# Pv3Rs: Plasmodium vivax relapse, recrudescence, and reinfection statistical genetic inference

## TL;DR

Pv3Rs is a statistical tool that helps determine the cause of Plasmodium vivax malaria recurrence using genetic data.

## Contribution

Pv3Rs introduces a new statistical method for inferring recurrence states in P. vivax infections using genetic data.

## Key findings

- Pv3Rs models genetic relationships to compute posterior probabilities of recurrence states.
- The tool works with various genetic data types like length polymorphic loci and amplicon sequencing data.
- Pv3Rs is freely available on CRAN for use in clinical and research settings.

## Abstract

A Plasmodium vivax recurrence can be caused by activation of dormant liver-stage hypnozoites (relapse), failure to successfully treat a blood-stage infection (recrudescence), or a new mosquito inoculation (reinfection) (Pv3Rs). Inference of the cause of recurrence is important, especially in clinical trials, where molecular correction is used to improve estimates of antimalarial treatment efficacy. Pv3Rs implements statistical inference of P. vivax recurrence states (recrudescence, relapse, reinfection) from P. vivax genetic data. Under various simplifying assumptions, we model genetic relationships between parasites within and across infections to compute the posterior probabilities of recurrence states. Pv3Rs is applicable to a variety of genetic data types, including length polymorphic loci and amplicon sequencing data.

Pv3Rs is freely available on CRAN under the GNU license. Its CRAN DOI is 10.32614/CRAN.package.Pv3Rs. Source code and installation instructions can be found at https://cran.r-project.org/web/packages/Pv3Rs/index.html.