Evaluation of the potential of next generation sequencing to monitor transmitted HIV-1 drug resistance mutations in newly diagnosed therapy naïve patients.
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ABSTRACT:
PROVIDER: PRJEB22839 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3385870.fastq.gz | Fastqsanger.gz | |||
| ERR3385880.fastq.gz | Fastqsanger.gz | |||
| ERR3385890.fastq.gz | Fastqsanger.gz | |||
| ERR3385900.fastq.gz | Fastqsanger.gz | |||
| ERR3385910.fastq.gz | Fastqsanger.gz |
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Project description:HIV-1 replication is rapid and highly error-prone. Transmission of a drug-resistant HIV-1 strain is possible and occurs within the HIV-1-infected population. In this study, we aimed to determine the prevalence of transmitted drug resistance mutations (TDRMs) in 1,306 newly diagnosed untreated HIV-1-infected patients from 21 cities across six regions of Turkey between 2010 and 2015. TDRMs were identified according to the criteria provided by the World Health Organization's 2009 list of surveillance drug resistance mutations. The HIV-1 TDRM prevalence was 10.1% (133/1,306) in Turkey. Primary drug resistance mutations (K65R, M184V) and thymidine analogue-associated mutations (TAMs) were evaluated together as nucleos(t)ide reverse transcriptase inhibitor (NRTI) mutations. NRTI TDRMs were found in 8.1% (107/1,306) of patients. However, TAMs were divided into three categories and M41L, L210W, and T215Y mutations were found for TAM1 in 97 (7.4%) patients, D67N, K70R, K219E/Q/N/R, T215F, and T215C/D/S mutations were detected for TAM2 in 52 (3.9%) patients, and M41L + K219N and M41L + T215C/D/S mutations were detected for the TAM1 + TAM2 profile in 22 (1.7%) patients, respectively. Nonnucleoside reverse transcriptase inhibitor-associated TDRMs were detected in 3.3% (44/1,306) of patients (L100I, K101E/P, K103N/S, V179F, Y188H/L/M, Y181I/C, and G190A/E/S) and TDRMs to protease inhibitors were detected in 2.3% (30/1,306) of patients (M46L, I50V, I54V, Q58E, L76V, V82A/C/L/T, N83D, I84V, and L90M). In conclusion, long-term and large-scale monitoring of regional levels of HIV-1 TDRMs informs treatment guidelines and provides feedback on the success of HIV-1 prevention and treatment efforts.
| S-EPMC4692107 | biostudies-literature
Project description:BackgroundTransmitted drug resistance (TDR) is still a critical aspect for the management of individuals living with HIV-1. Thus, its evaluation is crucial to optimize HIV care.MethodsOverall, 2386 HIV-1 protease/reverse transcriptase and 1831 integrase sequences from drug-naïve individuals diagnosed in north and central Italy between 2015 and 2021 were analysed. TDR was evaluated over time. Phylogeny was generated by maximum likelihood. Factors associated with TDR were evaluated by logistic regression.ResultsIndividuals were mainly male (79.1%) and Italian (56.2%), with a median (IQR) age of 38 (30-48). Non-B infected individuals accounted for 44.6% (N = 1065) of the overall population and increased over time (2015-2021, from 42.1% to 51.0%, P = 0.002). TDR prevalence to any class was 8.0% (B subtype 9.5% versus non-B subtypes 6.1%, P = 0.002) and remained almost constant over time. Overall, 300 transmission clusters (TCs) involving 1155 (48.4%) individuals were identified, with a similar proportion in B and non-infected individuals (49.7% versus 46.8%, P = 0.148). A similar prevalence of TDR among individuals in TCs and those out of TCs was found (8.2% versus 7.8%, P = 0.707).By multivariable analysis, subtypes A, F, and CFR02_AG were negatively associated with TDR. No other factors, including being part of TCs, were significantly associated with TDR.ConclusionsBetween 2015 and 2021, TDR prevalence in Italy was 8% and remained almost stable over time. Resistant strains were found circulating regardless of being in TCs, but less likely in non-B subtypes. These results highlight the importance of a continuous surveillance of newly diagnosed individuals for evidence of TDR to inform clinical practice.
| S-EPMC11368429 | biostudies-literature
Project description:BACKGROUND: One out of ten newly diagnosed patients in Europe was infected with a virus carrying a drug resistant mutation. We analysed the patterns over time for transmitted drug resistance mutations (TDRM) using data from the European Spread program. METHODS: Clinical, epidemiological and virological data from 4317 patients newly diagnosed with HIV-1 infection between 2002 and 2007 were analysed. Patients were enrolled using a pre-defined sampling strategy. RESULTS: The overall prevalence of TDRM in this period was 8.9% (95% CI: 8.1-9.8). Interestingly, significant changes over time in TDRM caused by the different drug classes were found. Whereas nucleoside resistance mutations remained constant at 5%, a significant decline in protease inhibitors resistance mutations was observed, from 3.9% in 2002 to 1.6% in 2007 (p = 0.001). In contrast, resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) doubled from 2.0% in 2002 to 4.1% in 2007 (p = 0.004) with 58% of viral strains carrying a K103N mutation. Phylogenetic analysis showed that these temporal changes could not be explained by large clusters of TDRM. CONCLUSION: During the years 2002 to 2007 transmitted resistance to NNRTI has doubled to 4% in Europe. The frequent use of NNRTI in first-line regimens and the clinical impact of NNRTI mutations warrants continued monitoring.
| S-EPMC4223652 | biostudies-literature
Project description:Transmitted drug resistance (TDR) is a clinical and epidemiological problem because it may contribute to failure of antiretroviral treatment. The prevalence of TDR varies geographically, and its prevalence in Sweden during the last decade has not been reported. Plasma samples from 1,463 patients newly diagnosed with HIV-1 infection between 2003 and 2010, representing 44% of all patients diagnosed in Sweden during this period, were analyzed using the WHO 2009 list of mutations for surveillance of TDR. Maximum likelihood phylogenetic analyses were used to determine genetic subtype and to investigate the relatedness of the sequences. Eighty-two patients showed evidence of TDR, representing a prevalence of 5.6% (95% CI: 4.5%-6.9%) without any significant time trends or differences between patients infected in Sweden or abroad. Multivariable logistic regression showed that TDR was positively associated with men who have sex with men (MSM) and subtype B infection and negatively associated with CD4 cell counts. Among patients with TDR, 54 (68%) had single resistance mutations, whereas five patients had multi-drug resistant HIV-1. Phylogenetic analyses identified nine significantly supported clusters involving 29 of the patients with TDR, including 23 of 42 (55%) of the patients with TDR acquired in Sweden. One cluster contained 18 viruses with a M41L resistance mutation, which had spread among MSM in Stockholm over a period of at least 16 years (1994-2010). Another cluster, which contained the five multidrug resistant viruses, also involved MSM from Stockholm. The prevalence of TDR in Sweden 2003-2010 was lower than in many other European countries. TDR was concentrated among MSM, where clustering of TDR strains was observed, which highlights the need for continued and improved measures for targeted interventions.
| S-EPMC3308981 | biostudies-literature
Project description:BackgroundThe widespread use of antiretroviral therapy (ART) has led to considerable concerns about the prevalence of transmitted drug resistance (TDR). Sexual contact, particularly men who have sex with men (MSM) was the most prevalent form of HIV transmission in Shijiazhuang. Hence, we conducted an epidemiological surveillance study on TDR among newly diagnosed individuals who infected-HIV through sexual contact in from 2014-2015.MethodsGenotypic resistance mutations were defined using the WHO-2009 surveillance list. Potential impact on antiretroviral drug was predicted according to the Stanford HIV db program version 7.0. The role of transmission clusters in drug resistant strains was evaluated by phylogenetic and network analyses.ResultsIn this study, 589 individuals were recruited and 542 samples were amplified and sequenced successfully. The over prevalence of TDR was 6.1%: 1.8% to nucleoside reverse transcriptase inhibitors (NRTIs), 2.0% to non- NRTIs (NNRTIs) and 2.4% to protease inhibitors (PIs), respectively. We did not find significant differences in the TDR prevalence by demographic and clinical characteristics (p > 0.05). Using network and phylogenetic analysis, almost 60.0% sequences were clustered together. Of these clusters, 2 included at least two individuals carrying the same resistance mutation, accounting for 21.2% (7/33) individuals with TDR. No significant difference was observed in the clustering rate between the individuals with and without TDR.ConclusionsWe obtained a moderate level TDR rate in studied region. These findings enhance our understanding of HIV-1 drug resistance prevalence in Shijiazhuang, and may be helpful for the comprehensive prevention and control of HIV-1.
| S-EPMC5988301 | biostudies-literature
Project description:ObjectiveTo evaluate the diagnostic yield of baseline chest radiographs (CXRs) of children with acute lymphoblastic leukemia (ALL).Study designWe reviewed the CXR findings at diagnosis for 990 patients aged 1-18 years with ALL treated during the Total XV and XVI studies at St. Jude Children's Research Hospital and evaluated the associations of these findings with clinical characteristics and initial management.ResultsCommon findings were peribronchial/perihilar thickening (n = 187 [19.0%]), pulmonary opacity/infiltrate (n = 159 [16.1%]), pleural effusion/thickening (n = 109 [11.1%]), mediastinal mass (n = 107 [10.9%]), and cardiomegaly (n = 68 [6.9%]). Portable CXRs provided results comparable with those obtained with 2-view films. Forty of 107 patients with a mediastinal mass (37.4%) had tracheal deviation/compression. Mediastinal mass, pleural effusion/thickening, and tracheal deviation/compression were more often associated with T-cell ALL than with B-cell ALL (P < .001 for all). Pulmonary opacity/infiltrate was associated with younger age (P = .003) and was more common in T-cell ALL than in B-cell ALL (P = .001). Peribronchial/perihilar thickening was associated with younger age (P < .001) and with positive central nervous system disease (P = .012). Patients with cardiomegaly were younger (P = .031), more often black than white (P = .007), and more often categorized as low risk than standard/high risk (P = .017). Patients with a mediastinal mass, pleural effusion/thickening, tracheal deviation/compression, or pulmonary opacity/infiltrate were more likely to receive less invasive sedation and more intensive care unit admissions and respiratory support (P ≤ .001 for all). Cardiomegaly was associated with intensive care unit admission (P = .008). No patients died of cardiorespiratory events during the initial 7 days of management.ConclusionsThe CXR can detect various intrathoracic lesions and is helpful in planning initial management.
| S-EPMC7388067 | biostudies-literature
Project description:BackgroundHypertension and diabetes mellitus are often jointly present, especially in early onset cases of either disease. We investigated clinical characteristics of hypertensive patients with newly diagnosed diabetes and diabetic patients with newly diagnosed hypertension.MethodsOur study subjects were recruited in a China nationwide multicenter registry of hypertension and diabetes (n?=?2510). We performed logistic regression to compare patients seen for hypertension in cardiology, with newly diagnosed diabetes (n?=?137) and patients seen for diabetes mellitus in endocrinology, with newly diagnosed hypertension (n?=?155). Albuminuria was defined as a urinary albumin-to-creatinine ratio of???30 mg/g, and left ventricular hypertrophy according to the Cornell product index.ResultsThese two groups of patients with both hypertension and diabetes mellitus were similar in most of the characteristics (P???0.06). However, hypertensive patients with newly diagnosed diabetes, compared to diabetic patients with newly diagnosed hypertension, had a significantly greater body mass index (26.3 vs. 25.4 kg/m2, P?=?0.03) and slower heart rate (73.7 vs. 78.1 beats/min, P?=?0.01). In logistic regression analyses adjusted for sex (48.3% women) and age (mean 60.0?±?11.5 years), the odds ratio for newly diagnosed diabetes mellitus versus newly diagnosed hypertension was 1.27 (95% CI 1.03-1.56) and 0.80 (95% CI 0.66-0.96) for body mass index (+?3 kg/m2) and heart rate (+?10 beat/min), respectively. Hypertensive patients with newly diagnosed diabetes also had a lower prevalence of albuminuria (16.0% vs. 30.1%, P?=?0.02) and slightly and non-significantly higher prevalence of left ventricular hypertrophy (5.1% vs. 1.9%, P?=?0.14) than diabetic patients with newly diagnosed hypertension.ConclusionsEarlier or later onset of hypertension than diabetes mellitus may have different risk factors and organ damage.
| S-EPMC6708242 | biostudies-literature
Project description:OBJECTIVE:Seventeen years after the start of the IBAARV (Beninese initiative for access to antiretrovirals), transmitted drug resistance mutations in ARV-naïve patients and HIV-1 genetic diversity were investigated in Benin. RESULTS:Drug resistance mutations were detected in (27/248; 10.9%) according to the WHO SDRM 2009 list, with a predominance of mutations directed against NNRTIs drugs (24/248; 10%). Phylogenetic and recombination analyses showed a predominance of CRF02_AG strains (165/248; 66.5%) and a high genetic diversity with five other variants and 39 URFs (15.7%) which contained portions of strains that co-circulate in Benin. Eight recent transmission chains revealed active ongoing transmission of HIV-1 strains among ARV-naïve patients. Our study showed a moderate primary drug resistance mutations rate and also provided recent data on the HIV-1 variants that circulate in Benin. Regular monitoring of primary drug resistance is required to adapt HIV-1 treatment strategies and adoption of new WHO recommendations in Benin.
| S-EPMC7330984 | biostudies-literature
Project description:Acute Myeloid Leukemia (AML) is a heterogenous disease characterized by immature blasts at different maturation stage. We used single cell sequencing technique to analyze newly diagnosed AML patients.
2023-12-18 | GSE239721 | GEO
Project description:The iperactivation of self-renewal mechanisms, like Hedgehog (HH) pathway, which govern the refuel of Multiple Myeloma neoplastic clone, is critical to relapse events. The bulk of current knowledge is mainly based on the CD138+ cells molecular characterization, but in the light of the recent evidences, which attributed growing relevance to immature precursor clones, we become aware that multiple myeloma disease heterogeneity have more deepen roots. Here, we report on a high-throughput transcriptome study of gene expression profiles in newly diagnosed MM patients analyzed both in the CD138+ plasmacell fraction and in the CD19+ B cells compartment. Resulted data demonstrated that Hedgehog pathway, and in particular, a 10 HH-genes signature was heterogeneously expressed among MM patients, both in mature plasmacells and also in B cells at transcriptional level. Interestingly, this signature divide patients in two subgroups, and it seems that exists a sort of “ying-yang effect” between mature and immature cell compartments that are tightly regulate in order to express this relevant self-renewal pathway according to their maturation state.
2016-05-31 | GSE68999 | GEO