HIV-1 Subtype C Phylodynamics in the Global Epidemic
Abstract
:1. Introduction
2. Results and Discussion
2.1. The in vivo dynamics of gag diversity
2.2. Amino acid frequency in HIV-1 subtype C Gag
2.3. Synonymous and non-synonymous changes
2.4. Changing amino acids and CTL epitopes
Gag cleavage product | Amino acid position | Number of associated CTL epitopes | Epitope | HXB2 | HIV-1 Subtype | HLA restriction | |
---|---|---|---|---|---|---|---|
start | end | ||||||
p17 | 11 | 1 | ASILRGGKLDK | 5 | 15 | C | |
28 | 10 | RLRPGGKKHY | 20 | 29 | C | A*3002 | |
RLRPGGKKHYM | 20 | 30 | C | ||||
RPGGKKHY | 22 | 29 | A, C, D | B42, B7 | |||
RPGGKKRYM | 22 | 30 | C | B35, Cw*0602 | |||
RPGGKKKYML | 22 | 31 | A, C, D | B*0702, B*5801, B*8101 | |||
KRYMIKHLV | 27 | 35 | C | Cw*0602 | |||
HYMLKHIVW | 28 | 36 | A, C | A*2301 | |||
34 | 7 | HYMLKHLVW | 28 | 36 | A, B, C | A*2301, A*2402, A24 | |
HYMLNHIVW | 28 | 36 | A, C, D | B*0702, B*5801, B*8101 | |||
HYMLKHLVWAS | 28 | 38 | C | ||||
HLVWASREL | 33 | 41 | C | Cw*0602, Cw*0804 | |||
LVWASRELERF | 34 | 44 | C | A*3002, A30, B*5703, B57 | |||
76 | 2 | EELRSLYNTV | 73 | 82 | C | B*4006 | |
RSLYNTVATLY | 76 | 86 | B, C | A*30, A*3002, A30, B57, B58, B63 | |||
111 | 0 | ||||||
119 | 0 | ||||||
p24 | 342 | 4 | RALGPGATL | 335 | 343 | A, B, C, D | B7 |
ALGPGASLEEM | 336 | 346 | C | ||||
GPGATLEEM | 338 | 346 | A, C, D | B*0702, B*5801, B*8101 | |||
ATLEEMMTA | 341 | 349 | B, C, CRF01_AE | A*0201, A*0206, A*0220, A*0234, A*0236, A2 | |||
p2 | 375 | 0 |
Gag cleavage product | Amino acid position | Number of associated CTL epitopes | Epitope | HXB2 | HIV-1 Subtype | HLA restriction | |
---|---|---|---|---|---|---|---|
start | end | ||||||
p17 | 7 | 1 | ASILRGGKLDK | 5 | 15 | C | |
15 | 2 | ELDRWEKIRL | 12 | 21 | B, C | B63 | |
18 | 2 | KIRLRPGGKK | 18 | 27 | B, C, multiple | A*0301, A11, A3, B27 | |
20 | 4 | RLRPGGKKHY | 20 | 29 | C | A*3002 | |
30 | 7 | RLRPGGKKHYM | 20 | 30 | C | ||
RPGGKKRYM | 22 | 30 | C | B35, Cw*0602 | |||
31 | 6 | RPGGKKKYML | 22 | 31 | A, C, D | B*0702, B*5801, B*8101 | |
KRYMIKHLV | 27 | 35 | C | Cw*0602 | |||
HYMLKHIVW | 28 | 36 | A, C | A*2301 | |||
HYMLKHLVW | 28 | 36 | A, B, C | A*2301, A*2402, A24 | |||
HYMLNHIVW | 28 | 36 | A, C, D | B*0702, B*5801, B*8101 | |||
HYMLKHLVWAS | 28 | 38 | C | ||||
61 | 0 | ||||||
62 | 0 | ||||||
65 | 0 | ||||||
69 | 0 | ||||||
79 | 6 | EELRSLYNTV | 73 | 82 | C | B*4006 | |
RSLYNTVATLY | 76 | 86 | B, C | A*30, A*3002, A30, B57, B58, B63 | |||
SLYNTVATL | 77 | 85 | A, B, C, CRF02_AG, D, F, G, K | A*02.01, A*0201, A*0202, A*0205, A*0214, A*0220, A*0234, A*0236, A*68, A02, A2, B*1503 | |||
SLFNTVATLY | 77 | 86 | C | ||||
LYNTVATLY | 78 | 86 | C | A*2902, A29, B*4403 | |||
LFNTVATLY | 78 | 86 | C | A*2902 | |||
p17 | 90 | 1 | YCVHAGIEVRD | 86 | 96 | C | |
91 | 1 | ||||||
93 | 1 | ||||||
95 | 1 | ||||||
120 | 0 | ||||||
p24 | 163 | 8 | VKVIEEKAF | 156 | 164 | C | B*1503 |
VKVVEEKAF | 156 | 164 | B, C | B*1503 | |||
IEEKAFSPEV | 159 | 168 | C | B*4006 | |||
IEEKAFSPEVI | 159 | 169 | C | B*4501 | |||
EEKAFSPEV | 160 | 168 | A, C | B*4415, B*4501 | |||
EKAFSPEV | 161 | 168 | C | Cw*0602 | |||
KAFSPEVIPMF | 162 | 172 | A, B, C, CRF02_AG, G | A*310102, A*6603, B*440302, B*5701, B*5703, B*5801, B57, B58, B63, B8, Cw*040101, Cw*07 | |||
AFSPEVIPMFT | 163 | 173 | C | ||||
215 | 3 | AAEWDRLHPVH | 209 | 219 | C | ||
AEWDRLHPV | 210 | 218 | B, C | A2, B*04, B*4006, Cw*0602 | |||
223 | 4 | RLHPVHAGPIA | 214 | 224 | C | ||
HPVHAGPIA | 216 | 224 | B, C | B*3910, B07, B35, B7 | |||
HPVHAGPVA | 216 | 224 | A, B, C, D | B7 | |||
GPIAPGQM | 221 | 228 | C, D | B35 | |||
248 | 3 | TSTLQEQIGW | 240 | 249 | B, C, HIV-2 | A*310102, A*6603, B*440302, B*5701, B*5703, B*58, B*5801, B27, B35, B57, B58, B63, B7, Cw*040101, Cw*07 | |
TSTLQEQIAW | 240 | 249 | B, C | B*5701, B*5703, B*5801, B57 | |||
TLQEQIGWM | 242 | 250 | B, C | A*0201, A*0220, A*0234, A*0236, A2 | |||
260 | 6 | PPIPVGDIY | 254 | 262 | B, C | B*3501, B*3502, B35 | |
PPVPVGDIY | 254 | 262 | C | B35 | |||
PPIPVGEIY | 254 | 262 | A, B, C, D | B35, B53, B7 supertype | |||
PVGDIYKRWII | 257 | 267 | C | ||||
GEIYKRWII | 259 | 267 | A, B, C, CRF02_AG, D | A*01, A*6801, B*0801, B*51, B8, Cw*07, Cw15, DQ2, DQ3, DR3, DR4 | |||
DIYKRWII | 260 | 267 | B, C | B*0801, B8 | |||
286 | 0 | ||||||
312 | 3 | TLRAEQATQD | 303 | 312 | C | Cw*0304 | |
RAEQATQDVKN | 305 | 315 | C | ||||
QATQDVKNW | 308 | 316 | C | B*5301, B*5801, B57 | |||
319 | 0 | ||||||
335 | 2 | NPDCKTILRAL | 327 | 337 | C | B*3910 | |
336 | 1 | RALGPGATL | 335 | 343 | A, B, C, D | B7 | |
339 | 3 | ALGPGASLEEM | 336 | 346 | C | ||
GPGATLEEM | 338 | 346 | A, C, D | B*0702, B*5801, B*8101 | |||
p2 | 370 | 1 | CLAEAMSQV | 362 | 370 | B, C | A*0201, A*0220, A*0234, A*0236 |
371 | 0 | ||||||
374 | 0 | ||||||
p7 | 377 | 0 | |||||
380 | 0 | ||||||
381 | 0 | ||||||
389 | 0 | ||||||
401 | 1 | IAKNCRAPRKK | 401 | 411 | C | ||
p1 | 441 | 1 | FLGKIWPSHK | 433 | 442 | A, B, C, CRF01_AE | A*0201, A*0205, A2 |
p6 | 451 | 0 | |||||
467 | 0 | ||||||
472 | 0 | ||||||
490 | 1 | PLTSLKSLFGS | 485 | 495 | C | ||
498 | 0 |
2.5. Dating of HIV-1 subtype C divergence
3. Experimental Section
Country | n | 1986 | 1987 | 1988 | 1989 | 1990 | 1991 | 1992 | 1993 | 1994 | 1995 | 1996 | 1997 | 1998 | 1999 | 2000 | 2001 | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 | 2008 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Botswana | 49 | 10 | 7 | 4 | 25 | 3 | ||||||||||||||||||
Ethiopia | 12 | 1 | 4 | 3 | 1 | 1 | 2 | |||||||||||||||||
India | 41 | 4 | 5 | 2 | 23 | 4 | 2 | 1 | ||||||||||||||||
Israel | 22 | 1 | 4 | 17 | ||||||||||||||||||||
Malawi | 11 | 1 | 3 | 7 | ||||||||||||||||||||
South Africa | 431 | 3 | 17 | 27 | 72 | 73 | 22 | 111 | 79 | 24 | 3 | |||||||||||||
Tanzania | 18 | 2 | 11 | 5 | ||||||||||||||||||||
Zambia | 30 | 1 | 1 | 6 | 11 | 8 | 3 | |||||||||||||||||
Others: | 39 | 1 | 2 | 2 | 1 | 5 | 0 | 4 | 6 | 2 | 2 | 5 | 2 | 5 | 1 | 1 | ||||||||
Total: | 653 | 1 | 0 | 5 | 1 | 2 | 2 | 1 | 5 | 5 | 0 | 14 | 4 | 34 | 58 | 131 | 111 | 39 | 117 | 84 | 26 | 8 | 4 | 1 |
4. Conclusions
Acknowledgments
References
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Novitsky, V.; Wang, R.; Lagakos, S.; Essex, M. HIV-1 Subtype C Phylodynamics in the Global Epidemic. Viruses 2010, 2, 33-54. https://doi.org/10.3390/v2010033
Novitsky V, Wang R, Lagakos S, Essex M. HIV-1 Subtype C Phylodynamics in the Global Epidemic. Viruses. 2010; 2(1):33-54. https://doi.org/10.3390/v2010033
Chicago/Turabian StyleNovitsky, Vlad, Rui Wang, Stephen Lagakos, and Max Essex. 2010. "HIV-1 Subtype C Phylodynamics in the Global Epidemic" Viruses 2, no. 1: 33-54. https://doi.org/10.3390/v2010033