Table 1.
Lineage assignment of SARS-CoV-2 from participants enrolled in the AGILE CST-2 phase IIa molnupiravir clinical trial
| Lineage | Placebo | Molnupiravir |
|---|---|---|
| Total (passed) | Total (passed) | |
| B.1.1.7 (Alpha) | 20 (14) | 17 (11) |
| B.1.1.1 | 1 (1) | 0 (0) |
| B.1.177 (EU1) | 13 (10) | 15 (8) |
| Delta (all) | 35 (24) | 37 (28) |
| B.1.617.2 | 2 (0) | 2 (2) |
| AY.120 | 1 (1) | 0 (0) |
| AY.33 | 0 (0) | 1 (1) |
| AY.4 | 28 (21) | 30 (22) |
| AY.43 | 0 (0) | 1 (1) |
| AY.4.2 | 2 (1) | 2 (2) |
| AY.4.2.1 | 1 (1) | 0 (0) |
| AY.98 | 1 (0) | 1 (1) |
| Omicron (all) | 19 (16) | 20 (12) |
| BA.1 | 12 (9) | 15 (11) |
| BA.2 | 6 (6) | 5 (1) |
| XE | 1 (1) | 0 (0) |
| Failed to assign | 2 (0) | 1 (0) |
| Trial total | 90 (65) | 90 (59) |
Viral RNA from nasopharyngeal swabs obtained from participants enrolled in the phase IIa clinical trial was sequenced as described in Methods. The consensus SARS-CoV-2 genome for each sample, assembled after mapping to the Wuhan-Hu-1 reference genome, was used to assign the lineage of SARS-CoV-2 that each patient was infected with upon entering the trial, using the software tool, Pangolin (version 4.0.6). Only participants that passed criteria of all samples (Days 1, 3 and 5) with a minimum 90% genome coverage at 200X were included in downstream analyses – numbers indicated in brackets for each (sub-)lineage. Sub-lineages denoted in italics. Lineages that only had one patient or an uneven balance of placebo:drug were excluded from the analysis (B.1.1.1. and BA.2).