Ansuvimab-zykl cell culture resistance studies have been performed using replication competent recombinant vesicular stomatitis virus expressing the EBOV surface glycoprotein (rVSV-EBOV GP). The rVSV-EBOV GP virus was sequentially sub-cultured in six experiments for up to 5 passages in the presence of a concentration range of ansuvimab-zykl (0.08 to 50 µg/mL) to determine if escape mutants developed via selective pressure. A total of seven different amino acid substitutions in the EBOV GP were found (
Table 4). Three of the seven were detected at less than 1% sequence frequency and were not within the ansuvimab-zykl GP epitope or within 5Å of the epitope, and therefore were excluded from further analysis.
Table 4 Identification of Ebola GP Substitutions in Cell Culture Studies| a Frequency range of the sequences in 6 replicate experiments identified at the highest ansuvimab-zykl concentration of 50 µg/mL
|
GP Substitutions | % Frequency of
Sequences with the
Substitution
a
| Ansuvimab-zykl Amino Acid Substitutions Selected at
50 µg/mL
|
R29S | <1 | Excluded |
P116H | 71–94 | Resistant |
T144M | 71–100 | Resistant |
N228H | <1 | Excluded |
R299K | 71 | No Resistance - Equivalent ansuvimab-zykl neutralization to
Kikwit reference GP sequence
|
N434K | 73 | No Resistance - Equivalent ansuvimab-zykl neutralization to
Kikwit reference GP sequence
|
T634A | <1 | Excluded |
The four remaining GP amino acid substitutions (P116H, T144M, R299K and N434K) were further evaluated in a single-cycle neutralization assay using a replication-defective lentiviral vector not expressing envelope pseudotyped with EBOV GP containing each of the substitutions. The P116H and T144M substitutions exhibited resistance to ansuvimab-zykl based on no neutralization detected at the highest concentrations assessed (10 µg/mL) resulting in a >56-fold reduction in susceptibility for each substitution compared to the wild type EBOV GP.
Two additional substitutions within the EBOV GP conserved region (G118E and G118R), which were not found in the studies described above, have been reported in the literature from similar cell culture resistance studies and these substitutions were able to confer >29- and >34-fold reductions in susceptibility to ansuvimab-zykl, respectively.
1
Of the four resistant substitutions identified under selective pressure in cell culture (P116H, G118E, G118R, and T144M), only G118R has been identified in naturally infected Ebola virus disease patients in low frequency through NGS sequencing.
In Clinical Studies
A post-hoc detailed analysis of currently available EBOV GP sequences in the public database (as of November 2022) was performed to identify all amino acid polymorphisms in the ansuvimab-zykl epitope (GP positions 111-119) and amino acids within 5Å of the epitope. A total of nine sequences out of 3324 available EBOV genomes had amino acid changes, of which two were within the ansuvimab-zykl linear epitope (L111I and L111F) and two within 5Å of the epitope compared to the Kikwit variant (I170L and I170F). Of the nine EBOV GP sequences, six were at the same amino acid location with the same amino acid substitution (I170L), one was at the same location as the previous six, but with a different amino acid substitution (I170F). The remaining two were at the same location but with different amino acid substitutions (L111I and L111F). Overall, four of the nine EBOV GP sequences expressed distinct amino acid substitutions at only two different positions. Phenotypic assessments of these amino acid changes inside of, or within 5Å of the ansuvimab-zykl linear epitope (111-119) were performed with a single-cycle neutralization assay using a replication-defective lentiviral vector not expressing envelope pseudotyped with EBOV GP containing each of the substitutions. The EBOV-GP pseudotyped lentiviral vectors with the I170F and I170L substitutions were found to be inactive and unable to infect target cells. EBOV-GP pseudotyped lentiviral vectors with the L111I and L111F were fully neutralized by ansuvimab-zykl with a potency similar to the Ituri wild type variant and historic Mayinga variant EC
50values and therefore none of the four identified amino acid substitutions are expected to be resistant to ansuvimab-zykl.
PALM Clinical study and MEURI EAP
Samples from a total of 95 participants (79 participants enrolled in the PALM randomized controlled clinical study and 16 participants from the MEURI EAP) including samples from 40 deceased participants and from 36 surviving participants with paired samples taken at baseline (pre-treatment) and after treatment with ansuvimab-zykl where available for EBOV glycoprotein (GP) sequencing. A total of 147 EBOV (GP) genome sequences were produced. When compared to the Kikwit and the Ituri variants, 26 and 14 amino acid substitutions, respectively, were found outside of the region of the ansuvimab-zykl epitope in EBOV GP from PALM trial participants. These amino acid changes were located predominantly in the less conserved mucin-like domain of the EBOV GP. None of these amino acid changes were associated with mortality nor appeared to be driven by ansuvimab-zykl treatment.
The amino acid substitution G118R, which was identified in cell culture selection experiments and had a >34-fold reduction in susceptibility to ansuvimab-zykl, was detected at 9% to 13% frequency by Next Generation Sequencing (NGS) in 10 participant samples (9 of which were survivors) collected prior to treatment with ansuvimab-zykl in the PALM and MEURI EAP
1; the clinical significance of this substitution is unknown.
Additional post-hoc analysis of NGS data from the viral sequences detected several amino acid substitutions located in the ansuvimab-zykl epitope (K115, P116L, D117G) and within 5Å of the ansuvimab-zykl epitope (Y109C/H, L122P/S, V141A, P146L, C147K, Y171C, F176L). These substitutions, along with two controls that have known resistance (L111F, P116H), were evaluated for reductions in susceptibility to ansuvimab-zykl in comparison to the wild-type EBOV (Mayinga strain) using EBOV GP pseudotyped virus-like particle (PsVLP) infection of HEK293T cells. Out of the 18 PsVLPs produced (including the two controls), P116L showed significant reductions in susceptibility to ansuvimab-zykl, resulting in a mean 29.2-fold change compared to the wild-type EBOV GP. Three substitutions (K115N, D117G, and P146L) exhibited a range of 3.2- to 4.3-fold reduction in susceptibility based on mean reductions relative to wild-type control. Infectivity of the variants in this analysis ranged from 0.21 to 0.86 (where wild-type EBOV infectivity = 1).
Table 5provides an overview of the infectivity and fold change of the four variants and two controls from this analysis. The clinical significance of these substitutions is unknown.
Table 5 Infectivity and Mean Reductions in Susceptibility in Cell Culture of Select Ebolavirus Glycoprotein (EBOV GP) Variants (Pseudotyped Virus-Like Particles) compared to Wild-Type EBOVN/A = Not applicable.
a The pseudotyped virus-like particle variants K115N, P116L and D117G contain amino acid substitutions at the Ebanga EBOV GP target epitope; while variant P146L is within 5 Å of the Ebanga EBOV GP target epitope.
b Infectivity and reductions in susceptibility values are relative to wild-type (WT) EBOV (Mayinga strain). Relative Infectivity values of <1 indicates the variant exhibits lower infectivity compared to the WT (WT Infectivity =1).
c There was no neutralization detected at the highest concentration evaluated (18 µg/mL) for control variant P116H.
|
EBOV GP Variant
a
| Infectivity
b
| Mean Fold Change
b
|
L111F (control) | 0.90 | 2.6 |
K115N | 0.31 | 4.3 |
P116H (control) | 0.80 | N/Ac |
P116L | 0.75 | 29.2 |
D117G | 0.86 | 3.2 |
P146L | 0.21 | 3.2 |