Table 4.
Multivariable logistic regression analysis evaluating the association between SGTF infection during Oct 1–Nov 30, 2021, compared with delta variant infection during April 1–Nov 9, 2021, and severe disease among hospitalised individuals with a known outcome, South Africa* (n=1036)
| Severe disease† | Adjusted odds ratio (95% CI) | p value | |
|---|---|---|---|
| SARS-CoV-2 variant (n=1037) | |||
| SGTF | 57/244 (23·4%) | 0·3 (0·2–0·5) | <0·001 |
| Delta (B.1.617.2) | 496/793 (62·5%) | 1 (ref) | .. |
| Age group (n=1037) | |||
| <5 years | 7/41 (17·1%) | 0·5 (0·2–1·6) | 0·23 |
| 5–12 years | 4/16 (25·0%) | 0·7 (0·2–2·9) | 0·61 |
| 13–18 years | 3/22 (13·6%) | 0·2 (0·0–0·8) | 0·023 |
| 19–24 years | 15/42 (35·7%) | 1 (ref) | .. |
| 25–39 years | 71/243 (29·2%) | 0·8 (0·4–1·9) | 0·66 |
| 40–59 years | 189/309 (61·2%) | 2·2 (1·0–5·0) | 0·048 |
| ≥60 years | 264/364 (72·5%) | 3·8 (1·7–8·6) | 0·001 |
| Sex (n=1036) | |||
| Male | 248/425 (58·4%) | 1 (ref) | .. |
| Female | 305/611 (49·9%) | 0·7 (0·5–1·0) | 0·032 |
| Province (n=1037) | |||
| Eastern Cape | 42/47 (89·4%) | 3·5 (1·2–10·3) | 0·023 |
| Free State | 2/4 (50·0%) | 1·1 (0·1–24·3) | 0·94 |
| Gauteng | 210/432 (48·6%) | 1·1 (0·7–1·9) | 0·61 |
| KwaZulu-Natal | 28/48 (58·3%) | 2·1 (0·9–4·7) | 0·089 |
| Limpopo | 78/103 (75·7%) | 1·9 (1·0–3·7) | 0·050 |
| Mpumalanga | 44/60 (73·3%) | 1·8 (0·8–4·0) | 0·13 |
| North West | 87/148 (58·8%) | 1 (ref) | .. |
| Northern Cape | 23/26 (88·5%) | 5·9 (1·4–24·3) | 0·014 |
| Western Cape | 39/169 (23·1%) | 0·1 (0·1–0·2) | <0·001 |
| Comorbidity‡(n=1037) | |||
| Absent | 270/658 (41·0%) | 1 (ref) | .. |
| Present | 283/379 (74·7%) | 2·8 (2·0–4·0) | <0·001 |
| Health-care sector (n=1037) | |||
| Public | 472/787 (60·0%) | 1 (ref) | .. |
| Private | 81/250 (32·4%) | 0·7 (0·4–1·3) | 0·28 |
| Days between diagnosis and admission (n=1037) | |||
| 1–7 days before diagnosis | 154/267 (57·7%) | 1 (ref) | .. |
| 0–6 days after diagnosis | 351/686 (51·2%) | 0·7 (0·5–1·0) | 0·061 |
| 7–21 days after diagnosis | 48/84 (57·1%) | 0·9 (0·5–1·8) | 0·85 |
| Reinfection§(n=1037) | |||
| No | 541/1000 (54·1%) | 1 (ref) | .. |
| Yes | 12/37 (32·4%) | 1·1 (0·5–2·7) | 0·80 |
| SARS-CoV-2 vaccination¶(n=1037) | |||
| No | 141/207 (68·1%) | 1 (ref) | .. |
| Yes | 21/38 (55·3%) | 0·6 (0·2–1·5) | 0·25 |
| Unknown | 391/792 (49·4%) | 1·1 (0·7–1·7) | 0·79 |
Data are n/N (%), unless otherwise specified. SGTF=S gene target failure.
Patients with COVID-19 followed up for in-hospital outcome until Dec 21, 2021.
Severe disease was defined as a hospitalised patient meeting at least one of the following criteria: admitted to an intensive care unit; received oxygen treatment; was ventilated; received extracorporeal membrane oxygenation; had acute respiratory distress syndrome; or had died.
Comorbidity was defined as the presence of at least one of the following conditions: hypertension, diabetes, chronic cardiac disease, chronic kidney disease, asthma, chronic obstructive pulmonary disease, malignancy, HIV, and active or previous tuberculosis.
Reinfection was defined by an individual having at least one positive SARS-CoV-2 test more than 90 days before the current positive SARS-CoV-2 test.
Vaccination was defined as having at least one dose of a SARS-CoV-2 vaccine (Ad.26.COV2.S [Johnson & Johnson] or BNT162b2 [Pfizer–BioNTech]).