Short communication: Emergence of novel A/G recombinant HIV-1 strains in Argentina

Abstract

The predominant circulating HIV-1 strains in South America are subtype B and B/F recombinants with different distributions among countries. However, the emergence of other subtypes is a matter of concern and needs continuous monitoring. We identified three different A/G recombinants in Argentina, two of them in vertically infected children from unlinked mothers and one in an adult female. HIV-1 pol sequences from the children showed novel A/G recombination patterns and no phylogenetic relationship with previously reported South American A/G sequences. The third A/G recombinant was a CRF06_cpx with African origin. The detection of new or unusual subtypes is important to avoid false-negative PCR HIV-1 early diagnosis due to detection failures and for future vaccine development.

FIG. 1.

Maximum likelihood phylogenetic trees of the HIV-1 pol region, encompassing the protease and part of the reverse transcriptase of newly identified A/G recombinants from Argentina and subtype reference strains. Bootstrap support values are represented at the nodes for each cluster. (a) Analysis of newly identified sequences from Argentina with the reference sequence from the parental HIV-1 subtypes and CRF06_cpx. (b) Analysis of newly identified sequences from Argentina with A, G, or A/G recombinants from South America and Africa. Sequences marked with lined boxes are the newly identified sequences from Argentina in a woman (FFCA) and two children (5707 and 4707). The sequence marked with a black square is the previously identified A/G recombinant from Argentina.

FIG. 2.

Bootscanning plot of (a) 4707_M86 and (b) 5707_U864 sequences from Argentina. Black curve represents subtype G and light gray curve subtype A. Subtypes C and D were used as outgroups for 4707 and 5707, respectively. In bootscan analyses performed with SimPlot, bootstrap values were determined in neighbor-joining trees constructed using the Kimura two-parameter model, based on 100 resamplings, supporting branching with the consensus sequences within a 200-bp window moving in steps of 20 bases.

FIG. 3.

Schematic representation of the recombination pattern of (a) 4707_M86 and (b) 5707_U864. Illustrations were obtained from the Recombinant HIV-1 Drawing Tool (www.hiv.lanl.gov/content/sequence/DRAW_CRF/recom_mapper.html). Phylogenetic trees for the nucleotide sequences of regions with different subtypes were constructed using the maximum-likelihood approach. Bootstrap values above 70 are shown at the branch nodes. The clusters containing the query sequences are highlighted and the black square represents the newly identified sequences from Argentina 4707 or 5707, respectively.