Analysis Of The Distribution Of HIV-1 Subtype And The Prediction Of Coreceptor Among MSM In Guangzhou

ObjectiveTo understand the dynamic distribution of HIV-1 subtypes among MSM in Guangzhou from 2008 to 2012, and to explore if new CRFs and URFs emerged in the research objects. To analysis the mutations of HIV-1 envelop V3 Loop in the target population, and predict the coreceptor of HIV-1 among MSM in Guangzhou. MethodsViral RNA was extracted from 986 positive serum samples among HIV-1 infected MSM population in Guangzhou from 2008 to 2012. The gag gene region and env gene region were amplified by Nested-PCR and were sequenced and analyzed. After two rounds of PCR amplification, the products of the second round PCR are purified and sequenced by sequencing company according to results of agarose gel electrophoresis.To edite and analysis gene sequence in Chromas software, and use the MEGA6.0 software for alignment and calibration according to the gene sequence of gag zone and env zone. Using the method（Neighbor Joining） to construct the phylogenetic tree. The analysis results of subtypes under considering the gag gene region and env region. Geno2pheno[coreceptor]2.5 tool is used to predict HIV-1 coreceptor. Using chi–test to make a statistical inference according to the characteristics of demography by SPSS17.0 software. Resulsts1. Most HIV-1 infected MSM’age in Guangzhou is between 20 to 39 years old, accounted for more than eighty percent. Most of them are unmarried, accounted for more than thirty-nine percent. Most of them are college educated, accounted for more than twenty percent.2. The distribution of the HIV-1 subtypes: From 2008 to 2012 among MSM in Guangzhou area, there are B, A, F1, CRF01_AE, CRF07_BC, CRF59₀1B, CRF54₀1B. CRF01_AE and CRF07_BC are the most typical variants, the second is B subtype. But the proportion of B subtype is decreased and the proportion of URF is increased from 2008 to 2012.3. The analysis of V3 loop amino acid sequence revealed that CRF01_AE had six types of V3 loop central motif: GPGQ（88.1%）, GPGR（7.3%）, GPGK（3.4%）, GPGA（0.2%）, GPGS（0.7%）, GPGM（0.2%）, mosts are GPGQ. B subtype had 13 kinds of V3 loop central motif, as GPGR 、 GPGS 、 GWGR 、 APGR 、 AGGR, et al. Most CRF07_BC have GPGQ（99.4%）, GPGR（0.3%）, GPAQ（0.3%）. CRF59₀1B type exists only in 5 cases of GPGR（45.5%） and 6 cases of GPGK（54.5%）. 1 CRF54₀1B has GPGQ.4. In the 861 samples, about 65.5% strains using CCR5 as coreceptor, and 34.5% using CXCR4 or CCR5/CXCR4 as coreceptor coreceptor. 64.7% CRF01_AE virus using CXCR4 or CCR5/CXCR4 as a coreceptor, 85.7% CRF07_BC virus and 99% B subtype using CCR5 as coreceptor. Only one case of CRF54₀1B is predicted for CXCR4, 72.7% CRF59₀1B are predicted for CCR5, 78% URF using CCR5 as a coreceptor. Conclusion1. Most HIV-1 infected MSM’ average age in Guangzhou is about 30 years old, within the age group 20 to 39, a large number of them are young adults. And they regularly have a higher cultural level.2. From 2008 to 2012 among MSM in Guangzhou area, there are many HIV-1 subtypes, including B, A, F1, CRF01_AE, CRF07_BC, CRF59₀1B, CRF54₀1B. CRF01_AE and CRF07_BC are the most typical variants, the second is B subtype. But the proportion of B subtype is decreased and the proportion of URF is increased from 2008 to 2012. In recent years, two new epidemic strains emerged in MSM, as CRF59₀1B and CRF54₀1B.3. CRF01_AE had six types of V3 loop central motif: GPGQ, GPGR, GPGK, GPGA, GPGS, GPGM, mosts are GPGQ. B subtype had 13 kinds of V3 loop central motif, B has a more significant variation than CRF01_AE in the V3 loop central motif. Most CRF07_BC have GPGQ, showing a higher conservatism. CRF59₀1B only have 5 cases of GPGR and 6 cases of GPGK.4. In the research samples, there are 65.5% strains may use CCR5 as a co receptor, and these are NSI viruses. About 34.5% viruses are predicted for the CXCR4 or CCR5/CXCR4 coreceptor. Different auxiliary receptor in HIV-1 subtype showed different features.