Influence of treatment with neutralizing monoclonal antibodies on the SARS-CoV-2 nasopharyngeal load and quasispecies

Abstract

Objectives: To evaluate the impact of neutralizing monoclonal antibody (mAb) treatment and to determine whether the selective pressure of mAbs could facilitate the proliferation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with spike protein mutations that might attenuate mAb effectiveness.

Patients and methods: We evaluated the impact of mAbs on the nasopharyngeal (NP) viral load and virus quasispecies of mAb-treated patients using single-molecule real-time sequencing. The mAbs used were: Bamlanivimab alone (four patients), Bamlanivimab/Etesevimab (23 patients) and Casirivimab/Imdevimab (five patients).

Results: The NP SARS-CoV-2 viral load of mAb-treated patients decreased from 8.2 log₁₀ copies/mL before administration to 4.3 log₁₀ copies/mL 7 days after administration. Five immunocompromised patients given Bamlanivimab/Etesevimab were found to have mAb activity-reducing spike mutations. Two patients harboured SARS-CoV-2 variants with a Q493R spike mutation 7 days after administration, as did a third patient 14 days after administration. The fourth patient harboured a variant with a Q493K spike mutation 7 days post-treatment, and the fifth patient had a variant with a E484K spike mutation on day 21. The emergence of the spike mutation was accompanied by stabilization or rebound of the NP viral load in three of five patients.

Conclusion: Two-mAb therapy can drive the selection of resistant SARS-CoV-2 variants in immunocompromised patients. Patients given mAbs should be closely monitored and measures to limit virus spread should be reinforced.

Keywords: Coronavirus disease 2019; Mutations; Neutralizing monoclonal antibodies; Quasispecies; Receptor-binding domain; Severe acute respiratory syndrome coronavirus 2; Single-molecular real-time sequencing; Spike protein.

Fig. 1

(a) Evolution of the viral load in nasopharyngeal (NP) samples from monoclonal antibody (mAb) -treated patients between days 0 and 7. The horizontal black line of the histogram indicates the median of difference (day 7 – day 0). Red: Bamlanivimab alone (n = 4), dark grey: Bamlanivimab/Imdevimab (n = 23) and blue: Casirivimab/Imdevimab (n = 5). (b) Differences in the viral load in NP samples from mAb-treated patients between days 0 and 7. The horizontal black line of the histogram indicates the median of difference (day 7 – day 0). Red: Bamlanivimab alone (n = 4), dark grey: Bamlanivimab/Etesevimab (n = 23) and blue: Casirivimab/Imdevimab (n = 5).

Fig. 2

Changes in nasopharyngeal (NP) viral load, detection of spike protein mutations and SARS-CoV-2 genetic diversity in five Bamlanivimab/Etesevimab-treated patients. NP samples were analysed for: clade, spike protein mutations in the receptor binding domain, and percentage of haplotypes detected. Red stars indicate the appearance of key monoclonal antibody (mAb) activity-reducing mutations. Red: key mutation, blue: minor mutations.

Fig. S1

Differences in the viral loads (days 0 to 7) in NPs from untreated control solid organ transplant patients and from monoclonal antibody-treated solid organ transplant patients.