Acta Tropica 160 (2016) 23–34 Contents lists available at ScienceDirect Acta Tropica jo ur nal home p age: www.elsevier.com/locate/actatropica Population genetics structure of Plasmodium vivax circumsporozoite protein during the elimination process in low and unstable malaria transmission areas, southeast of Iran Samaneh Hemati Shabani a,b , Sedigheh Zakeri a,∗ , Akram Abouie Mehrizi a , Yousef Mortazavi b , Navid Dinparast Djadid a a Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Pasteur Avenue, P.O. Box 1316943551, Tehran, Iran b Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran a r t i c l e i n f o Article history: Received 21 November 2015 Received in revised form 14 April 2016 Accepted 15 April 2016 Available online 19 April 2016 Keywords: Plasmodium vivax Circumsporozoite protein (CSP) Genetic diversity Population structure Elimination Iran a b s t r a c t In Iran, the prevalence of Plasmodium falciparum and Plasmodium vivax has dropped after a national malaria elimination program was launched. To estimate the likelihood of success and to measure the outcome of malaria intervention tools during elimination programs (2008–2012), the population genetic surveys of Iranian P. vivax isolates (n = 60) were carried out using the CSP genetic marker. The results were compared with a similar work that was carried out during a control phase (2000–2003) in the same study areas. Based on PCR-RFLP analysis, 49 (81.67%) of 60 studied samples were VK210 and 11 (18.33%) were VK247 with no mixed genotypes. However, 10.97% of P. vivax isolates of control phase harbored the mixed genotypes. Sequencing analysis of 50 pvcsp gene showed 14 distinct haplotypes, of which 11 and 3 were VK210 and VK247 types, respectively. However, during the control phase, 19 distinct subtypes (11 VK210 and 8 VK247) were reported. Also, 7 of 11 VK210 and the VK247F subtypes were new, and 3 out of 7 new VK210 and VK247F were isolated from the patients with Pakistani nationality. The lower nucleotide diversity per site ( = 0.02017 ± 0.00436 and  = 0.04525 ± 0.00255) and haplotype diversity (Hd = 0.513 ± 0.093 and Hd = 0.691 ± 0.128) as well as lower In/Del haplotype [Hd(i) = 0.243 and 0] and nucleotide diversity [(i) = 0.00078 and 0] were recorded for VK210 and VK247of the elimination samples, respectively. In conclusion, the comparison of PRMs and RATs in CRR along with the polymorphism analysis of the sequence lengths, SNPs, and In/Del polymorphisms in all analyzed samples showed lower genetic diversity for PvCSP in the elimination samples. Also, although there is a turnover of P. vivax parasite genotypes in the study areas, reduction in genetic diversity and transmission was detected due to scaling-up of the intervention tools during an elimination program in Iran. This notable challenge of the elimination program must be taken into account and controlled by active surveillance for limiting both reintroductions of new allelic forms as well as the spread of drug-resistant parasite to prevent any disease outbreaks. © 2016 Elsevier B.V. All rights reserved. 1. Introduction Plasmodium vivax is the most widespread of five human malaria parasites and prevalent species in non-African endemic areas. Despite a decrease in Plasmodium falciparum cases worldwide, the incidence of P. vivax has been increasing (Kasehagen et al., 2006; Ferreira et al., 2007; Jun et al., 2009; Carme et al., 2009). How- ever, research on P. vivax malaria has been relatively neglected, ∗ Corresponding author. E-mail addresses: zakeris@yahoo.com, zakeris@pasteur.ac.ir (S. Zakeri). and much detail of the biology, pathogenesis, and epidemiology of this parasite remains unknown. In the new malaria campaigns, the Malaria Eradication Research Agenda (malERA) Consultative Group on basic science suggested that no campaign for control or elimination can be succeed without having knowledge about the disease epidemiology and host-parasite-vector interactions, as well as knowing how these interactions are affected by intensifying intervention tools (Baum et al., 2011). Therefore, it has been suggested that understand- ing and mapping of global and local P. vivax population structure are essential for defining accurately the transmission dynamics of P. vivax and also for predicting how quick novel antigenic vari- http://dx.doi.org/10.1016/j.actatropica.2016.04.006 0001-706X/© 2016 Elsevier B.V. All rights reserved.