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One marker that has seen extensive use is the gene encoding merozoite surface protein 3-alpha (MSP-3\u03b1), a blood-stage antigen known to be highly variable among<jats:italic>P. vivax<\/jats:italic>isolates. Here, a sample of complete<jats:italic>msp-3\u03b1<\/jats:italic>gene sequences is analysed in order to assess its utility as a molecular marker for epidemiologic investigations.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Amplification, cloning and sequencing of additional<jats:italic>P. vivax<\/jats:italic>isolates from different geographic locations, including a set of Venezuelan field isolates (n\u2009=\u200910), yielded a sample of 48 complete<jats:italic>msp<\/jats:italic>-<jats:italic>3\u03b1<\/jats:italic>coding sequences. Characterization of standard population genetic measures of diversity, phylogenetic analysis, and tests for recombination were performed. This allowed comparisons to patterns inferred from the<jats:italic>in silico<\/jats:italic>simulation of a polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) protocol used widely.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The larger sample of MSP-3\u03b1 diversity revealed incongruence between the observed levels of nucleotide polymorphism, which were high in all populations, and the pattern of PCR-RFLP haplotype diversity. Indeed, PCR-RFLP haplotypes were not informative of a population\u2019s genetic diversity and identical haplotypes could be produced from analogous bands in the commonly used protocol. Evidence of frequent and variable insertion-deletion mutations and recurrent recombination between MSP-3\u03b1 haplotypes complicated the inference of genetic diversity patterns and reduced the phylogenetic signal.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The genetic diversity of<jats:italic>P. vivax msp-3\u03b1<\/jats:italic>involves intragenic recombination events. Whereas the high genetic diversity of<jats:italic>msp-3\u03b1<\/jats:italic>makes it a promising marker for some epidemiological applications, the ability of<jats:italic>msp-3\u03b1<\/jats:italic>PCR-RFLP analysis to accurately track parasites is limited. Local studies of the circulating alleles are needed before implementing PCR-RFLP approaches. Furthermore, evidence from the global sample analysed here suggests such<jats:italic>msp-3\u03b1<\/jats:italic>PCR-RFLP methods are not suitable for broad geographic studies or tracking parasite populations for an extended period of time.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1475-2875-12-288","type":"journal-article","created":{"date-parts":[[2013,8,21]],"date-time":"2013-08-21T08:14:16Z","timestamp":1377072856000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Merozoite surface protein-3 alpha as a genetic marker for epidemiologic studies in Plasmodium vivax: a cautionary note"],"prefix":"10.1186","volume":"12","author":[{"given":"Benjamin L","family":"Rice","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M\u00f3nica M","family":"Acosta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria Andre\u00edna","family":"Pacheco","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ananias A","family":"Escalante","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,8,21]]},"reference":[{"key":"2905_CR1","doi-asserted-by":"publisher","first-page":"e1814","DOI":"10.1371\/journal.pntd.0001814","volume":"6","author":"PW Gething","year":"2012","unstructured":"Gething PW, Elyazar IRF, Moyes CL, Smith DL, Battle KE, Guerra CA, Patil AP, Tatem AJ, Howes RE, Myers MF, George DB, Horby P, Wertheim HFL, Price RN, M\u00fceller I, Baird JK, Hay SI: A long neglected world malaria map: Plasmodium vivax endemicity in 2010. 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