Data Science in the Real World

A Data Scientist Perspective

For the latest information and advice on COVID-19 visit the official WHO website: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/advice-for-public

With a surge in COVID-19 cases around the world, there is increasing apprehension about its impact and containment. Below is an accessible, initial exploration of Chinese epidemiological data for COVID-19, with an emphasis on implications for intervention policy.

Insights from China

Here, epidemiological data on the COVID-19 outbreak from China was obtained and used to generate choropleth maps of cases globally, in China, and the originating province of Hubei.

To examine more closely the spread of disease in Hubei, and the efficacy of containment measures, historical data was obtained at city-level granularity. These data were left-truncated to the date of the first death to facilitate the development of log-logistic forecasting models for each city (indicated in blue/red).

The x-axis represents the number of days since the first death in each city, and the y-axis the number of cumulative confirmed cases (left of pair) or deaths (right of pair). Perhaps the most striking observation is the plateau in new cases or deaths, underscoring the efficacy of government interventions in preventing new infections. Outside of Wuhan, within ~20 days of the first reported death, ~95% of new cases were being prevented, and the reproductive number dropped from ~3.86 to ~0.32.

Government interventions

The implementation of government interventions occurred in two stages. From 23rd January, an unprecedented policy of cordon sanitaire was introduced, in addition to further transport and social distancing measures: -

Initial block on outbound transport followed by suspension of public transport and a ban on all vehicular traffic in the city.

Social distancing measures introduced, with compulsory mask-wearing enforced in public places, and cancellation of social gatherings.

The increased availability of medical resources allowed the implementation of further interventions on 2nd February: -

A policy of centralized quarantine and treatment implemented for all confirmed and suspected cases, including those with fever or respiratory symptoms, including the close contacts of confirmed cases.

Social distancing measures extended, with temperature monitoring and stay-at-home policies enforced for all city residents.

Forecasting a no-intervention scenario

The cordon sanitaire policy was introduced early, on 23rd January, at a time when Hubei reported ~500 cases and ~17 deaths. Cities throughout the world are approaching — or have recently surpassed — a comparable stage in the outbreak. The breaking news of today, Sunday 8th March, reports 273 confirmed cases in the United Kingdom including 38 cases in London. The next 1–2 weeks will likely witness this ‘Hubei-threshold’ surpassed in many major cities.

A scenario of disease progression without aggressive intervention was modeled by building a linear model (blue) for confirmed cases on data up to 10th February in the cities of Hubei province, China: -

Here, the vertical dashed line represents 2nd February — the date of introduction of centralized quarantine and additional strict social distancing measures. After an approximate two-week period of sustained increases, there is a marked decline in new cases, consistent with the COVID-19 incubation period of 1–14 days.

The blue line represents a no-intervention scenario forecast with a linear model, revealing a predicted 2–3x increase in cases over the actual observed cases; this is consistent with recently published forecasting models (Wang et al., 2020), and highlights the efficacy of government intervention measures in preventing new cases.

Summary

Extensive early countermeasures have effectively controlled the COVID-19 outbreak in China. As other countries witness a surge in cases, it is clear that in the absence of viable drugs or vaccines, there is an urgent need for aggressive government intervention. China has provided a clear template, and the burden of COVID-19 will be shaped most profoundly by our ability to act quickly. Special efforts will also be required to protect the most vulnerable populations, including the elderly and healthcare workers.

References

Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19) https://www.who.int/docs/default-source/coronaviruse/who-china-joint-mission-on-covid-19-final-report.pdf

Chaolong Wang, Li Liu, Xingjie Hao, Huan Guo, Qi Wang, Jiao Huang, Na He, Hongjie Yu, Xihong Lin, An Pan, Sheng Wei, Tangchun Wu. Evolving Epidemiology and Impact of Non-pharmaceutical Interventions on the Outbreak of Coronavirus Disease 2019 in Wuhan, China. doi: https://doi.org/10.1101/2020.03.03.20030593

Tianzhi Wu, Xijin Ge, Guangchuang Yu. An R package and a website with real-time data on the COVID-19 coronavirus outbreak. medRxiv, 2020.02.25.20027433. doi: https://doi.org/10.1101/2020.02.25.20027433