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Evaluating the Performance of Malaria Genetics for Inferring Changes in Transmission Intensity Using Transmission Modeling

Evaluating the Performance of Malaria Genetics for Inferring Changes in Transmission Intensity Using Transmission Modeling

Authors :
Lucy C Okell
Hannah C Slater
Joel Hellewell
Hsiao-Han Chang
Azra C. Ghani
H. Juliette T. Unwin
Oliver J Watson
Robert Verity
Kirk A. Rockett
Christina Hubbart
Irene Omedo
Philip Bejon
Joaniter I. Nankabirwa
Robert W. Snow
Bryan Greenhouse
Abdisalan M. Noor
Wellcome Trust
The Royal Society
The Royal Society of Medicine
Medical Research Council (MRC)
Source :
Molecular Biology and Evolution
Publication Year :
2020
Publisher :
Oxford University Press (OUP), 2020.

Abstract

Substantial progress has been made globally to control malaria, however there is a growing need for innovative new tools to ensure continued progress. One approach is to harness genetic sequencing and accompanying methodological approaches as have been used in the control of other infectious diseases. However, to utilize these methodologies for malaria, we first need to extend the methods to capture the complex interactions between parasites, human and vector hosts, and environment, which all impact the level of genetic diversity and relatedness of malaria parasites. We develop an individual-based transmission model to simulate malaria parasite genetics parameterized using estimated relationships between complexity of infection and age from five regions in Uganda and Kenya. We predict that cotransmission and superinfection contribute equally to within-host parasite genetic diversity at 11.5% PCR prevalence, above which superinfections dominate. Finally, we characterize the predictive power of six metrics of parasite genetics for detecting changes in transmission intensity, before grouping them in an ensemble statistical model. The model predicted malaria prevalence with a mean absolute error of 0.055. Different assumptions about the availability of sample metadata were considered, with the most accurate predictions of malaria prevalence made when the clinical status and age of sampled individuals is known. Parasite genetics may provide a novel surveillance tool for estimating the prevalence of malaria in areas in which prevalence surveys are not feasible. However, the findings presented here reinforce the need for patient metadata to be recorded and made available within all future attempts to use parasite genetics for surveillance.

Details

ISSN :
15371719 and 07374038
Volume :
38
Database :
OpenAIRE
Journal :
Molecular Biology and Evolution
Accession number :
edsair.doi.dedup.....23e0328d718177d89fea30dfab9a052f
Full Text :
https://doi.org/10.1093/molbev/msaa225