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Genetic and functional characterization of human immunodeficiency virus type 1 VprC variants from north India: presence of unique recombinants with mosaic genomes from B, C and D subtypes within the open reading frame of Vpr

Aalia S. Bano^1,

Vikas Sood^1,

Ujjwal Neogi^1,

¹ Virology, National Institute of Immunology, JNU Campus, New Delhi 110067, India
² Post Graduate Institute of Medical Education and Research, Chandigarh, India

Correspondence
Akhil C. Banerjea
akhil{at}nii.res.in or
akhil_banerjea{at}yahoo.com

The human immunodeficiency virus type 1 (HIV-1) epidemic in India is predominantly caused by genetic subtype C, though other minor subtypes have also been reported. One of the major accessory proteins of HIV-1, namely Vpr, is known to influence key steps in viral replication, cell cycle progression, promoter activation, apoptosis and pathogenesis. Therefore, we carried out a genetic and functional analysis of the Vpr variants from eight HIV-1-infected individuals from north India. The sequence analyses revealed that six of eight samples clustered with ancestral subtype C. Remarkably, five of these showed a conserved and region-specific L64P mutation, located in the predicted third -helix. This change adversely affected their ability to activate the HIV-1 long terminal repeat promoter without compromising their ability to cause apoptosis. Bootscan, phylogenetic and SimPlot analysis of the remaining two samples (VprS2 and A6) revealed very interesting mosaic genomes derived from B, C and D subtypes. The N-terminal half of the VprS2 gene consisted of genomic segments derived from subtypes B/D, C and D but the C-terminal half was derived predominantly from subtype C. Interestingly the N-terminal half of sample A6 also showed similar B/D, C and D inter-subtype recombinant structure but the C-terminal half was entirely derived from the consensus B subtype. Multiple breakpoints in a short stretch of 291 nt encoding the Vpr gene strongly suggest that this region is a potential hot-spot for the formation of inter-subtype recombinants and also highlight the importance of the rapidly evolving HIV-1 epidemic in the north Indian region due to multiple genetic subtypes.

These authors contributed equally to this work.

The GenBank/EMBL/DDBJ accession numbers for the sequences obtained in this paper are EU446123 [GenBank] , EU446124 [GenBank] , EU493256 [GenBank] and EU541271 [GenBank] (NII-PGI-IND-VprS1, S2, S3 and A6, respectively).

Two supplementary figures, showing bootscan and phylogenetic analysis of three Vpr variants and breakpoint and predicted hairpin formation analysis, are available with the online version of this paper.