Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas

Edwin Sutanto, Zuleima Pava, Diego F. Echeverry, Tatiana M. Lopera-Mesa, Lidia Madeline Montenegro, Maria F. Yasnot-Acosta, Ernest Diez Benavente, Richard D. Pearson, Sócrates Herrera, Myriam Arévalo-Herrera, Hidayat Trimarsanto, Angela Rumaseb, Rintis Noviyanti, Dominic P. Kwiatkowski, Ric N. Price, Sarah Auburn

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Colombia aims to eliminate malaria by 2030 but remains one of the highest burden countries in the Americas. Plasmodium vivax contributes half of all malaria cases, with its control challenged by relapsing parasitaemia, drug resistance and cross-border spread. Using 64 Colombian P. vivax genomes collected between 2013 and 2017, we explored diversity and selection in two major foci of transmission: Chocó and Córdoba. Open-access data from other countries were used for comparative assessment of drug resistance candidates and to assess cross-border spread. Across Colombia, polyclonal infections were infrequent (12%), and infection connectivity was relatively high (median IBD = 5%), consistent with low endemicity. Chocó exhibited a higher frequency of polyclonal infections (23%) than Córdoba (7%), although the difference was not significant (P = 0.300). Most Colombian infections carried double pvdhfr (95%) and single pvdhps (71%) mutants, but other drug resistance mutations were less prevalent (< 10%). There was no evidence of selection at the pvaat1 gene, whose P. falciparum orthologue has recently been implicated in chloroquine resistance. Global population comparisons identified other putative adaptations. Within the Americas, low-level connectivity was observed between Colombia and Peru, highlighting potential for cross-border spread. Our findings demonstrate the potential of molecular data to inform on infection spread and adaptation.

Original languageEnglish
Article number19779
Pages (from-to)1-17
Number of pages17
JournalScientific Reports
Issue number1
Publication statusPublished - Dec 2023

Bibliographical note

Funding Information:
We thank the patients who contributed their samples to the study, the health workers and field teams who assisted with the sample collections, and the staff of the Wellcome Sanger Institute Sample Logistics, Sequencing, and Informatics facilities for their contributions. We also thank Alberto Tobon Castaño for helpful guidance on the study. The patient sampling and metadata collection from Colombia were supported by Colciencias Colombia (FP44842-503-445 awarded to DFE). The study was also supported by the Bill and Melinda Gates Foundation (INV-043618 awarded to SA), the National Health and Medical Research Council of Australia (APP2001083 awarded to SA), and the Wellcome Trust (200909 and ICRG GR071614MA Senior Fellowships in Clinical Science to RNP). The whole genome sequencing component of the study was supported by the Medical Research Council and UK Department for International Development (award number M006212 to DPK) and the Wellcome Trust (award numbers 206194 and 204911 to DPK).

Publisher Copyright:
© 2023, The Author(s).


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