Genetic analysis of human immunodeficiency virus type 1 nef in portugal: Subtyping, identification of mosaic genes, and amino acid sequence variability

Abstract

Extending our previous genetic characterization of human immunodeficiency virus type 1 (HIV-1) strains circulating in Portugal, we here report the first phylogenetic and putative amino acid sequence variability analyses of nef accessory gene. Viral sequences (n = 53) were amplified by nested PCR from proviral DNA purified from peripheral blood mononuclear cells of HIV-1 infected individuals (n = 49). Phylogenetic inference analysis demonstrated a distribution of the viral sequences between subtypes A (sub-subtype A1), B, D, F (sub-subtype F1), G, H, and J, with subtypes G and B accounting altogether for more than half of the genotypes found. A significant number of the proviral DNA sequences analyzed (18.4%) were shown to correspond to intragenic nef recombinants, with the majority having the typical CRF02_AG nef structure. In addition, three novel intragenic recombinant structures were found (B/G/B, CRF02_AG/H, and D/G). From phylogenetic analysis, it was concluded that part of the non-recombinant nef genes might have actually been amplified from mosaic viruses: CRF06_cpx, CRF14_BG, and a new envA/nefJ recombinant. While comparing all the putative Nef sequences, significant amino acid sequence variability was observed. However, most of the described nef functional motifs were relatively well conserved in the majority of the sequences analyzed and numerous amino acid changes fell outside these regions. The results presented unambiguously endorse the high level of complexity of HIV-1 epidemics in Portugal.

Analysis of a Local HIV-1 Epidemic in Portugal Highlights Established Transmission of Non-B and Non-G Subtypes

“…In the last decade, other local epidemics with CRF14_BG have been described among IDU in Spain and Portugal (20,22). Our results are in line with the data showing a decrease in the prevalence of HIV-1 among IDU in Portugal (28), consequently reducing the transmission of BG recombinant viruses.…”

“…Portugal contrasts with the rest of western Europe in its distribution of HIV-1 subtypes. In addition to the B subtype, Portugal also has a high prevalence of the G subtype (18)(19)(20)(21)(22)(23). The high prevalences of the B and G subtypes are thought to have promoted the appearance among intravenous drug users (IDU) of different types of B/G recombinant strains, namely, CRF14_BG, which is considered to have emerged in Portugal in the early 1990s and then spread to Spain and other European countries (24)(25)(26).…”

Molecular Epidemiology of HIV Type 1 CRF02_AG in Cameroon and African Patients Living in Italy

“…13 Recent data from Yaoundé also indicate that the CRF02_AG strain represents up to 50% of the total infection. 15 CRF02_AG prevalence has been increasing not only in West and West-Central Africa, 8,[13][14][15][19][20][21][22][23] but also in different countries of Europe, [24][25][26][27] such as Italy, [28][29][30][31][32] because of migrations from the sub-Saharan region. This viral variant is one of the most prevalent recombinant forms of HIV-1 in the world, responsible for at least 5% of infections.…”

Meta-Analysis To Test the Association of HIV-1 nef Amino Acid Differences and Deletions with Disease Progression

“…The nef amino acid sequence has been reported to be highly polymorphic even within a particular subtype (4,22,28,29,40,42,53). Single amino acid deletions have been found predominantly at three locations that are structurally less defined loop regions: positions 8 to 11, 49 to 51, and 155 to 162 (25) (32).…”