AIDS research and human retroviruses最新文献

{"title":"Near Full-Length Genomic Characterization of a Novel HIV-1 Unique Recombinant (A1/D/K) from an Immigrant Worker in China Using Nanopore Sequencing.","authors":"Haibo Wang, Huina Huang, Weigang Li, Cheng Yuan, Ying Su, Xiaojian Zhou, Xinbin Chen, Yuxiang Huang","doi":"10.1089/aid.2024.0108","DOIUrl":"https://doi.org/10.1089/aid.2024.0108","url":null,"abstract":"<p><p>Recombination contributes substantially to the genetic diversity of HIV-1. Here we reported a novel HIV-1 recombinant detected from a Chinese labor who had been to Uganda as an immigrant worker using nanopore sequencing. Near full-length genome (NFLG) phylogenetic analysis showed that the novel HIV-1 recombinant HIV-sd1801 stood in a distinct branch between the CRF130_A1B/CRF131_A1B and CRF50_A1D/CRF84_A1D reference sequences. Recombinant analysis showed that the NFLG of HIV-sd1801 was composed of subtypes A1, D, and K, with 19 recombinant breakpoints observed in the <i>gag, pol, tat, rev, vpu, env,</i> and <i>nef</i> regions. This is the first detection of a novel HIV-1 recombinant (A1/D/K) in immigrant workers in China, which indicated the continuous evolution of HIV-1 among this population and underscored the importance of continuous surveillance of the dynamic changes of HIV-1.</p>","PeriodicalId":7544,"journal":{"name":"AIDS research and human retroviruses","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular HIV Surveillance: Beyond Cluster Detection and Response.","authors":"Sanjay R Mehta, Antoine Chaillon, Alan B Wells, Susan J Little","doi":"10.1089/aid.2024.0084","DOIUrl":"https://doi.org/10.1089/aid.2024.0084","url":null,"abstract":"<p><p>There has been significant controversy surrounding the use of HIV sequence data to identify outbreaks of HIV transmission since the initiation of molecular HIV surveillance (MHS) in the US. The current approach to MHS is comprehensive cluster detection and response (CDR), in which clusters of related infections are identified and used as the basis for cluster-based or population-based interventions. With CDR, there are ethical and stigma concerns around the impingement of individual privacy, as well as legal concerns around the inference of transmission in regions where HIV criminalization laws and statutes exist. Here we propose an alternative approach to the analysis of HIV sequence and public health data that focuses on regions and populations rather than clusters, and still provides useful data for public health agencies.</p>","PeriodicalId":7544,"journal":{"name":"AIDS research and human retroviruses","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequence Notes: Identification of Three Novel HIV-1 Recombinant Strains with Different Recombination Patterns in Hebei Province, China.","authors":"Sisi Chen, Haoxi Shi, Zhen Zhang, Lijuan Yin, Jianru Jia, Weiguang Fan","doi":"10.1089/aid.2024.0115","DOIUrl":"https://doi.org/10.1089/aid.2024.0115","url":null,"abstract":"<p><p>The global human immunodeficiency virus 1 (HIV-1) pandemic is driven by the extraordinary genetic diversity of the virus, largely resulting from frequent recombination events. These events generate circulating recombinant forms (CRFs) and unique recombinant forms, which significantly contribute to the complexity of HIV-1 epidemiology, especially within key populations, such as men who have sex with men (MSM). Here, we identified three novel HIV-1 recombinant strains consisting of the CRF01_AE and CRF07_BC subtypes from HIV-positive MSM in Baoding City, Hebei Province, China. Using near-full-length genome analysis and phylogenetic reconstruction, the strains-designated BDL017, BDL036, and BDSB006-were shown to exhibit distinct mosaic structures. Each strain contained multiple inserted fragments from CRF07_BC and CRF01_AE within various genomic regions, highlighting their complex recombination patterns. Our study emphasizes the need for continuous molecular surveillance among MSM in Hebei Province to monitor these recombinant forms and prevent their spread to the broader population.</p>","PeriodicalId":7544,"journal":{"name":"AIDS research and human retroviruses","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a Novel HIV-1 Second-Generation Circulating Recombinant Form (CRF117_0107) in China.","authors":"Xiaorui Wang, Bo Zhu, Hanping Li, Jingwan Han, Xiaolin Wang, Lei Jia, Bohan Zhang, Jingyun Li, Yongjian Liu, Hongling Wen, Lin Li","doi":"10.1089/aid.2024.0106","DOIUrl":"https://doi.org/10.1089/aid.2024.0106","url":null,"abstract":"<p><p>Under the background of the main epidemic HIV strains (CRF01_AE and CRF07_BC) co-circulation in China, more HIV second-generation recombinant (SGR) strains with CRF01_AE and CRF07_BC as the backbone were also emerging. In this study, we characterize a novel HIV-1 second-generation circulating recombinant form (CRF117_0107) consisting of CRF01_AE and CRF07_BC fragments from three epidemiologically unrelated HIV-1-infected individuals. One near full-length genome (NFLG) sequence was amplified, sequenced, and spliced in two halves using RNA extracted from the plasma of a homosexual in Shenzhen, Guangdong Province. Two other NFLG sequences were obtained from the Los Alamos HIV Sequence Database under accession numbers KY201177 and MK397789, which were isolated from men who have sex with men (MSM) in Guangdong Province and Zhejiang Province, respectively. Phylogenetic analysis revealed that these NFLG sequences formed a monophyletic cluster with a high bootstrap value of 1.0. Recombination analysis demonstrated that the genome of CRF117_0107 was separated into three segments by two breakpoints. Further subregional phylogenetic analysis was performed that showed segment I+III (790-5990nt, 8295-9412nt) of CRF117_0107 originated from the CRF07_BC cluster, and Segment I+III (5991-8294nt) originated from the CRF01_AE cluster. The appearance of CRF117_0107 further highlights that HIV-1 SGR strains containing CRF01_AE and CRF07_BC will be generated more frequently and will most likely be more conducive to accelerating the spread of HIV in China. This study suggested it's essential to monitor HIV-1 second-generation CRFs among high-risk populations such as MSM for the epidemic and evolution dynamics of HIV-1 in China.</p>","PeriodicalId":7544,"journal":{"name":"AIDS research and human retroviruses","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HIV-1 DNA Genotypic Drug Resistance Testing Guides Antiretroviral Therapy in Patients with Low-Level Viremia.","authors":"Bianchuan Cao, Mei Liu, Shaofang Song, Mingxian Guo, Lingyu Tang, Ping Ding, Tianru Yuan, Tong Wang, Li Zhong","doi":"10.1089/aid.2024.0088","DOIUrl":"https://doi.org/10.1089/aid.2024.0088","url":null,"abstract":"<p><p>In 2023, we published a case study involving a 10-year-old HIV-1-infected child with low-level viremia (LLV). We showed that this child patient achieved successful viral suppression by modifying the antiretroviral therapy (ART) regimen according to the HIV-1 DNA genotypic drug resistance testing. In this study, we aimed to address whether HIV-1 DNA genotypic drug resistance testing could direct successfully virological suppression in HIV-1-infected patients experiencing persistent LLV based on evidence from a cohort study. The subjects of this study were all people living with HIV-1 who received ART and followed in the Yuexi County (Liangshan, China) from December 2010 to February 2024. From June 2021 to February 2024, a total of 10 mL of peripheral blood was collected from each subject at each follow-up and separated. HIV-1 RNA and HIV-1 DNA were quantified, followed by HIV-1 genotypic drug resistance testing. ART regimens were accordingly adjusted, while follow-up tests were performed in terms of HIV-1 RNA and DNA measurements. The prevalent HIV-1 DNA drug resistance mutations (DRMs) included M184V, K103N, K101E/P, and V108I. The primary resistance mutations observed for nucleoside reverse transcriptase inhibitor (NRTI) were against abacavir, lamivudine, and emtricitabine. For non-NRTI, the primary DRMs were associated with efavirenz and nevirapine. Five out of the six patients were subjected to regimen adjustments according to HIV-1 DNA DRMs, while one patient was continuously treated with unchanged regimen. Viral suppression was achieved in all five ART-changed cases, with observation of remarkable of HIV-1 DNA decline. The ART-unchanged case showed progressive treatment failure with drastic increase of plasma HIV-1 RNA and whole blood HIV-1 DNA. For patients with LLV, HIV-1 DNA genotypic drug resistance testing directed ART regimen considerations are highly recommended for achieving viral suppression.</p>","PeriodicalId":7544,"journal":{"name":"AIDS research and human retroviruses","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142977190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical Benefit of a Conservative Treatment for High-Risk Human Papillomavirus Lesions in Patients with HIV.","authors":"Jesús Joaquín Hijona Elósegui, Antonio Luis Carballo García, Ana Cristina Fernández Rísquez, Jesús Carlos Presa Lorite, Gabriel Fiol Ruiz","doi":"10.1089/aid.2024.0067","DOIUrl":"https://doi.org/10.1089/aid.2024.0067","url":null,"abstract":"<p><p>Infection with Human immunodeficiency virus (HIV) shows a higher risk of infection by Human papillomavirus (HPV). We aim to provide evidence about the effect of a <i>Coriolus versicolor</i>-based vaginal gel (Papilocare®) for treating HPV in women with HIV. Women ≥25 years coinfected by endocervical HPV and with low-grade abnormal cervicovaginal cytology were treated for 6 months with Papilocare® in this observational, prospective, non-controlled pilot study. Cytology, colposcopy, biopsy, hybrid capture test, and 5-point Likert scale were assessed to evaluate cervical lesions repair, HPV clearance, and changes in cervical reepithelization, respectively, at 6 months. Fifteen patients (25-54 years) were included. Overall HPV clearance and cytological normalization rates were 73.3% and 80.0%, respectively, and 55.6% of the abnormal colposcopies were normalized. Re-epithelialization index improved in 66.7% of cases. Papilocare® may be effective for managing endocervical HPV infection in patients living with HIV.</p>","PeriodicalId":7544,"journal":{"name":"AIDS research and human retroviruses","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142942479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of an Invisible HIV-1 Circulating Recombinant Form (CRF149_01B) in China.","authors":"Min Chen, Huichao Chen, Jie Dai, Lijuan Dong, Yanling Ma, Manhong Jia","doi":"10.1089/aid.2024.0099","DOIUrl":"https://doi.org/10.1089/aid.2024.0099","url":null,"abstract":"<p><p>In this study, by analyzing the available near full-length genome (NFLG) sequences of CRF55_01B, it was found that two of the NFLG sequences could not be clustered with other NFLG sequences. Recombination analysis and phylogenetic analysis suggested that these two NFLG sequences arose by recombination with subtype B based on CRF55_01B, rather than by recombination directly derived from CRF01_AE and subtype B. In addition, two other HIV-1 partial gene fragments found in the database shared the same characteristics as these two NFLG sequences in the key recombination region. These sequences may therefore represent a previously unrecognized circulating recombinant form (CRF), which has been named CRF149_01B. Evolutionary analyses suggested that CRF149_01B emerged between approximately 2005 and 2007. The discovery of CRF149_01B highlights the complexity of HIV recombinant evolution and advances the refinement of the HIV genotyping system. A deeper understanding of HIV-1 genetics will facilitate molecular tracing and provide a basis for studying the biological properties of HIV.</p>","PeriodicalId":7544,"journal":{"name":"AIDS research and human retroviruses","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142942477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Confirmation of Two Novel HIV-1 CRF01_AE/CRF07_BC Recombinant Forms Among Men Who Have Sex with Men in Hebei, China.","authors":"Yapeng Guan, Jun Wang, Meng Liu, Xinli Lu","doi":"10.1089/aid.2024.0104","DOIUrl":"https://doi.org/10.1089/aid.2024.0104","url":null,"abstract":"<p><p>Acquired immune deficiency syndrome caused by human immunodeficiency virus (HIV) is a serious infectious disease because of its' high genetic variability. Nowadays, homosexual contact has become the most predominant transmission route in Hebei province, China, leading to the emergence of novel HIV-1 recombinant forms. The neighbor-joining (N-J) phylogenetic trees were constructed using MEGA 6.0 in order to identify the subtypes of H22063 and H22144. Recombination breakpoints were identified using online resources jpHMM, RIP 3.0, and Simplot 3.5.1. In this study, we identified two novel HIV-1 unique recombinant forms (URFs) _0107 from three men who have sex with men in Hebei province, including H22063 and H22144. The near full-length genome analysis showed H22063 has seven gene recombination sub-regions, including three subtype CRF07_BC gene fragments inserted into the CRF01_AE backbone. H22144 has nine gene recombination sub-regions, including four subtype CRF07_BC gene fragments inserted into the CRF01_AE backbone. This study confirms the emergence of novel recombinant forms and suggests we should strengthen the monitoring of novel HIV recombinant forms in order to deal with the complex HIV-1 epidemiological trend in Hebei province, China.</p>","PeriodicalId":7544,"journal":{"name":"AIDS research and human retroviruses","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142942480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interpreting the Epidemiological Characteristics of HIV-1 in Heterosexually Transmitted Population Based on Molecular Transmission Network in Kunming, Yunnan: A Retrospective Cohort Study.","authors":"Peng Cheng, Bao-Cui He, Zhi-Xing Wu, Jia-Fa Liu, Jia-Li Wang, Cui-Xian Yang, Sha Ma, Mi Zhang, Xing-Qi Dong, Jian-Jian Li","doi":"10.1089/aid.2023.0137","DOIUrl":"10.1089/aid.2023.0137","url":null,"abstract":"<p><p>Heterosexuals have become the most prevalent group of HIV-1 in Kunming, Yunnan Province. Utilizing the principle of genetic similarity between their gene sequences, we built a molecular transmission network by gathering data from earlier molecular epidemiological studies. This allowed us to analyze the epidemiological features of this group and offer fresh concepts and approaches for the prevention and management of HIV-1 epidemics. Cytoscope was used to visualize and characterize the network following the processing of the sample gene sequences by BioEdit and HyPhy. The number of possible links and the size of the clusters were investigated as influencing factors using a zero-inflated Poisson model and a logistic regression model, respectively. A scikit-learn-based prediction model was developed to account for the dynamic changes in the HIV-1 molecular network. Six noteworthy modular clusters with network scores ranging from 4 to 9 were found from 150 clusters using Molecular Complex Detection analysis at a standard genetic distance threshold of 0.01. The size of the number of possible links and the network's clustering rate were significantly impacted by sampling time, marital status, and CD4⁺ T lymphocytes (all <i>p</i> < 0.05). The gradient boosting machine (GBM) model had the highest area under the curve value, 0.884 ± 0.051, according to scikit-learn. Though not all cluster subtypes grew equally, the network clusters were relatively specific and aggregated. The largest local transmission-risk group for HIV-1CRF08_BC is now the heterosexual transmission population. The most suitable model for constructing the HIV-1 molecular network dynamics prediction model was found to be the GBM model.</p>","PeriodicalId":7544,"journal":{"name":"AIDS research and human retroviruses","volume":" ","pages":"1-10"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HIV DNA Levels in Persons Who Acquired HIV in the Setting of Long-Acting Cabotegravir for HIV Prevention: Analysis of Cases from HPTN 083 and 084.","authors":"Jessica M Fogel, Deborah Persaud, Estelle Piwowar-Manning, Paul Richardson, Joseph Szewczyk, Mark A Marzinke, Zhe Wang, Xu Guo, Marybeth McCauley, Jennifer Farrior, Ha Viet Tran, Chaiwat Ungsedhapand, Carrie-Anne Mathew, Juliet Mpendo, Alex R Rinehart, James F Rooney, Myron S Cohen, Brett Hanscom, Beatriz Grinsztejn, Mina C Hosseinipour, Sinead Delany-Moretlwe, Raphael J Landovitz, Susan H Eshleman","doi":"10.1089/aid.2024.0049","DOIUrl":"10.1089/aid.2024.0049","url":null,"abstract":"<p><p>We evaluated HIV DNA levels in individuals who received long-acting cabotegravir (CAB-LA) or tenofovir disoproxil fumarate/emtricitabine (TDF/FTC) pre-exposure prophylaxis in the HPTN 083 and 084 trials and had HIV DNA testing performed to help determine HIV status. HIV DNA testing was performed using peripheral blood mononuclear cell (PBMC) samples collected after a reactive HIV test was obtained at a study site. DNA was quantified using droplet digital PCR (lower limit of detection [LLOD]: 4.09 copies/million PBMCs). Final HIV status and the timing of the first HIV-positive visit were determined by an independent adjudication committee based on HIV test results from real-time site testing and retrospective testing at a centralized laboratory. HIV DNA testing was performed for 133 participants [21 HIV-positive (7 CAB-LA arm, 14 TDF/FTC arm) and 112 HIV-negative; 1-6 tests/person]. For persons with HIV, the time between the first HIV-positive visit and collection of the first sample for DNA testing was a median of 81 days for those receiving CAB-LA (range 41-246) and 11 days for those receiving TDF/FTC (range 3-127). Four (57.1%) of the seven CAB-LA cases with infection had a low initial DNA result [three detected <LLOD; one near the LLOD (4.2 copies/10⁶ PBMCs); in 2/4 cases, the DNA level was still <10 copies/10⁶ PBMCs ≥40 weeks after the first HIV-positive visit. In contrast, only 3/14 (21.4%) of the TDF/FTC cases had a low or negative initial DNA test result (one not detected; two <10 copies/10⁶ PBMCs). In this study, the time between the first HIV-positive visit and the first DNA test was longer in the CAB-LA cases than the TDF/FTC cases. Despite this difference, low or undetectable DNA levels were more frequently observed in the CAB-LA cases. This suggests that CAB-LA exposure may limit seeding of the HIV reservoir in early infection.</p>","PeriodicalId":7544,"journal":{"name":"AIDS research and human retroviruses","volume":" ","pages":"30-36"},"PeriodicalIF":1.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}