PvGTSeq and PvCRiSP: Two amplicon-based targeted sequencing panels for Plasmodium vivax
1
Issued Date
2026-05-01
Resource Type
eISSN
19352735
Scopus ID
2-s2.0-105039766578
Pubmed ID
42133746
Journal Title
Plos Neglected Tropical Diseases
Volume
20
Issue
5
Rights Holder(s)
SCOPUS
Bibliographic Citation
Plos Neglected Tropical Diseases Vol.20 No.5 (2026) , e0013663
Suggested Citation
Manrique-Valverde P.C., Hasund C.M., Kelley K.A., Amaya-Romero J.E., Arévalo-Herrera M., Brosula R., Calzada J.E., Chenet S.M., Corredor V., Early A.M., Fontecha G., Forero-Peña D.A., Herrera S., Lana J.T., Laws M., Niles-Robin R., Obaldia N., Santamaria A.M., Schwabl P., Auburn S., Neafsey D.E. PvGTSeq and PvCRiSP: Two amplicon-based targeted sequencing panels for Plasmodium vivax. Plos Neglected Tropical Diseases Vol.20 No.5 (2026) , e0013663. doi:10.1371/journal.pntd.0013663 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/117022
Title
PvGTSeq and PvCRiSP: Two amplicon-based targeted sequencing panels for Plasmodium vivax
Author's Affiliation
Harvard T.H. Chan School of Public Health
Broad Institute
Nuffield Department of Medicine
Friedrich-Loeffler-Institute
Menzies School of Health Research
Mahidol Oxford Tropical Medicine Research Unit
Universidad de Panamá
Universidad Nacional Autónoma de Honduras
Universidad Nacional de Colombia, Facultad de Medicina
Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas
Clinton Health Access Initiative, Inc.
Ministry of Health
Malaria Vaccine and Drug Development Center
Caucaseco Scientific Research Center
Biomedical Research and Therapeutic Vaccines Institute
Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES)
Broad Institute
Nuffield Department of Medicine
Friedrich-Loeffler-Institute
Menzies School of Health Research
Mahidol Oxford Tropical Medicine Research Unit
Universidad de Panamá
Universidad Nacional Autónoma de Honduras
Universidad Nacional de Colombia, Facultad de Medicina
Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas
Clinton Health Access Initiative, Inc.
Ministry of Health
Malaria Vaccine and Drug Development Center
Caucaseco Scientific Research Center
Biomedical Research and Therapeutic Vaccines Institute
Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES)
Corresponding Author(s)
Other Contributor(s)
Abstract
Plasmodium vivax is the main cause of malaria outside of sub-Saharan Africa, and in many settings it presents significant challenges to malaria elimination efforts. Despite some control successes in the Americas, regional annual case counts of malaria have increased by over 25% between 2014 and 2023, largely driven by P. vivax. Genomic surveillance can play a key role in understanding the extent to which disease persistence represents indigenous transmission as opposed to introduction of new strains through migration, and whether specific variants evade control measures. Efforts to make P. vivax genomic surveillance more cost-effective have led to the development of targeted sequencing-based methods, which strike a varying balance between assay sensitivity and breadth/informativeness. We introduce two new highly sensitive multiplexed amplicon sequencing panels for P. vivax: PvGTSeq and PvCRiSP. PvGTSeq requires selective whole-genome amplification (sWGA) and contains 249 amplicons-36 for antimalarial resistance and 213 for population structure-optimized for Latin America but applicable to all continents. PvCRiSP features four highly polymorphic amplicons that operate without sWGA and is designed to estimate complexity of infection (COI), identify instances of clonal transmission, and characterize recurrent episodes. Both panels use a single multiplex PCR with non-proprietary reagents, achieve ≥75% amplicon recovery at parasitemias as low as five parasites/μL, and PvCRiSP remains effective with low quality DNA. PvGTSeq showed high sequencing accuracy (error rate 3.85e-4% - 2.87e-3%), and both panels efficiently detected alleles from minority clones in simulated polyclonal infections. We validated both panels with samples from Colombia, Guyana, Honduras, Panama, and Venezuela, and performed in-silico assessments using data from 16 countries worldwide, confirming that these two panels have high power to discriminate samples and assign global geographic origin to imported cases. These panels will therefore be useful tools for P. vivax molecular surveillance in diverse geographic settings.