Table S2. List of Pol Sequences

Taxon Accession number Seq Length
1 A1.TZ.01.A341_AY253314 AY253314 1003
2 A1.KE.00.KER2008_AF457052 AF457052 1003
3 A1.KE.00.KER2009_AF457053 AF457053 1003
4 A1.KE.00.KER2012_AF457055 AF457055 1003
5 A1.KE.00.KNH1144_AF457066 AF457066 1003
6 A1.KE.00.KNH1199_AF457067 AF457067 1003
7 A1.KE.00.KNH1207_AF457068 AF457068 1000
8 A1.KE.00.KNH1209_AF457069 AF457069 1003
9 A1.KE.00.KNH1211_AF457070 AF457070 1003
10 A1.KE.00.KSM4024_AF457077 AF457077 1003
11 A1.KE.00.KSM4030_AF457079 AF457079 1003
12 A1.KE.00.MSA4069_AF457080 AF457080 1003
13 A1.KE.00.MSA4070_AF457081 AF457081 1003
14 A1.KE.00.MSA4072_AF457083 AF457083 1002
15 A1.KE.00.MSA4076_AF457084 AF457084 1000
16 A1.KE.00.MSA4079_AF457086 AF457086 1003
17 A1.KE.00.NKU3005_AF457089 AF457089 1003
18 A1.KE.86.ML013_10_AY322184 AY322184 1003
19 A1.KE.86.ML170_1986_AF539405 AF539405 1003
20 A1.KE.94.Q23_17_AF004885 AF004885 1003
21 A1.KE.97.ML013_2_AY322185 AY322185 1003
22 A1.KE.97.ML605_3_AY322190 AY322190 1003
23 A1.KE.97.ML752_AY322193 AY322193 1003
24 A1.KE.99.KNH1088_AF457063 AF457063 1003
25 A1.KE.99.KNH1135_AF457065 AF457065 1001
26 A1.KE.99.KSM4021_AF457075 AF457075 1003
27 A1.SE.94.SE7253_AF069670 AF069670 1003
28 A1.SE.94.SE7535_AF069671 AF069671 1001
29 A1.SE.95.SE8538_AF069669 AF069669 1003
30 A1.SE.95.SE8891_AF069673 AF069673 251
31 A1.SE.95.UGSE8131_AF107771 AF107771 997
32 A.SN.01.DDI579_AY521629 AY521629 1002
33 A.SN.01.DDJ369_AY521631 AY521631 1002
34 A.SN.96.DDJ360_AY521630 AY521630 1002
35 A1.TZ.01.A173_AY253305 AY253305 1003
36 A1.TZ.01.A195_AY253306 AY253306 1003
37 A1.TZ.97.97TZ02_AF361872 AF361872 1003
38 A1.TZ.97.97TZ03_AF361873 AF361873 473
39 A1.UA.00.98UA0116_AF413987 AF413987 1003
40 A1.UG.92.UG029_AB098333 AB098333 1003
41 A1.UG.x.UG031_AB098331 AB098331 1003
42 A1.UG.85.U455_M62320 M62320 1002
43 A1.UG.92.92UG037_U51190 U51190 565
44 A1.UG.98.98UG57134_AF484507 AF484507 844
45 A1.UG.98.98UG57135_AF484508 AF484508 1005
46 A1.UG.98.98UG57136_AF484509 AF484509 1003
47 A1.UG.98.98UG57142_AF484512 AF484512 1003
48 A1.UG.99.99UGA07072_AF484478 AF484478 1003
49 A1.UG.99.99UGG03379_AF484493 AF484493 1003
50 A1.UZ.02.02UZ0659_AY829209 AY829209 1003
51 A1.UZ.02.02UZ0663_AY829210 AY829210 351
52 A2.CD.97.97CDKFE4_AF286240 AF286240 995
53 A2.CD.97.97CDKTB48_AF286238 AF286238 997
54 A2.CY.94.94CY017_41_AF286237 AF286237 1003
55 B.GB.x.MANC_U23487 U23487 1003
56 B.AR.00.ARMS008_AY037269 AY037269 1003
57 B.AR.98.ARCH054_AY037268 AY037268 1003
58 B.AR.99.ARMA132_AY037282 AY037282 1003
59 B.AU.x.1181_AF538302 AF538302 1005
60 B.AU.x.1182_AF538303 AF538303 1003
61 B.AU.x.C24_AF538304 AF538304 1008
62 B.AU.x.C76_AF538306 AF538306 1003
63 B.AU.x.C92_AF538307 AF538307 1003
64 B.AU.x.VH_AF146728 AF146728 1003
65 B.AU.04.Phcsffull04_AY818644 AY818644 1003
66 B.AU.86.MBC200_AF042100 AF042100 1003
67 B.AU.87.MBC925_AF042101 AF042101 1005
68 B.AU.93.MBC18_AF042102 AF042102 1015
69 B.AU.95.MBCC54_AF042103 AF042103 1003
70 B.AU.96.MBCC98_AF042104 AF042104 1004
71 B.AU.96.MBCD36_AF042105 AF042105 1003
72 B.BO.99.BOL0122_AY037270 AY037270 1004
73 B.CA.99.CAN11FULL_AY779558 AY779558 1003
74 B.CA.00.CANA6FULL_AY779552 AY779552 1003
75 B.CA.97.CANB3FULL_AY779553 AY779553 1006
76 B.CA.98.CANB4FULL_AY779554 AY779554 1006
77 B.CA.98.CANB5FULL_AY779555 AY779555 1006
78 B.CA.99.CANB6FULL_AY779556 AY779556 1003
79 B.CA.92.CANC2FULL_AY779559 AY779559 1003
80 B.CA.94.CANC3FULL_AY779560 AY779560 1003
81 B.CA.92.CANC5FULL_AY779561 AY779561 1003
82 B.CA.93.CANC6FULL_AY779562 AY779562 1003
83 B.CA.96.CANC8FULL_AY779563 AY779563 1003
84 B.CN.x.CNHN24_AY180905 AY180905 1003
85 B.CN.x.RL42_U71182 U71182 1003
86 B.CN.02.02HNsc11_AY275556 AY275556 1003
87 B.CN.02.02HNsmx2_AY275557 AY275557 996
88 B.CN.02.02HNsq4_AY275555 AY275555 1003
89 B.CO.01.PCM023_AY561242 AY561242 1003
90 B.CO.01.PCM031_AY561244 AY561244 1002
91 B.CO.01.PCM001_AY561236 AY561236 1003
92 B.CO.01.PCM013_AY561237 AY561237 1007
93 B.CO.01.PCM034_AY561238 AY561238 1004
94 B.CO.01.PCM039_AY561239 AY561239 1011
95 B.CO.01.PCM074_AY561240 AY561240 565
96 B.DE.86.D31_U43096 U43096 1003
97 B.DE.86.HAN_U43141 U43141 1002
98 B.EC.89.EC003_AY173959 AY173959 1007
99 B.EC.89.EC102_AY173960 AY173960 1009
100 B.FR.83.HXB2_LAI_IIIB_BRU_K03455 K03455 1003
101 B.GA.88.OYI_M26727 M26727 1003
102 B.GB.83.CAM1_D10112 D10112 1003
103 B.GB.86.GB8_AJ271445 AJ271445 1009
104 B.KR.97.WK_AF224507 AF224507 846
105 B.MM.99.mSTD101_AB097870 AB097870 1004
106 B.NL.00.671_00T162_AY423383 AY423383 1013
107 B.NL.86.3202A21_U34604 U34604 1003
108 B.RU.04.04RU129005_AY751406 AY751406 1009
109 B.RU.04.04RU139089_AY751407 AY751407 1003
110 B.RU.04.04RU139095_AY819715 AY819715 1002
111 B.RU.04.04RU128005_AY682547 AY682547 1003
112 B.TH.90.BK132_AY173951 AY173951 1003
113 B.TW.94.TWCYS_AF086817 AF086817 1003
114 B.US.x.NL43E9_AF070521 AF070521 1003
115 B.CA.96.WC10C_10_AY314061 AY314061 1003
116 B.US.01.Ac_06_AY268493 AY268493 1003
117 B.US.83.RF_M17451 M17451 1002
118 B.US.83.SF2_K02007 K02007 1003
119 B.US.84.MNCG_M17449 M17449 564
120 B.US.84.SF33_AY352275 AY352275 1006
121 B.US.86.AD87_AF004394 AF004394 1003
122 B.US.86.JRCSF_M38429 M38429 1007
123 B.US.86.JRFL_U63632 U63632 1003
124 B.US.86.YU_2_M93258 M93258 1003
125 B.US.87.BC_L02317 L02317 1003
126 B.US.88.WR27_AF286365 AF286365 1003
127 B.US.89.P896_U39362 U39362 1003
128 B.US.90.US1_AY173952 AY173952 1003
129 B.US.90.US2_AY173953 AY173953 1003
130 B.US.90.US3_AY173954 AY173954 1003
131 B.US.90.US4_AY173955 AY173955 1002
132 B.US.90.WEAU160_U21135 U21135 1003
133 B.US.91.DH12_3_AF069140 AF069140 1001
134 B.US.95.P2C995_AF156844 AF156844 1001
135 B.US.96.1027_03_AY332237 AY332237 1004
136 B.US.96.1057_01_AY331292 AY331292 1007
137 B.US.96.1299_d22_AY308761 AY308761 1003
138 B.US.97.1001_07_AY331282 AY331282 1003
139 B.US.97.1006_08_AY331284 AY331284 1003
140 B.US.97.1012_08_AY331285 AY331285 997
141 B.US.97.1013_03_AY331287 AY331287 1003
142 B.US.97.1018_06_AY331289 AY331289 1003
143 B.US.97.ARES2_AB078005 AB078005 1002
144 B.US.97.Ac_06_AY247251 AY247251 1004
145 B.US.97.PT4_5_97_AF156850 AF156850 1006
146 B.US.98.1058_08_AY331294 AY331294 1000
147 B.US.98.98USHVTN1925c1_AY560107 AY560107 1003
148 B.US.98.98USHVTN3605c9_AY560108 AY560108 1003
149 B.US.98.98USHVTN8229c6_AY560109 AY560109 1003
150 B.US.98.98USHVTN941c1_AY560110 AY560110 1003
151 B.US.99.PRB959_03_AY331296 AY331296 1003
152 C.AR.01.ARG4006_AY563170 AY563170 999
153 C.BR.04.04BR013_AY727522 AY727522 1008
154 C.BR.04.04BR021_AY727523 AY727523 999
155 C.BR.04.04BR038_AY727524 AY727524 1006
156 C.BR.04.04BR073_AY727525 AY727525 1002
157 C.BR.04.04BR137_AY727526 AY727526 1010
158 C.BR.04.04BR142_AY727527 AY727527 1010
159 C.BR.92.BR025_d_U52953 U52953 238
160 C.BR.98.98BR004_AF286228 AF286228 999
161 C.BW.00.00BW07621_AF443088 AF443088 999
162 C.BW.00.00BW076820_AF443089 AF443089 1000
163 C.BW.00.00BW087421_AF443090 AF443090 1011
164 C.BW.00.00BW147127_AF443091 AF443091 560
165 C.BW.00.00BW16162_AF443092 AF443092 1007
166 C.BW.00.00BW1686_AF443093 AF443093 1000
167 C.BW.00.00BW17593_AF443094 AF443094 1000
168 C.BW.00.00BW17732_AF443095 AF443095 999
169 C.BW.00.00BW17835_AF443096 AF443096 1006
170 C.BW.00.00BW17956_AF443097 AF443097 1000
171 C.BW.00.00BW18113_AF443098 AF443098 408
172 C.BW.00.00BW18595_AF443099 AF443099 999
173 C.BW.00.00BW18802_AF443100 AF443100 999
174 C.BW.00.00BW192113_AF443101 AF443101 999
175 C.BW.00.00BW20361_AF443102 AF443102 1003
176 C.BW.00.00BW20636_AF443103 AF443103 997
177 C.BW.00.00BW20872_AF443104 AF443104 1007
178 C.BW.00.00BW2127214_AF443105 AF443105 1006
179 C.BW.00.00BW21283_AF443106 AF443106 1010
180 C.BW.00.00BW22767_AF443107 AF443107 1005
181 C.BW.00.00BW38193_AF443108 AF443108 1002
182 C.BW.00.00BW38428_AF443109 AF443109 1009
183 C.BW.00.00BW38713_AF443110 AF443110 999
184 C.BW.00.00BW3876_9_AF443111 AF443111 999
185 C.BW.00.00BW3886_8_AF443112 AF443112 1006
186 C.BW.00.00BW3891_6_AF443113 AF443113 487
187 C.BW.00.00BW3970_2_AF443114 AF443114 999
188 C.BW.00.00BW5031_1_AF443115 AF443115 1005
189 C.BW.96.96BW01B03_AF110959 AF110959 999
190 C.BW.96.96BW0402_AF110962 AF110962 999
191 C.BW.96.96BW0502_AF110967 AF110967 1009
192 C.BW.96.96BW1104_AF110969 AF110969 997
193 C.BW.96.96BW1210_AF110972 AF110972 1000
194 C.BW.96.96BW15B03_AF110973 AF110973 1000
195 C.BW.96.96BW1626_AF110978 AF110978 999
196 C.BW.96.96BW17_AF110979 AF110979 1000
197 C.BW.96.96BWM032_AF443075 AF443075 1001
198 C.BW.96.96BWMO1_5_AF443074 AF443074 1002
199 C.BW.98.98BWMC122_AF443076 AF443076 999
200 C.BW.98.98BWMC134_AF443077 AF443077 998
201 C.BW.98.98BWMC14A3_AF443078 AF443078 999
202 C.BW.98.98BWMO1410_AF443079 AF443079 1007
203 C.BW.98.98BWMO18D5_AF443080 AF443080 1008
204 C.BW.98.98BWMO36A5_AF443081 AF443081 1006
205 C.BW.98.98BWMO37D5_AF443082 AF443082 1000
206 C.BW.99.99BW393212_AF443083 AF443083 1011
207 C.BW.99.99BW46424_AF443084 AF443084 999
208 C.BW.99.99BW4745_AF443085 AF443085 1005
209 C.BW.99.99BW47547_AF443086 AF443086 999
210 C.BW.99.99BWMC168_AF443087 AF443087 1005
211 C.ET.86.ETH2220_U46016 U46016 1010
212 C.IL.99.99ET14_AY255825 AY255825 1003
213 C.IL.99.99ET17_AY255826 AY255826 1003
214 C.IL.99.99ET1_AY255823 AY255823 1003
215 C.IL.99.99ET7_AY255824 AY255824 999
216 C.IL.98.98IS002_AF286233 AF286233 1004
217 C.IN.93.93IN101_AB023804 AB023804 999
218 C.IN.93.93IN904_AF067157 AF067157 999
219 C.IN.93.93IN9999_AF067154 AF067154 1008
220 C.IN.94.94IN11246_AF067159 AF067159 999
221 C.IN.94.94IN476_AF286223 AF286223 1000
222 C.IN.98.98IN012_AF286231 AF286231 999
223 C.IN.98.98IN022_AF286232 AF286232 1002
224 C.IN.99.01IN565_10_AY049708 AY049708 999
225 C.KE.00.KER2010_AF457054 AF457054 999
226 C.MM.99.mIDU101_3_AB097871 AB097871 999
227 C.TZ.01.A125_AY253304 AY253304 1000
228 C.TZ.01.A207_AY253307 AY253307 999
229 C.TZ.01.A246_AY253308 AY253308 1009
230 C.TZ.01.A260_AY253310 AY253310 1000
231 C.TZ.01.A301_AY253312 AY253312 998
232 C.TZ.01.A388_AY253317 AY253317 1004
233 C.TZ.01.A93_AY253303 AY253303 1006
234 C.TZ.01.BD16_10_AY253320 AY253320 998
235 C.TZ.01.BD22_11_AY253321 AY253321 1000
236 C.TZ.01.BD39_8_AY253313 AY253313 1000
237 C.TZ.01.BD9_11_AY253322 AY253322 1006
238 C.TZ.97.97TZ04_AF361874 AF361874 1005
239 C.TZ.97.97TZ05_AF361875 AF361875 1005
240 C.TZ.98.98TZ013_AF286234 AF286234 816
241 C.TZ.98.98TZ017_AF286235 AF286235 1006
242 C.UY.01.TRA3011_AY563169 AY563169 999
243 C.ZA.00.1134MB_AY463217 AY463217 999
244 C.ZA.00.1162MB_AY463224 AY463224 999
245 C.ZA.00.1165MB_AY463230 AY463230 1000
246 C.ZA.00.1168MB_AY463231 AY463231 1005
247 C.ZA.00.1170MB_AY463225 AY463225 999
248 C.ZA.00.1171MB_AY463232 AY463232 1000
249 C.ZA.00.1176MB_AY463218 AY463218 999
250 C.ZA.00.1178MB_AY463233 AY463233 999
251 C.ZA.00.1192M3M_AY463219 AY463219 1000
252 C.ZA.00.1195MB_AY463220 AY463220 999
253 C.ZA.00.1197MB_AY463234 AY463234 999
254 C.ZA.00.1210MB_AY463221 AY463221 999
255 C.ZA.00.1214MB_AY463236 AY463236 999
256 C.ZA.00.1217MB_AY463226 AY463226 999
257 C.ZA.00.1225MB_AY463227 AY463227 999
258 C.ZA.00.1228MB_AY463222 AY463222 999
259 C.ZA.00.1157M3M_AY585266 AY585266 999
260 C.ZA.00.J38MA_AY463228 AY463228 1013
261 C.ZA.01.01ZATM45_AY228557 AY228557 1006
262 C.ZA.01.2134MB_AY463237 AY463237 999
263 C.ZA.01.J54Ma_AY463223 AY463223 999
264 C.ZA.03.SK023B2_AY772690 AY772690 1000
265 C.ZA.03.SK029B2_AY772691 AY772691 997
266 C.ZA.03.SK033B2_AY772692 AY772692 999
267 C.ZA.03.SK040B1_AY703908 AY703908 1004
268 C.ZA.03.SK041B1_AY772693 AY772693 1004
269 C.ZA.03.SK043B1_AY772700 AY772700 1011
270 C.ZA.03.SK065B1_AY772694 AY772694 1011
271 C.ZA.03.SK112B1_AY772695 AY772695 1005
272 C.ZA.03.SK116B1_AY772696 AY772696 999
273 C.ZA.04.SK134B1_AY703909 AY703909 1004
274 C.ZA.04.SK143B1_AY703910 AY703910 914
275 C.ZA.04.SK144B1_AY703911 AY703911 999
276 C.ZA.04.SK164B1_AY772699 AY772699 999
277 C.ZA.97.97ZA003_AY118165 AY118165 999
278 C.ZA.97.97ZA009_AY118166 AY118166 1012
279 C.ZA.97.97ZA012_AF286227 AF286227 1001
280 C.ZA.98.98ZA445_AY158533 AY158533 1000
281 C.ZA.98.98ZA502_AY158534 AY158534 1000
282 C.ZA.98.98ZA528_AY158535 AY158535 1005
283 C.ZA.98.TV001_AY162223 AY162223 1005
284 C.ZA.98.TV002_AY162224 AY162224 1003
285 C.ZA.98.TV012_AY162225 AY162225 994
286 C.ZA.00.1119MB_AY463229 AY463229 999
287 C.ZA.99.99ZACM9_AF411967 AF411967 1000
288 C.ZA.99.99ZATM10_AY228556 AY228556 1005
289 C.ZA.98.CTSC2_AY043176 AY043176 979
290 C.ZA.99.DU151_AY043173 AY043173 999
291 C.ZA.99.DU179_AY043174 AY043174 999
292 C.ZA.99.DU422_AY043175 AY043175 1000
293 C.ZA.99.ZASW7_AF411966 AF411966 1006
294 C.ZM.x.HIV1084i_AY805330 AY805330 999
295 C.ZM.96.96ZM651_AF286224 AF286224 999
296 C.ZM.96.96ZM751_AF286225 AF286225 1005
297 CD.BW.00.00BWMO351_AY074891 AY074891 993
298 CD.KE.00.MSA4077_AF457085 AF457085 1000
299 CD.KE.97.ML249_AY322187 AY322187 1002
300 CD.TZ.01.A247_AY253309 AY253309 1000
301 CD.TZ.97.97TZ07_AF361877 AF361877 1002
302 CD.UG.99.99UGK10192_AF484500 AF484500 1002
303 D.CD.83.ELI_K03454 K03454 1002
304 D.CD.83.NDK_M27323 M27323 1002
305 D.CD.84.84ZR085_U88822 U88822 1004
306 D.CD.85.Z2Z6_M22639 M22639 1002
307 D.CM.01.01CM_0009BBY_AY371155 AY371155 1004
308 D.CM.01.01CM_0175BA_AY371156 AY371156 1004
309 D.CM.01.01CM_4412HAL_AY371157 AY371157 1004
310 D.KE.97.ML415_2_AY322189 AY322189 1002
311 D.KE.01.NKU3006_AF457090 AF457090 1003
312 D.TD.99.MN011_AJ488926 AJ488926 1004
313 D.TD.99.MN012_AJ488927 AJ488927 713
314 D.TZ.01.A280_AY253311 AY253311 1004
315 D.UG.92.92UG001_AJ320484 AJ320484 1002
316 D.UG.94.94UG114_U88824 U88824 1004
317 D.UG.98.98UG57128_AF484502 AF484502 1002
318 D.UG.98.98UG57131_AF484505 AF484505 1002
319 D.UG.98.98UG57132_AF484506 AF484506 1002
320 D.UG.98.98UG57140_AF484511 AF484511 1002
321 D.UG.98.98UG57143_AF484514 AF484514 1002
322 D.UG.98.98UG57146_AF484513 AF484513 1001
323 D.UG.98.99UGJ32228_AF484516 AF484516 1002
324 D.UG.99.99UGA03349_AF484518 AF484518 1001
325 D.UG.99.99UGA07412_AF484477 AF484477 1002
326 D.UG.99.99UGA08483_AY304496 AY304496 1002
327 D.UG.99.99UGB21875_AF484480 AF484480 1003
328 D.UG.99.99UGB25647_AF484481 AF484481 1002
329 D.UG.99.99UGB32394_AF484483 AF484483 1002
330 D.UG.99.99UGD23550_AF484485 AF484485 1002
331 D.UG.99.99UGD26830_AF484486 AF484486 1007
332 D.UG.99.99UGE08364_AF484487 AF484487 1002
333 D.UG.99.99UGE13613_AF484515 AF484515 1002
334 D.UG.99.99UGE23438_AF484489 AF484489 1002
335 D.UG.99.99UGF03726_AF484519 AF484519 1003
336 D.UG.99.99UGF05734_AF484490 AF484490 1002
337 D.UG.99.99UGG10555_AF484494 AF484494 1002
338 D.UG.99.99UGG35093_AF484495 AF484495 1002
339 D.UG.99.99UGJ27597_AF484497 AF484497 1002
340 D.UG.99.99UGK09259_AF484498 AF484498 1002
341 D.UG.99.99UGK09958_AF484499 AF484499 1002
342 D.ZA.84.R2_AY773338 AY773338 1003
343 D.ZA.85.R214_AY773339 AY773339 998
344 D.ZA.85.R286_AY773340 AY773340 1001
345 D.ZA.86.R482_AY773341 AY773341 1002
346 F1.BE.93.VI850_AF077336 AF077336 1004
347 F1.BR.89.BZ126_AY173957 AY173957 1003
348 F1.BR.93.93BR020_1_AF005494 AF005494 1003
349 F1.FR.96.MP411_AJ249238 AJ249238 1005
350 F2.CM.02.02CM_0016BBY_AY371158 AY371158 1003
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