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Background  The R2 repeat region of GLURP has been reported as a good genetic marker for  Plasmodium falciparum  genotyping. Proper knowledge of the extent and nature of  P. falciparum  genetic diversity using highly immunogenic R2 repeat region in malaria-endemic areas is a crucial element to understand various aspects related to immunity acquisition and disease pathogenesis.    Methods  Population diversity of  P. falciparum  GLURP and amino acid sequence repeats in GLURP R2 region was studied in malaria-endemic Assam state, northeast India and compared at an interval of five years during 2005 (Group-A) and 2011 (Group-B).    Results  Of the 66 samples, a total of 55 samples showed positive PCR bands for GLURP R2 region and altogether ten types of alleles with size ranging from 501 bp to 1,050 bp (50 bp bin) were observed and coded as genotypes I-X. In Group-A (n = 29), 24 samples were found infected with single, four with double and one with triple  P. falciparum  genotype, while in Group-B (n = 26), single genotype was found in 23 samples, double in two samples and triple in one sample. Genotype IV showed significant increase (p = 0.002) during 2011 (Group-B). Genotypes I to V were more common in Group-B (62%), however genotypes VI to X were more frequently distributed in Group-A. The expected heterozygosity was found slightly higher in Group-A (H E  = 0.87) than Group-B (H E  = 0.85), whereas multiplicity of infection (MOI) in Group-A (MOI = 1.21 ± 0.49) and Group-B (MOI = 1.12 ± 0.43) did not display significant variation. The amino acid repeat sequence unit (AAU) DKNEKGQHEIVEVEEILPE (called ‘a’) was more frequent in the well-conserved part of R2 repeat region.    Conclusion  The present study is the first extensive study in India which has generated substantial data for understanding the type and distribution of naturally evolved genetic polymorphism at amino acid sequence level in GLURP R2 repeat region in  P. falciparum . There was decrease in the PCR amplicon size as well as the number of AAU [amino acid repeat unit] in Group-B displaying the bottleneck effect. The present study described a new type of AAU ‘d’ which varied from the other previous known AAUs.    Electronic supplementary material  The online version of this article (doi:10.1186/1475-2875-13-450) contains supplementary material, which is available to authorized users.

Genetic polymorphism and amino acid sequence variation in Plasmodium falciparum GLURP R2 repeat region in Assam, India, at an interval of five years