Report author: Lily Geidelberg
Authors: Erik M Volz, Han Fu 1 , Haowei Wang 1 , Xiaoyue Xi 2 , Wei Chen 3 , Dehui Liu 3 , Yingying Chen 3 , Mengmeng Tian 3 , Wei Tan 4 , Junjie Zai 5 , Wanying Sun 6 , Jiandong Li 6 , Junhua Li 6 , Xingguang Li 7, Qing Nie 3**
1. Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, Imperial College London,2.Department of Mathematics, Imperial College London,3. Department of Microbiology, Weifang Center for Disease Control and Prevention, Weifang, 4. Department of Respiratory Medicine, Weifang People's Hospital, Weifang, 5. Immunology Innovation Team, School of Medicine, Ningbo University, Ningbo,6. Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 7. Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China
Report prepared on 2020-04-09
This is analysis is based on :
- 20 whole genomes sampled from within Weifang
- 50 whole genomes sampled from outside of Weifang
- Samples within Weifang were collected between 2020-01-24 and 2020-02-10
How many are infected in Weifang?
Figure 1: Cumulative estimated infections through time. Points represent reported cases in Weifang. The dashed line indicates the date of last sample in Weifang in this analysis.
Estimated cumulative infections at last sample (2020-02-10): 223 [38-827] median [95%CI]
Cumulative confirmed infections reported at 2020-02-10: 38
Figure 2: Daily estimated infections through time. Points represent reported cases in Weifang. The dashed line indicates the date of last sample in Weifang in this analysis.
Figure 3: Reproduction number through time. The dashed line indicates the date of last sample in Weifang in this analysis.
Reproduction number at last sample (2020-02-10): 0.0911 [0.0129-0.532] median [95% CrI]
How quickly has the epidemic in Weifang grown?
|Quantile||Reproduction number||Growth rate (per day)||Doubling time (days)|
Table 1: Reproduction number, growth rate and doubling times
How has SARS-CoV 2 evolved in Weifang?
Figure 4: Time scaled phylogeny co-estimated with epidemiological parameters. The colour of the tips corresponds to location sampling; red tips were sampled from within Weifang, blue tips from outside.
Molecular clock rate of evolution: 0.0012 [0.000874-0.00163] median [95% CrI]
Details on methods and priors can be found here.
Model version: seijr0.0.0
Report version: 20200409-105433-91378a08
This work was supported by the MRC Centre for Global Infectious Disease Analysis at Imperial College London.