1. Epidemiology and Global Health
  2. Microbiology and Infectious Disease

Association of close-range contact patterns with SARS-CoV-2: a household transmission study

  1. Jackie Kleynhans  Is a corresponding author
  2. Lorenzo Dall'Amico
  3. Laetitia Gauvin
  4. Michele Tizzoni
  5. Lucia Maloma
  6. Sibongile Walaza
  7. Neil A Martinson
  8. Anne von Gottberg
  9. Nicole Wolter
  10. Mvuyo Makhasi
  11. Cheryl Cohen
  12. Ciro Cattuto
  13. Stefano Tempia
  14. SA-S-HTS Group
  1. Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, South Africa
  2. School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, South Africa
  3. ISI Foundation, Italy
  4. Institute for Research on Sustainable Development, France
  5. Department of Sociology and Social Research, University of Trento, Italy
  6. Perinatal HIV Research Unit, University of the Witwatersrand, South Africa
  7. Johns Hopkins University Center for TB Research, United States
  8. School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, South Africa
  9. Department of Informatics, University of Turin, Italy
https://doi.org/10.7554/eLife.84753
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Cite this article
  1. Jackie Kleynhans
  2. Lorenzo Dall'Amico
  3. Laetitia Gauvin
  4. Michele Tizzoni
  5. Lucia Maloma
  6. Sibongile Walaza
  7. Neil A Martinson
  8. Anne von Gottberg
  9. Nicole Wolter
  10. Mvuyo Makhasi
  11. Cheryl Cohen
  12. Ciro Cattuto
  13. Stefano Tempia
  14. SA-S-HTS Group
(2023)
Association of close-range contact patterns with SARS-CoV-2: a household transmission study
eLife 12:e84753.
https://doi.org/10.7554/eLife.84753
  2. Download BibTeX
  3. Download .RIS
4 figures, 6 tables and 1 additional file

Figures

Figure 1
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Participants screened, enrolled, included in household transmission study, and included in contact analysis, Klerksdorp and Soweto, South Africa, 2020–2021.
Figure 2
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Contact parameters related to the duration of all close-range proximity events within households by age group (year) and site, Klerksdorp (n=143) and Soweto (n=197), South Africa, September 2020–October 2021.

Median daily duration: median of cumulative duration of close-range proximity events for each day of deployment, in minutes. Maximum duration: longest duration of a close-range proximity event during deployment, in minutes. Median average daily duration: median of cumulative duration of close-range proximity events in the day divided by the cumulative number of close-range proximity events during that day, in minutes. Cumulative time in contact: cumulative duration of close-range proximity events over the deployment period divided by the number of days sensor was worn, in minutes. Horizontal line represents the median, box represents the 25th and 75th percentile, whiskers represent the 1st and 99th percentile, and circles indicate outliers.

Figure 3
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Contact parameters related to the frequency of all close-range proximity events within households by age group (year) and site, Klerksdorp (n=143) and Soweto (n=197), South Africa, September 2020–October 2021.

Median daily frequency: median of number of close proximity events for each day of deployment. Maximum frequency: highest number of close proximity events in one day during deployment. Daily average frequency: cumulative duration of close-range proximity events over the deployment period divided by the cumulative number of close-range proximity events during the deployment period. Horizontal line represents the median, box represents the 25th and 75th percentile, whiskers represent 1st and 99th percentile, and circles indicate outliers.

Figure 4
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Aged-based contact matrices based close-proximity event duration (A–C) and frequency (D–E) for the entire deployment period overall (A, D) Klerksdorp (B,D, n=143), and Soweto (C,F, n=193), September 2020–October 2021.

Teal denotes the lowest value, purple highest, and white no data for age group combination.

Tables

Table 1
Baseline characteristics of SARS-CoV-2 index cases (n=124) and their household contacts (n=373) included in the household cumulative infection risk study and included in the contact study, Klerksdorp and Soweto, South Africa, September 2020–October 2021.
OverallNo contact dataIncluded in contact analysisp-value
n=497n=157n=340
Site
Klerksdorp234 (47.1)91 (58.0)143 (42.1)0.001
Soweto263 (52.9)66 (42.0)197 (57.9)
Index
Index124 (24.9)36 (22.9)88 (25.9)0.551
Contact373 (75.1)121 (77.1)252 (74.1)
Household size
3–5347 (69.8)122 (77.7)225 (66.2)0.012
6–10150 (30.2)35 (22.3)115 (33.8)
Rooms used for sleeping
1–2244 (49.1)76 (48.4)168 (49.4)0.387
3–4203 (40.8)69 (43.9)134 (39.4)
>450 (10.1)12 (7.6)38 (11.2)
Crowding
No353 (71.0)112 (71.3)241 (70.9)1
Yes144 (29.0)45 (28.7)99 (29.1)
Child <5 years
No423 (85.1)136 (86.6)287 (84.4)0.611
Yes74 (14.9)21 (13.4)53 (15.6)
HH member smokes inside
No401 (80.7)116 (73.9)285 (83.8)0.013
Yes96 (19.3)41 (26.1)55 (16.2)
Main water source inside home
No350 (70.4)120 (76.4)230 (67.6)0.059
Yes147 (29.6)37 (23.6)110 (32.4)
Main cooking fuel
Electricity480 (96.6)152 (96.8)328 (96.5)1
Gas/Paraffin17 (3.4)5 (3.2)12 (3.5)
Monthly household income (US$)
0–5042 (8.5)20 (12.7)22 (6.5)0.125
51–10041 (8.2)16 (10.2)25 (7.4)
101–19090 (18.1)25 (15.9)65 (19.1)
191–37577 (15.5)21 (13.4)56 (16.5)
376–75036 (7.2)12 (7.6)24 (7.1)
>75020 (4.0)9 (5.7)11 (3.2)
Refused to disclose191 (38.4)54 (34.4)137 (40.3)
Age (years)
<519 (3.8)8 (5.1)11 (3.2)0.711
5–1273 (14.7)25 (15.9)48 (14.1)
13–1760 (12.1)18 (11.5)42 (12.4)
18–34130 (26.2)45 (28.7)85 (25.0)
35–59163 (32.8)47 (29.9)116 (34.1)
60+52 (10.5)14 (8.9)38 (11.2)
Sex
Male196 (39.4)61 (38.9)135 (39.7)0.935
Female301 (60.6)96 (61.1)205 (60.3)
Level of education*
No schooling/kindergarten18 (3.6)5 (3.2)13 (3.8)0.959
Primary23 (4.6)8 (5.1)15 (4.4)
Secondary110 (22.1)32 (20.4)78 (22.9)
Matriculation169 (34.0)52 (33.1)117 (34.4)
Post-secondary20 (4.0)7 (4.5)13 (3.8)
Unknown157 (31.6)53 (33.8)104 (30.6)
Employment*
Unemployed170 (34.2)52 (33.1)118 (34.7)0.876
Student33 (6.6)9 (5.7)24 (7.1)
Employed109 (21.9)34 (21.7)75 (22.1)
Unknown185 (37.2)62 (39.5)123 (36.2)
Smoking cigarettes ‡
No65 (13.1)22 (14.0)43 (12.6)0.558
Yes426 (85.7)132 (84.1)294 (86.5)
Unknown6 (1.2)3 (1.9)3 (0.9)
Living with HIV
No241 (48.5)87 (55.4)154 (45.3)0.095
Yes56 (11.3)17 (10.8)39 (11.5)
Unknown200 (40.2)53 (33.8)147 (43.2)
Underlying illness†
No416 (83.7)128 (81.5)288 (84.7)0.395
Yes71 (14.3)24 (15.3)47 (13.8)
Unknown10 (2.0)5 (3.2)5 (1.5)
Body-mass index
Underweight28 (5.6)8 (5.1)20 (5.9)0.757
Normal weight207 (41.6)67 (42.7)140 (41.2)
Overweight100 (20.1)31 (19.7)69 (20.3)
Obese152 (30.6)46 (29.3)106 (31.2)
Unknown10 (2.0)5 (3.2)5 (1.5)
SARS-CoV-2 infection
Negative153 (30.8)54 (34.4)99 (29.1)0.478
Positive (index)124 (24.9)36 (22.9)88 (25.9)
Positive (not index)220 (44.3)67 (42.7)153 (45.0)

  1. Values in headers indicate the number of individuals. p-values calculated using the Chi-squared test.

  2. *

    For individuals ≥18 years old.

  3. †

    Self-reported history of diabetes, hypertension, asthma, lung disease, heart disease, stroke, spinal cord injury, epilepsy, cancer, liver disease, renal disease, and pre-maturity.

  4. ‡

    For individuals ≥15 years old.

Table 2
Close-range proximity event parameters by age group (year) and site, Klerksdorp and Soweto, South Africa, September 2020–October 2021.
Median daily duration *Maximum duration †Median average daily duration ‡Cumulative time in contact (per day) §Median daily frequency Maximum frequency **Daily average frequency ††
Both sitesnMedian (IQR)
Overall34018.2 (6.6–45.1)60.5 (25.0–141.7)0.7 (0.5–0.8)3.3 (1.5–8.0)25.5 (10.0–58.1)75.0 (32.8–134.2)4.0 (2.0–8.7)
<51140.7 (17.3–87.2)163.0 (37.3–200.8)0.7 (0.6–0.8)7.0 (3.4–11.8)73.5 (24.5–105.2)209.0 (48.5–277.0)9.5 (4.4–16.2)
5–124858.0 (22.1–106.3)134.3 (58.3–296.7)0.8 (0.6–1.0)8.4 (3.7–18.9)72.2 (24.8–112.5)139.0 (52.5–273.5)9.9 (4.6–19.8)
13–174222.4 (7.7–51.2)82.0 (40.8–164.1)0.6 (0.6–0.8)4.6 (2.1–11.1)33.2 (14.1–63.5)96.0 (38.5–169.5)5.6 (3.0–10.0)
18–348514.7 (4.0–43.2)59.0 (16.7–134.3)0.7 (0.6–0.8)2.8 (1.2–6.7)19.0 (5.5–47.0)66.0 (23.0–116.0)3.0 (1.8–7.3)
35–5911614.2 (5.6–35.3)52.2 (23.8–99.5)0.6 (0.5–0.8)2.4 (1.3–4.3)20.8 (8.4–37.6)67.5 (32.8–105.5)3.3 (1.8–5.2)
≥603814.0 (6.6–25.4)42.0 (17.4–79.6)0.6 (0.5–0.7)2.6 (1.2–5.7)19.8 (12.2–36.9)55.5 (28.8–89.8)3.8 (1.8–6.8)
Klerksdorp
Overall14320.0 (6.5–56.8)66.7 (29.2–149.2)0.7 (0.5–0.9)3.3 (1.6–8.1)25.5 (9.8–65.2)80.0 (36.0–163.0)4.0 (2.2–8.7)
<5520.0 (20.0–137.2)48.7 (41.0–294.3)0.8 (0.7–0.9)3.6 (3.3–22.9)29.5 (25.0–163.5)69.0 (58.0–290.0)4.9 (4.0–20.1)
5–122167.5 (21.3–159.7)133.3 (59.0–336.3)0.7 (0.6–1.1)8.2 (3.7–23.7)78.0 (20.5–192.0)138.0 (51.0–273.0)8.4 (3.5–20.5)
13–172330.7 (8.8–75.7)140.0 (45.8–282.8)0.7 (0.6–0.9)6.0 (2.4–12.0)34.0 (14.8–81.2)129.0 (53.0–179.0)8.0 (3.5–10.3)
18–343815.0 (3.5–48.0)61.5 (11.0–134.8)0.6 (0.6–0.8)3.1 (1.2–6.8)19.5 (4.0–61.6)63.5 (13.5–144.5)3.1 (1.8–7.4)
35–594213.8 (6.1–32.8)54.5 (26.8–98.1)0.6 (0.5–0.7)2.6 (1.3–5.2)20.8 (9.0–32.8)64.5 (36.5–98.8)3.4 (1.8–4.8)
≥601422.2 (6.8–41.9)51.7 (19.8–114.7)0.5 (0.5–0.7)2.2 (1.2–4.8)31.0 (10.8–45.9)80.5 (34.0–104.0)3.4 (2.1–4.7)
Soweto
Overall19716.7 (6.7–40.8)59.0 (22.3–122.7)0.6 (0.5–0.8)3.2 (1.4–7.1)25.5 (10.5–56.0)71.0 (32.0–116.0)4.1 (2.0–8.6)
<5**652.5 (21.2–71.6)167.8 (53.5–184.4)0.6 (0.6–0.7)7.9 (6.4–8.9)86.2 (36.4–103.1)215.0 (74.0–253.2)9.9 (9.3–11.9)
5–122757.0 (23.7–95.8)135.3 (57.7–294.0)0.8 (0.6–0.9)9.1 (4.3–16.1)66.5 (35.5–111.8)140.0 (73.0–263.5)10.2 (6.1–18.3)
13–171921.3 (7.2–32.5)62.3 (20.0–98.3)0.6 (0.5–0.7)4.0 (1.2–5.7)33.0 (12.5–43.5)80.0 (28.5–105.0)4.2 (1.6–7.1)
18–344713.3 (4.1–39.2)59.0 (20.8–120.2)0.7 (0.6–0.9)2.1 (1.3–6.4)19.0 (6.0–41.2)67.0 (28.0–108.5)2.9 (1.9–6.9)
35–597414.8 (5.6–39.0)50.2 (22.6–98.8)0.6 (0.5–0.8)2.3 (1.1–4.1)20.5 (8.1–49.1)69.0 (30.0–109.8)3.3 (1.8–5.3)
≥602411.0 (7.0–20.7)37.0 (18.2–62.8)0.6 (0.5–0.7)3.6 (1.2–5.9)19.2 (12.8–30.0)49.0 (29.8–77.8)4.9 (1.6–7.2)
  1. *

    Median daily duration (median of cumulative duration of close-range proximity events for each day of deployment, in minutes).

  2. †

    Maximum duration (longest duration of a close-range proximity event during deployment, in minutes).

  3. ‡

    Median average daily duration (median of cumulative duration of close-range proximity events in the day divided by the cumulative number of close-range proximity events during that day, in minutes).

  4. §

    Cumulative time in contact (cumulative duration of close-range proximity events over the deployment period divided by the number of days sensor was worn, in minutes).

  5. Median daily frequency (median of number of close proximity events for each day of deployment).

  6. **

    Maximum frequency (highest number of close proximity events in one day during deployment).

  7. ††

    Daily average frequency (cumulative duration of close-range proximity events over the deployment period divided by the cumulative number of close-range proximity events during the deployment period).

Table 3
Association of contact parameters with SARS-CoV-2 household acquisition * using the Wilcoxon rank-sum test, Klerksdorp and Soweto, South Africa, September 2020–October 2021.
Contact parameterp-value (including all households)
Median daily duration with index †0.83
Maximum duration with index ‡0.32
Median average daily duration with index §0.78
Cumulative time in contact with index 0.83
Median daily frequency with index **0.71
Maximum frequency with index ††0.57
Daily average frequency with index ‡ ‡0.54
Median daily duration with infected household members †0.25
Maximum duration with infected household members ‡0.79
Median average daily duration with infected household members §0.27
Cumulative time in contact with infected household members 0.14
Median daily frequency with infected household members **0.32
Maximum frequency with infected household members ††0.76
Daily average frequency with infected household members ‡ ‡0.18
  1. *

    Outcome investigated: testing positive for SARS-CoV-2.

  2. †

    Median daily duration (median of cumulative duration of close-range proximity events for each day of deployment, in minutes).

  3. ‡

    Maximum duration (longest duration of a close-range proximity event during deployment, in minutes).

  4. §

    Median average daily duration (median of cumulative duration of close-range proximity events in the day divided by the cumulative number of close-range proximity events during that day, in minutes).

  5. Cumulative time in contact (cumulative duration of close-range proximity events over the deployment period divided by the number of days sensor was worn, in minutes).

  6. **

    Median daily frequency (median of number of close proximity events for each day of deployment).

  7. ††

    Maximum frequency (highest number of close proximity events in one day during deployment).

  8. ‡ ‡

    Daily average frequency (cumulative duration of close-range proximity events over the deployment period divided by the cumulative number of close-range proximity events during the deployment period).

Table 4
Factors associated with SARS-CoV-2 household transmission from index cases and acquisition in household contacts (contact parameters with index case), Klerksdorp and Soweto, South Africa, 2020–2021 (n=252).
SARS-CoV-2 infection*Univariate analysisMultivariable analysisMultivariable analysis (including contact parameter)
Negative
n=99		Positive
n=153		OR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)
Index Characteristics
Site
Klerksdorp47/106 (44%)59/106 (56%)Reference
Soweto52/146 (36%)94/146 (64%)1.73 (0.72–4.14)
Age (years)
18–3436/76 (47%)40/76 (53%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
35–5948/137 (35%)89/137 (65%)2.20 (0.80–6.02)2.21 (0.80–6.14)2.24 (0.79–6.32)2.17 (0.77–6.14)2.21 (0.79–6.15)2.51 (0.85–7.40)2.43 (0.85–6.94)2.19 (0.77–6.23)2.64 (0.89–7.85)
≥6015/39 (38%)24/39 (62%)1.86 (0.47–7.37)2.08 (0.51–8.50)2.10 (0.50–8.82)1.96 (0.47–8.25)2.06 (0.49–8.57)2.40 (0.55–10.49)2.34 (0.55–9.98)2.03 (0.48–8.59)2.43 (0.55–10.80)
Minimum Ct value
>3517/21 (81%)4/21 (19%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
30–3523/50 (46%)27/50 (54%)7.58 (1.21–47.43)7.07 (0.75–66.23)7.23 (0.76–68.84)6.83 (0.72–64.85)6.88 (0.72–65.28)7.98 (0.79–80.47)7.62 (0.78–74.23)6.59 (0.68–64.07)8.06 (0.78–83.67)
<3058/178 (33%)120/178 (67%)16.84 (3.05–93.06)10.60 (1.40–80.08)10.77 (1.41–82.26)10.39 (1.36–79.27)10.36 (1.36–79.23)11.04 (1.38–88.37)11.08 (1.42–86.47)10.04 (1.29–78.05)11.05 (1.35–90.60)
Unknown1/3 (33%)2/3 (67%)15.69 (0.31–793.51)7.22 (0.12–438.47)7.27 (0.12–450.06)6.79 (0.11–423.55)7.37 (0.12–465.42)7.55 (0.11–503.58)7.42 (0.12–467.86)6.85 (0.10–453.16)7.92 (0.11–558.92)
SARS-CoV-2 variant
non-Alpha/Beta/Delta5/14 (36%)9/14 (64%)1.22 (0.22–6.93)2.04 (0.31–13.41)2.12 (0.32–14.08)2.15 (0.32–14.51)2.06 (0.31–13.72)2.00 (0.29–13.76)1.99 (0.30–13.26)1.99 (0.29–13.61)2.07 (0.29–14.67)
Alpha2/13 (15%)11/13 (85%)4.81 (0.59–39.19)5.02 (0.52–48.39)5.15 (0.48–55.49)5.48 (0.53–57.15)4.71 (0.43–51.12)3.45 (0.33–36.67)4.59 (0.47–44.90)5.02 (0.50–50.59)4.91 (0.47–51.69)
Beta70/171 (41%)101/171 (59%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
Delta8/38 (21%)30/38 (79%)3.24 (0.93–11.32)3.76 (0.97–14.55)3.90 (0.99–15.29)3.79 (0.96–14.95)3.81 (0.97–14.89)3.86 (0.96–15.53)3.88 (0.99–15.27)3.87 (0.97–15.53)3.94 (0.96–16.23)
Variant Unknown14/16 (88%)2/16 (12%)0.06 (0.01–0.41)0.15 (0.01–1.60)0.16 (0.02–1.67)0.16 (0.01–1.66)0.15 (0.01–1.57)0.14 (0.01–1.56)0.14 (0.01–1.50)0.14 (0.01–1.55)0.14 (0.01–1.61)
Contact characteristics
Age (years)
<58/11 (73%)3/11 (27%)0.17 (0.03–1.05)0.28 (0.04–1.90)0.30 (0.04–2.04)0.31 (0.05–2.11)0.28 (0.04–1.90)0.24 (0.03–1.66)0.24 (0.03–1.70)0.27 (0.04–1.97)0.22 (0.03–1.59)
5–1221/48 (44%)27/48 (56%)0.69 (0.25–1.93)0.54 (0.19–1.52)0.53 (0.18–1.54)0.55 (0.19–1.56)0.51 (0.18–1.46)0.49 (0.17–1.42)0.47 (0.16–1.37)0.51 (0.17–1.48)0.48 (0.17–1.41)
13–1711/42 (26%)31/42 (74%)2.55 (0.78–8.32)2.41 (0.72–8.08)2.42 (0.72–8.16)2.42 (0.72–8.17)2.38 (0.70–8.03)2.47 (0.72–8.45)2.46 (0.73–8.34)2.39 (0.71–8.12)2.57 (0.75–8.83)
18–3422/60 (37%)38/60 (63%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
35–5927/68 (40%)41/68 (60%)0.72 (0.28–1.87)0.60 (0.23–1.57)0.60 (0.23–1.59)0.61 (0.23–1.61)0.59 (0.22–1.56)0.60 (0.23–1.59)0.59 (0.22–1.57)0.58 (0.22–1.55)0.62 (0.23–1.65)
≥6010/23 (43%)13/23 (57%)0.78 (0.21–2.93)0.61 (0.17–2.24)0.61 (0.17–2.27)0.61 (0.17–2.27)0.61 (0.16–2.23)0.65 (0.17–2.46)0.64 (0.17–2.37)0.61 (0.16–2.26)0.66 (0.17–2.54)
Sex
Male52/108 (48%)56/108 (52%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
Female47/144 (33%)97/144 (67%)2.51 (1.25–5.02)2.38 (1.17–4.84)2.37 (1.15–4.86)2.44 (1.18–5.03)2.32 (1.14–4.74)2.25 (1.09–4.63)2.20 (1.07–4.53)2.36 (1.14–4.88)2.21 (1.07–4.59)
Sleep in same room as index
No68/171 (40%)103/171 (60%)Reference
Yes31/81 (38%)50/81 (62%)0.94 (0.47–1.88)
Cared for by index
No84/212 (40%)128/212 (60%)Reference
Yes15/40 (38%)25/40 (62%)0.92 (0.36–2.34)
Median daily duration †5 (1-11)4 (2-12)0.99 (0.98–1.01)1.00 (0.98–1.02)
Maximum duration ‡17 (5–48)14 (4–38)1.00 (0.99–1.00)1.00 (0.99–1.01)
Median average daily duration §0.53 (0.43–0.69)0.56 (0.44–0.67)1.15 (0.60–2.21)1.08 (0.50–2.30)
Cumulative time in contact 0.87 (0.37–1.80)0.90 (0.33–2.27)1.04 (0.92–1.17)1.08 (0.94–1.25)
Median daily frequency 6 (3-15)7 (3-15)1.00 (0.98–1.02)1.01 (0.99–1.03)
Maximum frequency **22 (8–52)19 (7–41)1.00 (0.99–1.01)1.00 (0.99–1.01)
Daily average frequency ††1.00 (0.57–2.77)1.16 (0.53–2.70)1.06 (0.95–1.18)1.10 (0.96–1.25)
  1. *

    n/ row N (%); Median (interquartile range).

  2. †

    Median daily duration (median of cumulative duration of close-range proximity events for each day of deployment, in minutes).

  3. ‡

    Maximum duration (longest duration of a close-range proximity event during deployment, in minutes).

  4. §

    Median average daily duration (median of cumulative duration of close-range proximity events in the day divided by the cumulative number of close-range proximity events during that day, in minutes).

  5. Cumulative time in contact (cumulative duration of close-range proximity events over the deployment period divided by the number of days sensor was worn, in minutes).

  6. **

    Maximum frequency (highest number of close proximity events in one day during deployment).

  7. ††

    Daily average frequency (cumulative duration of close-range proximity events over the deployment period divided by the cumulative number of close-range proximity events during the deployment period). aOR: adjusted odds ratio. Significant associations on multivariable analysis in boldface. Factors investigated but not found significant on multivariable analysis: index sex, HIV status, underlying conditions, body mass index, current smoking, episode duration, serostatus at follow-up end; contact HIV status, underlying conditions, body mass index, current smoking, cared for by index.

Table 5
Factors associated with SARS-CoV-2 household transmission from index cases and acquisition in household contacts (contact parameters with index case) in households with no members excluded from analysis, Klerksdorp and Soweto, South Africa, 2020–2021, (n=192).
SARS-CoV-2 infection*Univariate analysisMultivariable analysisMultivariable analysis (including contact parameter)
Negative
n=66		Positive
n=126		OR (95% CI)aOR (95% CI)aOR (95% CI)
Index Characteristics
Site
Klerksdorp25/70 (36%)45/70 (64%)Reference
Soweto41/122 (34%)81/122 (66%)1.30 (0.42–4.00)
Age (years)
18–3420/48 (42%)28/48 (58%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
35–5932/111 (29%)79/111 (71%)2.52 (0.70–9.13)2.13 (0.60–7.55)1.88 (0.58–6.15)1.99 (0.60–6.55)2.09 (0.63–6.97)1.98 (0.55–7.11)2.02 (0.59–6.89)1.86 (0.54–6.38)2.09 (0.63–7.00)
≥6014/33 (42%)19/33 (58%)1.01 (0.20–5.19)1.41 (0.24–8.22)1.22 (0.23–6.62)1.31 (0.24–7.23)1.38 (0.24–7.84)1.34 (0.23–7.74)1.35 (0.24–7.72)1.26 (0.23–6.94)1.43 (0.26–7.91)
Minimum Ct value
>3516/18 (89%)2/18 (11%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
30–3515/38 (39%)23/38 (61%)22.18 (2.39–205.39)23.38 (1.23–445.33)21.38 (1.41–325.01)22.55 (1.43–354.91)23.36 (1.40–389.09)21.73 (1.24–381.17)21.25 (1.30–347.22)18.86 (1.18–301.62)22.49 (1.37–368.46)
<3034/133 (26%)99/133 (74%)48.47 (5.80–404.75)39.72 (2.69–585.90)37.61 (3.28–431.72)38.32 (3.24–452.80)39.80 (3.20–495.62)37.67 (2.76–513.85)36.87 (3.03–448.62)32.87 (2.61–413.51)38.58 (3.14–473.57)
Unknown1/3 (33%)2/3 (67%)30.11 (0.61–1,497.22)14.55 (0.18–1,148.81)13.46 (0.22–836.17)14.11 (0.22–923.86)15.49 (0.22–1,110.09)14.21 (0.20–1,025.63)13.14 (0.19–918.99)11.86 (0.19–755.20)13.83 (0.20–952.08)
SARS-CoV-2 variant
non-Alpha/Beta/Delta3/8 (38%)5/8 (62%)0.68 (0.09–5.16)0.68 (0.09–5.16)1.79 (0.13–24.54)1.71 (0.14–20.48)1.76 (0.14–21.84)1.85 (0.14–23.74)1.75 (0.14–22.72)1.71 (0.13–21.95)1.60 (0.13–20.06)
Alpha1/11 (9.1%)10/11 (91%)7.00 (0.47–103.30)7.00 (0.47–103.30)5.58 (0.32–96.65)8.18 (0.32–206.89)6.52 (0.32–132.55)5.76 (0.25–133.53)7.47 (0.29–194.23)5.51 (0.29–103.13)5.83 (0.36–94.07)
Beta45/130 (35%)85/130 (65%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
Delta7/33 (21%)26/33 (79%)2.17 (0.61–7.64)2.17 (0.61–7.64)3.01 (0.67–13.53)2.82 (0.68–11.69)2.90 (0.68–12.35)3.01 (0.69–13.17)2.91 (0.68–12.50)2.85 (0.66–12.41)2.73 (0.65–11.51)
Variant Unknown10/10 (100%)0/10 (0%)NANANANANANANANANA
Contact characteristics
Age (years)
<57/8 (88%)1/8 (12%)0.01 (0.00–0.27)0.03 (0.00–0.50)0.03 (0.00–0.51)0.03 (0.00–0.48)0.03 (0.00–0.46)0.03 (0.00–0.52)0.03 (0.00–0.48)0.03 (0.00–0.65)0.03 (0.00–0.44)
5–1214/37 (38%)23/37 (62%)0.38 (0.10–1.40)0.33 (0.09–1.20)0.38 (0.10–1.34)0.35 (0.10–1.23)0.33 (0.10–1.16)0.34 (0.09–1.23)0.35 (0.10–1.24)0.37 (0.10–1.37)0.33 (0.09–1.14)
13–177/33 (21%)26/33 (79%)1.68 (0.38–7.41)1.66 (0.34–8.03)1.57 (0.33–7.58)1.63 (0.33–7.96)1.65 (0.33–8.22)1.61 (0.34–7.72)1.68 (0.34–8.31)1.63 (0.35–7.65)1.66 (0.33–8.25)
18–3410/42 (24%)32/42 (76%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
35–5923/57 (40%)34/57 (60%)0.36 (0.11–1.19)0.35 (0.11–1.13)0.36 (0.11–1.10)0.35 (0.11–1.10)0.35 (0.11–1.09)0.34 (0.10–1.09)0.36 (0.11–1.11)0.36 (0.11–1.16)0.34 (0.11–1.08)
≥605/15 (33%)10/15 (67%)0.47 (0.08–2.68)0.42 (0.08–2.30)0.41 (0.08–2.09)0.42 (0.08–2.16)0.43 (0.08–2.22)0.41 (0.08–2.19)0.43 (0.08–2.23)0.41 (0.08–2.19)0.41 (0.08–2.12)
Sex
Male33/79 (42%)46/79 (58%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
Female33/113 (29%)80/113 (71%)2.40 (1.05–5.46)2.28 (0.96–5.43)2.42 (1.04–5.66)2.38 (1.01–5.62)2.30 (0.99–5.36)2.36 (0.99–5.63)2.34 (0.99–5.55)2.45 (1.02–5.87)2.29 (0.97–5.39)
Sleep in same room as index
No46/133 (35%)87/133 (65%)Reference
Yes20/59 (34%)39/59 (66%)0.90 (0.39–2.08)
Cared for by index
No54/160 (34%)106/160 (66%)Reference
Yes12/32 (38%)20/32 (62%)0.60 (0.19–1.86)
Median daily duration †6 (1-14)4 (1-12)0.99 (0.97–1.01)0.99 (0.97–1.02)
Maximum duration ‡18 (5–51)13 (3–37)1.00 (0.99–1.00)1.00 (0.99–1.01)
Median average daily duration §0.53 (0.43–0.75)0.52 (0.42–0.67)1.10 (0.53–2.27)1.00 (0.42–2.34)
Cumulative time in contact 1.01 (0.37–2.26)0.88 (0.32–2.34)0.98 (0.85–1.12)0.96 (0.80–1.16)
Median daily frequency **9 (3-16)7 (3-15)0.99 (0.97–1.01)1.00 (0.97–1.02)
Maximum frequency ††24 (8–68)19 (6–40)0.99 (0.98–1.00)0.99 (0.98–1.01)
Daily average frequency ‡ ‡1.40 (0.60–3.15)1.07 (0.50–2.70)0.98 (0.84–1.15)0.98 (0.81–1.18)
  1. *

    n/ row N (%); Median (interquartile range).

  2. †

    Median daily duration (median of cumulative duration of close-range proximity events for each day of deployment, in minutes).

  3. ‡

    Maximum duration (longest duration of a close-range proximity event during deployment, in minutes).

  4. §

    Median average daily duration (median of cumulative duration of close-range proximity events in the day divided by the cumulative number of close-range proximity events during that day, in minutes).

  5. Cumulative time in contact (cumulative duration of close-range proximity events over the deployment period divided by the number of days sensor was worn, in minutes).

  6. **

    Median daily frequency (median of number of close proximity events for each day of deployment).

  7. ††

    Maximum frequency (highest number of close proximity events in one day during deployment).

  8. ‡ ‡

    Daily average frequency (cumulative duration of close-range proximity events over the deployment period divided by the cumulative number of close-range proximity events during the deployment period). aOR: adjusted odds ratio. Significant associations on multivariable analysis in boldface.

Table 6
Factors associated with SARS-CoV-2 acquisition within the household (contact parameters with SARS-CoV-2 infected household members), Klerksdorp and Soweto, South Africa, 2020–2021, (n=340).
SARS-CoV-2 infectionUnivariate analysisMultivariable analysisMultivariable analysis (including contact parameter)
Negative
n=99		Positive
n=241		OR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)aOR (95% CI)
Site
Klerksdorp47/143 (33%)96/143 (67%)Reference
Soweto52/197 (26%)145/197 (74%)1.70 (0.64–4.51)
Contact Age (years)
<58/11 (73%)3/11 (27%)0.06 (0.01–0.41)1.88 (0.25–14.08)0.09 (0.01–0.71)0.12 (0.01–0.96)0.11 (0.01–0.89)0.08 (0.01–0.65)0.09 (0.01–0.75)0.15 (0.02–1.21)0.08 (0.01–0.63)
5–1221/48 (44%)27/48 (56%)0.20 (0.07–0.57)9.43 (1.17–75.88)0.17 (0.05–0.56)0.24 (0.08–0.75)0.21 (0.07–0.62)0.16 (0.05–0.48)0.18 (0.05–0.59)0.25 (0.08–0.76)0.15 (0.05–0.48)
13–1711/42 (26%)31/42 (74%)0.87 (0.28–2.70)10.08 (1.34–76.04)0.96 (0.28–3.28)1.00 (0.30–3.36)1.12 (0.34–3.74)0.93 (0.28–3.06)0.95 (0.28–3.25)1.05 (0.32–3.44)0.92 (0.28–3.04)
18–3422/85 (26%)63/85 (74%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
35–5927/116 (23%)89/116 (77%)0.98 (0.41–2.30)8.79 (1.14–67.74)0.87 (0.34–2.23)0.91 (0.36–2.30)0.84 (0.34–2.12)0.86 (0.35–2.13)0.88 (0.34–2.24)0.92 (0.37–2.27)0.87 (0.35–2.15)
≥6010/38 (26%)28/38 (74%)1.11 (0.34–3.58)8.71 (0.98–77.54)0.86 (0.24–3.05)0.86 (0.25–3.00)0.82 (0.24–2.78)0.85 (0.25–2.87)0.87 (0.25–3.05)0.89 (0.27–2.97)0.85 (0.25–2.88)
Contact Sex
Male52/135 (39%)83/135 (61%)Reference
Female47/205 (23%)158/205 (77%)2.64 (1.40–4.95)
Body mass index
Normal weight50/140 (36%)90/140 (64%)Reference
Underweight7/20 (35%)13/20 (65%)0.89 (0.22–3.53)0.90 (0.22–3.67)0.87 (0.20–3.87)1.04 (0.24–4.56)0.88 (0.21–3.73)0.78 (0.19–3.29)0.90 (0.20–3.96)1.01 (0.25–4.09)0.81 (0.19–3.38)
Overweight22/69 (32%)47/69 (68%)1.61 (0.70–3.71)1.17 (0.49–2.76)1.17 (0.47–2.91)1.15 (0.47–2.83)1.17 (0.49–2.78)1.18 (0.49–2.82)1.16 (0.47–2.89)1.14 (0.48–2.67)1.17 (0.49–2.80)
Obese17/106 (16%)89/106 (84%)7.47 (3.10–17.98)4.14 (1.54–11.11)4.31 (1.54–12.03)3.83 (1.40–10.48)3.91 (1.44–10.62)4.40 (1.62–11.92)4.20 (1.51–11.69)3.84 (1.44–10.23)4.33 (1.60–11.69)
Unknown3/5 (60%)2/5 (40%)0.53 (0.03–10.58)NANANANANANANANA
Current smoking
Yes18/43 (42%)25/43 (58%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
No80/294 (27%)214/294 (73%)3.02 (1.19–7.63)3.24 (1.15–9.18)3.12 (1.04–9.39)3.33 (1.12–9.94)3.54 (1.23–10.15)3.14 (1.10–8.97)3.16 (1.05–9.53)3.42 (1.21–9.69)3.10 (1.09–8.80)
Unknown1/3 (33%)2/3 (67%)8.06 (0.17–386.04)NANANANANANANANA
SARS-CoV-2 variant
non-Alpha/Beta/Delta5/19 (26%)14/19 (74%)1.21 (0.15–9.96)1.19 (0.14–10.06)1.13 (0.12–10.46)1.61 (0.18–14.66)1.27 (0.13–12.50)1.08 (0.12–9.43)1.17 (0.13–10.77)1.49 (0.18–12.64)1.08 (0.13–9.25)
Alpha2/17 (12%)15/17 (88%)3.19 (0.24–42.01)4.61 (0.31–69.26)3.79 (0.24–60.31)7.77 (0.49–122.66)18.70 (0.95–368.10)3.19 (0.19–53.63)4.30 (0.28–65.69)5.42 (0.36–82.77)3.92 (0.26–60.08)
Beta70/230 (30%)160/230 (70%)ReferenceReferenceReferenceReferenceReferenceReferenceReferenceReferenceReference
Delta8/50 (16%)42/50 (84%)3.00 (0.64–13.99)3.00 (0.60–14.89)2.78 (0.54–14.39)3.63 (0.72–18.44)4.08 (0.73–22.94)2.29 (0.44–11.95)2.92 (0.57–14.94)3.40 (0.69–16.67)2.33 (0.45–12.09)
Variant Unknown14/24 (58%)10/24 (42%)0.48 (0.09–2.57)0.45 (0.08–2.48)0.45 (0.08–2.67)0.47 (0.08–2.72)0.37 (0.06–2.29)0.46 (0.08–2.56)0.46 (0.08–2.70)0.46 (0.09–2.44)0.46 (0.08–2.56)
Median daily duration *460 (165–1,250)680 (160–1,760)1.00 (1.00–1.00)1.00 (1.00–1.00)
Maximum duration †39 (10–81)39 (13–96)0.99 (0.99–1.00)1.00 (0.99–1.00)
Median average daily duration ‡33 (28–44)37 (28–47)0.98 (0.96–0.99)0.98 (0.96–0.99)
Cumulative time in contact §95 (46–198)127 (40–363)1.00 (1.00–1.00)1.00 (1.00–1.00)
Median daily frequency 13 (5–27)18 (4–38)0.99 (0.99–1.00)1.00 (0.99–1.01)
Maximum frequency **41 (15–83)46 (18–100)0.99 (0.99–1.00)1.00 (0.99–1.00)
Daily average frequency ††2.4 (1.0–3.7)2.9 (1.0–6.8)1.01 (0.98–1.04)1.03 (0.97–1.10)

  1. 1 n/ row N (%); Median (interquartile range).

  2. *

    Median daily duration (median of cumulative duration of close-range proximity events for each day of deployment, in minutes).

  3. †

    Maximum duration (longest duration of a close-range proximity event during deployment, in minutes).

  4. ‡

    Median average daily duration (median of cumulative duration of close-range proximity events in the day divided by the cumulative number of close-range proximity events during that day, in minutes).

  5. §

    Cumulative time in contact (cumulative duration of close-range proximity events over the deployment period divided by the number of days sensor was worn, in minutes).

  6. Median daily frequency (median of number of close proximity events for each day of deployment).

  7. **

    Maximum frequency (highest number of close proximity events in one day during deployment).

  8. ††

    Daily average frequency (cumulative duration of close-range proximity events over the deployment period divided by the cumulative number of close-range proximity events during the deployment period). aOR: adjusted odds ratio. Significant associations on multivariable analysis in boldface. Factors investigated but not found significant on multivariable analysis: sex, HIV status, and underlying conditions.

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  1. Jackie Kleynhans
  2. Lorenzo Dall'Amico
  3. Laetitia Gauvin
  4. Michele Tizzoni
  5. Lucia Maloma
  6. Sibongile Walaza
  7. Neil A Martinson
  8. Anne von Gottberg
  9. Nicole Wolter
  10. Mvuyo Makhasi
  11. Cheryl Cohen
  12. Ciro Cattuto
  13. Stefano Tempia
  14. SA-S-HTS Group
(2023)
Association of close-range contact patterns with SARS-CoV-2: a household transmission study
eLife 12:e84753.
https://doi.org/10.7554/eLife.84753