Analysis of genetic diversity and amino acid sequence of HIV-1 Vpr from a patient with AIDS dementia complex

Abstract

Objective To study the sequence characteristics and variation of HIV-1 Vpr gene in different parts of an AIDS dementia complex (ADC) patient and provide basis for the study of the neurologic pathogenesis of HIV-1-assciatd dementia. Methods Genomic DNA was extracted from peripheral samples (lymph nodes, spleen, liver) and central nervous system (meninges, frontal lobe, temporal lobe gray matter, frontal white matter, basal ganglia cortex) of an ADC patient, The Vpr gene was amplified with nested polymerase chain reaction (PCR). PCR products were cloned into the pMD19-T vector. After transformation into DH5α competent E. coli, five positive clones were sequenced. The phylogenetic tree was built and genetic distance was calculated through MEGA6, and the values of ds/dn was calculated through SNAP, then the changes of the amino acid sites were analyzed. Results HIV-1 Vpr genes isolated from different tissues of the ADC patient had variations. Vpr HIV-1 gene sequences from central nervous system and peripheral tissues were intercrossed together in the phylogenetic tree. Central nervous system and peripheral HXB2 Vpr had no significant differences in genetic distance. The ds/dn of all the HIV-1 Vpr gene sequences were 3.3749. Conclusions The HIV-1 Vpr sequences were different in the ADC patient, and there were different variations in different parts of the peripheral and central regions. Whether these variations are related to the pathogenesis of ADC remains to be further studied. Key words: Human immunodeficiency virus 1 (HIV-1); Vpr; AIDS dementia complex; Genetic diversity