Table I.

CH77 3′ SGA direct sequencing spanning CTL epitopes

Day SGA clone ENV 343-363 (CH77.s) NEF 17-35 (CH77.aa) NEF 75-94 (CH77.cc) 
0 Consensus SHVVDKLREQFRNKTIVFNH RERRRRDEPAAVGVGPASQ PVRPMTYKAALDLSHFLKEK 
14 CH77_WGA_B3a ...........K........ ................... .................... 
14 CH77_WGA_C7 ...........K........ ................... .................... 
14 CH77_WGA_C9 ...........K........ ................... .................... 
14 CH77_WGA_C4 ...........K........ ................... .................... 
14 CH77_WGA_D5 ...........K........ ................... .................... 
14 CH77_WGA2b .................... ................... .................... 
14 CH77E_L7 ...........S........ ......N............ .................... 
14 CH77E_L8 ...........K........ .....K............. .................... 
14 CH77E_M6 ..............A..... ....K.............. .................... 
32 CH77_WK03_3_B1 ...........K........ ....G.............. .......Q............ 
32 CH77_WK03_3_D1 ...........K........ ........S.......... ............I....... 
32 CH77_WK03_3_D2 ...........K........ ......E............ .......P............ 
32 CH77_WK03_3_D3 ...........K........ .....K............. .......Q............ 
32 CH77_WK03_3_TB1 ...........K........ .....K............. .......Q............ 
32 CH77_WK03_3_TB2 ...........K........ ......E............ .......T............ 
32 CH77_WK03_3_TB4 ...........K........ ........S.......... ..........H......... 
32 CH77_WK03_3_TB5 ...........K........ ......N............ .......Q............ 
32 CH77_WK03_3_TB6 ...........K........ ..GA.ERR........... .......Q............ 
32 CH77_WK03_3_TB7 ...........K........ .....K............. .......Q............ 
32 CH77_WK03_3_TB8 ...........K........ ......E............ .......T............ 
32 CH77_WK03_3_TC1 ...........K........ ......N............ .......Q............ 
102 CH77_WK12_3_E1 .Y.........K........ ......N............ .L.....Q............ 
102 CH77_WK12_3_TA1 ...........K........ .....K............. .L.....Q............ 
102 CH77_WK12_3_TA2 ...........N........ .....T............. .L.....Q............ 
102 CH77_WK12_3_TB1 ...........K........ ....G.............. ........G........... 
102 CH77_WK12_3_TB2 ...........K........ .....G............. ....I...G........... 
159 CH77_WK24_3_TA1 ...........K........ K.....E............ .L......G........#.. 
159 CH77_WK24_3_TA2 ...N.......K........ .....G.........T... .L.....Q........... 
159 CH77_WK24_3_TA3 ...........K........ .....G....-------.. .L.....Q............ 
159 CH77_WK24_3_TA4 ...........K........ ......N........S... .L.....Q............ 
159 CH77_WK24_3_TA6 ...N.......K........ ......E............ .L......G........... 
159 CH77_WK24_3_TB1 ...N.......K........ .....G............R .L.....Q.........#.. 
159 CH77_WK24_3_TB2 N..........K........ .....T............. .L.....Q............ 
159 CH77_WK24_3_TB3 ...N.......K........ .....K..........V.. .L.....Q............ 
159 CH77_WK24_3_TB4 ...........N........ .....K..........V.. .L.....Q............ 
159 CH77_WK24_3_TB5 G..........N........ .....T............R .L......G........... 
159 CH77_WK24_3_TB6 ...N.......K........ ......E.........V.. .L......G........... 
159 CH77_WK24_3_TB7 ...N.......K........ .....G............. .L......G........... 
592 CH77_WK84_J1 .Y.........K........ ....GK............R ........G........... 
592 CH77_WK84_G7 .Y.........K..A..... ....GK............R ........G........... 
592 CH77_WK84_H12 ...A.......KD....... ....GK............R ........G........... 
592 CH77_WK84_C9 .Y.........K........ ......E...........R .L......G........... 
592 CH77_WK84_H3 .Y.........K........ .....G............R ........G........... 
592 CH77_WK84_D10 .Y.........K........ ....GK............R ........G........... 
Day SGA clone ENV 343-363 (CH77.s) NEF 17-35 (CH77.aa) NEF 75-94 (CH77.cc) 
0 Consensus SHVVDKLREQFRNKTIVFNH RERRRRDEPAAVGVGPASQ PVRPMTYKAALDLSHFLKEK 
14 CH77_WGA_B3a ...........K........ ................... .................... 
14 CH77_WGA_C7 ...........K........ ................... .................... 
14 CH77_WGA_C9 ...........K........ ................... .................... 
14 CH77_WGA_C4 ...........K........ ................... .................... 
14 CH77_WGA_D5 ...........K........ ................... .................... 
14 CH77_WGA2b .................... ................... .................... 
14 CH77E_L7 ...........S........ ......N............ .................... 
14 CH77E_L8 ...........K........ .....K............. .................... 
14 CH77E_M6 ..............A..... ....K.............. .................... 
32 CH77_WK03_3_B1 ...........K........ ....G.............. .......Q............ 
32 CH77_WK03_3_D1 ...........K........ ........S.......... ............I....... 
32 CH77_WK03_3_D2 ...........K........ ......E............ .......P............ 
32 CH77_WK03_3_D3 ...........K........ .....K............. .......Q............ 
32 CH77_WK03_3_TB1 ...........K........ .....K............. .......Q............ 
32 CH77_WK03_3_TB2 ...........K........ ......E............ .......T............ 
32 CH77_WK03_3_TB4 ...........K........ ........S.......... ..........H......... 
32 CH77_WK03_3_TB5 ...........K........ ......N............ .......Q............ 
32 CH77_WK03_3_TB6 ...........K........ ..GA.ERR........... .......Q............ 
32 CH77_WK03_3_TB7 ...........K........ .....K............. .......Q............ 
32 CH77_WK03_3_TB8 ...........K........ ......E............ .......T............ 
32 CH77_WK03_3_TC1 ...........K........ ......N............ .......Q............ 
102 CH77_WK12_3_E1 .Y.........K........ ......N............ .L.....Q............ 
102 CH77_WK12_3_TA1 ...........K........ .....K............. .L.....Q............ 
102 CH77_WK12_3_TA2 ...........N........ .....T............. .L.....Q............ 
102 CH77_WK12_3_TB1 ...........K........ ....G.............. ........G........... 
102 CH77_WK12_3_TB2 ...........K........ .....G............. ....I...G........... 
159 CH77_WK24_3_TA1 ...........K........ K.....E............ .L......G........#.. 
159 CH77_WK24_3_TA2 ...N.......K........ .....G.........T... .L.....Q........... 
159 CH77_WK24_3_TA3 ...........K........ .....G....-------.. .L.....Q............ 
159 CH77_WK24_3_TA4 ...........K........ ......N........S... .L.....Q............ 
159 CH77_WK24_3_TA6 ...N.......K........ ......E............ .L......G........... 
159 CH77_WK24_3_TB1 ...N.......K........ .....G............R .L.....Q.........#.. 
159 CH77_WK24_3_TB2 N..........K........ .....T............. .L.....Q............ 
159 CH77_WK24_3_TB3 ...N.......K........ .....K..........V.. .L.....Q............ 
159 CH77_WK24_3_TB4 ...........N........ .....K..........V.. .L.....Q............ 
159 CH77_WK24_3_TB5 G..........N........ .....T............R .L......G........... 
159 CH77_WK24_3_TB6 ...N.......K........ ......E.........V.. .L......G........... 
159 CH77_WK24_3_TB7 ...N.......K........ .....G............. .L......G........... 
592 CH77_WK84_J1 .Y.........K........ ....GK............R ........G........... 
592 CH77_WK84_G7 .Y.........K..A..... ....GK............R ........G........... 
592 CH77_WK84_H12 ...A.......KD....... ....GK............R ........G........... 
592 CH77_WK84_C9 .Y.........K........ ......E...........R .L......G........... 
592 CH77_WK84_H3 .Y.........K........ .....G............R ........G........... 
592 CH77_WK84_D10 .Y.........K........ ....GK............R ........G........... 

Italics, nonsynonymous mutation occurring two or more times; underline, confirmed optimal T cell epitope; -, deletion; #, insertion; ., amino acids that are identical to the transmitted form.

a

Representative of five further SGA clones (unpublished data).

b

Representative of one further SGA clone (unpublished data).

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