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).