Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa
- University of California, San Francisco, United States
- Johns Hopkins Bloomberg School of Public Health, United States
- University of Namibia, Namibia
- University of Southampton, United Kingdom
- Clinton Health Access Initiative, United States
- University of Washington, United States
- University of Texas Southwestern Medical Center, United States
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.
Data availability
All data generated or analyzed during this study are included in the manuscript and supplementary files.
Article and author information
Author details
Sofonias K Tessema
Funding
Bill and Melinda Gates Foundation
- Sofonias K Tessema
- Bryan Greenhouse
Burroughs Wellcome Fund
- Amy Wesolowski
National Institutes of Health
- Amy Wesolowski
Chan Zuckerberg Biohub
- Bryan Greenhouse
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Ben Cooper, Mahidol Oxford Tropical Medicine Research Unit, Thailand
Ethics
Human subjects: Ethical approval for the study was obtained from the Institutional Review Boards of the University of Namibia and the University of California, San Francisco (Identification numbers 15-17422 and 14-14576). Informed consent was obtained from all participants or the parents of all children participated in the Zambezi study. For the Kavango study, IRB approval was obtained but no informed consent was collected as all samples (used RDTs) and de-identified data were collected during routine surveillance.
Version history
- Received: November 9, 2018
- Accepted: March 6, 2019
- Accepted Manuscript published: April 2, 2019 (version 1)
- Version of Record published: April 23, 2019 (version 2)
Copyright
© 2019, Tessema et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa
eLife 8:e43510.
https://doi.org/10.7554/eLife.43510
Further reading
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Genetic analyses help to pinpoint where people got infected with malaria, enabling better interventions on the ground.
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- Epidemiology and Global Health
Background:
The Zanzibar archipelago of Tanzania has become a low-transmission area for Plasmodium falciparum. Despite being considered an area of pre-elimination for years, achieving elimination has been difficult, likely due to a combination of imported infections from mainland Tanzania and continued local transmission.
Methods:
To shed light on these sources of transmission, we applied highly multiplexed genotyping utilizing molecular inversion probes to characterize the genetic relatedness of 282 P. falciparum isolates collected across Zanzibar and in Bagamoyo district on the coastal mainland from 2016 to 2018.
Results:
Overall, parasite populations on the coastal mainland and Zanzibar archipelago remain highly related. However, parasite isolates from Zanzibar exhibit population microstructure due to the rapid decay of parasite relatedness over very short distances. This, along with highly related pairs within shehias, suggests ongoing low-level local transmission. We also identified highly related parasites across shehias that reflect human mobility on the main island of Unguja and identified a cluster of highly related parasites, suggestive of an outbreak, in the Micheweni district on Pemba island. Parasites in asymptomatic infections demonstrated higher complexity of infection than those in symptomatic infections, but have similar core genomes.
Conclusions:
Our data support importation as a main source of genetic diversity and contribution to the parasite population in Zanzibar, but they also show local outbreak clusters where targeted interventions are essential to block local transmission. These results highlight the need for preventive measures against imported malaria and enhanced control measures in areas that remain receptive to malaria reemergence due to susceptible hosts and competent vectors.
Funding:
This research was funded by the National Institutes of Health, grants R01AI121558, R01AI137395, R01AI155730, F30AI143172, and K24AI134990. Funding was also contributed from the Swedish Research Council, Erling-Persson Family Foundation, and the Yang Fund. RV acknowledges funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/R015600/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 program supported by the European Union. RV also acknowledges funding by Community Jameel.
