First generate stan model output for all 9 models + other sensitivity analyses

or, load pregenerated stan model output

Figure 1. Epidemic curve and recruitment period

Figure 2. Estimated median probability of infection

Figure 3. ORs of infection from the main model (model 5)

SFigure 2. Frequency of households of different sizes in the study, proportion seropositive by household size, and distribution of the number of seropositive people in household by size

SFigure 3. Figure representation of Table 1

Table 1. Number of recruited and seropositive individuals by age-group, sex and household size of the households they reside in.

my_var hhsize1 hhsize2 hhsize3 hhsize4 hhsize5 overall OR
HOUSEHOLDS
0 819/860 95%(94,96) 807/889 91%(89,93) 190/229 83%(78,87) 188/239 79%(73,83) 41/50 82%(69,90) 2045/2267 90%(89,91) NA
1 41/860 5%(4,6) 52/889 6%(4,8) 29/229 13%(9,18) 38/239 16%(12,21) 5/50 10%(4,21) 165/2267 7%(6,8) NA
1+ NA 30/889 3%(2,5) 10/229 4%(2,8) 13/239 5%(3,9) 4/50 8%(3,19) 57/2267 3%(2,3) NA
INDIVIDUALS
Age
5-9 NA 0/6 0%(0,0) 1/38 3%(0,13) 5/97 5%(2,12) 2/26 8%(2,24) 8/167 5%(2,9) 0.5 (0.2,1.0)
10-19 NA 2/21 10%(3,29) 8/99 8%(4,15) 14/248 6%(3,9) 7/91 8%(4,15) 31/459 7%(5,9) 0.7 (0.5,1.1)
20-49 14/227 6%(4,10) 39/361 11%(8,14) 23/249 9%(6,13) 36/375 10%(7,13) 7/90 8%(4,15) 119/1302 9%(8,11) NA
50-64 17/316 5%(3,8) 38/607 6%(5,8) 18/253 7%(5,11) 22/224 10%(7,14) 1/43 2%(0,12) 96/1443 7%(5,8) 0.7 (0.5,0.9)
65+ 10/317 3%(2,6) 33/783 4%(3,6) 1/48 2%(0,11) 0/12 0%(0,0) 0/3 0%(0,0) 44/1163 4%(3,5) 0.4 (0.3,0.6)
Sex
female 28/558 5%(3,7) 40/900 4%(3,6) 27/364 7%(5,11) 34/475 7%(5,10) 8/135 6%(3,11) 137/2432 6%(5,7) NA
male 13/302 4%(3,7) 72/878 8%(7,10) 24/323 7%(5,11) 43/481 9%(7,12) 9/118 8%(4,14) 161/2102 8%(7,9) 1.4 (1.1,1.8)
Symptom
asym 7/602 1%(1,2) 36/1277 3%(2,4) 19/449 4%(3,7) 24/643 4%(3,5) 5/176 3%(1,6) 91/3147 3%(2,4) NA
sym 34/258 13%(10,18) 76/501 15%(12,19) 32/238 13%(10,18) 53/313 17%(13,21) 12/77 16%(9,25) 207/1387 15%(13,17) 5.9 (4.6,7.6)
Reduced contact
Oui 33/788 4%(3,6) 107/1672 6%(5,8) 40/569 7%(5,9) 63/707 9%(7,11) 11/178 6%(3,11) 254/3914 6%(6,7) 0.8 (0.5,1.5)
Non 8/71 11%(6,21) 1/70 1%(0,8) 5/37 14%(6,28) 3/39 8%(3,20) 0/7 0%(0,0) 17/224 8%(5,12) NA
NA 0/1 0%(0,0) 4/36 11%(4,25) 6/81 7%(3,15) 11/210 5%(3,9) 6/68 9%(4,18) 27/396 7%(5,10) NA
Number of extra-HH contacts/week
0 3/64 5%(2,13) 14/188 7%(4,12) 7/72 10%(5,19) 5/88 6%(2,13) 1/12 8%(0,35) 30/424 7%(5,10) NA
1 à 2 10/207 5%(3,9) 26/375 7%(5,10) 7/134 5%(3,10) 15/180 8%(5,13) 2/49 4%(1,14) 60/945 6%(5,8) 0.9 (0.6,1.4)
3 à 5 12/283 4%(2,7) 32/563 6%(4,8) 7/158 4%(2,9) 12/152 8%(5,13) 3/47 6%(2,17) 66/1203 5%(4,7) 0.8 (0.5,1.2)
6 à 10 10/115 9%(5,15) 22/266 8%(6,12) 8/86 9%(5,17) 12/132 9%(5,15) 1/26 4%(0,19) 53/625 8%(7,11) 1.2 (0.8,2.0)
plus de 10 6/190 3%(1,7) 14/350 4%(2,7) 16/156 10%(6,16) 22/194 11%(8,17) 4/51 8%(3,18) 62/941 7%(5,8) 0.9 (0.6,1.5)
NA 0/1 0%(0,0) 4/36 11%(4,25) 6/81 7%(3,15) 11/210 5%(3,9) 6/68 9%(4,18) 27/396 7%(5,10) NA
Overall
overall 41/860 5%(4,6) 112/1778 6%(5,8) 51/687 7%(6,10) 77/956 8%(6,10) 17/253 7%(4,10) 298/4534 7% (6,7) NA

SFigure 4. sensitivity analyses, by sero-positivity definition

SFigure 5. sensitivity analyses, by enrollment week

SFigure 6. sensitivity analyses, by definition of symptomatic infections

SFigure 7. Prob of infection by weeks

SFigure 8. Proportion of infections that occurred within a household of various household sizes

SFigure 9. Distribution of the total number of transmission generations within a household by number of seropositives in a household.

STable 1. Household composition over the study period.

week total HH % HH with <10yrs old (n) % HH with >65yrs old (n) % HH size = 1 (n) average HH size (IQR)
1 85 11.8% (10) 18.8% (16) 30.6% (26) 2.33 (1, 3)
2 111 5.4% (6) 27.9% (31) 29.7% (33) 2.19 (1, 3)
3 155 3.2% (5) 32.9% (51) 41.9% (65) 1.95 (1, 2)
4 153 9.8% (15) 28.1% (43) 33.3% (51) 2.12 (1, 3)
5 217 8.8% (19) 25.8% (56) 38.7% (84) 2.07 (1, 3)
6 226 4.9% (11) 31.9% (72) 35% (79) 2.04 (1, 2)
7 183 9.8% (18) 31.1% (57) 25.1% (46) 2.33 (1.5, 3)
8 218 2.3% (5) 39.4% (86) 45% (98) 1.83 (1, 2)
9 185 6.5% (12) 40.5% (75) 39.5% (73) 1.98 (1, 2)
10 232 4.7% (11) 36.2% (84) 37.9% (88) 1.92 (1, 2)
11 232 3.4% (8) 47.4% (110) 40.1% (93) 1.81 (1, 2)
12 270 4.4% (12) 48.5% (131) 45.9% (124) 1.84 (1, 2)
all 2267 5.8% (132) 35.8% (812) 37.9% (860) 2 (1, 2)

STable 2. Outputs from models 1-3

Model 1;
age
Model 2;
age + sex
Model 3;
age/sex interaction
Extra-household
Within Household
Extra-household
Within Household
Extra-household
Within Household
Category Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI)
Age
5-9 0.5 (0.2, 1.0) 0.4 (0.1, 1.4) 0.5 (0.2, 1.0) 0.4 (0.1, 1.5) 0.4 (0.1, 1.1) 0.3 (0.0, 1.4)
10-19 0.5 (0.2, 0.9) 0.9 (0.3, 2.3) 0.5 (0.2, 0.9) 0.9 (0.3, 2.1) 0.4 (0.1, 0.9) 1.4 (0.4, 4.6)
50-64 0.7 (0.5, 1.0) 1.1 (0.5, 2.3) 0.7 (0.5, 1.0) 1.0 (0.4, 2.4) 0.6 (0.4, 1.0) 0.8 (0.2, 2.6)
65+ 0.4 (0.3, 0.6) 2.2 (0.7, 5.6) 0.4 (0.3, 0.6) 2.2 (0.8, 5.9) 0.3 (0.2, 0.6) 1.1 (0.2, 4.3)
Sex
Male NA NA 1.4 (1.0, 1.9) 1.6 (0.6, 3.9) 1.1 (0.7, 1.7) 1.6 (0.5, 5.2)
Age-sex interaction
5-9M NA NA NA NA 1.3 (0.3, 6.1) 1.7 (0.2, 13.1)
10-19M NA NA NA NA 1.4 (0.5, 4.7) 0.4 (0.1, 2.1)
50-64M NA NA NA NA 1.3 (0.7, 2.6) 1.6 (0.3, 9.1)
65+M NA NA NA NA 1.5 (0.7, 3.5) 5.2 (0.7, 43.7)

STable 2. Outputs models 4-6

Model 4:
age + sex + symptom
Model 5:
Model 4 + reduced contact
Model 6:
Model 4 + reduced contact + extra HH contacts
Extra-household
Within Household
Extra-household
Within Household
Extra-household
Within Household
Category Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI)
Age
5-9 0.5 (0.2, 0.9) 0.4 (0.1, 1.6) 0.3 (0.1, 0.8) 0.4 (0.1, 1.4) 0.4 (0.1, 1.3) 0.4 (0.1, 1.4)
10-19 0.5 (0.2, 0.8) 1.0 (0.4, 2.3) 0.3 (0.2, 0.7) 0.9 (0.3, 2.2) 0.4 (0.1, 1.2) 0.9 (0.3, 2.1)
50-64 0.7 (0.5, 0.9) 1.1 (0.5, 2.3) 0.7 (0.5, 1.0) 1.1 (0.5, 2.3) 0.7 (0.5, 1.0) 1.0 (0.4, 2.2)
65+ 0.4 (0.3, 0.6) 2.7 (0.9, 7.9) 0.2 (0.1, 0.9) 2.7 (0.9, 7.4) 0.3 (0.0, 1.5) 2.8 (1.0, 7.5)
Sex
Male 1.4 (1.0, 2.0) 1.4 (0.6, 3.1) 1.4 (1.0, 1.9) 1.4 (0.6, 3.2) 1.4 (1.0, 1.9) 1.3 (0.6, 3.0)
Symptomatic
sym NA 3.3 (1.5, 8.9) NA 3.3 (1.5, 8.4) NA 3.4 (1.5, 8.5)
Reduced contact among 20-64 yo
age2064:reduced_contact NA NA 0.7 (0.4, 1.2) NA 0.7 (0.4, 1.2) NA
Reduced contact among 65+ yo
age65+:reduced_contact NA NA 1.1 (0.4, 4.3) NA 1.1 (0.3, 5.7) NA
Extra HH contacts among 20-64 yo
age2064:0 NA NA NA NA 1.6 (0.9, 2.9) NA
age2064:1 à 2 NA NA NA NA 1.2 (0.7, 2.0) NA
age2064:6 à 10 NA NA NA NA 1.8 (1.1, 3.0) NA
age2064:plus de 10 NA NA NA NA 1.2 (0.7, 1.9) NA
Extra HH contacts among 65+ yo
age65+:0 NA NA NA NA 0.5 (0.1, 1.8) NA
age65+:1 à 2 NA NA NA NA 1.6 (0.7, 4.1) NA
age65+:6 à 10 NA NA NA NA 2.0 (0.8, 5.2) NA
age65+:plus de 10 NA NA NA NA 0.4 (0.1, 1.7) NA

STable 2. Outputs from models 7-9

Model 7:
infectors’ age/sex + infectors’ age
Model 8:
infectees’ sex + infectors’ age
Model 9:
Model 2 + infectors’ age
Extra-household
Within a household
Extra-household
Within a household
Extra-household
Within a household
Category Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI)
Age of infectees
5-9 0.4 (0.2, 1.0) 0.4 (0.1, 1.5) NA NA 0.5 (0.2, 1.0) 0.5 (0.1, 1.6)
10-19 0.6 (0.2, 1.1) 0.7 (0.2, 2.2) NA NA 0.5 (0.2, 1.1) 0.7 (0.1, 2.3)
50-64 0.7 (0.5, 1.0) 1.0 (0.4, 2.5) NA NA 0.7 (0.5, 1.0) 0.9 (0.3, 2.2)
65+ 0.4 (0.3, 0.6) 1.8 (0.4, 9.0) NA NA 0.4 (0.3, 0.6) 2.1 (0.4, 8.0)
Sex
Male 1.4 (1.0, 2.0) 1.3 (0.5, 3.2) 1.5 (1.1, 2.1) 1.1 (0.5, 2.4) 1.4 (1.0, 1.9) 1.6 (0.7, 4.0)
Symptomatic
alpha_sym NA 3.6 (1.5, 10.4) NA 3.9 (1.7, 10.6) NA NA
Age of infectors
alpha5-9 NA 0.7 (0.0, 4.7) NA 0.7 (0.0, 4.7) NA 0.5 (0.0, 2.8)
alpha10-19 NA 1.9 (0.2, 6.8) NA 1.9 (0.2, 6.8) NA 1.9 (0.2, 6.8)
alpha50-64 NA 1.2 (0.4, 3.6) NA 1.2 (0.4, 3.6) NA 1.2 (0.4, 3.6)
alpha65+ NA 1.9 (0.3, 8.7) NA 1.9 (0.3, 8.7) NA 1.9 (0.3, 8.7)

STable 2. Model performance

model waic delta_waic
model0 2006.908 0.00000
model1 1992.135 -14.77317
model2 1986.719 -20.18896
model3 1987.754 -19.15403
model4 1977.342 -29.56585
model5 1977.519 -29.38908
model6 1976.897 -30.01148
model7 1982.200 -24.70796
model8 1991.846 -15.06215
model9 1991.426 -15.48261

STable 3. Attributable fraction of extra-household infections, within household infections by symptomatics, and within household infections by asymptomatics

category model0 model1 model2 model3 model4 model5 model6 model7 model8 model9
2 23.2 (18.6, 25.9) 23.2 (19.6, 25.9) 23.2 (19.5, 26.8) 23.2 (18.8, 25.9) 23.2 (18.6, 26.0) 23.2 (19.6, 26.8) 23.2 (19.6, 25.9) 23.2 (19.5, 25.9) 23.2 (20.3, 26.0) 23.2 (20.5, 25.9)
3 21.6 (17.4, 23.5) 21.6 (15.7, 23.5) 19.6 (15.4, 23.5) 19.6 (17.4, 23.5) 19.6 (13.7, 23.5) 21.6 (15.7, 23.5) 19.6 (15.7, 23.5) 19.6 (15.7, 23.5) 19.6 (13.7, 23.5) 19.6 (15.7, 23.5)
4 31.2 (25.8, 33.8) 29.9 (25.8, 33.8) 29.9 (24.7, 32.7) 29.9 (26.0, 33.8) 31.2 (24.7, 33.8) 29.9 (27.3, 33.8) 31.2 (26.9, 33.8) 29.9 (26.0, 33.8) 29.9 (25.6, 33.8) 29.9 (26.0, 33.8)
5 41.2 (35.3, 47.1) 41.2 (28.5, 47.1) 41.2 (28.5, 47.1) 41.2 (29.4, 47.1) 41.2 (29.4, 47.1) 41.2 (29.4, 47.1) 41.2 (29.4, 47.1) 41.2 (29.4, 47.1) 41.2 (35.3, 47.1) 41.2 (29.4, 47.1)
all 22.5 (20.1, 24.5) 22.5 (20.1, 24.2) 22.5 (19.7, 23.9) 22.1 (20.1, 24.2) 22.5 (20.1, 24.2) 22.5 (20.4, 24.2) 22.5 (20.8, 23.9) 22.1 (20.4, 24.5) 22.5 (20.1, 24.5) 22.1 (20.8, 23.9)
asym
14.9 (8.5, 22.3) 13.8 (7.5, 21.2) 14.1 (8.9, 20.6) 14.1 (7.6, 20.1) 13.6 (7.9, 20.0)

STable 4. Numbers in Fig 2

Extra-household transmission (95%CI)
Household transmission
Age group combined male female combined male female
5-9 3.6 (1.4, 7.4) 4.1 (1.6, 8.5) 3.1 (1.2, 6.2) 7.6 (1.4, 20.7) 9.4 (1.7, 26.6) 6.1 (1.3, 18.1)
10-19 3.7 (2.0, 6.1) 4.4 (2.3, 7.4) 3.2 (1.7, 5.7) 15.8 (7.4, 26.1) 18.0 (8.2, 30.9) 12.4 (4.7, 23.6)
20-49 7.4 (6.0, 9.1) 8.5 (6.6, 10.7) 6.4 (4.8, 8.2) 16.5 (10.3, 24.2) 20.1 (11.0, 31.6) 13.9 (6.8, 23.2)
50-64 5.2 (4.2, 6.6) 6.1 (4.7, 8.0) 4.6 (3.3, 6.1) 17.4 (9.7, 26.0) 20.7 (10.5, 33.7) 14.3 (6.7, 24.6)
65+ 3.1 (2.2, 4.2) 3.5 (2.4, 5.0) 2.6 (1.8, 3.7) 29.9 (14.0, 49.2) 36.2 (14.1, 59.6) 26.1 (11.3, 45.8)
Combined 5.1 (4.5, 5.8) NA NA 17.3 (13.7, 21.7) NA NA

STable 6. Sensitivity analyses using expanded population and a different definition of symptomatic infection.

Model 5:
with kids
Model 5:
all household
Model 5:
symptom def
Model 5:
main analysis
Extra-household
Within Household
Extra-household
Within Household
Extra-household
Within Household
Extra-household
Within Household
Category Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) Odds Ratio (95% CI) NA NA
Age
5-9 0.3 (0.1, 0.7) 0.4 (0.1, 1.3) 0.2 (0.1, 0.5) 0.3 (0.1, 1.0) 0.3 (0.1, 0.8) 0.4 (0.1, 1.5) 0.3 (0.1, 0.8) 0.4 (0.1, 1.4)
10-19 0.4 (0.2, 0.8) 1.1 (0.4, 2.7) 0.4 (0.2, 0.8) 1.3 (0.7, 2.4) 0.3 (0.2, 0.7) 0.9 (0.3, 2.2) 0.3 (0.2, 0.7) 0.9 (0.3, 2.2)
50-64 0.7 (0.5, 0.9) 1.2 (0.5, 2.6) 0.7 (0.6, 0.9) 1.2 (0.7, 2.0) 0.7 (0.5, 1.0) 1.1 (0.5, 2.3) 0.7 (0.5, 1.0) 1.1 (0.5, 2.3)
65+ 0.3 (0.1, 0.9) 3.0 (1.0, 8.3) 0.6 (0.2, 1.3) 2.7 (1.2, 5.8) 0.3 (0.1, 0.9) 2.8 (0.9, 8.3) 0.2 (0.1, 0.9) 2.7 (0.9, 7.4)
Sex
Male 1.4 (1.0, 1.8) 1.3 (0.6, 2.8) 1.3 (1.0, 1.6) 1.1 (0.6, 1.9) 1.4 (1.0, 2.0) 1.3 (0.6, 2.9) 1.4 (1.0, 1.9) 1.4 (0.6, 3.2)
Symptomatic
sym NA 3.4 (1.6, 8.9) NA 3.1 (1.6, 7.1) NA 4.1 (1.8, 10.1) NA 3.3 (1.5, 8.4)
Reduced contact among 20-64 yo
age2064:reduced_contact 0.7 (0.4, 1.3) NA 0.8 (0.5, 1.1) NA 0.7 (0.4, 1.1) NA 0.7 (0.4, 1.2) NA
Reduced contact among 65+ yo
age65+:reduced_contact 1.1 (0.3, 4.4) NA 0.6 (0.3, 1.7) NA 1.0 (0.3, 4.1) NA 1.1 (0.4, 4.3) NA