Introduction
Patients and methods
Study design and setting
Target population and data collection
Study period
Sample collection and processing
SARS-CoV-2 whole-genome sequencing
Sequence alignment and phylogenetic analysis
Data analysis methods
Results
Phylogenetic analysis of SARS-CoV-2 genomes
Distribution of SARS-CoV-2 lineages and clades
Analysis of omicron genome sequences
Genomic variation and mutation signature
Spike gene
Other genes of SARS-CoV-2
Comparison of omicron and previous SARS-CoV-2 variants
Incidence rate and demographic characteristics of COVID-19
Characteristics | Omicron (N = 60,665) | Other variants (N = 441,964) | OR | 95% CI | P value | ||
---|---|---|---|---|---|---|---|
Number | Percent | Number | Percent | ||||
Age group | |||||||
1–15 | 1,573 | 2.6% | 9,664 | 2.2% | 1.2 | 1.13–1.26 | < 0.001 |
16–50 | 34,781 | 57.3% | 232,966 | 52.7% | 1.2 | 1.19–1.23 | < 0.001 |
51–65 | 12,306 | 20.3% | 118,523 | 26.8% | 0.7 | 0.68–0.71 | < 0.001 |
> 65 | 12,005 | 19.8% | 80,811 | 18.3% | 1.1 | 1.10–1.13 | < 0.001 |
Gender | |||||||
Male | 28,671 | 47.3% | 219,885 | 49.8% | 0.9 | 0.89–0.92 | < 0.001 |
Female | 31,994 | 52.7% | 222,027 | 50.2% | |||
Missing | 0 | 52 | 0.0% | ||||
Region | |||||||
Urban | 30,446 | 50.2% | 205,768 | 46.6% | 1.2 | 1.14–1.18 | < 0.001 |
Upper Egypt | 19,019 | 31.4% | 146,977 | 33.3% | 0.9 | 0.90–0.93 | < 0.001 |
Lower Egypt | 9,176 | 15.1% | 77,943 | 17.6% | 0.8 | 0.81–0.85 | < 0.001 |
Frontier | 2,024 | 3.3% | 11,276 | 2.6% | 1.3 | 1.26–1.38 | < 0.001 |
Duration onset – seeking healthcare | |||||||
0–2 | 25,854 | 42.6% | 162,098 | 36.7% | 1.3 | 1.26–1.31 | < 0.001 |
3–10 | 17,406 | 28.7% | 147,090 | 33.3% | 0.8 | 0.79–0.82 | < 0.001 |
> 10 | 1,084 | 1.8% | 9,289 | 2.1% | 0.8 | 0.79–0.90 | < 0.001 |
Missing | 16,321 | 26.9% | 123,487 | 27.9% | 0.9 | 0.93–0.97 | < 0.001 |
Comorbidities | 11,385 | 18.8% | 92,754 | 21.0% | 0.9 | 0.85–0.89 | < 0.001 |
Symptoms | |||||||
Fever | 34,223 | 56.4% | 277,232 | 62.7% | 0.8 | 0.76–0.78 | < 0.001 |
Dyspnea | 18,278 | 30.1% | 161,767 | 36.6% | 0.7 | 0.73–0.76 | < 0.001 |
Diarrhea | 5,115 | 8.4% | 55,595 | 12.6% | 0.6 | 0.62–0.66 | < 0.001 |
Pneumonia | 8,232 | 13.6% | 90,784 | 20.5% | 0.6 | 0.58–0.62 | < 0.001 |
Case fatality rate | 3,884 | 6.4% | 34,438 | 7.8% | 0.8 | 0.78–0.84 | < 0.001 |
Hospitalized | 13,395 | 22.1% | 145,237 | 32.9% | 0.6 | 0.57–0.59 | < 0.001 |
Hospital stay (days) | |||||||
0–7 | 7,536 | 56.3% | 68,665 | 47.3% | 1.4 | 1.38–1.49 | < 0.001 |
8–14 | 2,237 | 16.7% | 26,135 | 18.0% | 0.9 | 0.87–0.96 | < 0.001 |
> 14 | 906 | 6.8% | 11,166 | 7.7% | 0.9 | 0.81–0.93 | < 0.001 |
Missing | 2,716 | 20.3% | 39,271 | 27.0% | 0.7 | 0.66–0.72 | < 0.001 |
ICU admission | 2,108 | 15.7% | 13,656 | 9.4% | 1.8 | 1.71–1.89 | < 0.001 |
Ventilation | 1,154 | 8.6% | 9,051 | 6.2% | 1.4 | 1.33–1.51 | < 0.001 |
Died at hospital | 2,775 | 20.7% | 24,005 | 16.5% | 1.3 | 1.26–1.38 | < 0.001 |
The relative risk of death from omicron compared to other variants
Characteristic | Omicron (N = 3,884) | Other variants (N = 34,438) | OR | 95% CI | P value | ||
---|---|---|---|---|---|---|---|
No. | Percent | No. | Percent | ||||
Case fatality rate | 3884 | 6.4% | 34,438 | 7.8% | 0.8 | 0.78–0.84 | < 0.001 |
Age group (years) | |||||||
1—15 | 39 | 1.0% | 157 | 0.5% | 2.2 | 1.56–3.15 | < 0.001 |
16–50 | 285 | 7.3% | 4475 | 13.0% | 0.5 | 0.47–0.60 | < 0.001 |
51–65 | 908 | 23.4% | 12,093 | 35.1% | 0.6 | 0.53–0.61 | < 0.001 |
> 65 | 2652 | 68.3% | 17,713 | 51.4% | 2.0 | 1.89–2.18 | < 0.001 |
Male sex | 1996 | 51.4% | 17,105 | 49.7% | 1.1 | 1.00-1.14 | 0.042 |
Region | |||||||
Lower Egypt | 1552 | 40.0% | 11,466 | 33.3% | 1.3 | 1.25–1.43 | < 0.001 |
Upper Egypt | 1124 | 28.9% | 12,009 | 34.9% | 0.8 | 0.71–0.82 | < 0.001 |
Urban | 1055 | 27.2% | 10,064 | 29.2% | 0.9 | 0.84–0.97 | 0.007 |
Frontier | 153 | 3.9% | 899 | 2.6% | 1.5 | 1.281.82 | < 0.001 |
Comorbidity | 1719 | 44.3% | 14,206 | 41.3% | 1.1 | 1.06–1.21 | < 0.01 |
Hospitalized | 2775 | 71.5% | 24,005 | 69.7% | 1.1 | 1.01–1.17 | 0.026 |
Onset - admission | |||||||
0–2 | 1165 | 42.0% | 9518 | 39.7% | 1.1 | 1.01–1.19 | 0.019 |
3–10 | 1477 | 53.2% | 12,330 | 51.4% | 1.1 | 1.00-1.17 | 0.070 |
> 10 | 63 | 2.3% | 625 | 2.6% | 0.9 | 0.67–1.13 | 0.323 |
Missing | 70 | 2.5% | 1532 | 6.4% | 0.4 | 0.30–0.48 | < 0.001 |
Hospital stay (days) | |||||||
0–7 | 1607 | 57.9% | 12,482 | 52.0% | 1.3 | 1.17–1.38 | < 0.001 |
8–14 | 638 | 23.0% | 5168 | 21.5% | 1.1 | 1.00-1.20 | 0.08 |
> 14 | 328 | 11.8% | 2675 | 11.1% | 1.1 | 0.95–1.21 | 0.229 |
Missing | 202 | 7.3% | 3680 | 15.3% | 0.4 | 0.37–0.50 | < 0.001 |
ICU admitted | 839 | 21.6% | 5428 | 15.8% | 1.5 | 1.36–1.60 | < 0.001 |
Ventilated | 471 | 12.1% | 3088 | 9.0% | 1.4 | 1.26–1.55 | < 0.001 |