Table S1. Social-demographic characteristics of HIV-1 infected IDUs in Northern Myanmar. Variable (n=83) (%)

Transcription

1 Table S1. Social-demographic characteristics of HIV-1 infected IDUs in Northern Myanmar. Variable (n=83) Count (%) HIV-1 recombinants (Prevalence, %) Location Maizayang town 31(37.3) 25(80.6) Laza city 52(62.7) 43(82.7) Marital status Unmarried 46(55.4) 38(82.6) Married 25 (30.1) 19(76) Divorced 12 (14.5) 11(91.7) Education level 0 year 9(10.8) 6(66.7) Elementary 34(41.0) 27(79.4) Junior high 17(20.5) 15(88.2) Senior high 11(13.3) 10(90.9) College 12(14.5) 10(83.3) Age (years old) (2.4) 1(50) (51.8) 40(90.9) (36.1) 22(73.3) (7.2) 4(66.7) (2.4) 2() Age at first injection (years old) (14.5) 10(83.3) (57.8) 41(85.4) (24.1) 14(70) (1.2) 1() (2.4) 2() Nationality Han 19(22.9) 15(78.9) Dai 8(9.6) 6(75) Lahujingpo 40(48.2) 32(80) Bammar 9(10.8) 9() Sam myan 2(2.4) 2() Lili 1(1.2) 1() Hui 1(1.2) 1() Other 3(3.6) 1(33.3) Occupation Farmer 35(42.2) 27(77.1) Entertainment 2(2.4) 1(50) Businessman 6(7.2) 6() Soldier 1(1.2) 1() Worker 8(9.6) 7(87.5) Casual worker 15(18.1) 14(93.3) Unemployment 11(13.3) 9(81.8) Civil servant 2(2.4) 1(50) Driver 2(2.4) 1(50) Other 1(1.2) 1() RF: recombination forms

2 Table S2. Information of the primer pairs used in this study. Genomic fragments Reactions Primer Sequence (5-3 ) Location in pnl4.3 (nt) P17 1 st PCR Forward PBS-172A ATCTCTAGCAGTGGCGCCCGAACAG 2-26 Reverse p24-173b CTGATAATGCTGAAAACATGGGTAT nd PCR Forward PSI-174A CTCTCGACGCAGGACTCGGCTTGCT Reverse p17-175b CCCATGCATTCAAAGTTCTAGGTGA C2/V3 1 st PCR Forward ED-5 ATGGGATCAAAGCCTAAAGCCATGTG Reverse ED-12 AGTGCTTCCTGCTGCTCCCAAGAACCCAAG nd PCR Forward ED-31 CCTCAGCCATTACACAGGCCTGTCCAAAG Reverse ED-33 TTACAGTAGAAAAATTCCCCTC Pol 1 st PCR Forward AW26 TGGAAATGTGGAAAGGAAGGAC Reverse RT21 CTGTATTTCTGCTATTAAGTCTTTTGATGGG nd PCR Forward PRO-1 CAGAGCCAACAGCCCCACCA Reverse RT20 CTGCCAGTTCTAGCTCTGCTTC vif-vpr 1 st PCR Forward VIF-362A GGCAGGTGATGATTGTGTGGC Reverse VIF-364B GGCTGACTTCCTGGATGGTTCCAGGGC nd PCR Forward VIF-363A GGATGAGGATTAGAACATGG Reverse VIF-365B GCCTATTCTGCTATGTTGACACCC vpr-env 1 st PCR Forward VIF-368A GCCCCAGAAGACCAAGGGCC Reverse ENV-360B GGGGTCTGTGGGTACACAGGCATGTGT nd PCR Forward VIF-369A GACATTTTCCTAGGCCATGGC Reverse ENV-370B GTGGGTACACAGGCATGTGTGGC

3 Table S3. Summary of primary screening of HIV-1 genotypes in Northern Myanmar. Genomic Size Num Subtypes (%) Recombinants (%) fragments (nt) ber B C CRF01_ CRF07_ Recombinan BC CRF01_AE CRF0 CRF01_AE AE BC ts /B 1_AE /B/C /C P (8.0) 47(62.7) 10(13.3) 0 12(16) 1(8.3) 0 11(91. 7) 0 pol (7.2) 8(11.6) 2(2.9) 0 54(78.3) 50(92.6) 0 1(1.9) 3(5.6) vif-env (4.1) 4(8.2) 4(8.2) 1(1.4) 38(77.6) 22(57.9) (42.1) Env (6.7) 37(61.7) 9(15) 0 10(16.7) 0 0 9(90) 1(10)

4 Figure S1. Phylogenetic tree of p17 fragments (A) and bootscanning plots of some recombinants (B). The recombination was determined using bootscan analyses (SimPlot software). Because some recombinants (i.e. CRF01_AE/C recombinants) shared identical breakpoint, only one representative bootscanning plot is shown. The HIV-1 subtype references used in bootscan analyses are: subtypes A (PS1044 and 92UG037), B (RL42, BK132, 671_00T36, and 1058_11), C (95IN21068, BR025-D, ETH2220, and SK16481), and CRF01_AE (93TH051 and CM240). For other details, please see Fig. 2.

5 Figure S2. Phylogenetic tree of C2V3 fragments of HIV-1 strains isolated from Northern Myanmar. A, phylogenetic tree. B, bootscanning plots of some recombinants. Please see Figs. s. 2 and S1 for other details.

6 Figure S3. Bootscanning plots of pol fragments of HIV-1 intersubtype recombinants from IDUs in Northern Myanmar. For other details, please see Figs. 2 and S1. CRF07_BC CRF08_BC 09mIDU020 (09mIDU033) 09mIDU087 09mIDU082 09mIDU070 09mIDU014 09mIDU031 09mIDU094 09mIDU076 09mIDU039 (09mIDU002) 09mIDU074 09mIDU073 09mIDU045 09mIDU064 09mIDU053 09mIDU005 09mIDU034 (09mIDU088; 09mIDU009) 09mIDU051 09mIDU047 09mIDU041 09mIDU078 09mIDU093 09mIDU035 (09mIDU030; 09mIDU003; 09mIDU027; 09mIDU029; 09mIDU010)

7 Figure S3 (Continued). Bootscanning plots of pol fragments of HIV-1 intersubtype recombinants from IDUs in Northern Myanmar. For other details, please see Figs. 2 and S1. 09mIDU065 09mIDU036 09mIDU044 (09mIDU092) 09mIDU069 09mIDU090 CRF01_AE/B/C recombinants 09mIDU042 09mIDU072 09mIDU007 (09mIDU024) 09mIDU mIDU043 09mIDU008 09mIDU017 (09mIDU016) 09mIDU054 09mIDU032 CRF01_AE/C recombinants 09mIDU052 09mIDU089 09mIDU018 (09mIDU019) 09mIDU015 09mIDU038

8 Figure S4. Bootscanning plots of vif-env fragments of HIV-1 intersubtype recombinants from IDUs in Northern Myanmar. For other details, please see Figs. 2 and S1. CRF07_BC 09mIDU003 (09mIDU030) 09mIDU018 09mIDU084 09mIDU051 09mIDU005 09mIDU043 09mIDU073 09mIDU002 09mIDU057 (09mIDU076) 09mIDU032 09mIDU089 09mIDU082 09mIDU053 09mIDU015 09mIDU095 09mIDU041 09mIDU044 09mIDU048 09mIDU033 09mIDU034 09mIDU092

9 Figure S4 (Continued). Bootscanning plots of vif-env fragments of HIV-1 intersubtype recombinants from IDUs in Northern Myanmar. For other details, please see Figs. 2 and S1. 09mIDU065 (09mIDU031) 09mIDU094 09mIDU036 (09mIDU047 09mIDU054 09mIDU014 09mIDU069) 09mIDU088 09mIDU045 09mIDU078 09mIDU087 09mIDU072 09mIDU090 09mIDU093 09mIDU064

10 Figure S5. Phylogenetic tree of vif-vpr fragments of HIV-1 strains isolated from Northern Myanmar. For other details, please see Figs. 2 and S1. 07 BC.CN.97.97CN001.AF mIDU007 09mIDU BC.CN.05.XJDC EF BC.CN.05.XJDC6441.EF mIDU010 09mIDU mIDU026 B/C recombinant 09mIDU040 C.IN.95.95IN21068.AF mIDU028 09mIDU004 09mIDU BC.CN.97.97CNGX 6F.AY BC.CN.98.98CN006.AF C.ET.86.ETH2220.U46016 C.BR.92.BR025 d.u BC.BR.04.04BR142.AY C.ZA.04.SK164B1.AY B.US AY mIDU B.CN.-.RL42 B B.NL T36.AY B.TH.90.BK132.AY D.TZ.01.A280.AY D.UG.94.94UG114.U88824 H.BE.93.VI991.AF H.CF AF J.SE.93.SE7887.AF J.SE.94.SE7022.AF F2.CM.02.02CM 0016BBY.AY F2.CM.95.MP255.AJ K.CD.97.EQTB11C.AJ K.CM.96.MP535.AJ F1.FI.93.FIN9363.AF F1.FR.96.MP411.AJ A2.CD.97.97CDKTB48.AF A2.CY.94.94CY AF A1.AU.03.PS1044 Day0.DQ A1.UG.92.92UG037.AB G.PT.x.PT2695.AY BG.DE AY G.BE.96.DRCBL.AF B.MY.05.05MYKL007 1.DQ B.MY.05.05MYKL045 1.DQ AE.TH.90.CM240.U AE.TH.93.93TH051.AB B.TH.99.OUR2478P.EF B.TH.99.99TH MU2079.AF B.TH.99.99TH R2399.AF CPZ.CM.05.SIVcpzMT145.DQ C CRF07_BC 0.05

11 Figure S6. Phylogenetic tree of vpr-env fragments of HIV-1 strains isolated from Northern Myanmar. For other details, please see Figs. 2 and S1. CRF07_BC 09mIDU025 09mIDU BC.CN.05.XJDC6441.EF BC.CN.97.97CN001.AF BC.CN.05.XJDC EF mIDU022 B/C recombinant 09mIDU017 B/C recombinant 09mIDU025 B/C recombinant B.US AY B.CN..RL42 B.NL T36.AY B.TH.90.BK132.AY mIDU035 09mIDU086 09mIDU024 CRF01_AE/B recombinants 78 09mIDU037 09mIDU039 B/C recombinant C.BR.92.BR025 d.u BC.BR.04.04BR142.AY C.ET.86.ETH2220.U46016 C.ZA.04.SK164B1.AY mIDU020 09mIDU023 C 84 C.IN.95.95IN21068.AF mIDU BC.CN.97.97CNGX 6F.AY BC.CN.98.98CN006.AF D.TZ.01.A280.AY D.UG.94.94UG114.U88824 J.SE.93.SE7887.AF J.SE.94.SE7022.AF H.BE.93.VI991.AF H.CF AF K.CD.97.EQTB11C.AJ K.CM.96.MP535.AJ F2.CM.02.02CM 0016BBY.AY F2.CM.95.MP255.AJ F1.FI.93.FIN9363.AF F1.FR.96.MP411.AJ G.BE.96.DRCBL.AF G.PT.x.PT2695.AY BG.DE AY A2.CD.97.97CDKTB48.AF A2.CY.94.94CY AF A1.AU.03.PS1044 Day0.DQ A1.UG.92.92UG037.AB mIDU052 CRF01_AE/B/C recombinant B.TH.99.99TH MU2079.AF B.TH.96.M169.DQ B.TH.99.99TH R2399.AF mIDU mIDU058 09mIDU042 CRF01_AE 33 01B.MY.05.05MYKL045 1.DQ B.MY.05.05MYKL007 1.DQ B.TH.99.OUR2478P.EF AE.TH.90.CM240.U AE.TH.93.93TH051.AB CPZ.CM.05.SIVcpzMT145.DQ mIDU035 09mIDU017 09mIDU048 ( 09mIDU024 09mIDU037) 09mIDU mIDU039

12 Figure S7. Phylogenetic tree based on concatenated sequences from 47 HIV-1 strains isolated from Northern Myanmar. The sequences were concatenated in an order of p17, pol, vif-env, and C2V3. For other details, please see Figs. 2 and S1.