1.Structural and epitope characterization of HIV-1 V1V2 highly effective neutralizing antibodies based on AlphaFold 3
Junjie ZHANG ; Qianying WANG ; Ying LIU ; Shuhui WANG ; Li REN ; Shuo WANG ; Yutao SHI ; Yuhua RUAN ; Xiaojing LIU ; Xinran DU ; Yanling HAO ; Dan LI
Chinese Journal of Experimental and Clinical Virology 2025;39(5):548-555
Objective:To screen broadly neutralizing antibodies in human immunodeficiency virus-1(HIV-1)chronically infected individuals and characterize their molecular features and to provide new strategies for rational vaccine development and antibody-based therapeutics.Methods:A total of 34 treatment-na?ve individuals with chronic HIV-1 infection were enrolled. Plasma antibody binding levels were measured against two HIV-1 envelope proteins. Single antigen-specific memory B cells were sorted from high-binding samples,and antibody variable region genes were amplified by PCR for paired expression. The monoclonal antibodies were evaluated for neutralizing activity using pseudovirus assays,and their structural features were analyzed by integrating AlphaFold 3 prediction with Discovery Studio molecular docking.Results:Plasma samples showed strong binding to DU422-GP140 and BG505-GP140. Eight monoclonal antibodies were isolated from two donors. Among them,antibodies 0919-A4,0919-A9 and 0808-A2 could cross-react with GP140 from HIV-1 subtypes AE,BC and B. The monoclonal antibody 0919-A9 demonstrated potent neutralizing activity against SF162(Tier 1)and CH181(Tier 2)pseudoviruses,with somatic hypermutation rates of 13.27%(heavy chain)and 15.58%(light chain). Structural modeling revealed its specific targeting of the V1V2 region on GP120.Conclusion:The isolated antibody 0919-A9 effectively neutralizes Tier 2 pseudoviruses. Its high somatic mutation frequency and V1V2-targeting property underlie its neutralizing activity,providing both a promising candidate and mechanistic insights for HIV vaccine development and antibody-based therapeutic strategies.
2.Development and application of dental scenario-based clinical thinking teaching and examination system
Haojue RUAN ; Jingyi ZHANG ; Yuhua LIN ; Jiawei ZHENG
Chinese Journal of Medical Education Research 2025;24(1):115-120
Objective:To explore the application of dental scenario-based clinical thinking teaching and examination system in oral education.Methods:A total of 70 resident physicians from the 2022 class at the dental base of Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine were selected and randomly divided into a control group (30 participants) and an experimental group (40 participants). The control group was taught using traditional teaching methods, and the experimental group was taught and trained using the dental scenario-based clinical thinking teaching and examination system. After one year of teaching, both groups participated in a unified annual assessment. Finally, the teaching effectiveness was evaluated through a questionnaire survey on the experimental group. The questionnaire data were analyzed using the Chi-square test in IBM SPSS 24.0 statistical software, and the t-test was conducted using GraphPad Prism 8.0.2 software. Results:The average score before teaching was (78.83±2.61) in the control group and (78.28±3.29) in the experimental group, with no statistical significant difference between the two groups ( t=0.77, P=0.447). The average score in the annual assessment after teaching was (78.57±3.50) in the control group and (81.75±4.63) in the experimental group, with statistical significant difference between the two groups ( t=3.15, P=0.002). The questionnaire survey indicated that students highly recognized the dental scenario-based clinical thinking teaching and examination system, noting its advantages of innovative and interesting lectures, the ability to improve clinical thinking skills, and not being limited by location or time. Conclusions:The dental scenario-based clinical thinking teaching and examination system can stimulate students' interest and enthusiasm for independent learning. The system has received high levels of acceptance among students. The application and development of the dental scenario-based clinical thinking teaching and examination system hold significant value.
3.Development and application of dental scenario-based clinical thinking teaching and examination system
Haojue RUAN ; Jingyi ZHANG ; Yuhua LIN ; Jiawei ZHENG
Chinese Journal of Medical Education Research 2025;24(1):115-120
Objective:To explore the application of dental scenario-based clinical thinking teaching and examination system in oral education.Methods:A total of 70 resident physicians from the 2022 class at the dental base of Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine were selected and randomly divided into a control group (30 participants) and an experimental group (40 participants). The control group was taught using traditional teaching methods, and the experimental group was taught and trained using the dental scenario-based clinical thinking teaching and examination system. After one year of teaching, both groups participated in a unified annual assessment. Finally, the teaching effectiveness was evaluated through a questionnaire survey on the experimental group. The questionnaire data were analyzed using the Chi-square test in IBM SPSS 24.0 statistical software, and the t-test was conducted using GraphPad Prism 8.0.2 software. Results:The average score before teaching was (78.83±2.61) in the control group and (78.28±3.29) in the experimental group, with no statistical significant difference between the two groups ( t=0.77, P=0.447). The average score in the annual assessment after teaching was (78.57±3.50) in the control group and (81.75±4.63) in the experimental group, with statistical significant difference between the two groups ( t=3.15, P=0.002). The questionnaire survey indicated that students highly recognized the dental scenario-based clinical thinking teaching and examination system, noting its advantages of innovative and interesting lectures, the ability to improve clinical thinking skills, and not being limited by location or time. Conclusions:The dental scenario-based clinical thinking teaching and examination system can stimulate students' interest and enthusiasm for independent learning. The system has received high levels of acceptance among students. The application and development of the dental scenario-based clinical thinking teaching and examination system hold significant value.
4.Structural and epitope characterization of HIV-1 V1V2 highly effective neutralizing antibodies based on AlphaFold 3
Junjie ZHANG ; Qianying WANG ; Ying LIU ; Shuhui WANG ; Li REN ; Shuo WANG ; Yutao SHI ; Yuhua RUAN ; Xiaojing LIU ; Xinran DU ; Yanling HAO ; Dan LI
Chinese Journal of Experimental and Clinical Virology 2025;39(5):548-555
Objective:To screen broadly neutralizing antibodies in human immunodeficiency virus-1(HIV-1)chronically infected individuals and characterize their molecular features and to provide new strategies for rational vaccine development and antibody-based therapeutics.Methods:A total of 34 treatment-na?ve individuals with chronic HIV-1 infection were enrolled. Plasma antibody binding levels were measured against two HIV-1 envelope proteins. Single antigen-specific memory B cells were sorted from high-binding samples,and antibody variable region genes were amplified by PCR for paired expression. The monoclonal antibodies were evaluated for neutralizing activity using pseudovirus assays,and their structural features were analyzed by integrating AlphaFold 3 prediction with Discovery Studio molecular docking.Results:Plasma samples showed strong binding to DU422-GP140 and BG505-GP140. Eight monoclonal antibodies were isolated from two donors. Among them,antibodies 0919-A4,0919-A9 and 0808-A2 could cross-react with GP140 from HIV-1 subtypes AE,BC and B. The monoclonal antibody 0919-A9 demonstrated potent neutralizing activity against SF162(Tier 1)and CH181(Tier 2)pseudoviruses,with somatic hypermutation rates of 13.27%(heavy chain)and 15.58%(light chain). Structural modeling revealed its specific targeting of the V1V2 region on GP120.Conclusion:The isolated antibody 0919-A9 effectively neutralizes Tier 2 pseudoviruses. Its high somatic mutation frequency and V1V2-targeting property underlie its neutralizing activity,providing both a promising candidate and mechanistic insights for HIV vaccine development and antibody-based therapeutic strategies.
5.Impact of early and timely treatment and initial antiviral treatment regimen on antiviral treatment mortality and attrition among HIV-infected patients in Liuzhou, Guangxi
QIN Litai ; HUANG Jinghua ; CHEN Huanhuan ; LAN Guanghua ; FENG Yi ; XING Hui ; ZHU Jinhui ; CAI Wenlong ; RUAN Yuhua ; ZHU Qiuying ; XIE Yihong
China Tropical Medicine 2024;24(2):126-
Objective To understand the impact of early and timely treatment and initial antiviral treatment regimen on mortality and attrition of antiretroviral therapy. Methods A retrospective cohort study was conducted using download data on antiretroviral therapy for HIV-infected patients in Liuzhou City, Guangxi Province, from the database of the Basic Information System for AIDS Control and Prevention (BISAC) from 2010 to 2020. The Cox proportional risk regression model was used to analyze the influencing factors of mortality and attrition. Results A total of 15 713 infected patients were included, including 53.4% aged 18-<50 years, 69.4% male, 61.0% farmer, 75.1% CD4 count <350 cells /μL before initial antiviral treatment, the overall mortality rate was 4.30/100 person-years, and the overall attrition was 2.42/100 person-years. The results of Cox regression analysis showed that the influencing factors of mortality were pretreatment CD4 counts of 350-<500 cells/μL(AHR=0.72, 95%CI: 0.63-0.81) and ≥500 cells/μL (AHR= 0.64, 95%CI: 0.55-0.76); duration from diagnosis to initial antiviral treatment 91-180 days (AHR=1.25, 95%CI: 1.08-1.45), 181-365 days (AHR=1.26, 95%CI: 1.08-1.47), and ≥365 days (AHR=1.26, 95%CI: 1.11-1.44); initial antiviral treatment regimens of D4T+3TC+EFV/NVP (AHR=1.47, 95%CI: 1.32-1.63) and AZT/D4T/TDF+3TC+LPV/r (AHR=1.73, 95%CI: 1.50-1.99). Factors affecting attrition were pretreatment CD4 counts of 350-499 cells/μL (AHR=1.32, 95%CI: 1.16-1.50) and ≥500 cells/μL (AHR=1.28, 95%CI: 1.10-1.50); interval from HIV positivity confirmation to initial dosing ≥365 days (AHR=1.21, 95%CI: 1.04-1.40), initial antiviral treatment regimens of TDF+3TC+NVP (AHR=1.32, 95%CI: 1.13-1.55), AZT+3TC+EFV/NVP (AHR=1.43, 95%CI: 1.26-1.62) and AZT/D4T/TDF+3TC+LPV/r (AHR=1.33, 95CI%: 1.06-1.67). Conclusions Early and timely treatment and the initial antiviral treatment regimen of TDF+3TC+EFV have good efficacy, but attention should be paid to the high risk of attrition of HIV-infected people with high CD4 count before treatment.
6.The effect of Ba Duan Jin on the balance of community-dwelling older adults: a cluster randomized control trial
Leilei DUAN ; Yubin ZHAO ; Yuliang ER ; Pengpeng YE ; Wei WANG ; Xin GAO ; Xiao DENG ; Ye JIN ; Yuan WANG ; Cuirong JI ; Xinyan MA ; Cong GAO ; Yuhong ZHAO ; Suqiu ZHU ; Shuzhen SU ; Xin'e GUO ; Juanjuan PENG ; Yan YU ; Chen YANG ; Yaya SU ; Ming ZHAO ; Lihua GUO ; Yiping WU ; Yangnu LUO ; Ruilin MENG ; Haofeng XU ; Huazhang LIU ; Huihong RUAN ; Bo XIE ; Huimin ZHANG ; Yuhua LIAO ; Yan CHEN ; Linhong WANG
Chinese Journal of Epidemiology 2024;45(2):250-256
Objective:To assess the effectiveness of a 6-month Ba Duan Jin exercise program in improving the balance of community-dwelling older adults.Methods:A two arms, parallel-group, cluster randomized controlled trial was conducted in 1 028 community residents aged 60-80 years in 40 communities in 5 provinces of China. Participants in the intervention group (20 communities, 523 people) received Ba Duan Jin exercise 5 days/week, 1 hour/day for 6 months, and three times of falls prevention health education, and the control group (20 communities, 505 people) received falls prevention health education same as the intervention group. The Berg balance scale (BBS) score was the leading outcome indicator, and the secondary outcome indicators included the length of time of standing on one foot (with eyes open and closed), standing in a tandem stance (with eyes open and closed), the closed circle test, and the timed up to test.Results:A total of 1 028 participants were included in the final analysis, including 731 women (71.11%) and 297 men (28.89%), and the age was (69.87±5.67) years. After the 3-month intervention, compared with the baseline data, the BBS score of the intervention group was significantly higher than the control group by 3.05 (95% CI: 2.23-3.88) points ( P<0.001). After the 6-month intervention, compared with the baseline data, the BBS score of the intervention group was significantly higher than the control group by 4.70 (95% CI: 4.03-5.37) points ( P<0.001). Ba Duan Jin showed significant improvement ( P<0.05) in all secondary outcomes after 6 months of exercise in the intervention group compared with the control group. Conclusions:This study showed that Ba Duan Jin exercise can improve balance in community-dwelling older adults aged 60-80. The longer the exercise time, the better the improvement.
7.Analysis of pretreatment drug resistance and polymorphic sites in CRF08_BC strains among HIV-1 patients
Jiaxin ZHANG ; Jing HU ; Chang SONG ; Aobo DONG ; Miaomiao LI ; Yi FENG ; Yuhua RUAN ; Hui XING ; Lingjie LIAO
Chinese Journal of Microbiology and Immunology 2023;43(1):20-26
Objective:To investigate the prevalence of pretreatment drug resistance and the genetic polymorphism of CRF08_BC strains among HIV-1 patients in China.Methods:This cross-sectional survey involved the plasma samples of HIV patients in a national pretreatment HIV drug resistance survey conducted in 2018. RNA was extracted from the samples. The fragments containing protease and partial reverse transcriptase (PR/RT) regions were obtained and sequenced. Drug resistance was analyzed using Stanford HIVdb Program. Differences in polymorphic mutations between drug-resistant and non-drug-resistant HIV-1 strains were analyzed by Chi-square test or Fisher′s exact test. The association between drug-resistant and polymorphic mutations was evaluated using CorMut R package. Molecular transmission networks were constructed using HIV-TRACE software. Results:Totally 465 partial pol sequences were obtained from individuals with CRF08_BC infection in 25 provinces and cities. The total pretreatment drug resistance rate was 17.8% (83/465). The pretreatment drug resistance rates to non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs) were 16.6% (77/465), 1.1% (5/465) and 0.9% (4/465), respectively. The resistance rate to rilpivirine (RPV) was the highest (15.7%, 73/465). The most common mutation was E138A (11.6%, 54/465). There were six polymorphic mutations (S162C, K102Q, T200A, V179E, I202V, T200M) that co-variated with E138A. The molecular transmission network showed that patients infected with CRF08_BC strains carrying the resistant mutations at position E138 mainly gathered in clusters in Yunnan and Sichuan, and the highest degree of connection was in Lincang, Yunnan. Conclusions:In China, HIV-1 CRF08_BC-infected patients showed a high rate of pretreatment resistance to one of the second-generation NNRTIs, namely RPV. Further researches were warranted to evaluate the impacts of co-mutations of the E138A mutation and polymorphic sites on HIV resistance and replicative capacity.
8.Analysis on characteristics of virus isolation and unique recombinant forms from untreated HIV-1 infected patients in three provinces of China
Lijie WANG ; Yi FENG ; Lin HE ; Ruolei XIN ; Yan WANG ; Shu LIANG ; Yibo DING ; Shujia LIANG ; Yuanyuan ZHANG ; Caiqin HU ; Yuhua RUAN ; Hui XING ; Kunxue HONG ; Yiming SHAO ; Liying MA
Chinese Journal of Experimental and Clinical Virology 2022;36(3):263-269
Objective:To analyze the characteristics of viral isolation and unique recombinant from untreated HIV-1 patients infected through sexual transmission and injection drug use, so as to provide evidence for understanding the biological characteristics and precise prevention and control of HIV-1 infection in different transmission routes.Methods:In view of the different HIV-1 transmission risks, newly diagnosed untreated HIV-1 patients from Beijing, Guangxi and Sichuan were carefully selected. Venous blood was collected to detect the viral load and CD4 + T cell count, and peripheral blood lymphocytes were isolated for virus isolation. Viral RNAs were extracted from the virus supernatant, and the near full-length genome sequences were obtained using in-house method, then the recombination patterns were determined. Results:Among the 65 HIV-1 infection, 32(49.2%), 20(30.8%) and 13(20.0%) were infected via men who have sex with men (MSM), heterosexual and injection drug use (IDU), respectively; genotypes mainly included 26(40.0%) CRF07_ BC, 23(35.4%) CRF01_ AE, and 9(13.8%) unique recombinant types (URFs). A total of 46 HIV-1 clinical strains were isolated. The positive rate of HIV-1 isolation was significantly negatively correlated with CD4 + T cells ( X2=4.22, P=0.04), but positively correlated with viral load ( X2=22.4, P<0.001); the multi-variate generalized estimating equations(GEE) model analysis of HIV-1 P24 antigen content showed similar result. In addition, GEE model showed a positive correlation between viral P24 antigen content and virus-producing culture time (52.14, 95% CI: 9.42~94.87, P=0.017). Viral growth curve analysis showed that the level of viral P24 antigen in MSM Group was significantly higher than that in heterosexual group and IDU group (adjusted P values were p<0.01 and P<0.05, respectively), on the 14th day after culture. The proportion of URFs in MSM Group was higher than that in heterosexual group, and the recombinant breakpoints in MSM Group were more than that in heterosexual group. Conclusions:MSM population was more sensitive to HIV-1 virus isolation; there was unique diversity of recombinant forms of HIV-1 among those with sexually transmitted infections, especially in the MSM population.
9.Characteristics of amino acid and codon usage of Env genes in HIV-1 infected individuals with highly broad cross-neutralizing activity
Shasha SUN ; Yuanyuan HU ; Ying LIU ; Li REN ; Yuhua RUAN ; Liying MA ; Yiming SHAO ; Kunxue HONG
Chinese Journal of Microbiology and Immunology 2021;41(5):338-344
Objective:To study the amino acid and codon usage profile of HIV-1 Env gene in donors whose serum exhibit highly broad cross-neutralizing activity. Methods:The samples were divided into highly broad cross-neutralizing activity group (hBCN + group) and non-highly broad cross-neutralizing activity group (hBCN - group) based on whether the neutralization breadth was higher than 90% or not. Full-length Env genes were amplified by single genome amplification (SGA) method from patients′ plasma samples, and the characteristics of Env sequences in hBCN + group were compared with hBCN - group. The correspondence analysis (COA) on relative amino acid usage (RAAU), adaptability to host based on similarity index D( A, B) and relative synonymous codon usage (RSCU) values of Env genes (hBCN + and hBCN -) with respect to human host RSCU were analyzed. Results:Correspondence analysis showed that the RAAU data of hBCN + group and hBCN - group were distributed along the two main axes to form two relatively separated clusters, indicating that the Env genes of the two groups had relatively unique amino acid usage patterns; the similarity index calculation results showed that hBCN + group (0.097) was lower than the hBCN - group (0.102), in addition, the Env gene of the hBCN + group had less frequency of similarly selected codons with human host system compared to hBCN - group. Conclusions:Env genes in hBCN + group and hBCN - group may have relatively unique amino acid usage patterns, and virus strains in hBCN + group are less adaptable to the host than those in hBCN - group.
10.Analysis on drug resistance in people infected with HIV-1 CRF55_01B before antiviral therapy in China
Shan ZHENG ; Chang SONG ; Mengze GAN ; Qingyu HAN ; Jing HU ; Aobo DONG ; Lingjie LIAO ; Yi FENG ; Yuhua RUAN ; Hui XING
Chinese Journal of Experimental and Clinical Virology 2021;35(2):194-198
Objective:To explore the resistance to protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and integrase inhibitors (INSTIs) of HIV-1 CRF55_01B and the transmission of drug-resistant strains among HIV-1 CRF55_01B infected patients before antiviral treatment in China.Methods:HIV-1 RNA was extracted from plasma samples of the patients infected with CRF55_01B in the national surveillance of HIV drug resistance before antiviral treatment in 2018. A 1 056 bp gene fragment of protease/reverse transcriptase (PR/RT) region and an 846 bp gene fragment of integrase (IN) region were obtained and sequenced. Drug resistance was analyzed by using all drugs included in the Stanford University HIV db Program, HIV-1 molecular network analysis was performed with software HIV-TRACE and polymorphism mutations of CRF55_01B integrase gene region were analyzed.Results:A total of 178 samples from 26 provinces, municipalities and autonomous regions in China were analyzed, and 170 sequences of CRF55_01B PR/RT region and 170 sequences of IN region of corresponding samples were obtained. The drug resistance rate was 15.3% (26/170). The drug resistance rates of PIs, NRTIs, NNRTIs and INSTIs were 1.2% (2/170), 1.2% (2/170), 15.3% (26/170), 0.6% (1/170), respectively. The level of drug resistance was mostly low. NNRTIs drug resistance mutations were mainly V179D/E co-appeared with other mutations, and 84.1% (143/170) of the infected patients carrying V179D/E alone showed potential drug resistance. INSTIs drug resistance mutation was G163R, and showed low resistance to EVG and RAL. The molecular network access rate was 30.0%(51/170)according to the 0.9% gene distance threshold. The resistant strains were transmitted between men with homosexual transmission and heterosexually transmitted people, and both carried resistant mutations E138G and V179E. In the integrase region, CRF55_01B and CRF01_AE and B subtypes showed high mutation frequency difference in 5 sites (T215A、G134N、I135V, K136R and L101I/V).Conclusions:Before antiviral treatment, CRF55_01B infected patients in China had a high resistance to NNRTIs. Strains carrying both E138G and V179E resistance mutations were transmitting in clusters. The prevalence of CRF55_01B integrase inhibitor resistant strains is low, but some genetic polymorphisms with high mutation rate in the integrase gene region have potential influence on drug sensitivity. The influence of drug resistance of new recombinant strains on antiviral therapy in China needs to be further monitored and analyzed.

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