Genetic diversity and evolutionary perspectives of Pfcrt in Plasmodium falciparum: insights from Indian and global isolates.

Abstract

Background: Chloroquine resistance in Plasmodium falciparum (Pf) driven by mutations in the Pf chloroquine resistance transporter (Pfcrt) gene continues to pose a challenge to malaria control in endemic regions like India. Understanding the genetic diversity and evolutionary patterns of Pfcrt is important for guiding malaria surveillance and future national drug policy.

Methods: This study analysed 979 Indian (exon 2) and 719 global full-length Pfcrt sequences using molecular tools to assess genetic diversity, selection pressure and population structure. Comparative and temporal analyses were conducted across Indian states and global regions to explore evolutionary trends.

Results: Indian sequence analysis revealed regional and temporal variations in haplotype diversity with both widespread and region-specific variants. Haplotype networks identified three major haplotypes namely CVIET, SVMNT and CVMNK, with CVIET predominating, particularly in the North-East, while SVMNT and CVMNK showed variable prevalence across regions and time periods. The greatest diversity was recorded between 2010-2019 despite reduced malaria incidence, suggesting ongoing selection pressure. Mizoram exhibited the highest Tajima's D value (D = 3.310, p < 0.01) and Pfcrt sequences from North-East region showed a unique genetic structure reflecting a likely role of selection pressures from the Greater Mekong Subregion. Globally, 65 haplotypes were detected with highest diversity in Cambodia with strong genetic differentiation observed across countries. Distinct genetic clusters and limited haplotype sharing across countries suggest that region-specific evolutionary pressures have shaped Pfcrt diversity. Positive selection at 6 codons and linkage disequilibrium between key SNPs indicate functional adaptation under drug pressure.

Conclusion: This study highlights the variation in Pfcrt shaped by national drug policies and regional malaria transmission patterns. Continued molecular surveillance is essential to monitor emerging resistant lineages and guide effective malaria treatment strategies. This study highlights the variation in Pfcrt shaped by national drug policies and regional malaria transmission patterns.