Real-time monitoring the transmission potential of COVID-19 in Singapore, March 2020

Abstract

Background: As of March 31, 2020 the ongoing COVID-19 epidemic that started in China in December 2019 is now generating local transmission around the world. The geographic heterogeneity and associated intervention strategies highlight the need to monitor in real time the transmission potential of COVID-19. Singapore provides a unique case example for monitoring transmission, as there have been multiple disease clusters, yet transmission remains relatively continued.

Methods: Here we estimate the effective reproduction number, R_t, of COVID-19 in Singapore from the publicly available daily case series of imported and autochthonous cases by date of symptoms onset, after adjusting the local cases for reporting delays as of March 17, 2020. We also derive the reproduction number from the distribution of cluster sizes using a branching process analysis that accounts for truncation of case counts.

Results: The local incidence curve displays sub-exponential growth dynamics, with the reproduction number following a declining trend and reaching an estimate at 0.7 (95% CI: 0.3, 1.0) during the first transmission wave by February 14, 2020 while the overall R based on the cluster size distribution as of March 17, 2020 was estimated at 0.6 (95% CI: 0.4, 1.02). The overall mean reporting delay was estimated at 6.4 days (95% CI: 5.8, 6.9), but it was shorter among imported cases compared to local cases (mean 4.3 vs. 7.6 days, Wilcoxon test, p<0.001).

Conclusion: The trajectory of the reproduction number in Singapore underscores the significant effects of successful containment efforts in Singapore, but it also suggests the need to sustain social distancing and active case finding efforts to stomp out all active chains of transmission.

Keywords: COVID-19; Cluster distribution; Reporting delay; Reproduction number; SARS-CoV-2; Singapore; Transmission heterogeneity; Transmission potential.

Figure 1:

Cluster network of the cases in Singapore for the COVID-19 global pandemic as of March 17, 2020. The pink circles represent the cases linked to Wuhan, the green circles represent the non-Wuhan related case importations and the blue circles represent cases with no travel history to China. The larger dotted circles represent the COVID-19 disease clusters. Each blue arrow represents the direction in which the disease was transmitted. Pink arrows represent immediate family. Dates below the circles are the dates of case reporting.

Figure 2:

Map depicting the spatial distribution of the 6 largest COVID-19 clusters in Singapore; Grand Hayatt cluster, Yong Thai Hang cluster, Seletar Aerospace cluster, Wizlearn Technologies cluster, SAFRA Jurong cluster and The Grace Assembly of God Church and Life Church and Missions cluster as of March 17, 2020.

Figure 3:

Distribution of COVID-19 cluster sizes in Singapore as of March 17, 2020.

Figure 4:

Local and imported incidence cases by date of reporting as of March 17, 2020. The solid blue line represents the cumulative case count for the COVID-19 cases in Singapore.

Figure 5:

Reporting delay adjusted local incidence for the COVID-19 outbreak in Singapore as of March 17, 2020. Blue bars represent the raw incidence, red solid line represents the adjusted incidence, red dotted lines represent the 95% lower and upper bound of the adjusted incidence.

Figure 6:

The distribution of reporting delays for all cases as of March 17, 2020. The red line represents the fit of a gamma distribution to the data. The red circle represents the mean of gamma distribution and the horizontal line represents the 95% CI.

Figure 7:

Reporting delay distribution with mean (blue circle) and 95% CI (vertical lines) for each big cluster in Singapore; Grand Hayatt cluster, Yong Thai Hang cluster, Seletar Aerospace cluster, Wizlearn Technologies cluster, SAFRA Jurong cluster and The Grace Assembly of God Church and Life Church and Missions cluster as of March 17, 2020.

Figure 8:

The effective reproduction number reproduction number with 95% CI estimated by adjusting for the imported cases α = 0.15 during the first transmission wave by February 14, 2020. The effective reproduction number followed a declining trend with the latest estimate at 0.7 (95% CI: 0.3,1.0) by February 14, 2020.