Table 2. Consensus differences of HIV-1 Gag between 454 and Sanger clone-based sequencing methods overlapped with the functional of immunogenic sites in individuals.
| Patient IDa | Clade | HLA type | Positionb | Sequence | Functionc |
| ML1111 | A1 | N/A | 086–115 | YSVHQRIDVKDTKEALEKIEEEQN(N/K) KSKKKA(T/P) | NEUTRALIZINGVIRUSES |
| N/A | 121–132 | DTGNSS(S/N)QVSQNY | NEUTRALIZING VIRUSES | ||
| B*5703 | 162–169 | K(K/R)AFS(N/S)PEVI | CTL RESPONSES | ||
| B*5703 | 162–172 | K(K/R)AFS(N/S)PEVIPMF | CTL RESPONSES | ||
| B*4201 | 180–188 | T(T/I)PQDLNTNL | CTL RESPONSES | ||
| N/A | 217–224 | PVH(Q/H)AGPIA | CYCLOPHILIN A BINDING | ||
| ML1857 | C | A*0201 | 077–085 | SLY(Y/H)NT(T/A)VATL | CTL RESPONSES |
| B*3501 | 254–262 | PPI(V/I)PVGD(E/D)IY | CTL RESPONSES | ||
| A*0201 | 433–442 | FLGK(K/R)IWPS(P/S)Y(Y/H)K | CTL RESPONSES | ||
| ML1992 | A1 | A*0801 | 074–082 | EL(L/I)RSLYNTV | CTL RESPONSES |
| A*3002 | 076–086 | RSLY(F/Y)NTVATLY | CTL RESPONSES | ||
| A*0201 | 077–085 | SLY(F/Y)NTVATL | CTL RESPONSES | ||
| N/A | 086–115 | YSVHQRIDVKDTKEALEKIEEE Q(Q/K)NKSKKKA | NEUTRALIZING VIRUSES | ||
| N/A | 113-122 | KKAQQA(E/A)A(T/A)A(T/A)D(D/A)T | NEUTRALIZING VIRUSES | ||
| N/A | 121–132 | D(D/A)TGH(S/N)SSQ(N/Q)VSQNY | NEUTRALIZING VIRUSES | ||
| A*0801 | 329–337 | DCK(K/R)TILKAL | CTL RESPONSES | ||
| A*0201 | 433–442 | FLGK(K/R)IWPSYK | CTL RESPONSES | ||
| ML1876 | A1 | A*2602 | 028–036 | KYKL(L/M)KHI(I/L)VW | CTL RESPONSES |
| A*0202 | 077–085 | SLY(Y/F)NTVATL | CTL RESPONSES | ||
| N/A | 113–122 | KKAQQA(A/E)A(A/T)A(A/T)D(A/D)T | NEUTRALIZING VIRUSES | ||
| N/A | 121–132 | D(A/D)TGH(S/N)SSQ(Q/N)VSQNY | NEUTRALIZING VIRUSES | ||
| ML0795 | A1 | A*0202 | 077–085 | SLYNTV(V/I)AT(T/V)L | CTL RESPONSES |
| N/A | 392–407 | CFNC(C/Y)GKEGHLARNC | VIRAL ENCAPSIDATION | ||
| ML1003 | A1 | B*5301 | 308–316 | QASQE(D/E)VKN(N/C)W | CTL RESPONSES |
| ML1102 | D | N/A | 064 | L(I/L)->X | PARTICLE FORMATION |
| N/A | 113–121 | KKAQQAA(T/A)ADT | NEUTRALIZING VIRUSES | ||
| N/A | 121–132 | DTG(R/G)H(N/H)SSQVSQNY | NEUTRALIZING VIRUSES | ||
| A*0201 | 433–442 | FLGKIWPSY(H/Y)K | CTL RESPONSES | ||
| ML1317 | D | A*0201 | 433–442 | FLGKIWPSY(H/Y)K | CTL RESPONSES |
| ML1208 | A1 | N/A | 064 | L(I/L)->X | PARTICLE FORMATION |
| A*0201 | 077–085 | SLYNTVATL(L/I) | CTL RESPONSES | ||
| N/A | 121–132 | DTGHSSQ(Q/K)VSQNY | NEUTRALIZINGVIRUSES | ||
| ML1591 | C | A*0201 | 077–085 | SLYNTVAT(T/V)L | CTL RESPONSES |
| A*0201 | 433–442 | FLGKIWPSY(N/H)K | CTL RESPONSES | ||
| ML1660 | D | A*2402 | 028–036 | KYK(K/R)LKHIVW | CTL RESPONSES |
| N/A | 086–115 | YSVHQ(Q/E)R(R/K)ID(E/K)V(I/V)K(K/A) DTKEALEKIEEEQN(N/T)KSKKKA | NEUTRALIZING VIRUSES | ||
| N/A | 113–122 | KKAQQAA(A/T)ADT | NEUTRALIZINGVIRUSES | ||
| N/A | 121–132 | DTG(G/R)H(H/N)SSQVSQNY | NEUTRALIZINGVIRUSES | ||
| ML1739 | A1 | N/A | 113–122 | KKAQQAAAD(D/G)T | NEUTRALIZINGVIRUSE |
| ML0157 | A1 | A*0802 | 180–188 | TPQDLNT(P/M)ML | CTL RESPONSES |
| N/A | 217–226 | PVHAQPIA(A/P)P | CYCLOPHILIN A BINDING | ||
| ML0415 | A1 | A*0301 | 020–028 | RLRPGGKKK(K/Q) | CTL RESPONSES |
| A*0301 | 020–029 | RLRPGGKKK (K/Q) Y | CTL RESPONSES | ||
| ML0548 | A1 | B*57 | 248 | A(A/G)->G | B*57 ESCAPING[68] |
| ML1594 | A1 | N/A | 017–022 | EKIR(E/R)LR | NEUTRALIZING VIRUSES |
| B*0801 | 024–032 | GGK(R/K)KK(K/T)YK(K/R)L(M/L)K | CTL RESPONSES | ||
| B*0801 | 074–082 | ELRSLYNT(T/A)V | CTL RESPONSES | ||
| N/A | 121–132 | DT(T/A)GH(H/S)SS(S/K)Q(K/Q)VSQNY | NEUTRALIZING VIRUSES | ||
| N/A | 217–225 | PVH(P/H)AQPI(V/I)AP | CYCLOPHILIN A BINDING | ||
| ML1654 | A1 | N/A | 121–132 | DT(A/T)GH(S/N)SS(K/S)Q(Q/K)VSQNY | NEUTRALIZING VIRUSES |
| ML1768 | A1 | N/A | 121–132 | D(A/D)TGHSSQ(Q/K)V(V/I)SQNY | NEUTRALIZING VIRUSES |
| N/A | 217–225 | PVHAGPI(I/A)AP | CYCLOPHILIN A BINDING |
a
: patient IDs are from a cohort of the Pumwani Sex Worker in Nairobi, Kenya; b: positions are referred to HXB2 gag gene; c: CTL epitopes are derived from the best-defined CTL epitope summary (HIV Molecular Immunology 2009, Los Alamos National Laboratory, USA). The differences between consensus sequences are shown in bold.