Driver Project 8 - Characterizing COVID-19 Transmission Chains for Precision Mitigation Using Epidemiological Survey Data
To improve control measures for COVID-19 by applying statistical methods to existing datasets containing over 40,000 COVID-19 cases from five Asian countries to reconstruct transmission chains between individuals in households and communities.
Xiaofan Liu at the City University of Hong Kong and colleagues aimed to reconstruct COVID-19 transmission chains between individuals in communities and households using statistical methods applied to existing datasets to more reliably estimate COVID-19 transmission characteristics, such as reproduction rates, that are critical for planning effective control measures. Currently, transmission characteristics are estimated using aggregated-level data, which leads to inaccuracies. Ideally, data on how COVID-19 is transmitted between individuals are needed. They curated an existing collection of datasets containing over 40,000 COVID-19 cases in five Asian countries with person-to-person transmission evidence to reconstruct transmission chains. They then applied statistical tests and an analytical methodology called regression analysis to identify the most important transmission risk factors, including virus strain, transmission media, population density, and climate conditions.
| Title | Journal | Date |
Type | Abstract |
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| Lancet Global Health | Oct 2022 | Publication | The transmission dynamics of influenza were affected by public health and social measures (PHSMs) implemented globally since early 2020 to mitigate the COVID-19 pandemic. We aimed to assess the effect of COVID-19 PHSMs on the transmissibility of influenza viruses and to predict upcoming influenza epidemics… | |
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Modeling comparative cost-effectiveness of SARS-CoV-2 vaccine dose fractionation in India
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Nature Medicine |
Feb 2022 | Publication | Given global Coronavirus Disease 2019 (COVID-19) vaccine shortages and inequity of vaccine distributions, fractionation of vaccine doses might be an effective strategy for reducing public health and economic burden, notwithstanding the emergence of new variants of concern… |
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Reproduction Numbers of SARS-CoV-2 Variants: A Systematic Review and Meta-analysis |
Clinical Infectious Diseases |
Feb 2022 | Publication | The COVID-19 pandemic continues to pose substantial risks to public health, worsened by the emergence of SARS-CoV-2 variants which may have a higher transmissibility and reduce vaccine effectiveness… |
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Assessing the spread risk of COVID-19 associated with multi-mode transportation networks in China |
Science Direct | April 2022 | Publication | The spatial spread of COVID-19 during early 2020 in China was primarily driven by outbound travelers leaving the epicenter, Wuhan, Hubei province… |
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Grand Challenges ICODA Data Science Initiative – Blog 1
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Aridhia | Nov 2021 | Article | A few months ago, we reported on the launch of the Grand Challenges ICODA Data Science initiative by the Bill & Melinda Gates Foundation. These 10 projects will use the ICODA Workbench (powered by Aridhia’s DRE) to explore the answers to critical research questions relating to COVID-19. Over the coming weeks, we will take a look at some of these projects and what they aim to achieve… |
| iScience | Sep 2022 | Publication | Although open-access data are increasing common and useful to epidemiological research, curation of such datasets is resource-intensive and time-consuming | |
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| Title | Type | Description |
| COVID-19 Transmission Chains for using Epidemiological Survey Data from Asia | Metadata | This line-list dataset contains confirmed COVID-19 cases with specific information that can link them to others, such as close contacts and cooccurrence in the same place. The linkage information can be used for transmission chain reconstruction. The data are curated from the publicly available case reports disclosed by global governments or collected from published studies. |
| GitHub code | code |
Repository for the ICODA project DP-CHAIN. Hosted here is our infectious disease transmission chain inference algorithm utilizing epidemiological survey data. |
Video Transcription
We’re using epidemiological survey data from eight countries. The challenges so far of course is the data curation process – different data sets, they have different standards, they have different organisations and we have to identify the identical parts in the data and merge them together.
Once the project has been finished that is once the COVID-19 transmission chains have different variations in different worlds and a different culture, demographic features has been characterised. Well hopefully we can help the human beings understanding COVID-19 better and help the policymakers to make more scientific strategies.
We have already finished that data curation parts and we are really applying statistical models onto our data. Hopefully we can the results in three months.
I think the first priority of health’s data science right now is to opening up data. During our data collection process we have identified many papers that are characterising a specific set of transmission chain in a specific demographic or geographic settings. However, these data are not open. And also we have identified many useful databases that contain useful data for this project. But we don’t have access to those databases. We understand that there were privacy concerns in this line of research. That is the epidemiological survey data could sometimes be sensitive. In privacy prospective, however, we really hope that these databases can at least be open to the global size, sociality. The second priority for health data science is the normalisation and standardisation of the datasets. We spend a lot of time curating the data sets from different sources, they will be better if they had been prepared in a standardised way and that will save not only our time, but other researchers time so that they can put more time into an analysis instead of data processing.
It’s obvious that our research question cannot be answered without being shared. We rely on different data sources. For example, academic papers, and the government public reports for collecting and curating these epidemiologic reports or the traces of the transmission chains.