leedrake5 / ncov-cfr-shiny

R code and documentation to estimate case fatality ratio of COVID-19 from cases outside China

This is a shiny adaptation of this app. Origional app notes are below

Estimating case fatality ratio of COVID-19 from observed cases outside China

Updated report: 16 February 2020

Christian L. Althaus ([email protected]), Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland

Summary: We provide a preliminary estimate of the overall case fatality ratio (CFR) of COVID-19 at 2.2% (95% confidence interval: 0.6%-5.8%).

COVID-19 has spread rapidly in China with a basic reproduction number of 2.2 (90% high density interval: 1.4-3.8) (1) and a doubling time of around one week (2) during the early phase of the epidemic. To date, uncertainty remains regarding the case fatality ratio (CFR) of COVID-19. Naive estimates of CFR from the reported numbers of confirmed cases and deaths are difficult to interpret due to possible biases in observed cases and the right-censoring of cases with respect to the time delay from illness onset to death (3). We argue that reported COVID-19 cases and deaths outside China are less prone to bias and could provide more precise estimates of the absolute CFR (Figure 1, Table 1).

Figure 1. Reported COVID-19 cases outside China by onset of symptoms and time of death. The WHO Coronavirus disease 2019 (COVID-19) situation reports report onset of symptoms in cases outside China. Deaths outside China have been reported by WHO, ECDC and international media.

Table 1. List of fatal COVID-19 cases outside China.

Date	Country	Sex	Age	Comorbidities	Notes	Source
1 Feb 2020	Philippines	Male	44 y	Streptococcus pneumoniae and influenza B virus	Included	Link
13 Feb 2020	France	Male	80 y	-	Included	Link
14 Feb 2020	Japan	Female	80+ y	-	Included	Link
15 Feb 2020	Taiwan	Male	60+ y	Hepatitis B virus and diabetes	Not yet included	Link

First, we collect COVID-19 cases and deaths outside China from WHO, ECDC and international media (Figure 1). We then model the expected incidence of death due to COVID-19 given the CFR. To this end, we assume that the time from onset to death follows a gamma distribution with a mean of 15.3 days and a shape parameter of 5.0 (Figure 2) (4). Finally, we use a maximum-likelihood framework to estimate CFR by fitting the model to the data assuming the observed numbers of deaths are Poisson distributed (see R code file ncov_cfr.R).

Figure 2. Probability distribution of time from onset of COVID-19 symptoms to death. The distribution is based on the estimates by Linton et al. (4).

We estimate the CFR of COVID-19 at 2.2% (95% confidence interval: 0.6%-5.8%). Due to the small number of deaths, the uncertainty around this estimate remains wide. Increasing numbers of cases and deaths outside China will increase the precision of the estimate (Figure 3). Furthermore, the estimate could represent an upper bound because information on date of onset of symptoms is not available for all reported cases and asymptomatic cases are not included.

Figure 3. Change in precision of estimates of COVID-19 case fatality ratio. Future estimates including additional cases and deaths outside China are expected to become more precise.

References

1. Riou, J. and Althaus, C. L. (2020). Pattern of early human-to-human transmission of wuhan 2019 novel coronavirus (2019-ncov), December 2019 to January 2020. Eurosurveillance, 25(4).
2. Li, Q., Guan, X., Wu, P., Wang, X., Zhou, L., Tong, Y., et al. (2020). Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. N Engl J Med.
3. Jung, S., Akhmetzhanov, A. R., Hayashi, K., Linton, N. M., Yang, Y., Yuan, B., et al. (2020). Real time estimation of the risk of death from novel coronavirus (2019-nCoV) infection: Inference using exported cases. medRxiv.
4. Linton, N. M., Kobayashi, T., Yang, Y., Hayashi, K., Akhmetzhanov, A. R., Jung, S., et al. (2020). Epidemiological characteristics of novel coronavirus infection: A statistical analysis of publicly available case data. medRxiv.