Age-specific patterns of DBLα var diversity can explain why residents of high malaria transmission areas remain susceptible to Plasmodium falciparum blood stage infection throughout life
We characterized age-specific patterns of *P. falciparum* variant antigen gene diversity in residents of a highly endemic setting in Bongo, Ghana and used these data to simulate the development of variant-specific immunity over an individuals lifetime.
By Shazia Ruybal-Pesántez, Kathryn E. Tiedje, Shai Pilosof, Gerry Tonkin-Hill1, Qixin He, Thomas S. Rask, Lucas Amenga-Etego, Abraham R. Oduro, Kwadwo A. Koram, Mercedes Pascual, Karen P. Day in Research
December 2, 2021
**This article has been accepted in International Journal for Parasitology **
Abstract
Motivation:
Recombination is a fundamental process in molecular evolution, and the identification of recombinant sequences is thus of major interest. However, current methods for detecting recombinants are primarily designed for aligned sequences. Thus they struggle with analyses of highly diverse genes, such as the var genes of the malaria parasite Plasmodium falciparum, which are known to diversify primarily through recombination.
Results:
We introduce an algorithm to detect recent recombinant sequences from a dataset without a full multiple alignment. Our algorithm can handle thousands of gene-length sequences without the need for a reference panel. We demonstrate the accuracy of our algorithm through extensive numerical simulations; in particular, it maintains its effectiveness in the presence of insertions and deletions. We apply our algorithm to a dataset of 17,335 DBLα types in var genes from Ghana, observing that sequences belonging to the same ups group or domain subclass recombine amongst themselves more frequently, and that non-recombinant DBLα types are more conserved than recombinant ones.
Availability:
Source code is freely available at https://github.com/qianfeng2/detREC_program.