Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study

Abstract

Background: Rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, prompted heightened surveillance in Shenzhen, China. The resulting data provide a rare opportunity to measure key metrics of disease course, transmission, and the impact of control measures.

Methods: From Jan 14 to Feb 12, 2020, the Shenzhen Center for Disease Control and Prevention identified 391 SARS-CoV-2 cases and 1286 close contacts. We compared cases identified through symptomatic surveillance and contact tracing, and estimated the time from symptom onset to confirmation, isolation, and admission to hospital. We estimated metrics of disease transmission and analysed factors influencing transmission risk.

Findings: Cases were older than the general population (mean age 45 years) and balanced between males (n=187) and females (n=204). 356 (91%) of 391 cases had mild or moderate clinical severity at initial assessment. As of Feb 22, 2020, three cases had died and 225 had recovered (median time to recovery 21 days; 95% CI 20-22). Cases were isolated on average 4·6 days (95% CI 4·1-5·0) after developing symptoms; contact tracing reduced this by 1·9 days (95% CI 1·1-2·7). Household contacts and those travelling with a case were at higher risk of infection (odds ratio 6·27 [95% CI 1·49-26·33] for household contacts and 7·06 [1·43-34·91] for those travelling with a case) than other close contacts. The household secondary attack rate was 11·2% (95% CI 9·1-13·8), and children were as likely to be infected as adults (infection rate 7·4% in children <10 years vs population average of 6·6%). The observed reproductive number (R) was 0·4 (95% CI 0·3-0·5), with a mean serial interval of 6·3 days (95% CI 5·2-7·6).

Interpretation: Our data on cases as well as their infected and uninfected close contacts provide key insights into the epidemiology of SARS-CoV-2. This analysis shows that isolation and contact tracing reduce the time during which cases are infectious in the community, thereby reducing the R. The overall impact of isolation and contact tracing, however, is uncertain and highly dependent on the number of asymptomatic cases. Moreover, children are at a similar risk of infection to the general population, although less likely to have severe symptoms; hence they should be considered in analyses of transmission and control.

Funding: Emergency Response Program of Harbin Institute of Technology, Emergency Response Program of Peng Cheng Laboratory, US Centers for Disease Control and Prevention.

Figure 1

Incubation period and serial interval of COVID-19 (A) Proportion of cases who developed symptoms of coronavirus disease 2019 (COVID-19) by days after infection (ie, the cumulative distribution function of the incubation period). (B) Proportion of cases infected by an index case who developed symptoms by a given number of days after the day of symptom onset of the index case (ie, the cumulative distribution function of the serial interval). The maximum-likelihood estimates for the parametric distribution of the cumulative distribution function are shown, along with 1000 parametric bootstrap estimates of the cumulative distribution function. The median incubation period of COVID-19 is estimated to be 4·8 days (95% CI 4·2–5·4). 5% of cases who develop symptoms will do so by 1·6 days (95% CI 1·3–2·0) after infection, and 95% by 14·0 days (12·2–15·9). We estimated that the median serial interval of COVID-19 is 5·4 days (95% CI 4·4–6·5). 5% of infected cases who develop symptoms will do so by 1·3 days (95% CI 0·9–1·9) after symptom onset of the index case, and 95% by 14·3 days (11·1–17·6).

Figure 2

Time between symptom onset and SARS-CoV-2 confirmation (A), admission to hospital (B), and isolation among cases (C) detected by contact-based and symptom-based surveillance The maximum-likelihood estimates for the parametric distribution of the cumulative distribution function are shown, along with 1000 parametric bootstrap estimates of the cumulative distribution function. Panel A shows estimates of the proportion of cases who are confirmed by RT-PCR, according to the number of days after symptom onset. We estimated that 50% of cases detected through symptom-based surveillance were confirmed by RT-PCR within 4·6 days (95% CI 4·2–5·0) after symptom onset, and 95% were confirmed by RT-PCR within 12·7 days (11·5–13·8) after symptom onset. Contact-based surveillance reduced the days from symptom onset to RT-PCR confirmation to 2·9 days (95% CI 2·4–3·4) in 50% of cases and to 6·6 days (5·3–8·0) in 95% of cases. Panel B shows estimates of the proportion of cases who were admitted to hospital, according to the number of days after symptom onset. We estimated that 50% of the cases detected through symptom-based surveillance were admitted to hospital by 3·4 days (95% CI 3·1–3·8) after symptom onset, and 95% by 12·4 days (10·9–13·8). Contact-based surveillance reduced the days from symptom onset to hospital admission to 2·1 days (95% CI 1·7–2·6) in 50% of cases, and 6·0 days (95% CI 4·5–7·5) in 95% of cases. Panel C shows estimates of the proportion of cases isolated, according to number of days after symptom onset. We estimated that 50% of cases detected through symptom-based surveillance were isolated by 3·4 days (95% CI 3·1–3·7) after symptom onset, and 95% by 12·2 days (95% CI 10·8–13·6). Contact-based surveillance reduced the days from symptom onset to isolation to 2·2 days (95% CI 1·7–2·6) in 50% of cases, and to 6·5 days (4·7–8·2) in 95% of cases.

Figure 3

Attack rate among close contacts, baseline severity, and proportion of cases without fever at initial assessment by age group *Proportion of close contacts for attack rate; proportion of all cases for those with severe symptoms or no fever at initial assessment.