Characteristics of index cases
Between July 3, 2020 and September 3, 2020, 291 laboratory-confirmed SARS-CoV-2 infected cases were identified in a densely populated district Chattogram, Bangladesh. Table 1 shows the demographic characteristics of all index cases. Among all cases, 103 (35.4%) were detected through contact-based surveillance while remaining 188 (64.6%) were found after symptom-based surveillance (Table 1). Among all reported cases, 213 (73.2%) were male and 78 (26.8%) were female. The mean age of all cases was 43.0 years (ranges from 19 to 83), and 29 (9.97%) cases were in the age group between 0–29, 224 (76.98%) cases were in the age group between 30–69 and remaining 38 (13.06%) cases were in the age group 70 and above. When patients were classified based on the disease severity, 145 (49.83%) cases were mild, 87 (29.9%) cases were moderate and 59 (20.3%) cases were severe/critical in nature. Of 291 cases, 258 (88.7%) were symptomatic, while 33 (11.34%) did not show any symptom (Table 1).
Table 1
Demographic and clinical characteristics of 291 Covid-19 index cases identified by contact based (n = 103) and symptom based (n = 188) surveillance.
All Index cases
n = 291
|
Contact based
surveillance
n = 103 (%)
|
Symptom based surveillance
n = 188 (%)
|
p-value
(Fisher
Exact -test)
|
Sex
|
Male
|
213 (73.20)
|
79 (76.70)
|
134 (71.28)
|
< 0.0001
|
Female
|
78 (26.80)
|
24 (23.30)
|
54 (28.72)
|
Age group (Years)
|
0–9
|
0
|
0
|
0
|
0.050
|
10–19
|
5 (1.72)
|
1 (0.97)
|
4 (4.13)
|
20–29
|
24 (8.25)
|
2 (1.94)
|
21 (11.17)
|
30–39
|
59 (20.27)
|
25 (24.27)
|
35 (18.62)
|
40–49
|
67 (23.02)
|
28 (27.18)
|
47 (25.0)
|
50–59
|
71 (24.40)
|
21 (20.39)
|
32 (17.02)
|
60–69
|
27 (9.28)
|
15 (14.56)
|
17 (9.04)
|
70–79
|
20 (6.87)
|
5 (4.85)
|
13 (6.91)
|
80+
|
18 (6.19)
|
6 (5.83)
|
19 (10.11)
|
Disease Severity
|
Mild
|
145 (49.83)
|
51 (49.51)
|
94 (14.89)
|
0.77
|
Moderate
|
87 (29.90)
|
29 (28.16)
|
58 (30.85)
|
Severe
|
59 (20.27)
|
23 (22.33)
|
36 (19.15)
|
Symptomatic cases
|
Yes
|
258 (88.66)
|
93 (90.29)
|
165 (87.77)
|
0.56
|
No
|
33 (11.34)
|
10 (9.71)
|
23 (12.23)
|
Symptoms
|
Fever-Yes
|
257 (88.32)
|
95 (92.23)
|
162 (86.17)
|
0.13
|
Fever-No
|
34 (11.68)
|
8 (7.77)
|
26 (13.83)
|
Cough-Yes
|
178 (61.17)
|
61(59.22)
|
117 (62.23)
|
0.61
|
Cough-No
|
113 (38.83)
|
42 (40.78)
|
71 (37.77)
|
Fatigue-Yes
|
88 (30.24)
|
51 (49.51)
|
37 (19.68)
|
< 0.0001
|
Fatigue-No
|
203 (69.76)
|
52 (50.49)
|
151 (80.32)
|
Diarrhea-Yes
|
49 (18.84)
|
21(20.39)
|
28 (14.89)
|
0.25
|
Diarrhea-No
|
242 (83.16)
|
82 (79.61)
|
160 (85.11)
|
Breathing difficulty-Yes
|
101(34.71)
|
39 (37.86)
|
62 (32.98)
|
0.44
|
Breathing difficulty-No
|
190 (65.29)
|
64 (62.14)
|
126 (67.02)
|
Cough-Yes
|
128 (43.99)
|
47 (45.63)
|
81 (43.09)
|
0.003
|
Cough-No
|
163 (56.01)
|
56 (54.37)
|
107 (56.91)
|
Runny nose-Yes
|
79 (27.15)
|
36 (34.95)
|
43 (22.87)
|
0.03
|
Runny nose-No
|
212 (72.85)
|
67 (65.05)
|
145 (77.13)
|
When comparing cases between contact-based and symptom-based surveillance, male cases 134 (71.3%) of 188 vs 79 (76.7%) of 103 cases were detected through symptom-traced surveillance (p < 0.0001). Majority of cases were detected between age group 30–69 (n = 89 [86.4%] of 103 vs 131 [69.7%] of 188; p = 0.05; Table 1) in both modes of detection. In the contact-based surveillance group, 9 [90.3%] of 103 cases showed the symptom of fever in compared to 165 (87.7%) cases of symptom-based surveillance; p = 0.56; Table 1).
Analysis Of Key Parameters For Index Cases
Going by the growth of the epidemic and based on patients with well-defined time of exposure and time of symptom onset, we estimated the onset to symptom period, median days in hospital stay, median onset to recovery and median onset to death for all index cases. In both surveillance modes, the majority of cases showed symptoms of the disease within 2 to 5 days, with the highest number of cases showing symptoms at day 4 (Fig. 1A). The estimated incubation period for COVID-19 cases was found to be 3.9 days and 4.1 days for contact-based and symptom-based surveillance respectively (95% CI 2.18–4.42; Fig. 1B; Supplementary Table S1). On the other hand, the serial interval for symptom-based surveillance was estimated as 3.0 days (95% CI 2.57–4.71), while cases detected through contact-based surveillance was 2.0 days (95% CI 1.79–3.23; Fig. 1C; Supplementary Table S1). 90% of patients showed symptoms within 6 days. Median hospital stays of 63 (21.7%) out of 291 cases was 9.5 days (95% CI 8.99–9.94; Supplementary Fig. S1A), and average onset to recovery of all cases was 21.1 days (95% CI 21.66–22.20; Supplementary Fig. S1B).
As of September, 2020, when assessing the final clinical outcome, 17 patients died from both surveillance categories. The mean time from onset-to-death to be 15.7 days (95% CI 14.34–17.39, Supplementary Fig S1C). The median age of the patients was 47.9 years (95% CI 43.77–77.06). Among all 17 cases of death, the male-female proportion was 14:3. We estimated the overall crude CFR (case fatality ratio) as 5.84% (95% CI 4.69–6.99; Supplementary Table S2). The highest CFR was estimated in 70–79 age group (25.0%, 95% CI 20.62–29.38), age 80+ (16.67%, 95% CI 120.5-21.29) and age 60–69 years (14.81%, 95% CI 11.03–18.58; Supplementary Table S2; Supplementary Fig. S1D). The least CFR was estimated for the younger age group between 0–49 inclusive (Supplementary Table S2, Supplementary Fig. S1D). A large proportion of deaths were recorded in the older (60 + age) cases (18.46%, 95% CI 16.03–20.89) (Supplementary Table S2).
Secondary infection rate and risk of transmission of close contacts in major exposure settings
We collected 1171 close contact cases who were linked to 291 index cases between the same time period. Of the 1171 close contacts, 79 (6.75%) were identified as funeral ceremonies contacts, 205 (17.1%) household contacts, 131 (11.19%) hospital facilities contacts, 177 (15.12%) workplaces contacts, 181 (15.56%) were family close contacts and remaining 398 (33.99%) cases belongs to others category (social gathering, food court, market places, public transportations). Table 2 summarizes detailed epidemiological characteristics of all close contact cases in different exposure settings. We identified six (6) clusters and the distribution of clusters in each exposure according to the number of index cases is presented and summarized in Fig. 2A (Supplementary Fig. S2; Table 3). Through contact tracing, we identified 39 secondary cases from 1171 close contacts in different exposure settings (Fig. 2B). Six clusters of exposure settings with one or more secondary cases (not including tertiary cases or subsequent cases) were identified (Table 3). All cases in these clusters were locally transmitted. Three asymptomatic of 39 cases were excluded from the subsequent transmission analysis because none of the three asymptomatic cases transmitted to secondary cases. Of the 33 secondary cases, 11 (33.33%) were in household setting, 3 (9.09%) in the hospital, 2 (6.08%) in funeral, 7 (21.21%) in work places, 7 (21.21%) in family and 6 (18.8%) in others (public transportations, market places, food court etc.) exposure settings (Fig. 2B; Table 4). We closely monitored these secondary contacts when they were under quarantine or isolated at least for two weeks and during this time all 36 out of 39 of the close contacts showed all the major symptoms of COVID-19 and tested positive for COVID-19 infection. For symptomatic secondary cases with confirmed COVID-19 diagnosis, the distribution of days of symptom to RT-PCR diagnosis, symptom onset and isolation start time is presented in Supplementary Figure S3.
Table 2
Characteristics of the 1171 close contacts by different exposure settings
Variables
|
Exposure. No. (%)
|
Funeral
Ceremony
n = 79
|
Household
n = 205
|
Hospital facilities n = 131
|
Work places n = 177
|
Family n = 181
|
Others1 n = 398
|
p-value
|
Sex
|
|
Male
|
51 (61.56)
|
142 (69.27)
|
91 (69.47)
|
129 (72.88)
|
107 (59.12)
|
252 (63.32)
|
0.05
|
Female
|
28 (35.44)
|
63 (30.73)
|
40 (30.53)
|
48 (27.12)
|
74 (40.88)
|
146 (36.68)
|
Age group-years
|
|
0–9
|
0
|
9 (4.39)
|
0
|
0
|
1(0.55)
|
9 (2.26)
|
0.0004
|
10–19
|
0
|
7 (3.41)
|
3 (2.29)
|
0
|
7 (3.87)
|
58 (14.57)
|
20–29
|
11 (10.26)
|
29 (14.15)
|
10 (7.63)
|
51 (28.81)
|
25 (13.81)
|
106 (26.63)
|
30–39
|
17 (17.95)
|
36 (17.56)
|
27 (20.61)
|
47 (26.55)
|
34 (18.78)
|
79 (19.85)
|
40–49
|
23 (30.77)
|
33 (16.10)
|
25 (19.08)
|
62 (35.03)
|
38 (20.99)
|
59 (14.82)
|
50–59
|
21 (20.51)
|
35 (17.07)
|
18 (13.74)
|
17 (9.60)
|
27 (14.92)
|
68 (17.09)
|
60–69
|
7 (20.51)
|
26 (12.68)
|
19 (14.50)
|
0
|
19 (10.50)
|
19 (4.78)
|
70–79
|
0
|
19 (9.27)
|
23 (17.56)
|
0
|
21 (11.60)
|
0
|
80+
|
0
|
16 (7.80)
|
6 (4.58)
|
0
|
9 (4.97)
|
0
|
Severity
|
|
Severe
|
29 (36.71)
|
49 (23.90)
|
29 (22.14)
|
39 (22.03)
|
27 (14.92)
|
37 (9.30)
|
0.0004
|
Moderate
|
31 (39.24)
|
75 (36.59)
|
37 (28.24)
|
63 (35.59)
|
68 (37.57)
|
118 (29.65)
|
Mild
|
19 (24.05)
|
81 (39.51)
|
65 (49.62)
|
75 (42.37)
|
86 (47.51)
|
243 (61.06)
|
Fever
|
|
Yes
|
31 (39.24)
|
68 (33.17)
|
33 (25.19)
|
29 (16.38)
|
51(28.18)
|
119 (29.90)
|
0.0004
|
No
|
48 (60.76)
|
137 (66.83)
|
98 (74.81)
|
148 (83.62)
|
130 (71.82)
|
279 (70.10)
|
1Others: includes food court, public transportations and market places
|
Table 3
Clusters, close contacts, and secondary cases distribution in differ exposure settings
Color codes: Clusters, Close contacts, Secondary cases
|
Cluster size
|
Household
|
Hospital
|
Funeral
|
Work places
|
Family
|
1
|
13/12/2
|
4/19/0
|
2/13/1
|
9/23/0
|
7/31/0
|
2
|
19/71/3
|
8/12/0
|
1/9/0
|
13/39/1
|
6/29/2
|
3
|
21/ 63/3
|
13/29/1
|
3/11/0
|
10/26/1
|
9/39/2
|
4
|
29/33/2
|
3/32/2
|
7/19/1
|
21/17/1
|
17/26/1
|
5
|
13/16/1
|
5/21/2
|
5/11/0
|
19/29/1
|
9/35/2
|
6
|
10/10/0
|
3/18/0
|
4/16/0
|
10/43/3
|
4/21/0
|
Total
|
105/205/11
|
36/131/3
|
21/79/2
|
77/177/7
|
52/181/7
|
Table 4
Secondary clinical attack rate among 1171 close contacts by age, exposure setting and disease severity
Variables
|
No. of close contacts (%)
|
No. of secondary contacts (asymptomatic case)
|
Secondary attack rate; % (95% CI)
|
p-values1
|
Risk ratio
(95% CI)
|
Overall
|
1171
|
36 (3)
|
3.07 (2.49–3.64)
|
|
|
Sex
|
Male
|
819 (69.94)
|
31 (2)
|
3.76 (3.08–4.44)
|
0.04
|
2.64 (2.07–3.21)
|
Female
|
352 (30.05)
|
5 (1)
|
1.42 (0.38–2.46)
|
1 (reference)
|
Age (years)
|
|
|
0–9
|
0
|
0
|
0
|
0.019
|
0
|
10–19
|
57 (4.87)
|
0
|
0
|
0
|
20–29
|
112 (9.56)
|
2 (0)
|
1.79 (0.06–3.65)
|
0.62 (-0.47-1.71)
|
30–39
|
139 (11.87)
|
4 (1)
|
2.89 (1.22–4.56)
|
1 (reference)
|
40–49
|
267 (22.80)
|
3 (1)
|
1.12 (0.07–2.32)
|
0.39 (-0.31-1.09)
|
50–59
|
251 (21.43)
|
15 (1)
|
5.98 (4.74–7.22)
|
2.07 (1.34–2.80)
|
60–69
|
117 (9.99)
|
8 (0)
|
6.83 (5.02–8.64)
|
2.36 (1.29–3.43)
|
70–79
|
115 (9.82)
|
4 (0)
|
3.47 (1.65–5.29)
|
1.20 (1.12–2.28)
|
80+
|
0
|
0
|
0
|
0
|
Exposure settings
|
|
|
Household
|
178 (15.20)
|
11 (1)
|
6.17 (4.70–7.64)
|
0.05
|
2.44 (1.51–3.36)
|
Hospital facility
|
131 (11.19)
|
3 (1)
|
2.29 (0.58–3.40)
|
0.91 (-0.17-1.99)
|
Funeral
|
79 (6.75)
|
2 (0)
|
2.53 (0.32–4.73)
|
1 (reference)
|
Work places
|
177 (15.12)
|
7 (0)
|
3.95 (2.48–5.42)
|
1.56 (0.63–2.49)
|
Family
|
181(15.46)
|
7 (1)
|
3.87 (2.41–5.33)
|
1.53 (0.61–2.45)
|
Other
|
425 (36.29)
|
6 (0)
|
1.41 (0.45–2.36)
|
0.56 (-0.04-1.16)
|
Disease severity
|
|
|
Severe
|
259 (22.12)
|
11 (0)
|
4.25 (3.03–5.47)
|
< 0.0001
|
1.45 (0.74–2.16)
|
Moderate
|
647 (55.25)
|
19 (1)
|
2.93 (2.16–3.70)
|
1 (reference)
|
Low
|
265 (22.63)
|
6 (2)
|
2.26 (1.06–3.46)
|
0.77 (0.06–1.47)
|
1 Fisher Exact test., CI-Confidence Interval
|
Using the data from 33 cases with well-defined exposure history, we estimated the estimated median incubation period of these 33-secondary cases for overall and for each exposure setting. The overall incubation period was 3.9 days (95% CI 3.41–4.79; Supplementary Table S3) and median serial interval was 4.1 day (95% CI 3.41–4.79, Supplementary Table S4; Figs. 3A; 3B). The incubation period for household setting was estimated as 1.5 days (95% CI 1.52–3.48) and serial interval was 3.3 days (95% CI 2.20–4.46; Figs. 3A; 3B; Supplementary Table S3; S4). The overall secondary clinical attack rate was 3.07% (95% CI 2.49–3.64) among all cases analyzed (Table 4). A higher percentage of males than females (3.76% [95% CI 3.08–4.44] to 1.42% [95% CI 0.38–2.46]) were infected, and these differences were statistically significant (p = 0.04; Table 4). The secondary attack rate was (6.83%% [95% CI 5.02–8.64; risk ratio 2.36, [95% CI 1.29–3.43]) higher in cases who were ages between 60 to 69, followed by ages age 50–59 (5.98% [95% CI 4.47–7.22; risk ratio 2.07, [95% CI 1.34–2.80]) and age 70–79 (3.47%, [95% CI 1.65–5.29.75; risk ratio 1.20, 95% CI 1.12–2.28]; Table 4). In term of exposure settings, household contact had a higher secondary attack rate (6.17%; 95% CI 4.70–7.64) and higher risk of secondary infection (risk ratio 2.44; 95% CI 1.51–3.36) compared to cases who were exposed to hospital facility (2.29%; 95% CI 0.58–3.40, risk ratio 0.91; 95% CI -0.17-1.99), workplaces contacts (3.95%, 95% CI 2.48–5.42; risk ratio 1.56, 95% CI 0.63–2.49), family contacts (3.87%, 95% CI 2.41–5.33, risk ratio 1.53; 95% CI 0.61–2.45) and other contact (1.41%, 95% CI 0.45–2.36, risk ratio 0.56 95% CI -0.04-1.16; Table 4). The secondary attack rate and risk ratio increased with the disease severity of the index cases. The secondary attack rate and risk ratio was 4.25% and 2.93 (95% CI 3.03–5.47; 1.45; 95% CI 0.74–2.16) for severe cases while the secondary attack rate was 2.26% (95% CI 1.06–3.46) and risk ratio was 0.77 (95% CI 0.06–1.17) for low risk cases (Table 4).