Table 1 Estimated fractions of SARS-CoV-2 nonsynonymous mutations that are lethal, deleterious, neutral, and beneficial

From: Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data

Region

n

Lethal

Deleterious

Neutral

Beneficial (fb)

ORF1ab

41757

10.0% (9.7–10.3%)

46.0% (45.6–46.5%)

43.2% (42.7–43.7%)

0.8% (0.7–0.9%)

S

7797

8.8% (8.2–9.5%)

39.2% (38.1–40.3%)

48.9% (47.8–50.0%)

3.1% (2.7–3.5%)

ORF3a

1640

1.2% (0.8–1.9%)

18.7% (16.8–20.6%)

76.2% (74.1–78.2%)

3.9% (3.0–5.0%)

E

448

6.0% (4.1–8.8%)

52.5% (47.7–57.1%)

39.5% (35.0–44.2%)

2.0% (1.0–3.9%)

M

1317

12.0% (10.3–13.9%)

46.7% (44.0–49.4%)

40.3% (37.7–43.0%)

1.0% (0.5–1.7%)

ORF6

374

0.3% (0.0–1.7%)

15.2% (11.8–19.4%)

81.6% (77.2–85.3%)

2.9% (1.6–5.4%)

ORF7a

715

0% (0.0–0.7%)

7.1% (5.4–9.3%)

86.3% (83.5–88.7%)

6.6% (4.9–8.7%)

ORF7b

251

0% (0.0–1.9%)

9.2% (6.0–13.6%)

87.3% (82.3–91.0%)

3.6% (1.8–6.9%)

ORF8

712

0% (0.0–0.7%)

12.6% (10.3–15.4%)

82.3% (79.3–85.0%)

5.1% (3.6–7.0%)

N

2502

7.7% (6.7–8.8%)

26.1% (24.4–27.9%)

62.8% (60.9–64.7%)

3.4% (2.7–4.2%)

ORF9b

585

6.0% (4.3–8.3%)

26.3% (22.8–30.1%)

62.1% (58.0–66.0%)

5.6% (4.0–7.9%)

ORF10

226

1.3% (0.3–4.1%)

23.9% (18.6–30.1%)

73.5% (67.1–79.0%)

1.3% (0.3–4.1%)

S:135–164

182

0% (0.0–2.6%)

16.5% (11.6–22.9%)

69.8% (62.5–76.2%)

13.7% (9.3–19.8%)

S:465–494

219

7.3% (4.4–11.8%)

25.6% (20.0–32.0%)

55.3% (48.4–61.9%)

11.9% (8.0–17.1%)

Genome

58324

9.1% (8.8–9.3%)

42.0% (41.6–42.4%)

47.4% (47.0–47.8%)

1.5% (1.4–1.6%)

  1. Results are based on the fitness effect estimates of Bloom and Neher19, downloaded from https://github.com/jbloomlab/SARS2-mut-fitness (aamut_fitness_all.csv, public_2023-10-01 dataset; accessed 2023/10/05). The central 95% of synonymous mutational fitness effects were used as the null (neutral) distribution. Specifically, nonsynonymous mutations were classified by their fitness effects as (1) lethal if ≤ −3.95; (2) deleterious if > −3.95 and < −1.75; (3) neutral if ≥ −1.75 and <1.20; and (4) beneficial if ≥ 1.20 (−3.95 is the median effect of stop mutations and −1.75–1.20 is the central 95% of synonymous mutational effects). Ranges indicate 95% binomial confidence intervals. Sites in putative overlapping ORFs25 were included. S:135–164 and S:465–494 refer to the 30-codon windows with the highest values of fb. The final row provides results for the full coding genome (bold). Scripts, analysis code, input data, and intermediate files are available at https://doi.org/10.5281/zenodo.10552831.
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