Polymorphisms and Mutational Covariation Associated with Death in a Prospective Cohort of HIV/AIDS Patients Receiving Long-Term ART in China.

BACKGROUND: HIV drug resistance is associated with faster clinical progression of AIDS. However, the effect of significant polymorphisms and mutational covariation on mortality among HIV/AIDS patients receiving long-term antiretroviral therapy (ART), have rarely been studied. METHODS: In this prospective cohort study from December 2003 to December 2014, we present a new computational modelling approach based on bioinformatics-based models and several statistical methods to elucidate the molecular mechanisms involved in the acquisition of polymorphisms and mutations on death in HIV/AIDS patients receiving long-term ART in China. RESULTS: This study involved 654 ART-treated patients, who had been followed for 5473.4 person-years, a median of 9.8 years, and 178 died (25.2%, 3.3/100 person-years). The first regimens included AZT/d4T + NVP+ ddI (78.9%) or AZT/d4T + NVP+ 3TC (20.0%). We calculated an individual Ka/Ks value for each specific amino acid mutation. Result showed that 20 polymorphisms (E6D, Q18H, E35D, S37N, T39A, K43E, S68N, L74I, I93L, K103N, V106A, E169D, Y181C, G190A, Q197K, T200V, T200E, T215I, E224D and P225H) were strongly associated with AIDS related deaths. Among them, 7 polymorphisms (L74I, K103N, V106A, Y181C, G190A, T215I and P225H) were known to be drug resistance mutations, 7 polymorphisms (E6D, E35D, S37N, I93L, E169D, T200V and T200E were considered to be potential drug resistance mutations, and 6 polymorphisms (T39A, K43E, S68N, Q197K, T200V and E224D) were newly found to have an association with drug resistance mutations, which formed a complex network of relationships. CONCLUSIONS: Some polymorphisms and mutational covariation may be the important influencing factors in the failure of treatment. Understanding these mechanisms is essential for the development of new therapies, designing optimal drug combinations, and determining effective clinical management of individual patients.

[Detection and analysis of 26 cases of long-term non-progressors who infected HIV in Henan province].

OBJECTIVE: To investigate the progression and drug resistance of long-term non-progressors during three follow-up in Henan province. METHODS: In May 2009, 26 cases of long-term non-progressors were recruited who infected HIV more than 10 years with blood collection and supply routes, did not receive anti-retroviral therapy, CD4(+)T lymphocyte count ≥350/µl and did not show typical symptoms of AIDS from Weishi, Shangcai, and Linying of Henan Province. Continuous follow-up were conducted three times since 2009 every two years with cohort analysis, the epidemiological information of infection routes, infection time and blood were collected, and 78 parts of 10 ml EDTA anticoagulated whole blood were collected. The changes of CD4 (+) T lymphocytes, viral load, and virus gene variety were characterized from 2009 to 2014. In-house methods were used to explore primary drug resistance of long-term non-progressors. Nonparametric Kruskal-Wallis test were used to compare CD4(+) T lymphocyte count and viral load changes during different follow-up times. RESULTS: The average age and infection time of 26 cases were (48.51 ± 6.75) years, (13.42 ± 4.26) years, respectively. Three follow-up times, CD4(+) T lymphocyte count P50 (P25-P75) was 573.5 (487.4-789.8), 499.8 (403.5-635.7), and 418.8 (297.6-537.8)/µl (H=63.99,P<0.001), respectively. And natural logarithm of viral load P50 (P25-P75) were 3.93 (3.43-4.55), 4.29 (3.78-4.75), 4.50 (4.01-4.81) (H=3.19,P=0.355), respectively. Subtype and phylogenetic analysis of HIV showed that prevalent cases were B subtype, accounting for 88.5% (23/26), and three cases showed restructuring changes. Two cases appeared highly resistant of 18 infected patients whose viral load >1 000 copies/ml. CONCLUSION: The CD4(+)T lymphocyte had a declining trend, virus subtype recombinant changes in a few cases, and primary drug resistance was found of long-term non-progressors in Henan province.

Population-based human immunodeficiency virus 1 drug resistance profiles among individuals who experienced virological failure to first-line antiretroviral therapy in Henan, China during 2010-2011.

BACKGROUND: In Henan, China, first-line antiretroviral treatment (ART) was implemented early in a large number of treatment-experienced patients who were more likely to have a drug resistance. Therefore, we investigated the human immunodeficiency virus (HIV)-1 drug resistance profiles among patients in Henan who experienced virological failure to ART. METHOD: A cross-sectional survey was administered in 10 major epidemic cities from May 2010 to October 2011. Adult patients who experienced virological failure (virus load ≥1,000 copies/mL) with >1 year of first-line antiretroviral treatment consented to provide blood for genotype resistance testing. The clinical and demographic data were obtained from the patients' medical records. Logistic regression analysis was performed to determine the factors associated with ≥1 significant drug resistance mutation. RESULTS: We included 3,235 patients with integral information and valid genotypic resistance data. The city, age, CD4 counts, virus load, treatment duration, and World Health Organization stage were associated with drug resistance, and 64.76% of patients acquired drug resistance. The nucleoside reverse transcriptase inhibitor (NRTI), non-(N)NRTI, and protease inhibitor resistance mutations were found in 50.26, 63.12, and 1.30% of subjects, respectively. Thymidine analogue mutations, NNRTI and even multidrug resistance complex were quite common in this patient cohort. CONCLUSION: Multiple and complex patterns of HIV-1 drug resistance mutations were identified among individuals who experienced virological failure to first-line ART in Henan, China during 2010-2011. Therefore, timely virological monitoring, therapy adjustments, and more varieties of drugs and individualized treatment should be immediately considered in this patient population.

[Analysis of HIV-1 drug resistance among 1 922 individuals experiencing virological failure of first-line antiretroviral therapy in Henan province].

OBJECTIVE: To study the condition of HIV-1 drug resistance mutation among failures of first-line antiretroviral therapy in Henan province. METHOD: The sub platform of China's legal infectious disease monitoring information reporting system-HIV/AIDS integrated prevention and control data information management system was used to collect the information of patients experiencing first-line antiretroviral treatment failure (virus load ≥ 1 000 copies/ml) more than one year among nine cities of Henan in 2011. A total of 40 cases with no information and 212 cases with incomplete drug resistance results were deleted, and 1 922 cases were included in this study and genotype resistance testing was carried out. Non-conditional logistic regression analysis was used to analyse the influencing factors of drug resistance mutation. RESULTS: A total of 1 922 cases were included in the analysis. 1 039 cases were males, 833 cases were females, the age was (45.7 ± 12.1) years, 82.73% (1 590) were married, and 87.93% (1 690) were transmitted by blood. 64.20% (1 234) patients acquired drug resistance. Nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI) and protease inhibitor (PI) resistance mutations were found in 62.59% (1 203), 49.74% (956) and 0.94% (18) of subjects, respectively. 42.09% (809) of patients harbored NRTI and NNRTI resistance mutations synchronously. ≥ 1TAM was the most commonly emerged NRTI resistance mutation (41.94% (806)), the prevalences of TAM-1 and TAM-2 were 8.48% (163) and 4.24% (81), respectively. K65R/N and Q151M complex existed in 23 and 4 patients, respectively. K103N/S was the most commonly emerged NNRTI resistance mutation (34.32% (659)). Non-conditional logistic regression analysis showed that, factors associated with high drug resistance were the following: transmitted by mother to child (OR = 9.05, 95% CI: 1.14-72.12), clinical stage was IV (OR = 1.70, 95% CI: 1.09-2.66) and 5-year-treated (OR = 1.59, 95% CI: 1.03-2.47). Factors associated with low drug resistance were the following: 1-year-treated (OR = 0.19, 95% CI: 0.13-0.27). CONCLUSION: Complex patterns of HIV-1 drug resistance mutations were identified among individuals experiencing failure of first-line antiretroviral therapy in Henan province. Factors associated with high drug resistance were lived in Luohe, Shangqiu, Nanyang, Xinyang, transmitted by mother to child, clinical stage was IV, and 5-year-treated.

[Prevalence of hepatitis C virus antibody among newly reported HIV infection cases in Henan, 2012-2014].

OBJECTIVE: To study the prevalence of antibody to hepatitis C virus (anti-HCV) among newly reported HIV infection cases in Henan province, 2012-2014. METHODS: HIV-1 BED incidence test and anti-HCV test were conducted in newly diagnosed HIV infection cases in Henan, which were reported through national AIDS information system between 1 July 2012 and 30 June 2014. RESULTS: The data of 4 267 newly reported HIV-1 infection cases were analyzed, the positive rate of anti-HCV was 13.19% (563/4 267). The anti HCV was highest in those infected with HIV through injection drug use (77.27%), the anti-HCV positive rates in those infected with HIV through blood donation/transfusion, heterosexual contact, homosexual contact and mother-to-child transmission were 15.06%, 15.81%, 3.74% and 8.96%, respectively. Kaifeng (32.04%), Nanyang (14.67%), Shangqiu (25.00%), Zhumadian (25.00%) and Zhoukou (18.86%) were the first five prefectures with the high anti-HCV positive rates. The anti-HCV positive rate in BED positive patients (recent HIV-1 infections) was 7.50% (86/1 146). The multivariate logistic regressions analysis revealed that BED negative, aged >40 years, being farmer, HIV infection though injection drug use and living in in Kaifeng, Nanyang, Shangqiu, Zhumadian and Zhoukou were the risk factors for HCV infection. CONCLUSION: The positive rate of anti-HCV declined between 2012-2014 in newly reported HIV infection cases in Henan, but the positive rate of anti-HCV was high in risk population and in some areas.

[A follow-up study of HIV long-term non-progress populations in Henan province].

OBJECTIVE: To explore the related testing indicators variation of HIV long-term non-progress populations. METHODS: The long-term non-progress populations in some areas of Henan were recruited, and the study was carried out according to different CD4(+)T lymphocytes counts for two groups. The dynamic characteristics of immune status and viral load between LTNP-1group (CD4(+)T lymphocytes ≥ 500/µl, 42 cases) and LTNP-2 group(350/µl ≤ CD4(+)T lymphocytes < 500/µl, 49 cases) from July 2010 to August 2013 were observed. The characteristics of HIV elite controllers during the follow-up were also described. RESULTS: LTNP were recruited, 56% (51 cases) were men, and 44% (40 cases) were women. The study population were aged from 38 to 65 years old. A total of 320 individuals were followed-up, 14 cases were lost, 2 deaths, and 16 cases had received antiretroviral therapy during four years. To analyze the annual changes of CD4(+)T lymphocytes and VL of the group from 2010 to 2013, LTNP-1 group CD4(+)T lymphocytes from 654.0(545.2-809.5) decreased to 494.0(341.0-574.7), and LTNP-2 group decreased from 493.0 (429.5-770.0) to 343.5(253.0-500.8), CD4(+)T lymphocytes decline of over times of two groups in longitudinal analysis (χ(2) = 50.32, P < 0.01; χ(2) = 31.03, P < 0.01). lg (VL) of LTNP-1 group were 3.52 (3.15-4.27), 3.71 (2.70-4.55), 3.86 (3.59-4.55), 3.96 (3.25-4.36), and lg (VL) of TNP-2 group were 4.35 (3.72-4.83), 4.35 (3.97-4.94), 4.71 (3.96-4.95), 5.04(4.78-5.26), respectively (P > 0.05). The same year inter-group comparison found CD4(+)T lymphocytes of LTNP-1 group were higher than LTNP-2 group (Z = 5.23, P < 0.01; Z = 3.06, P < 0.01; Z = 2.51, P < 0.05; Z = 2.47, P < 0.05). VL of LTNP-2 group increased from 4.35(3.97-4.94) to 5.04 (4.78-5.26) during 2011 to 2013, were higher than LTNP-1 group in the same year (Z = 2.28, P < 0.05; Z = 2.58, P < 0.05; Z = 2.76, P < 0.05). 65 cases HCV antibody were positive in 91 individuals, and the HCV antibody positive rate was 76% (32/42), 67% (33/49) between LTNP-1 group and LTNP-2 group. Six elite controllers maintained CD4(+)T lymphocytes ≥ 500/µl, VL<1 000 copies/ml during four years follow-up. CONCLUSION: The long-term non-progress populations in Henan were overall healthy, and VL were relatively stable, there was a decreased trend of CD4 year by year, and HCV co-infection rate was high.

[Epidemiological survey on the hepatitis C virus and its genotyping analysis in Henan province in 2012].

OBJECTIVE: To investigate the prevalence and distribution of hepatitis C virus (HCV) genotypes in Henan province in 2012. METHODS: A total of 32 203 permanent residents (1 to 74 years old) in Henan were recruited using multi-stage random samping method from March to June 2012. All participants were asked to complete a questionnaire to collect demographic information, past medical history and the exposure history of risk factors. A blood sample of 5 ml was collected at the same time. The condition of anti-HCV and HCV RNA was determined through the ELISA test and nested RT-PCR. HCV RNA positive samples were further subject to the nonstructural protein 5 region (NS5B) gene amplification and sequencing. The sequence was amplified for the phylogenetic tree and genetic analysis. The differences of the positive rate of anti-HCV and HCV RNA and the HCV genetic subtype distribution in different respondents'characteristics were analyzed. RESULTS: Among 32 203 subjects, the overall positive rate of anti-HCV and HCV RNA were 0.48% (153/32 203) and 0.24% (78/32 203), in which men were 0.42% (65/15 634), and 0.23% (36/15 634), and women were 0.53% (88/16 569) and 0.25% (42/16 596). The differences between men and women were not statistically significant (χ(2) values were 2.26, 0.18, respectively, both P values > 0.05). The results of NS5B genotyping and molecular evolution analysis showed that there were six subtypes in the 71 HCV RNA positive samples.In those six subtypes, the proportion of genotypes 1b, 6a, 3a, 2a, 3b and 1a were 56.3% (40/71), 19.7% (14/71), 11.3% (8/71), 8.5% (6/71), 2.8% (2/71) and 1.4% (1/71), respectively. The HCV genetic subtypes of infestor were mainly present with two branches of 1b and 6a, and the two subtypes Bootstrap values were 0.95. CONCLUSION: The prevalence of HCV infection was high in Henan. The major HCV genotypes in patients with HCV infection were 1b and 6a.

[A cross-sectional study on the prevalence of HIV drug resistance in patients receiving antiretroviral treatment in Shenqiu county, Henan province].

OBJECTIVE: To understand the prevalence of drug resistance in AIDS patients who had been receiving HAART in a long run, in Shenqiu county, Henan province. METHODS: This cross-sectional study included 120 HIV infected patients who began receiving ART (antiretroviral therapy) in 2003. Viral loads and CD(4)(+) T cells counts were measured, and In-house drug resistance test was performed in VL > 1000 copies/ml patients. RESULTS: 114 cases out of 120 patients had complete viral load data. Among them, 33 cases having viral loads less than 50 copies/ml, and the remaining viral loads showed an average of lg (4.09 ± 1.10) copies/ml. The average of CD(4)(+) T cell counts was (377 ± 218) cells/ml, with 64 (53.3%) cases showing their CD(4)(+) T cell counts higher than 350 cells/ml. In 67 patients, 58 of them showed genotypic resistance, and 40 cases showed reverse transcriptase inhibitors (RTIs) resistance. The ratios of nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs) resistance were 53.4% (31/58) and 67.2% (39/58), respectively. There were no differences of drug resistance ratio in the three treatment programs. The highest drug resistance rates in NRTIs and NNRTIs were zidovudine, lamivudine, nevirapine. However, protease inhibitors (PIs) resistance variants were not found. CONCLUSION: The prevalence of drug-resistant strains seemed to be high in Shenqiu country, Henan province. Long-term follow-up monitoring strategy should be developed to optimize the timely treatment programs.

[Men who have sex with men and its relationship with HIV-1 strains prevailing in the paid blood donors from Zhengzhou city, Henan].

OBJECTIVE: To clarify the genetic characteristics of human immunodeficiency virus (HIV) circulated in the population of men who have sex with men (MSM) in Zhengzhou, Henan and to analyze its relationship with HIV-1 prevailing in the paid blood donors (PBDs). METHODS: Thirty-one MSM who were confirmed as HIV positive individuals in 2010 together with 41 HIV-positive former PBDs were enrolled in the study. Information on related epidemiological characteristics and their plasma were collected. RT-PCR was used to amplify HIV-1 full length gag (1584 bp), pol (3147 bp) genes and partial env gene (C2V3 segment, 558 bp) followed by sequencing on those subjects. Online software available at LosAlamos HIV Database was used to identify the HIV subtypes based on the findings of the sequences. Phylogenetic tree was used to identify the possible relationship of transmission. RESULTS: Fifty-three full length gag, 38 full length pol and 48 partial env (C2V3) genes were collected from 72 participants. Among the 31 HIV(+) MSM individuals, 14 CRF01_AE strains, 5 CRF07_BC strains and 12 subtype B (1 subtype B and 11 B') strains were identified respectively. All of the 41 strains identified from former PBDs were infected by B' strains. The CRF01_AE strains identified in MSM showed a close relationship to those identified from both Hebei and Liaoning provinces. The CRF07_BC strains showed a close relationship with those from Shijiazhuang and Beijing cities. Among the 12 subtype B strains, 8 sequences grouped into 1 cluster with 1 sequence from the former PBDs. Two sequences grouped with 02HNseq4 suggested that B' had been prevailed in the MSM population might come from the former PBDs and were closely related to the strains identified in the MSM population. CONCLUSION: Complicated genetic background and multiple introductions of HIV in the MS population in Zhengzhou, were found. This was also the first report which noticed that the subtype B epidemic among Zhengzhou MSM was mainly originated from the B' among the former PBDs.

[Follow-up study on 84 AIDS patients having received the replaced therapy program for six months in one county of Henan, China].

OBJECTIVE: To analyze the situation of AIDS patients who had received replaced therapy program in Henan province. METHODS: 84 AIDS patients had been enrolled into the national free first-line antiretroviral treatment for more than 5 years and would soon be replaced with another antiretroviral treatment program, were selected to a follow-up program to be carried out six months later. Data on CD4(+) t-lymphocyte count, viral load and genotypic resistance were included in the study. RESULTS: The DDI+AZT+NVP treatment program was used by all the 84 patients at baseline. A replacement by 3TC + AZT + NVP (post first-line) in 31 patients and 3TC + TDF + LPV/r (second-line) in another 53 patients were taken place within a week. All the patients were followed for six months. RESULTS: showed that: all of the 84 patients appeared an amelioration of CD4(+) t-lymphocyte count median from the baseline of 374.00 cell/µl to 406.50 cell/µl (P = 0.005). Those patients who had changed to second-line treatment program also showed an improvement of CD4(+) t-lymphocyte count median from the baseline of 267.00 cell/µl to 365.00 cell/µl (P = 0.015), while patients who were on the post first-line program with their CD4(+) t-lymphocyte count mean did not show significant change as compared to the baseline (P = 0.158) data. All the 84 patients showed a decrease of virus load median from the baseline of 3.61 log(10)copies/ml to 0.00 log(10) copies/ml (P = 0.000). Both of the two types of patients who had been changed to different programs, had a lower virus load median in the end of the follow-up period (for post first-line: P = 0.007; for second-line: P = 0.000). 13 patients kept their viral load more than 1000 copies/ml, including 5 cases bore more than three thymidine analogue mutations (TAMs) a the end of the follow-up program. Another 4 patients had no resistance mutations detected and no significant variation of viral load (less than 3 times) in the pre- or post-surveys. CONCLUSION: AIDS patients who had received long-term first-line antiretroviral treatment program, showed an amelioration six months after changing of the treatment program. Timely and effective testing on drug resistance as well as the strengthening of the follow-up program still seemed to be the link to those patients who were receiving first-line treatment that should not be ignored.

[The primary HIV drug resistance in partial region of Henan province].

OBJECTIVE: To study the prevalence of primary HIV drug resistance in antiretroviral therapy (ART) areas of Henan province. METHODS: A total of 121 drug-naive long-term infected individuals and 154 patients with newly diagnosed from January 2011 to March 2012 were recruited, the questionnaires were surveyed and whole blood were collected to analyze the CD4(+)T cell counts and viral load. In-house method for genotypic resistance test was determined in those with viral load > 1000 copies/ml samples, the differences of demographic characteristics, immunological parameters and primary drug resistance were compared between the two groups. RESULTS: A total of 121 cases of long-term individuals who had infected (12.50 ± 3.21) years were mainly previous paid blood donors, and the age was (46.61 ± 9.32) years old. The infection route of the newly diagnosed were diversity, including blood, sexual transmission and others, the cases were 73, 73, 8, respectively, the confirmatory year was (0.91 ± 0.28) years, and average age was (22.21 ± 3.11) years old. The difference were statistically significant in the route of transmission, age and infection time from demographic analysis of the two groups (P < 0.05). The absolute M(P(25)-P(75)) counts of CD4(+)T lymphocytes of long-term group was 322 (217 - 422) cell/µl, which was lower than the newly diagnosed was 434(308 - 578) cell/µl (P < 0.05), and viral load was 4.0 (2.96 - 4.64) copies/ml, 3.77 (2.94 - 4.53) copies/ml, the difference was not significant (P > 0.05). The prevalence of primary drug resistance in long-term group and newly diagnosed was 5.79% (7/121), 9.09% (14/154), respectively, and the difference was statistically different (P < 0.05), and one PI-resistant strain was found in the newly diagnosed group. CONCLUSION: The primary drug resistant strains in untreated patients were found in Henan province of ART areas, and there was difference in degree of resistance between long-term infected individuals and newly diagnosed.

[Study on the situation of antiretroviral therapy against HIV/AIDS in Henan province based on the CD4+ T cells count and virus load].

OBJECTIVE: To analyze the CD4(+) T cells and virus load in HIV/AIDS affected population and to evaluate the HIV/AIDS antiretroviral therapy programs in Henan province. METHODS: "Henan HIV/AIDS Testing Laboratory Network Database" was used to collect the data on CD4(+) T cells and virus load (VL) value and corresponding information in HIV/AIDS population of Henan in 2009. Cross-sectional studies was used to study the constituent ratio of CD4(+) T cells and virus load value in individuals who had not received antiretroviral-treated (ART) and had joined first-line ART between the year of 2005 to 2008 among HIV/AIDS population of Henan. RESULTS: As to these people living with HIV/AIDS that had not received ART in the first half and the second half year of 2009, the constituent ratio of individuals whose CD4(+) T cells were less than 200 cells/µl both accounted for more than 20% (χ(2) = 2.059, P = 0.151). The constituent ratio of individuals whose CD4(+) T cells were in 200 - 350 cells/µl and more than 350 cells/µl increased from 27.61% to 29.41% (χ(2) = 4.636, P = 0.031) and decreased from 51.49% to 48.60% (χ(2) = 9.767, P = 0.002), respectively. Meanwhile, we saw 34.53% and 19.65% of the patients whose virus load was > 10 000 copy/ml and > 30 000 copy/ml in this population. Patients that joined first-line ART during 2005 - 2008 showed the following results: the longer of the therapy time, the higher constituent ratio of individuals whose CD4(+) T cells were more than 350 cells/µl (χ(2) = 148.689, P < 0.001) and the lower constituent ratio of individuals of whose CD4(+) T cells were less than 200 cells/µl (χ(2) = 46.686, P < 0.001). Simultaneously, the lower constituent ratio of individuals whose viral load was less than 500 copy/ml (χ(2) = 9.066, P = 0.003) and the higher constituent ratio of individuals whose virus load was more than 10 000 copy/ml (χ(2) = 6.597, P = 0.010). CONCLUSION: Significant curative effect had been achieved in AIDS first-line ART of Henan, but along with the increasing treatment time, the risk of treatment failure also increased. Drug resistance test and changing of treatment protocols were needed. To reach better and more efficient effects on therapy, factors as more detections and investments on ART, expanding the scope of treatment etc. were needed on those people living with HIV/AIDS that had not received ART.