Pathogens have evolved countermeasures to avoid immune clearance and prolong the period of infection in their vertebrate hosts. The type and degree of immune escape strategies depends on the in vivo ‘lifestyle’ the pathogen has adopted. Protozoan parasites use different strategies to coordinate their expression of phenotypic variation, which is used in many cases to fool the immune system, or to successfully invade new host cells. The protozoan pathogen Plasmodium falciparum, which infects up to 300 million people causing more than two million lives each year, undergoes antigenic variation to establish persistent blood stage infection. Several clonally variant gene families undergo antigenic variation in P. falciparum and are expressed during blood stage infection at the surface of infected red blood cells (iRBC). One family encoded by 60 var genes expresses the major virulence adhesion surface molecule causing severe malaria (capillary blockages in the brain and other organs mediated by iRBC). Switching expression between the 60-member var gene families avoids parasite immune clearance and prolongs the period of infection and transmission to the mosquito. Several laboratories have contributed to the deciphering of the underlying mechanisms of antigenic variation. Most findings concern factors that control the default silencing process of clonally variant gene families. This includes epigenetic factors such as histone modifications and a particular nuclear spatial location of the virulence gene family. The molecular events leading to ‘activation of a single member’, however, remain unknown in malaria parasites. Understanding the mechanism of mutually exclusive expression remains the Holy Grail in the field of antigenic variation and malaria pathogenesis. Here we propose a novel approach based on findings of the two participating teams. Our recent insight points to non-coding RNA (ncRNA) as a novel key regulator in virulence gene expression in malaria parasites and opens a new research avenue. We hypothesise that ncRNA produced from var gene introns and from GC-rich elements associated to var genes may be a missing link in the understanding of chronic infection and pathogenesis of malaria parasites. This idea is supported by our observation that links the upregulation of ncRNA of all GC elements (15 in total) in a mutant parasite (RNase II mutant gene) to the specific expression of a subgroup of var genes (type A). Type A vars are strongly associated to severe malaria. MalVir aims to explore var gene associated ncRNA as potential key regulators in different processes of antigenic variation. We have identified two candidate genes that apparently contribute to the control of two distinct types of ncRNA, one is a member of the ApiAP2 putative transcription activator family that binds to var introns (AP2varint). Var introns produce sense and antisense RNA, but their biological function remains unknown. The second is a novel nuclear RNase II that targets with high specificity ncRNA produced from GC-rich elements adjacent to many var genes. Both genes have been genetically manipulated to obtain protein knock down parasite lines. By studying these mutant parasites we expect to obtain exciting insights into the underlying principles of antigenic variation and malaria pathogenesis. The project is likely to reveal an Achilles Heel of the parasite’s immune evasion strategy, which could be targeted for future drug intervention strategies. The MalVir consortium represents a balanced collaboration between two matching teams exploring new ideas and tools in the field malaria parasite ncRNA. The work that has lead to this project has been initiated in 2010 in a collaborative study between both partner laboratories (initially with Prof. Pan and Dr Zhang from the Tongji University and currently with Dr. Zhang who is a very skilled group leader). MalVir will foster solid partnership between the Institut Pasteur Paris and the Tongji University.