High-throughput genotyping of Plasmodium vivax in the Peruvian Amazon via molecular inversion probes

Zachary R. Popkin-Hall (), Karamoko Niaré, Rebecca Crudale, Alfred Simkin, Abebe A. Fola, Juan F. Sanchez, Danielle L. Pannebaker, David J. Giesbrecht, Isaac E. Kim, Özkan Aydemir, Jeffrey A. Bailey, Hugo O. Valdivia and Jonathan J. Juliano
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Zachary R. Popkin-Hall: University of North Carolina
Karamoko Niaré: Brown University
Rebecca Crudale: Brown University
Alfred Simkin: Brown University
Abebe A. Fola: Brown University
Juan F. Sanchez: U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH)
Danielle L. Pannebaker: U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH)
David J. Giesbrecht: Brown University
Isaac E. Kim: The Warren Alpert Medical School of Brown University
Özkan Aydemir: UMass Chan Medical School
Jeffrey A. Bailey: Brown University
Hugo O. Valdivia: U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH)
Jonathan J. Juliano: University of North Carolina

Nature Communications, 2024, vol. 15, issue 1, 1-11

Abstract: Abstract Plasmodium vivax transmission occurs throughout the tropics and is an emerging threat in areas of Plasmodium falciparum decline, causing relapse infections that complicate treatment and control. Targeted sequencing for P. falciparum has been widely deployed to detect population structure and the geographic spread of antimalarial and diagnostic resistance. However, there are fewer such tools for P. vivax. Leveraging global variation data, we designed four molecular inversion probe (MIP) genotyping panels targeting geographically differentiating SNPs, neutral SNPs, putative antimalarial resistance genes, and vaccine candidate genes. We deployed these MIP panels on 866 infections from the Peruvian Amazon and identified transmission networks with clonality (IBD[identity by descent]>0.99), copy number variation in Pvdbp and multiple Pvrbps, mutations in antimalarial resistance orthologs, and balancing selection in 13 vaccine candidate genes. Our MIP panels are the broadest genotyping panel currently available and are poised for successful deployment in other regions of P. vivax transmission.

Date: 2024
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DOI: 10.1038/s41467-024-54731-y

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