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Identification of two unique naturally occurring Vpr sequence polymorphisms associated with clinical parameters in HIV‐1 chronic infection

HIV‐1 viral protein R (Vpr) plays important roles in HIV‐1 replication. Despite the identification of a number of HLA class I‐associated immune escape mutations; it is yet known whether immune‐driven Vpr polymorphisms are associated with disease outcome. Hereby, we comprehensively analyzed Vpr sequence polymorphisms and their association with disease outcome and host HLA genotypes, by using plasma viral RNA isolated from 444 HLA‐typed, treatment‐naïve, chronically HIV‐1 infected individuals. Vpr amino acid residues at positions 13, 37, 45, 55, 63, 77, 84, 85, 86, and 93 were significantly associated with patients’ plasma viral load and/or CD4 count. Further analysis revealed Ala at position 55 was significantly associated with lower plasma viral load; and Thr at position 63 was significantly associated with lower plasma viral load and higher CD4 count. Also, the number of amino acid residues at the two positions, located in a functionally important α‐helical domain, correlated inversely with plasma viral load and positively with CD4 count. Moreover, a phylogenetically corrected method revealed residues at positions 55 and 63 are associated with patients’ HLA genotypes. Taken together, our results suggest that Vpr polymorphisms at functionally important and immune‐reactive sites may contribute, at least in part, to viral replication and disease outcome in vivo. J. Med. Virol. 89:123–129, 2017. © 2016 Wiley Periodicals, Inc.