Diversity
Genetic diversity of malaria parasites and frequency of multiple clone infections are often associated with transmission rates, as a result of changes in the effective population size. We indeed observe that the genetic diversity of P. vivax populations in LAM (mean nucleotide diversity (pi ) across the genome of 0.00071 ± 0.00046) is significantly lower (p<0.0001) than in most other regions of the world (except MSEA, which includes mostly highly related samples from Malaysia; supplementary figure 4). Interestingly, several clonalP. vivax clusters (IBD-sharing ≥99% of the genome) are also observed within the LAM countries (supplementary figure 5).
Genetic diversity was significantly different in all pairwise comparisons between LAM countries (pairwise t-tests with no assumption of equal variances, p<0.0001, Figure 5B). From the LAM countries where genomes were available for this study, Brazil has the highest number of cases, which is reflected in the diversity, that was highest in Brazil, and lowest in Panama (Figure 5A and B). While currently the prevalence of malaria in Mexico is very low, observedpi was higher than in Panama (Figure 5B). However, these samples were collected before 2007, with the majority from 2002, when reported incidence in Mexico was higher than in Panama during the years 2007-2009. Therefore, results conform with the pattern of lower genetic diversity observed at lower transmission levels. The majority of samples from LAM had monoclonal P. vivax infections (Figure 5C), but in the countries with higher numbers of cases (Colombia, Brazil, Peru), polyclonal infections (FWS<0.95) were more frequent (15.6%, 19.0% and 10.0% of samples, respectively).