Sequence characterization of the protease and partial reverse transcriptase proteins of the NED panel, an international HIV type 1 subtype reference and standards panel

The NED panel (NIH-ENVA-DOD) was assembled by the Virology Quality Assurance Laboratory for use as an international HIV-1 subtype reference and standards panel. The panel contains 44 minimally cultured strains from diverse geographic areas donated by the Walter Reed Army Institute of Research and F. Brun-Vezinet (Hopital Bichat-Claude Bernard, Paris, France). The contributors assigned the strains to group M subtypes A (5), B (10), C (6), D (3), E (10), F (5), G (2), H (1), and 0 (2) before donation. Phylogenetic and recombination analyses of the protease gene and a partial sequence of the reverse transcriptase gene of each seed pool indicated potentially three more recombinants in the panel in addition to the two previously recognized recombinants. Alignments of the amino acids to corresponding regions of pNL4-3 showed protease amino acid sequence identity ranged from 68.5% (group 0) to 95.2% (subtype B). Reverse transcriptase amino acid identity ranged from 84.5% (group O) to 96.8% (clade B). Codons associated with antiretroviral resistance were primarily wild type and highly conserved among all the clades.