 196 DOR in vitro susceptibility results [7,8,9,10,11,12,13,14]. Five studies reporting 136 results were published by authors at MRL [7, 9,10,11,12]. Three studies reporting 60 susceptibility results were published by other research groups—National Cancer Institute (NCI) in the U.S., University of Sienna (Italy) and McGill University (Canada) [8, 13, 14]. The MRL studies used the PhenoSense assay for 109 results and an MT-2 cell reporter gene assay for 27  results.

Figure 1 shows the results published in the MRL studies according to type of isolate: (1) 89 were part of a Monogram Biosciences panel of clinical isolates containing common patterns of NNRTI DRMs (blue circles) [12]; (2) 21 were site-directed mutants containing common patterns of NNRTI DRMs including several selected in persons receiving DOR (black circles); (3) 16 results, each representing the median of viruses containing a single NNRTI DRM in the Monogram Biosciences database (green circles) [10]; and (4) 10 results on viruses containing patterns of NNRTI DRMs that were selected either in vitro or in persons receiving DOR (red circles).

Doravirine in vitro susceptibility data for isolates with one, two, or three NNRTI-resistance mutations. The Y-axis indicates the pattern of mutations and the X-axis indicates the fold-reduction in susceptibility on a log2 scale. Isolates with a fold-reduced susceptibility < 1.0 were jittered about 1.0 whereas those with a fold reduced susceptibility > 128 were jittered at this level. Each of the results were published by the Merck Research Laboratory and included 109 results generated by the Monogram Biosciences PhenoSense assay and 27 results generated by an in-house MT-2 cell reporter gene assay. Blue circles indicate clinical isolates containing common patterns of NNRTI DRMs. Green circles indicate median fold reduced susceptibilities of viruses containing a single NNRTI DRM from a selection of viruses in the Monogram database [10]. Black circles indicate site-directed mutants containing common patterns of NNRTI DRMs. Red circles indicate site-directed mutants containing patterns of NNRTI DRMs that were selected either in vitro or in persons receiving doravirine. Vertical lines indicate 3.0-fold and  10.0-fold reduced susceptibility

Susceptibility data from the MRL studies were available for 86 isolates with 22 different single NNRTI DRMs, 46 isolates with 20 different pairs of NNRTI DRMs, and 20 isolates with 12 different patterns containing three NNRTI DRMs. Among the 22 different single NNRTI DRMs, four had been selected in vitro and/or in vivo by DOR and had a reduced susceptibility ≥ 3.0 fold including Y188L (> 64-fold; 8 results), Y318F (11-fold; 2 result), V106A (9.6-fold; 3 results) and V106M (3.4-fold; 1 result). Three other DRMs also had a reduction in susceptibility ≥ 3.0 fold including G190E (18-fold; 1 result), Y181V (5.1-fold; 2 results), and G190S (3.0-fold; 6 results).

Among the 20 different pairs of NNRTI DRMs, 9 patterns containing V106A, Y188L, F227C/L, or M230L had median reductions in susceptibility ≥ 36-fold. Eight patterns without any of these canonical DOR-associated mutations had median reductions in susceptibility ranging from 3.3 to 7.9-fold including K103N + P225H (7.9-fold; 2 results), V108I + Y181C (6.9-fold; 2 results), L100I + K103N (5.7-fold; 9 results), K103N + V108I (4.6-fold; 2 results), A98G + K103N (4.0-fold, 1 result), K103N + Y181C (3.8-fold, 5 results), Y181C + G190A (3.5-fold, 3 results), and A98G + Y181C (3.3-fold, 1 result).

Among the 12 patterns of mutations containing three NNRTI DRMs, the five containing V106A, F227C, or M230L had > 64-fold reductions in susceptibility. Two patterns lacking any canonical DOR-resistance mutations had > tenfold reductions in susceptibility including L100I + K103N + V108I and K101E + Y181C + G190S.

Additional file 1: Table S1 summarizes in vitro susceptibility data published by the McGill, Sienna, and NCI research groups. The McGill research group tested cultured viruses selected in vitro by DOR including V106A/I/M, V108I, H221Y, F227L, M230L, L234I, and Y318F in a 7 day multi-cycle assay with a read-out based on RT activity. Their fold reductions in susceptibility differed from those of the MRL group in that isolates with V108I + Y318F or H221Y + L234I were associated with high-level reductions in DOR susceptibility.

The Sienna group tested a panel of 10 site-directed mutants containing representative patterns of two to four NNRTI DRMs in a 48 h recombinant virus luciferase reporter gene assay. Although this panel was created prior to the approval of DOR, three isolates lacking canonical DOR-associated DRMs had > tenfold reductions in susceptibility including K103N + V179F + Y181C, V106I + Y181C + G190A + H221Y, and A98G + K101E + E138K + Y181C.

The NCI group tested 32 site-directed mutants associated with reduced NNRTI susceptibility in a 48-h recombinant virus luciferase reporter gene assay. Its results diverged from the other research groups in that K103N, E138K, and the uncommon NRTI-resistance mutation D67E had 7.0, 8.2, and a 70-fold reduction in DOR susceptibility, respectively.

HIVDB contained 42,535 one-per-person RT sequences from ART-naïve persons during the five- year period encompassing 2017 to 2021 reported in 168 published studies. Overall, 3374 (7.9%) had sequences with a mutation that had a penalty score for DOR (Additional file 2: Table S2). Of these, 2,788 (82.6%) contained a single NNRTI DRM (n = 33 different mutations), 426 (12.6%) contained two DRMs (n = 79 pairs of mutations), and 143 (4.2%) contained three or more DRMs (n = 86 patterns of mutations). Of the 3,374 sequences with a mutation that had a DOR penalty score, the most common subtypes were B (49.7%), C (12.3%), A (8.2%), CRF01_AE (8.0%), and CRF02_AG (7.1%). The distribution of sequences by region included Asia (31.5%), Europe (29.7%), Africa (26.1%), Latin America (11.9%) and North America (0.7%).

Among the 2,788 sequences with a single NNRTI DRM, 112 (4.0%) were associated with ≥ 3.0 fold-reduced DOR susceptibility, 2,625 (94.2%) were associated with < 3.0 fold-reduced susceptibility (Table 1). The 112 sequences associated with ≥ 3.0 fold-reduced susceptibility included three with the canonical resistance mutations V106A, Y188L, and Y318F and four with the non-canonical resistance mutations V106M, Y181V, and G190S/E. Susceptibility data were not available for 12 individual mutations including two canonical doravirine DRMs, F227C and M230L that occurred in five sequences and 10 additional mutations L100V, K101P, V179F, Y181I, G190Q, F227I/V, M230I, L234I and P236L that occurred in 46 sequences (Additional file 3: Table S3).

Among the 426 sequences with two NNRTI DRMs, 180 (42.3%) were associated with ≥ 3.0 fold reduced DOR susceptibility, 32 (7.5%) were associated with < 3.0 fold reduced DOR susceptibility (Table 2). Susceptibility data were not available for 214 (50.2%) sequences including 57 containing one or more canonical resistance mutations or V106M, Y181V, or G190S/E. The remaining 157 sequences did not contain a DRM that individually was associated with ≥  3.0-fold reduced DOR susceptibility (Additional file 3: Table S3).