Plasmodium vivax: Microsatellite analysis of multiple-clone infections

High Genetic Diversity of Plasmodium vivax on the North Coast of Papua New Guinea

“…29 To investigate whether artifacts were introduced as a result of WGA, sequences of msp1F3 and MS16 alleles amplified from undiluted genomic DNA and subjected to WGA were compared. Consistent with previous reports, 26,27 results were concordant between the WGA and unamplified DNA (data not shown).…”

“…WGA, a method that has been used in similar molecular epidemiological studies, [25][26][27][28] was performed prior to genotyping to increase the amount of P. vivax DNA for analysis. The multiple displacement amplification (MDA) method used in this study has been shown to result in a higher yield of non-artifact DNA template and reduced amplification bias compared with PCR-based WGA methods.…”

A closer look at multiple-clone Plasmodium vivax infections: detection methods, prevalence and consequences

“…We found varying PCR amplification efficiencies of microsatellite alleles ( Fig. 1), suggesting that amplification biases may lead to the inaccurate assignment of predominant haplotypes in multiple-clone P. vivax infections (Havryliuk et al 2008). …”

“…Stutter peaks result from DNA strand slippage during PCR at intervals corresponding to nucleotide repeat sizes (de Valk et al 2007). A minimum value of either one-third (Anderson et al 2000, Imwong et al 2007a, Karunaweera et al 2008 or one-fourth (Anderson et al 1999) of the predominant allele peak height has been used as a cut-off to differentiate minor alleles from stutter or unspecific peaks, but the sensitivity and specificity of these criteria remain undetermined (Greenhouse et al 2006, Havryliuk et al 2008.…”

Recurrent Parasitemias and Population Dynamics of Plasmodium vivax Polymorphisms in Rural Amazonia

“…Multilocus haplotypes were defined as unique combinations of alleles at each locus analyzed; in most analysis, only the most abundant alleles were considered for haplotype assignment in multipleclone infections. 28 However, given the risk of misassigning haplotypes because of biased amplification of co-existing alleles in multiple-clone infections, 29 we considered all possible haplotypes when comparing acute infection and recrudescence parasites. For this purpose, we listed all combinations of alleles (considering major and minor peaks) for paired acute-phase and recrudescence samples and examined whether one of the possible haplotypes occurred in both samples of the pair.…”