Computational protocol: Contrasting Transmission Dynamics of Co-endemic Plasmodium vivax and P. falciparum: Implications for Malaria Control and Elimination

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Protocol publication

[…] An infection was defined as polyclonal if more than one allele was observed at one or more loci. The Multiplicity of infection (MOI) for a given sample was defined as the maximum number of alleles observed at any of the loci investigated. With the exception of measures of polyclonality and MOI, only the predominant allele at each locus in each isolate was used for analysis []. The expected heterozygosity (H E) was measured as an index of population diversity using the formula H E = [n/ (n-1)] [1-Σp i 2], where n is the number of isolates analyzed and pi is the frequency of the ith allele in the population. The pairwise F ST metric was used to gauge the genetic distance between populations. Calculations were undertaken using Arlequin software (version 3.5) []. Standardized measures (F’ST) were additionally calculated to adjust for high marker diversity []. Population structure was further assessed using STRUCTURE software version 2.3.3 []. Twenty replicates, with 100,000 burn-in and 100,000 post burn-in iterations were run for each of K (populations) from 1–10 using the model parameters of admixture with correlated allele frequencies. The most probable K was derived by applying the delta K method []. STRUCTURE results were displayed using bar plots prepared with distruct software version 1.1 []. Multi-locus haplotypes were reconstructed from the predominant allele at each locus in isolates with no missing data. Multi-locus linkage disequilibrium (LD) was measured by the standardised index of association (I A S) using the web-based LIAN 3.5 software []. The significance of the I A S estimates was assessed using 10,000 random permutations of the data. For each population, LD was assessed in 1) all samples, 2) samples with a maximum of one multi-allelic locus, and 3) with each unique haplotype represented just once. The genetic relatedness between sample pairs was assessed by measuring the proportion of alleles shared between multi-locus haplotype pairs (ps). Using (1-ps) as a measure of genetic distance [], an unrooted neighbour-joining tree [] was generated with the ape package in R []. Mantel’s r-test was used to assess the correlation between genetic and temporal distance using the ade4 package in R []. […]

Pipeline specifications

Software tools Arlequin, DISTRUCT, LIAN, APE
Applications Phylogenetics, Population genetic analysis
Organisms Plasmodium vivax, Plasmodium falciparum
Diseases Infection, Malaria, Malaria, Falciparum