Lamos National Laboratory, http://www.hiv.lanl.gov/content/ immunology) [54], theLamos National Laboratory, http://www.hiv.lanl.gov/content/ immunology) [54], the most comprehensive

Lamos National Laboratory, http://www.hiv.lanl.gov/content/ immunology) [54], the
Lamos National Laboratory, http://www.hiv.lanl.gov/content/ immunology) [54], the most comprehensive curated source of known HIV epitopes [55]. A total of 606 linear epitopes were collected, including 229 CTL epitopes that were described as the “best defined” CTL epitopes and were supported by strong experimental evidence, as defined by Frahm et al., 2007 [56], 296 T-Helper epitopes and 81 antibody epitopes (Table 2, Additional file 2). Because of the challenges in identifying primary sequence elements of structurally conserved discontiguous conformational epitopes (e.g., [57,58]), conformational epitopes were not included in the study. Only the epitopes proven to be immunogenic in human as per the HIV ImmunologyTable 1 Overview of HIV-1 sequences used in the analysesType of genome Non – recombinant Group M group Subtype A A1 A2 B C D F1 F2 G H J K M – Total N group O group N O Total Non-recombinants – Total Circulating Recombinant Forms (CRF) Totaldatabase were used in PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27385778 this study. The overview of epitope mapping techniques and challenges in epitope identification has been described elsewhere [59,60]. Although CTL and Th epitopes had representation from all nine proteincoding genes, Ab epitopes were absent in the Vif, Vpr, Rev and Vpu genes. The majority of the Ab epitopes (75 out of 81) belonged to the Env PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28298493 gene, while the Pol gene had three and the Gag, Tat and Nef genes had one epitope each [61-65]. It should be noted that because of the high amino acid sequence diversity of the Env gene that may differ by as much as 30 between subtypes [43], very few antibody epitopes if at all could be expected to be conserved across a broad range of HIV-1 sequences; thus, in this study we primarily focus on CTL and T-Helper epitopes. Restricting HLA (S)-(-)-BlebbistatinMedChemExpress (S)-(-)-Blebbistatin allele(s) for associated epitopes are given in Table 3 as per HIV Immunology database and IEDB http://www.immuneepitope.org/.Inclusion of epitopes in association-rule miningIn order to identify the most broadly represented epitopes, each epitope sequence was aligned with 90 reference sequences and the epitopes present in more than 75 of the reference sequences (i.e., perfect amino acid sequence match in more than 67 sequences) were selected for association rule mining. A total of 47 epitopes, including 33 CTL, 12 T-Helper and 2 antibody epitopes, were present in more than 75 of the referenceReference sequences# 4 3 5 4 4 4 4 4 3 3 2 40 3 4 7 47 43Non-reference sequences* 6 46 158 350 32 6 12 610 2 13 15 625 263Total (Global HIV-1 population^) 6 50 3 163 354 36 10 4 16 3 3 2 650 5 17 22 672 306The table shows numbers of HIV-1 sequences of different subtypes among reference sequences and global population used in the analyses. # Reference sequences used in the primary analyses to identify association rules * Non-reference sequences were collected from 2008 Web alignment of HIV Sequence database ^ Total number of sequences in the global HIV-1 population used in the analysisPaul and Piontkivska BMC Microbiology 2010, 10:212 http://www.biomedcentral.com/1471-2180/10/Page 4 ofTable 2 Overview of epitopes used in the analysesGene Gag Protein p17 p24 p2p7p1p6 Total Pol Gag-Pol Protease RT RTIntegrase Integrase Total Vif Vpr Tat Rev Vpu Env Nef Total#Total no. of epitopes CTL#Highly conserved epitopes* Total 50 131 24 205 1 8 62 2 23 96 11 13 11 9 2 197 62 606 CTL 1 8 2 11 1 12 1 5 19 2 32 Th 6 6 1 2 3 1 10 2 2 Ab Total 1 14 2 17 1 13 1 7 22 2 3No of associated epitopes^ CTL 8 2 10 1 12 1 4 18 2 30 Th 6 6 1.