Table 1 Comparison of demographic and clinical characteristics, shedding and cycle threshold (Ct) value of infection episodes with Beta and Delta variants vs ancestral in a rural and an urban community, South Africa, 2020-2021

Site

Urban

38/66 (58)

141/260 (54)

116/322 (36)

0.9 (0.5-1.5)

0.4 (0.2-0.7)

Age group (years)

<5

3/66 (5)

27/260 (10)

32/322 (10)

3.0 (0.8-10.8)

4.2 (1.2-15.2)

4.2 (0.9-19.7)

6.7 (1.4-31.2)

5-12

9/66 (14)

59/260 (23)

113/322 (35)

2.2 (0.9-5.1)

5.0 (2.2-11.5)

2.6 (1.1-6.6)

6.6 (2.6-16.7)

13-18

14/66 (21)

39/260 (15)

66/322 (21)

0.9 (.4-2.0)

1.9 (0.9-4.0)

0.8 (0.4-1.7)

1.5 (0.7-3.3)

19-39

23/66 (35)

69/260 (27)

58/322 (18)

Reference

Reference

Reference

Reference

40-59

12/66 (18)

38/260 (15)

32/322 (10)

1.1 (0.5-2.4)

1.1 (0.5-2.4)

0.9 (0.4-2.0)

0.9 (0.4-2.1)

≥60

5/66 (8)

28/260 (11)

21/322 (7)

1.9 (0.6-5.4)

1.7 (0.6-4.9)

1.7 (0.6-5.0)

1.5 (0.5-4.6)

Sex

Female

44/66 (67)

166/260 (64)

185/322 (57)

0.9 (0.5-1.6)

0.7 (0.4-1.2)

HIV and viral load copies/ml

Uninfected

52/66 (79)

200/260 (77)

270/322 (84)

Reference

Reference

Infected <400

7/66 (11)

35/260 (13)

26/322 (8)

1.3 (0.5-3.1)

0.7 (0.3-1.7)

Infected ≥400

3/66 (5)

14/260 (5)

7/322 ()2)

1.2 (0.3-4.4)

0.4 (0.1-1.8)

HIV and/or viral load unknown

4/66 (6)

11/260 (4)

19/322 (6)

0.7 (0.2-2.3)

0.9 (0.3-2.8)

Other underlying illness^a

Present

8/66 (12)

27/260 (10)

25/322 (8)

0.8 (0.4-1.9)

0.6 (0.3-1.4)

BMI^b

Underweight

2/66 (3)

18/260 (7)

32/320 (10)

2.2 (0.5-9.8)

2.6 (0.6-11.3)

Normal weight

29/66 (44)

121/260 (47)

181/320 (57)

Reference

Reference

Overweight

13/66 (20)

54/260 (21)

55/320 (17)

1.0 (0.5-2.1)

0.7 (0.3-1.4)

Obese

22/66 (33)

67/260 (26)

52/320 (16)

0.7 (0.4-1.4)

0.4 (0.2-0.7)

Symptoms

Present

7/66 (11)

44/260 (17)

46/322 (14)

1.7 (0.7-4.0)

1.4 (0.6-3.3)

Shedding duration

>4 days

48/66 (73)

208/260 (80)

255/322 (79)

1.5 (0.8-2.8)

1.4 (0.8-2.6)

Minimum Ct value

>35

10/66 (15)

19/260 (7)

18/322 (6)

Reference

Reference

Reference

Reference

30-35

6/66 (9)

6/260 (10)

36/322 (11)

2.3 (0.7-7.4)

3.3 (1.1-10.6)

2.8 (0.8-9.3)

4.5 (1.3-15.5)

<30

50/66 (76)

215/260 (83)

268/322 (83)

2.3 (1.0-5.2)

3.0 (1.3-6.8)

3.2 (1.3-7.9)

6.0 (2.3-15.7)

Previous infection^c

6/61 (10)

25/257 (10)

82/322 (25)

1.0 (0.4-2.5)

3.1 (1.3-7.5)

1.6 (0.6-4.3)

6.2 (2.3-16.4)

SARS-CoV-2 vaccine status before episode

Unvaccinated

62/66 (94)

237/260 (91)

297/322 (92)

Reference

Reference

Partially vaccinated

3/66 (5)

19/260 (7)

11/322 (3)

1.6 (05-5.8)

0.8 (0.2-2.8)

Fully vaccinated

1/66 (2)

4/260 (2)

14/322 (4)

1.0 (0.1-9.5)

2.9 (0.4-22.6)