Table 2. Characterization of expanded viruses.
| Sample ID | Infection route | Area of collection | HIV-1 subtype | CD4+T-cells (cells/μl) in plasma | VIDAS HIV p24 II (pg/ml) a | Domestic HIV-1 p24 assay(pg/ml) a | NucliSENS EasyQ HIV-1 v2.0(million copies/ml) a | COBAS Taqman v 2.0(million copies/ml) a | Coreceptor predicted by Webpssm | Coreceptor predicted by Geno 2 Pheno (FPR 2.5%) | The top 4 peptides of V3 | Number of glycosylation sites in V3 loop | Drug-resistant mutations |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GX2005002 | Heterosexual sex | Guangxi | CRF01_AE | 43 | 14800 | 6168 | 330 | 252 | X4/R5 | X4/R5 | GPGR | 10 | NRTI: K70KT |
| GX2005016 | Blood transfusion | Guangxi | CRF01_AE | 137 | 345 | 74 | 0.0068 | 1.07 | X4/R5 | X4/R5 | GPGR | 8 | None |
| GX2006183 | Unclear | Guangxi | CRF01_AE | 293 | 680 | 166 | 0.4 | 0.892 | X4/R5 | X4/R5 | GLGH | 11 | None |
| GX2006185 | Heterosexual sex | Guangxi | CRF01_AE | 114 | 371 | 173 | 0.15 | 0.747 | X4/R5 | X4/R5 | GPGH | 9 | None |
| GD2005003 | Blood transfusion | Guangdong | B | 8 | 11900 | 6664 | 1300 | 152 | R5 | X4/R5 | GPGR | 10 | None |
| GD2005004 | Heterosexual sex | Guangdong | CRF01_AE | 3 | 1472 | 498 | 4.3 | 8.15 | X4/R5 | X4/R5 | GPGH | 9 | None |
| GD2005006 | Heterosexual sex | Guangdong | CRF01_AE | 2 | 8630 | 2372 | 170 | 127 | X4/R5 | X4/R5 | GPGQ | 11 | None |
| GD2005025 | intravenous drug using | Guangdong | CRF01_AE | 10 | 622 | 270 | 0.32 | 1.51 | R5 | R5 | GPGQ | 9 | PI: K20KT, D30DE, V32EV, M46MR |
| GD2005028 | Blood transfusion | Guangdong | B | 36 | 86 | 28 | 2.5 | 1.16 | R5 | R5 | GPGR | 10 | PI: V82FIV* |
| SC2009001 | Occupational Exposure | Sichuan | CRF01_AE | 503 | 1390 | 498 | 9 | 10 | X4/R5 | X4/R5 | GPGR | 9 | None |
| SX2010001 | Blood transfusion | Shanxi | B | 76 | 14000 | 5742 | 170 | 203 | R5 | R5 | GPGR | 13 | NRTI: M41L*, M184V*, L210W*, T215Y*, K219KN; NNRTI: K103N*, M230L* |
| SD2010001 | Homosexual sex | Shandong | CRF01_AE | 1187 | 22170 | 7806 | 43 | 173 | R5 | R5 | GPGQ | 10 | None |
| HN2010001 | Blood donation | Henan | B | 265 | 595 | 314 | 8.8 | 4.24 | R5 | R5 | GQGR | 13 | None |
| HN2010002 | Blood donation | Henan | B | 432 | 14100 | 5609 | 130 | 251 | R5 | R5 | GQGR | 11 | PI: A71T |
| BJ2010001 | Homosexual sex | Henan | CRF01_AE | 1179 | 3576 | 909 | 13 | 28 | R5 | R5 | GPGQ | 10 | None |
| HN2010003 | Blood trasfusion | Henan | B | 312 | 7440 | 3766 | 180 | 140 | R5 | R5 | GQGR | 13 | None |
| HN2010004 | Blood donation | Henan | B | 219 | 3370 | 1289 | 32 | 43.9 | R5 | R5 | GPGQ | 13 | INI: L68V |
| BJ2010002 | Homosexual sex | Henan | B | 1187 | 101000 | 92819 | 5100 | 2010 | R5 | R5 | GWGR | 10 | PI: A71T; INI: A128T |
| XJ2010001 | Homosexual sex | Xinjiang | CRF07_BC | 1333 | 18500 | 7331 | 1700 | 1170 | R5 | R5 | GPGQ | 9 | PI: Q58E |
| HN2010005 | Blood donation | Henan | B | 248 | 18900 | 12021 | 860 | 359 | R5 | R5 | GPGR | 9 | None |
| BJ2010003 | Homosexual sex | Henan | CRF07_BC | 1528 | 2630 | 554 | 250 | 101 | R5 | R5 | GPGQ | 12 | INI: H51HQ |
| NX2005012 | Blood transfusion | Ningxia | B | 21 | 237 | 65 | 5.8 | 2.12 | R5 | R5 | GQGR | 11 | INI: L68V |
| SH2007052 | Heterosexual sex | Shanghai | G | ND | 363 | 50 | 0.66 | 0.823 | R5 | R5 | APGQ | 10 | None |
| HN2002024 | Blood trasfusion | Henan | B | ND | 80000 | 128722 | 1700 | 618 | X4/R5 | X4/R5 | GPGR | 10 | PI: I54M*, L23IL, A71V |
| SD2013001 | Homosexual sex | Shandong | CRF01_AE | 197 | 2575 | 1047 | 0.2 | 22.7 | X4/R5 | R5 | GPGQ | 11 | INI: P145PS, S153FS |
| SD2013005 | Homosexual sex | Shandong | CRF07_BC | 715 | 107 | 46 | 14 | 3.11 | R5 | R5 | GPGQ | 10 | None |
| SD2013008 | Homosexual sex | Shandong | CRF01_AE | 486 | 21500 | 11583 | 40 | 254 | X4/R5 | X4/R5 | GPGQ | 8 | None |
| BJ2006001 | Heterosexual sex | Beijing | B | 40 | 1500 | 866 | 4.6 | 2.49 | X4/R5 | X4/R5 | GRGR | 12 | NRTI: M41L*, L210W*, T215F*; NNRTI: A98G, K103N*, V179E*, Y181C*, G190A*; PI: L63P, V77I |
| SD2006001 | Blood trasfusion | Shandong | B | 74 | 1600 | 409 | 5.8 | 2.78 | X4/R5 | X4/R5 | GPGR | 13 | NRTI: M184V*; NNRTI: K103N*; PI: L63P, A71T, V77I, I93L |
| ZJ2006001 | Blood transfusion | Zhejiang | CRF07_BC | 38 | 4060 | 1488 | 9.9 | 17 | Unknown | Unknown | Unknown | Unknown | NRTI: K65R*, T69D, K219R; NNRTI: V106M*, Y181C*; PI: L63P, I93L, L10X |
| IIIB_LAI(Ref) | Unknown | France | B | Unknown | 79000 | 43925 | 2600 | 708 | X4/R5 | X4/R5 | GPGR | 11 | None |
| NL4-3(Ref) | Recombinant | France | B | Unknown | 78000 | 44829 | 2200 | 686 | X4/R5 | X4/R5 | GPGR | 12 | IN: V151I |
ND: Not done, envC2V3 PCR was negative.
a: Samples for p24 antigen tests(VIDAS HIV p24 II and the domestic HIV-1 p24 assay) and viral load tests(NucliSENS EasyQ HIV-1 v2.0 and COBAS Taqman v 2.0) are culture supernatant of the isolates after expansion.
*: NRTI/NNRTI/PI/INI Major drug-resistance mutations. Mutations without “*” are minor resistance mutations, accessory mutations or single nucleotide polymorphisms (SNP).
Ref: Reference virus. IIIB_LAI and NL4-3 are reference virus with clear background information and high replication capacity but are not primary isolates.
The expanded virus was characterized in terms of infection route, area of origin, CD4+T cells concentration in blood sample, viral RNA concentration (Roche TaqMan v2.0 and BioMerieux NucliSENS EasyQ HIV-1 v2.0), p24 concentration (BioMerieux VIDAS HIV p24 II and One domestic HIV-1 p24 antigen assay), coreceptor usage (Webpssm and Geno 2 Pheno (FPR 2.5%)), the four identical residues at the tip of v3 loop, number of glycosylation sites in v3-loop, and drug-resistance mutations in pol.