Publications
1.
Lai, Shengjie; Bogoch, Isaac I; Ruktanonchai, Nick W; Watts, Alexander; Lu, Xin; Yang, Weizhong; Yu, Hongjie; Khan, Kamran; Tatem, Andrew J
Assessing spread risk of COVID-19 within and beyond China in early 2020 Journal Article
In: Data Science and Management, 2022.
Abstract | Links | BibTeX | Tags: China, covid-19, Mobility
@article{,
title = {Assessing spread risk of COVID-19 within and beyond China in early 2020},
author = {Lai, Shengjie and Bogoch, Isaac I and Ruktanonchai, Nick W and Watts, Alexander and Lu, Xin and Yang, Weizhong and Yu, Hongjie and Khan, Kamran and Tatem, Andrew J},
doi = {10.1016/j.dsm.2022.08.004},
year = {2022},
date = {2022-08-26},
urldate = {2022-08-26},
journal = {Data Science and Management},
abstract = {A novel coronavirus emerged in Wuhan in late 2019 and has caused the COVID-19 pandemic announced by the World Health Organization on March 12, 2020. This study was originally conducted in January 2020 to estimate the potential risk and geographic range of COVID-19 spread within and beyond China at the early stage of the pandemic. A series of connectivity and risk analyses based on domestic and international travel networks were conducted using historical aggregated mobile phone data and air passenger itinerary data. We found that the cordon sanitaire of Wuhan was likely to have occurred during the latter stages of peak population numbers leaving the city, with travellers departing into neighbouring cities and other megacities in China. We estimated that 59,912 air passengers, of which 834 (95% uncertainty interval: 478–1349) had COVID-19 infection, travelled from Wuhan to 382 cities outside of mainland China during the two weeks prior to the city’s lockdown. Most of these destinations were located in Asia, but major hubs in Europe, the US and Australia were also prominent, with a strong correlation seen between the predicted risks of importation and the number of imported cases found. Given the limited understanding of emerging infectious diseases in the very early stages of outbreaks, our approaches and findings in assessing travel patterns and risk of transmission can help guide public health preparedness and intervention design for new COVID-19 waves caused by variants of concern and future pandemics to effectively limit transmission beyond its initial extent.},
keywords = {China, covid-19, Mobility},
pubstate = {published},
tppubtype = {article}
}
A novel coronavirus emerged in Wuhan in late 2019 and has caused the COVID-19 pandemic announced by the World Health Organization on March 12, 2020. This study was originally conducted in January 2020 to estimate the potential risk and geographic range of COVID-19 spread within and beyond China at the early stage of the pandemic. A series of connectivity and risk analyses based on domestic and international travel networks were conducted using historical aggregated mobile phone data and air passenger itinerary data. We found that the cordon sanitaire of Wuhan was likely to have occurred during the latter stages of peak population numbers leaving the city, with travellers departing into neighbouring cities and other megacities in China. We estimated that 59,912 air passengers, of which 834 (95% uncertainty interval: 478–1349) had COVID-19 infection, travelled from Wuhan to 382 cities outside of mainland China during the two weeks prior to the city’s lockdown. Most of these destinations were located in Asia, but major hubs in Europe, the US and Australia were also prominent, with a strong correlation seen between the predicted risks of importation and the number of imported cases found. Given the limited understanding of emerging infectious diseases in the very early stages of outbreaks, our approaches and findings in assessing travel patterns and risk of transmission can help guide public health preparedness and intervention design for new COVID-19 waves caused by variants of concern and future pandemics to effectively limit transmission beyond its initial extent.
2.
Lai, Shengjie; Sorichetta, Alessandro; Steele, Jessica; Ruktanonchai, Corrine W; Cunningham, Alexander D; Rogers, Grant; Koper, Patrycja; Woods, Dorothea; Bondarenko, Maksym; Ruktanonchai, Nick W; Shi, Weifeng; and Tatem, Andrew J.
Global holiday datasets for understanding seasonal human mobility and population dynamics Journal Article
In: Scientific Data, vol. 9, no. 17, 2022.
Abstract | Links | BibTeX | Tags: holidays, Mobility, Population
@article{nokey,
title = {Global holiday datasets for understanding seasonal human mobility and population dynamics},
author = {Lai, Shengjie and Sorichetta, Alessandro and Steele, Jessica and Ruktanonchai, Corrine W and Cunningham, Alexander D and Rogers, Grant and Koper, Patrycja and Woods, Dorothea and Bondarenko, Maksym and Ruktanonchai, Nick W and Shi, Weifeng and and Tatem, Andrew J.},
doi = {https://doi.org/10.1038/s41597-022-01120-z},
year = {2022},
date = {2022-01-20},
urldate = {2022-01-20},
journal = {Scientific Data},
volume = {9},
number = {17},
abstract = {Public and school holidays have important impacts on population mobility and dynamics across multiple spatial and temporal scales, subsequently affecting the transmission dynamics of infectious diseases and many socioeconomic activities. However, worldwide data on public and school holidays for understanding their changes across regions and years have not been assembled into a single, open-source and multitemporal dataset. To address this gap, an open access archive of data on public and school holidays in 2010–2019 across the globe at daily, weekly, and monthly timescales was constructed. Airline passenger volumes across 90 countries from 2010 to 2018 were also assembled to illustrate the usage of the holiday data for understanding the changing spatiotemporal patterns of population movements.},
keywords = {holidays, Mobility, Population},
pubstate = {published},
tppubtype = {article}
}
Public and school holidays have important impacts on population mobility and dynamics across multiple spatial and temporal scales, subsequently affecting the transmission dynamics of infectious diseases and many socioeconomic activities. However, worldwide data on public and school holidays for understanding their changes across regions and years have not been assembled into a single, open-source and multitemporal dataset. To address this gap, an open access archive of data on public and school holidays in 2010–2019 across the globe at daily, weekly, and monthly timescales was constructed. Airline passenger volumes across 90 countries from 2010 to 2018 were also assembled to illustrate the usage of the holiday data for understanding the changing spatiotemporal patterns of population movements.
3.
Li, Juan; Lai, Shengjie; Gao, George F; and Shi, Weifeng
The emergence, genomic diversity and global spread of SARS-CoV-2 Journal Article
In: Nature, vol. 600, pp. 408–418, 2021.
Abstract | Links | BibTeX | Tags: covid-19, Mobility
@article{nokey,
title = {The emergence, genomic diversity and global spread of SARS-CoV-2},
author = {Li, Juan and Lai, Shengjie and Gao, George F and and Shi, Weifeng},
doi = {https://doi.org/10.1038/s41586-021-04188-6},
year = {2021},
date = {2021-12-08},
urldate = {2021-12-08},
journal = {Nature},
volume = {600},
pages = {408–418},
abstract = {Since the first cases of COVID-19 were documented in Wuhan, China in 2019, the world has witnessed a devastating global pandemic, with more than 238 million cases, nearly 5 million fatalities and the daily number of people infected increasing rapidly. Here we describe the currently available data on the emergence of the SARS-CoV-2 virus, the causative agent of COVID-19, outline the early viral spread in Wuhan and its transmission patterns in China and across the rest of the world, and highlight how genomic surveillance, together with other data such as those on human mobility, has helped to trace the spread and genetic variation of the virus and has also comprised a key element for the control of the pandemic. We pay particular attention to characterizing and describing the international spread of the major variants of concern of SARS-CoV-2 that were first identified in late 2020 and demonstrate that virus evolution has entered a new phase. More broadly, we highlight our currently limited understanding of coronavirus diversity in nature, the rapid spread of the virus and its variants in such an increasingly connected world, the reduced protection of vaccines, and the urgent need for coordinated global surveillance using genomic techniques. In summary, we provide important information for the prevention and control of both the ongoing COVID-19 pandemic and any new diseases that will inevitably emerge in the human population in future generations.},
keywords = {covid-19, Mobility},
pubstate = {published},
tppubtype = {article}
}
Since the first cases of COVID-19 were documented in Wuhan, China in 2019, the world has witnessed a devastating global pandemic, with more than 238 million cases, nearly 5 million fatalities and the daily number of people infected increasing rapidly. Here we describe the currently available data on the emergence of the SARS-CoV-2 virus, the causative agent of COVID-19, outline the early viral spread in Wuhan and its transmission patterns in China and across the rest of the world, and highlight how genomic surveillance, together with other data such as those on human mobility, has helped to trace the spread and genetic variation of the virus and has also comprised a key element for the control of the pandemic. We pay particular attention to characterizing and describing the international spread of the major variants of concern of SARS-CoV-2 that were first identified in late 2020 and demonstrate that virus evolution has entered a new phase. More broadly, we highlight our currently limited understanding of coronavirus diversity in nature, the rapid spread of the virus and its variants in such an increasingly connected world, the reduced protection of vaccines, and the urgent need for coordinated global surveillance using genomic techniques. In summary, we provide important information for the prevention and control of both the ongoing COVID-19 pandemic and any new diseases that will inevitably emerge in the human population in future generations.
4.
Shepherd, Harry ER; Atherden, Florence S; Chan, Ho Man Theophilus; Loveridge, Alexandra; Tatem, Andrew J
Domestic and international mobility trends in the United Kingdom during the COVID-19 pandemic: an analysis of facebook data Journal Article
In: International Journal of Health Geographics, vol. 20, no. 46, 2021.
Abstract | Links | BibTeX | Tags: covid-19, Europe, Mobility, NPIs, United Kingdom
@article{nokey,
title = {Domestic and international mobility trends in the United Kingdom during the COVID-19 pandemic: an analysis of facebook data},
author = {Shepherd, Harry ER and Atherden, Florence S and Chan, Ho Man Theophilus and Loveridge, Alexandra and Tatem, Andrew J},
doi = {10.1186/s12942-021-00299-5},
year = {2021},
date = {2021-12-04},
urldate = {2021-12-04},
journal = {International Journal of Health Geographics},
volume = {20},
number = {46},
abstract = {Since early March 2020, the COVID-19 epidemic across the United Kingdom has led to a range of social distancing policies, which resulted in changes to mobility across different regions. An understanding of how these policies impacted travel patterns over time and at different spatial scales is important for designing effective strategies, future pandemic planning and in providing broader insights on the population geography of the country. Crowd level data on mobile phone usage can be used as a proxy for population mobility patterns and provide a way of quantifying in near-real time the impact of social distancing measures on changes in mobility.
Methods
Here we explore patterns of change in densities, domestic and international flows and co-location of Facebook users in the UK from March 2020 to March 2021.
Results
We find substantial heterogeneities across time and region, with large changes observed compared to pre-pademic patterns. The impacts of periods of lockdown on distances travelled and flow volumes are evident, with each showing variations, but some significant reductions in co-location rates. Clear differences in multiple metrics of mobility are seen in central London compared to the rest of the UK, with each of Scotland, Wales and Northern Ireland showing significant deviations from England at times. Moreover, the impacts of rapid changes in rules on international travel to and from the UK are seen in substantial fluctuations in traveller volumes by destination.
Conclusions
While questions remain about the representativeness of the Facebook data, previous studies have shown strong correspondence with census-based data and alternative mobility measures, suggesting that findings here are valuable for guiding strategies.},
keywords = {covid-19, Europe, Mobility, NPIs, United Kingdom},
pubstate = {published},
tppubtype = {article}
}
Since early March 2020, the COVID-19 epidemic across the United Kingdom has led to a range of social distancing policies, which resulted in changes to mobility across different regions. An understanding of how these policies impacted travel patterns over time and at different spatial scales is important for designing effective strategies, future pandemic planning and in providing broader insights on the population geography of the country. Crowd level data on mobile phone usage can be used as a proxy for population mobility patterns and provide a way of quantifying in near-real time the impact of social distancing measures on changes in mobility.
Methods
Here we explore patterns of change in densities, domestic and international flows and co-location of Facebook users in the UK from March 2020 to March 2021.
Results
We find substantial heterogeneities across time and region, with large changes observed compared to pre-pademic patterns. The impacts of periods of lockdown on distances travelled and flow volumes are evident, with each showing variations, but some significant reductions in co-location rates. Clear differences in multiple metrics of mobility are seen in central London compared to the rest of the UK, with each of Scotland, Wales and Northern Ireland showing significant deviations from England at times. Moreover, the impacts of rapid changes in rules on international travel to and from the UK are seen in substantial fluctuations in traveller volumes by destination.
Conclusions
While questions remain about the representativeness of the Facebook data, previous studies have shown strong correspondence with census-based data and alternative mobility measures, suggesting that findings here are valuable for guiding strategies.
Methods
Here we explore patterns of change in densities, domestic and international flows and co-location of Facebook users in the UK from March 2020 to March 2021.
Results
We find substantial heterogeneities across time and region, with large changes observed compared to pre-pademic patterns. The impacts of periods of lockdown on distances travelled and flow volumes are evident, with each showing variations, but some significant reductions in co-location rates. Clear differences in multiple metrics of mobility are seen in central London compared to the rest of the UK, with each of Scotland, Wales and Northern Ireland showing significant deviations from England at times. Moreover, the impacts of rapid changes in rules on international travel to and from the UK are seen in substantial fluctuations in traveller volumes by destination.
Conclusions
While questions remain about the representativeness of the Facebook data, previous studies have shown strong correspondence with census-based data and alternative mobility measures, suggesting that findings here are valuable for guiding strategies.
5.
Han, Shasha; Zhang, Ting; Lyu, Yan; Lai, Shengjie; Dai, Peixi; Zheng, Jiandong; Yang, Weizhong; Zhou, Xiaohua; Feng, Luzhao
Methods and Applications: The Incoming Influenza Season — China, the United Kingdom, and the United States, 2021–2022 Journal Article
In: China CDC Weekly, vol. 3, no. 49, pp. 1039, 2021.
Abstract | Links | BibTeX | Tags: influenza, Mobility, NPIs, Predictive clustering
@article{nokey,
title = {Methods and Applications: The Incoming Influenza Season — China, the United Kingdom, and the United States, 2021–2022},
author = {Han, Shasha and Zhang, Ting and Lyu, Yan and Lai, Shengjie and Dai, Peixi and Zheng, Jiandong and Yang, Weizhong and Zhou, Xiaohua and Feng, Luzhao},
doi = {10.46234/ccdcw2021.253},
year = {2021},
date = {2021-12-03},
urldate = {2021-12-03},
journal = {China CDC Weekly},
volume = {3},
number = {49},
pages = {1039},
abstract = {Seasonal influenza activity has declined globally since the widespread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. There has been scarce information to understand the future dynamics of influenza — and under different hypothesis on relaxation of non-pharmaceutical interventions (NPIs) in particular — after the disruptions to seasonal patterns.
Methods
We collected data from public sources in China, the United Kingdom, and the United States, and forecasted the influenza dynamics in the incoming 2021–2022 season under different NPIs. We considered Northern China and Southern China separately, due to the sharp difference in the patterns of seasonal influenza. For the United Kingdom, data were collected for England only.
Results
Compared to the epidemics in 2017–2019, longer and blunter influenza outbreaks could occur should NPIs be fully lifted, with percent positivity varying from 10.5 to 18.6 in the studying regions. The rebounds would be smaller if the mask-wearing intervention continued or the international mobility stayed low, but sharper if the mask-wearing intervention was lifted in the middle of influenza season. Further, influenza activity could stay low under a much less stringent mask-wearing intervention coordinated with influenza vaccination.
Conclusions
The results added to our understandings of future influenza dynamics after the global decline during the coronavirus disease 2019 (COVID-19) pandemic. In light of the uncertainty on the incoming circulation strains and the relatively low negative impacts of mask wearing on society, our findings suggested that wearing mask could be considered as an accompanying mitigation measure in influenza prevention and control, especially for seasons after long periods of low-exposure to influenza viruses.},
keywords = {influenza, Mobility, NPIs, Predictive clustering},
pubstate = {published},
tppubtype = {article}
}
Seasonal influenza activity has declined globally since the widespread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. There has been scarce information to understand the future dynamics of influenza — and under different hypothesis on relaxation of non-pharmaceutical interventions (NPIs) in particular — after the disruptions to seasonal patterns.
Methods
We collected data from public sources in China, the United Kingdom, and the United States, and forecasted the influenza dynamics in the incoming 2021–2022 season under different NPIs. We considered Northern China and Southern China separately, due to the sharp difference in the patterns of seasonal influenza. For the United Kingdom, data were collected for England only.
Results
Compared to the epidemics in 2017–2019, longer and blunter influenza outbreaks could occur should NPIs be fully lifted, with percent positivity varying from 10.5 to 18.6 in the studying regions. The rebounds would be smaller if the mask-wearing intervention continued or the international mobility stayed low, but sharper if the mask-wearing intervention was lifted in the middle of influenza season. Further, influenza activity could stay low under a much less stringent mask-wearing intervention coordinated with influenza vaccination.
Conclusions
The results added to our understandings of future influenza dynamics after the global decline during the coronavirus disease 2019 (COVID-19) pandemic. In light of the uncertainty on the incoming circulation strains and the relatively low negative impacts of mask wearing on society, our findings suggested that wearing mask could be considered as an accompanying mitigation measure in influenza prevention and control, especially for seasons after long periods of low-exposure to influenza viruses.
Methods
We collected data from public sources in China, the United Kingdom, and the United States, and forecasted the influenza dynamics in the incoming 2021–2022 season under different NPIs. We considered Northern China and Southern China separately, due to the sharp difference in the patterns of seasonal influenza. For the United Kingdom, data were collected for England only.
Results
Compared to the epidemics in 2017–2019, longer and blunter influenza outbreaks could occur should NPIs be fully lifted, with percent positivity varying from 10.5 to 18.6 in the studying regions. The rebounds would be smaller if the mask-wearing intervention continued or the international mobility stayed low, but sharper if the mask-wearing intervention was lifted in the middle of influenza season. Further, influenza activity could stay low under a much less stringent mask-wearing intervention coordinated with influenza vaccination.
Conclusions
The results added to our understandings of future influenza dynamics after the global decline during the coronavirus disease 2019 (COVID-19) pandemic. In light of the uncertainty on the incoming circulation strains and the relatively low negative impacts of mask wearing on society, our findings suggested that wearing mask could be considered as an accompanying mitigation measure in influenza prevention and control, especially for seasons after long periods of low-exposure to influenza viruses.
6.
Floyd, Jessica R.; Ogola, Joseph; Fèvre, Eric M.; Wardrop, Nicola; Tatem, Andrew J.; Ruktanonchai, Nick W.
Activity-specific mobility of adults in a rural region of western Kenya Journal Article
In: PeerJ, vol. 8, pp. e8798, 2020, ISSN: 2167-8359.
Abstract | Links | BibTeX | Tags: Activity, GPS, Mobility, Resource access
@article{10.7717/peerj.8798,
title = {Activity-specific mobility of adults in a rural region of western Kenya},
author = {Jessica R. Floyd and Joseph Ogola and Eric M. Fèvre and Nicola Wardrop and Andrew J. Tatem and Nick W. Ruktanonchai},
url = {https://doi.org/10.7717/peerj.8798},
doi = {10.7717/peerj.8798},
issn = {2167-8359},
year = {2020},
date = {2020-04-01},
journal = {PeerJ},
volume = {8},
pages = {e8798},
abstract = {Improving rural household access to resources such as markets, schools and healthcare can help alleviate poverty in low-income settings. Current models of geographic accessibility to various resources rarely take individual variation into account due to a lack of appropriate data, yet understanding mobility at an individual level is key to knowing how people access their local resources. Our study used both an activity-specific survey and GPS trackers to evaluate how adults in a rural area of western Kenya accessed local resources. We calculated the travel time and time spent at six different types of resource and compared the GPS and survey data to see how well they matched. We found links between several demographic characteristics and the time spent at different resources, and that the GPS data reflected the survey data well for time spent at some types of resource, but poorly for others. We conclude that demography and activity are important drivers of mobility, and a better understanding of individual variation in mobility could be obtained through the use of GPS trackers on a wider scale.},
keywords = {Activity, GPS, Mobility, Resource access},
pubstate = {published},
tppubtype = {article}
}
Improving rural household access to resources such as markets, schools and healthcare can help alleviate poverty in low-income settings. Current models of geographic accessibility to various resources rarely take individual variation into account due to a lack of appropriate data, yet understanding mobility at an individual level is key to knowing how people access their local resources. Our study used both an activity-specific survey and GPS trackers to evaluate how adults in a rural area of western Kenya accessed local resources. We calculated the travel time and time spent at six different types of resource and compared the GPS and survey data to see how well they matched. We found links between several demographic characteristics and the time spent at different resources, and that the GPS data reflected the survey data well for time spent at some types of resource, but poorly for others. We conclude that demography and activity are important drivers of mobility, and a better understanding of individual variation in mobility could be obtained through the use of GPS trackers on a wider scale.
7.
Tessema, Sofonias; Wesolowski, Amy; Chen, Anna; Murphy, Maxwell; Wilheim, Jordan; Mupiri, Anna-Rosa; Ruktanonchai, Nick W; Alegana, Victor A; Tatem, Andrew J; Tambo, Munyaradzi; Didier, Bradley; Cohen, Justin M; Bennett, Adam; Sturrock, Hugh JW; Gosling, Roland; Hsiang, Michelle S; Smith, David L; Mumbengegwi, Davis R; Smith, Jennifer L; Greenhouse, Bryan
Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa Journal Article
In: eLife, vol. 8, pp. e43510, 2019, ISSN: 2050-084X.
Abstract | Links | BibTeX | Tags: genetic epidemiology, malaria, Mobility, parasite genomics
@article{10.7554/eLife.43510,
title = {Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa},
author = {Sofonias Tessema and Amy Wesolowski and Anna Chen and Maxwell Murphy and Jordan Wilheim and Anna-Rosa Mupiri and Nick W Ruktanonchai and Victor A Alegana and Andrew J Tatem and Munyaradzi Tambo and Bradley Didier and Justin M Cohen and Adam Bennett and Hugh JW Sturrock and Roland Gosling and Michelle S Hsiang and David L Smith and Davis R Mumbengegwi and Jennifer L Smith and Bryan Greenhouse},
editor = {Ben Cooper and Neil M Ferguson and Samir Bhatt and Thomas S Churcher},
url = {https://doi.org/10.7554/eLife.43510},
doi = {10.7554/eLife.43510},
issn = {2050-084X},
year = {2019},
date = {2019-04-01},
journal = {eLife},
volume = {8},
pages = {e43510},
publisher = {eLife Sciences Publications, Ltd},
abstract = {Local and cross-border importation remain major challenges to malaria elimination and are difficult to measure using traditional surveillance data. To address this challenge, we systematically collected parasite genetic data and travel history from thousands of malaria cases across northeastern Namibia and estimated human mobility from mobile phone data. We observed strong fine-scale spatial structure in local parasite populations, providing positive evidence that the majority of cases were due to local transmission. This result was largely consistent with estimates from mobile phone and travel history data. However, genetic data identified more detailed and extensive evidence of parasite connectivity over hundreds of kilometers than the other data, within Namibia and across the Angolan and Zambian borders. Our results provide a framework for incorporating genetic data into malaria surveillance and provide evidence that both strengthening of local interventions and regional coordination are likely necessary to eliminate malaria in this region of Southern Africa.},
keywords = {genetic epidemiology, malaria, Mobility, parasite genomics},
pubstate = {published},
tppubtype = {article}
}
Local and cross-border importation remain major challenges to malaria elimination and are difficult to measure using traditional surveillance data. To address this challenge, we systematically collected parasite genetic data and travel history from thousands of malaria cases across northeastern Namibia and estimated human mobility from mobile phone data. We observed strong fine-scale spatial structure in local parasite populations, providing positive evidence that the majority of cases were due to local transmission. This result was largely consistent with estimates from mobile phone and travel history data. However, genetic data identified more detailed and extensive evidence of parasite connectivity over hundreds of kilometers than the other data, within Namibia and across the Angolan and Zambian borders. Our results provide a framework for incorporating genetic data into malaria surveillance and provide evidence that both strengthening of local interventions and regional coordination are likely necessary to eliminate malaria in this region of Southern Africa.
