Mobility, exposure, and epidemiological timelines of COVID-19 infections in China outside Hubei province

Abstract

The 2019 coronavirus disease (COVID-19) is pseudonymously linked to more than 100 million cases in the world as of January 2021. High-quality data are needed but lacking in the understanding of and fighting against COVID-19. We provide a complete and updating hand-coded line-list dataset containing detailed information of the cases in China and outside the epicenter in Hubei province. The data are extracted from public disclosures by local health authorities, starting from January 19. This dataset contains a very rich set of features for the characterization of COVID-19’s epidemiological properties, including individual cases’ demographic information, travel history, potential virus exposure scenario, contacts with known infections, and timelines of symptom onset, quarantine, infection confirmation, and hospitalization. These cases can be considered the baseline COVID-19 transmissibility under extreme mitigation measures, and therefore, a reference for comparative scientific investigation and public policymaking.

Inferring time-varying generation time, serial interval, and incubation period distributions for COVID-19

“…The original data was extracted from the publicly available case reports provided by more than 200 municipal health commissions in Mainland China and reported in earlier studies 6 , 18 , 27 , and further integrated and compiled by ref. 28 . The line-list data contains the information on the case demography (age, sex, occupation, residence place), exposure and contact history, onset and hospitalization dates, and potential transmission links in addition.…”

COVID-19 spreading patterns in family clusters reveal gender roles in China

“…We collected the epidemiological survey reports of COVID-19 cases from 264 municipal governments outside Hubei province in mainland China. Data include cases' demographic characteristics, social relations of the close contacts, travel and contact diaries, and symptoms timelines [25]. This dataset covers 12 667 confirmed cases from 19 January to 20 November 2020, accounting for 71.1% of all confirmed cases outside Hubei Province.…”

“…That is to say, the imported case of a family is the first-infected case in this family, who could be infected in her/his hometown or other cities, in her/his working place or other places outside the family. We use curated epidemiological survey data with fine-grained features [25] and reconstruct the transmission chains during the Chinese New Year (20 January to 18 February 2020). Then, we apply statistical tests and construct null models to test the following two hypotheses.…”

Linking genomic and epidemiologic information to advance the study of COVID-19

“…Different kinds of sequence data are available, including raw sequencing data, virus genome sequences, and protein sequences. Furthermore, COVID-19 data can be found in epidemiological news and reports, produced and disseminated by the World Health Organization, public health authorities, Wikipedia, and other websites 16 , 17 . These data have addressed COVID-19 and the SARS-CoV-2 viruses from different perspectives, but it was difficult to obtain a comprehensive understanding of COVID-19 and SARS-CoV-2 virus from these data.…”

“…Most of the datasets available to date contain only epidemiological data 16 , 17 , without linking these data to the genome. Matching epidemiologic information with genomic information is beneficial for the surveillance of virus transmission and reconstruction of infection paths.…”