In my opinon you can assess the SPOROZOITE'S SPECIFIC PROTEIN(ANTIGEN) GENE using PCR and well designed specific primers for defining reinfection from relapse in P vivax malaria.
How to distinguish between the two is not currently known. Hence your question. Furthermore, there might be more origins of Plasmodium vivax malarial recurrence and genetic variation than just true relapse and reinfection. See, for example, the "Discussion" section (and associated literature citations) in Delgado-Ratto, C. et al., 2014, "Population structure and spatio-temporal transmission dynamics of Plasmodium vivax after radical cure treatment in a rural village of the Peruvian Amazon", Malaria Journal 13: 8. Also, read the comment re hypnozoites in the "An historical perspective on PE stages" subsection of Menard, R. et al., 2013, "Looking under the skin: the first steps in malarial infection and immunity", Nature Reviews Microbiology 11: 701-712. Lastly, it should be noted that aspects of what is covered in the following publication could apply to P. vivax malaria: Markus, M.B., 2012, "Source of clinical malaria in mixed-species infections", Journal of Travel Medicine 19: 275.
The main goal of malaria elimination program interrupt local transmission. Positive cases are occasionally reported that no evidence of transmission of malaria in the region does not exist. It appears this is due to Plasmodium vivax relapse. Because of this separation of recurrence of new transmission is very important to remove the program.
We are seeking a scientific method for to distinguish between reinfection and relaps cases of Plasmodium vivax .
Part of the answer can be find in a WHO report on parasite genotyping http://www.mmv.org/sites/default/files/uploads/docs/news/MalariaGenotyping2.pdf
There is no consensus on the markers to distinguish between reinfection and relapse. A paper from N White also stressed that point. Radical cure of vivax patients with primaquine (check G6PD) is probably needed to solve part of the problem.
Stephane Picot is correct, Habibollah, about there not being distinguishing markers at this time. On 3 November 2014, I gave a presentation in New Orleans (at the annual meeting of the American Society of Tropical Medicine & Hygiene) that was related to this subject. It was entitled "Plasmodium vivax: a genotypic interpretational problem".
Further to the original question, it is possible that single-cell genomic analysis might help, but the technique would not be suitable for routine use. See: S. Nair et al. 2014. Single-cell genomics for dissection of complex malaria infections. Genome Research 24: 1028-1038.
The authors of the following paper think that targeted deep sequencing might help to distinguish relapse from reinfection: Lin, J.T. et al. 2015. Using amplicon deep sequencing to detect genetic signatures of Plasmodium vivax relapse. Journal of Infectious Diseases (in press).
Dear Turki, I don't have many information about it but the only think I can advice you is to read the Celine Barnadas thesis. She deeply worked on P. vivax (as I supose you already know it).
Here is the link of her (very intresting) thesis, directed by S. Picot who answered you above)