1. Epidemiology and Global Health
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Evidence for transmission of COVID-19 prior to symptom onset

  1. Lauren C Tindale
  2. Jessica E Stockdale
  3. Michelle Coombe
  4. Emma S Garlock
  5. Wing Yin Venus Lau
  6. Manu Saraswat
  7. Louxin Zhang
  8. Dongxuan Chen
  9. Jacco Wallinga
  10. Caroline Colijn  Is a corresponding author
  1. University of British Columbia, Canada
  2. Simon Fraser University, Canada
  3. National University of Singapore, Singapore
  4. Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Netherlands
  5. Leiden University Medical Center, Netherlands
Research Article
Cite this article as: eLife 2020;9:e57149 doi: 10.7554/eLife.57149
9 figures, 6 tables and 1 additional file

Figures

Singapore COVID-19 cases.

(a) Daily hospitalized cases and cumulative hospitalized and discharged cases. (b) Daily incidence with probable source of infection. (C) Disease timeline, including dates at which each case is unexposed, exposed, symptomatic, hospitalized, and discharged. Not all cases go through each status as a result of missing dates for some cases.

Tianjin COVID-19 cases.

(a) Daily and cumulative confirmed cases, cumulative discharges and daily death cases. (b) Daily incidence with probable source of infection. (c) Disease progression timeline; not all cases go through each status as a result of missing dates for some cases.

Fitted gamma COVID-19 incubation period distributions (without intermediates).

Cases are defined as ‘early’ if they have symptom onset on or prior to January 31, and are classified ‘late’ otherwise.

COVID-19 incubation period Kaplan-Meier curves for (a) Singapore and (b) Tianjin.

Top panels show unstratified data (all cases with symptom onset given). Bottom panels show ‘early’ and ‘late’ cases, where early cases are defined as those with symptom onset on or prior to January 31, and late otherwise.

Mean incubation period and generation time estimates from the incubation period intermediates analysis, under the assumption that the scale parameter for both distributions is equal, shown with dependence on the mean number of unknown intermediate cases per day of the empirical time elapsed between exposure and symptom onset.

The incubation period is longer than the generation time, so this analysis suggests that symptom onset occurs after infectiousness begins. Top: Singapore. Bottom: Tianjin. The means are the scale times the shape, which is fixed at 2.1 in Singapore and 2.2 in Tianjin. Varying this fixed value for the shape parameter was not found to significantly impact the results.

Serial intervals of possible case pairs in (a) Singapore and (b) Tianjin.

Pairs represent a presumed infector and their presumed infectee plotted by date of symptom onset. Cases are defined as 'early' if they have symptom onset on or prior to January 31st.

Network diagram for (a) Singapore (b) Tianjin.
Pre-symptomatic infection as estimated by samples of (serial interval - incubation period), accounting for covariation.

Top: Singapore. Bottom: Tianjin. Left: without intermediates. Right: accounting for intermediates. Grey vertical line: 0. Samples below zero indicate pre-symptomatic transmission. In all cases there is substantial pre-symptomatic transmission.

Appendix 1—figure 1
Bootstrap values of the mean serial interval for (left) Singapore and (right) Tianjin, based on 100 replicates using the first four cases in each cluster.

Tables

Table 1
Mean incubation period, serial interval and pre-symptomatic transmission.

Incubation periods are based on the gamma estimates because these are the most convenient for taking the covariation of serial intervals and incubation periods into account (done throughout the table). 95% CIs are provided in brackets.

Without intermediatesIncubation (days)Serial interval (days)Mean difference (days)Portion pre-symptomatic(-)
Singapore (all)5.99 (4.97, 7.14)4.0 (2.73, 5.57)1.990.74
Singapore (early)5.91 (4.50,7.64)1.910.742
Singapore (late)6.06 (4.70, 7.67 )2.060.744
Tianjin (all)8.68 (7.72, 9.7)5.0 (3.82, 6.12)3.680.81
Tianjin (early)6.88 (5.97,7.87)1.880.72
Tianjin (late)12.4 (11.1,13.7)7.40.96
Account for intermediates
Singapore r=0.054.914.17 (2.44, 5.89)0.770.53
Singapore r=0.14.430.260.46
Singapore r=0.154.12−0.050.41
Singapore r=0.23.89−0.280.38
Tianjin r=0.057.544.31 (2.91, 5.72)3.230.79
Tianjin r=0.16.892.580.74
Tianjin r=0.156.301.990.67
Tianjin r=0.25.911.60.64
Appendix 1—table 1
Incubation period estimates (without intermediates) using gamma, Weibull and log normal distributions.

95% confidence intervals for the shape and scale (log mean and sd for log normal) parameters are shown in brackets.

GammaMedianShapeScale
Singapore Cluster5.323.05 (2.0, 3.84)1.95 (1.23, 2.34)
Tianjin Cluster8.064.74 (3.35, 5.72)1.83 (1.29, 2.04)
WeibullMedianShapeScale
Singapore Cluster5.661.83 (1.45, 2.30)6.91 (5.77, 8.29)
Tianjin Cluster8.592.41 (1.99, 2.90)10.01 (8.94, 11.20)
Log normalMedianLog meanStandard deviation
Singapore Cluster4.831.57 (1.38, 1.81) (mean 4.81)0.60 (0.47, 0.76)
Tianjin Cluster7.662.04 (1.92, 2.22) (mean 7.69)0.47 (0.39, 0.56)
Appendix 1—table 2
Incubation period estimates (without intermediates) using stratified data
Tianjin
GammaMedianShapeScale
Early6.486.01 (3.61, 7.26)1.140 (0.66,1.276)
Late12.117.78 (9.52, 21.47)0.695 (0.379,0.778)
WeibullMedianShapeScale
Early6.732.88 (2.16, 3.48)7.643 (6.735, 8.553)
Late12.64.34 (3.10, 5.24)13.661 (12.245, 15.289)
Log normalMedianLog meanStandard deviation
Early6.301.84 (1.70,2.03)0.426 (0.331,0.547)
Late12.02.48 (2.38,2.67)0.233 (0.172,0.315)
Singapore
GammaMedianShapeScale
Early5.263.22 (1.67, 4.05)1.818 (0.847,2.18)
Late5.352.96 (1.68,3.72)2.034 (1.132,2.439)
WeibullMedianShapeScale
Early5.512.05 (1.34,2.58)6.587 (5.077,7.897)
Late5.671.75 (1.29,2.21)6.989 (5.408,8.38)
Log normalMedianLog meanStandard deviation
Early4.911.59 (1.33,1.82)0.598 (0.421,0.848)
Late4.721.55 (1.25,1.78)0.606 (0.441,0.834)
Appendix 1—table 3
Serial interval estimates: accounting for intermediates.
orderingNumber cases per clusterμ (Tianjin)σ (Tianjin)μ (Singapore)σ (Singapore)
Onset34.170.9984.031.06
Onset44.310.9354.171.06
Onset54.430.9994.431.09
Onset64.541.054.761.15
Last Exposure45.091.274.261.17
Bootstrap44.49 (sd 0.716)0.995 (sd 0.307)3.83 (sd 0.882)1.24 (sd 0.538)
Appendix 1—table 4
Serial interval estimates: accounting for intermediates and using imputed dates of symptom onset
orderingNumber cases per clusterμ (Tianjin)σ (Tianjin)μ (Singapore)σ (Singapore)
Onset34.350.9074.181.05
Onset44.400.8644.271.04
Onset54.480.9094.410.981
Onset64.550.9484.711.08
Last Exposure44.810.9484.622.11
Bootstrap44.53 (sd 0.585)0.941 (sd 0.358)4.31 (sd 1.03)1.50 (sd 0.629)
Appendix 1—table 5
Mean incubation period and mean serial interval estimates for COVID-19 generated by other studies.
DataNumber of CasesMean Incubation Period (days)Mean Serial Interval (days)Reference
Wuhan first cases4255.2 (95CI 4.1-7.0)7.5 (95CI 5.3-19)Li et al., 2020b
South Korea first cases243.64.6Ki and Task Force for 2019-nCoV, 2020
Travellers from Wuhan886.4 (95CI 5.6-7.7)-Backer et al., 2019
Diagnosis outside Wuhan (excluding Wuhan residents)525.0 (95CI 4.2-6.0)-Linton et al., 2020
Diagnosis outside Wuhan (including Wuhan residents)1585.6 (95CI 5.0-6.3)-Linton et al., 2020
Transmission chains in Hong Kong21 chains-4.4 (95CI 2.9-6.7)Zhao et al., 2020
Infector-infectee pairs*28 pairs-4.0 (95CI 3.1-4.9)Nishiura et al., 2020
  1. *Note: included 3 infector-infectee pairs from this Singapore cluster. Remainder from Vietnam (4), South Korea (7), Germany (4), Taiwan (1) and China (9).

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