Publications

Total: 139
Mapping vaccination coverage to explore the effects of delivery mechanisms and inform vaccination strategies
Nature Communications 10, Article number: 1633 (2019).
Author(s): C. Edson Utazi, Julia Thorley, Victor A. Alegana, Matthew J. Ferrari, Saki Takahashi, C. Jessica E. Metcalf, Justin Lessler, Felicity T. Cutts & Andrew J. Tatem
Type: method. Year: 2019
DOI: 10.1038/s41467-019-09611-1.

Abstract: The success of vaccination programs depends largely on the mechanisms used in vaccine delivery. National immunization programs offer childhood vaccines through fixed and outreach services within the health system and often, additional supplementary immunization activities (SIAs) are undertaken to fill gaps and boost coverage. Here, we map predicted coverage at 1 × 1 km spatial resolution in five low- and middle-income countries to identify areas that are under-vaccinated via each delivery method using Demographic and Health Surveys data. We compare estimates of the coverage of the third dose of diphtheria-tetanus-pertussis-containing vaccine (DTP3), which is typically delivered through routine immunization (RI), with those of measles-containing vaccine (MCV) for which SIAs are also undertaken. We find that SIAs have boosted MCV coverage in some places, but not in others, particularly where RI had been deficient, as depicted by DTP coverage. The modelling approaches outlined here can help to guide geographical prioritization and strategy design.
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Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa
eLife 2019;8:e43510.
Author(s): Sofonias Tessema, Amy Wesolowski, Anna Chen, Maxwell Murphy, Jordan Wilheim, Anna-Rosa Mupiri, Nick W Ruktanonchai, Victor A Alegana, Andrew J Tatem, Munyaradzi Tambo, Bradley Didier, Justin M Cohen, Adam Bennett, Hugh JW Sturrock, Roland Gosling, Michelle S Hsiang, David L Smith, Davis R Mumbengegwi, Jennifer L Smith, Bryan Greenhouse
Type: method. Year: 2019
DOI: 10.7554/eLife.43510.

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.
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The epidemic potential of avian influenza A (H7N9) virus in humans in mainland China: A two-stage risk analysis
Plos One Journals.
Author(s): Xuzheng Shan, Shengjie Lai, Hongxiu Liao , Zhongjie Li, Yajia Lan , Weizhong Yang
Type: method. Year: 2019
DOI: 10.1371/journal.pone.0215857.

Abstract: Background From 2013 to 2017, more than one thousand avian influenza A (H7N9) confirmed cases with hundreds of deaths were reported in mainland China. To identify priorities for epidemic prevention and control, a risk assessing framework for subnational variations is needed to define the epidemic potential of A (H7N9). Methods We established a consolidated two-stage framework that outlined the potential epidemic of H7N9 in humans: The Stage 1, index-case potential, used a Boosted Regression Trees model to assess population at risk due to spillover from poultry; the Stage 2, epidemic potential, synthesized the variables upon a framework of the Index for Risk Management to measure epidemic potential based on the probability of hazards and exposure, the vulnerability and coping capacity. Results Provinces in southern and eastern China, especially Jiangsu, Zhejiang, Guangzhou, have high index-case potential of human infected with A (H7N9), while northern coastal provinces and municipalities with low morbidity, i.e. Tianjin and Liaoning, have an increasing risk of A (H7N9) infection. Provinces in central China are likely to have high potential of epidemic due to the high vulnerability and the lack of coping capacity. Conclusions This study provides a unified risk assessment of A (H7N9) to detect the two-stage heterogeneity of epidemic potential among different provinces in mainland China, allowing proactively evaluate health preparedness at subnational levels to improve surveillance, diagnostic capabilities, and health promotion.
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Tracking progress towards malaria elimination in China: estimates of reproduction numbers and their spatiotemporal variation
bioRxiv.
Author(s): Isobel Routledge, Shengjie Lai, Katherine E Battle, Azra C Ghani, Manuel Gomez-Rodriguez, Kyle B Gustafson, Swapnil Mishra, Joshua L Proctor, Andrew J Tatem, Zhongjie Li, Samir Bhatt
Type: method. Year: 2019
DOI: 10.1101/628842 .

Abstract: China reported zero locally-acquired malaria cases in 2017 and 2018. Understanding the spatio-temporal pattern underlying this decline, especially the relationship between locally-acquired and imported cases, can inform efforts to maintain elimination and prevent re-emergence. This is particularly pertinent in Yunnan province, where the potential for local transmission is highest. Using a geo-located individual-level dataset of cases recorded in Yunnan province between 2011 and 2016, we jointly estimate the case reproduction number, Rc, and the number of unobserved sources of infection. We use these estimates within spatio-temporal geostatistical models to map how transmission varied over time and space, estimate the timeline to elimination and the risk of resurgence. Our estimates suggest that, maintaining current intervention efforts, Yunnan is unlikely to experience sustained local transmission up to 2020. However, even with a mean Rc of 0.005 projected for the year 2019, locally-acquired cases are possible due to high levels of importation.
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