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1.
Clin Infect Dis ; 63(6): 836-843, 2016 09 15.
Article in English | MEDLINE | ID: mdl-27307507

ABSTRACT

BACKGROUND: Washington, DC, has 2.5% human immunodeficiency virus (HIV) prevalence, 3.9% among African Americans. Antiretrovirals (ARTs) are the cornerstone for treatment and prevention. Monitoring changes in transmitted drug resistance (TDR) is critical for effective HIV care. METHODS: HIV genotype data for individuals enrolled in research studies in metropolitan Washington, D.C., were used to identify TDR using the World Health Organization mutation list [Bennett DE, Camacho RJ, Otelea D, et al. Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PloS One 2009; 4:e4724]. HIV phylogenies were reconstructed using maximum likelihood and Bayesian methods. HIV transmission clusters were supported by 1000 bootstrap values >0.70 and posterior probability >0.95 of having a common ancestor. RESULTS: Among 710 individuals enrolled in 1994-2013, the median age was 38.6 years, 46.2% were female, and 53.3% were African-American. TDR was 22.5% among 566 treatment-naive individuals; 15.8% had nucleoside/nucleotide reverse transcriptase inhibitor (NRTI) resistance, 9.8% had nonnucleoside reverse-transcriptase inhibitor (NNRTI) resistance, and 4.2% had protease inhibitor (PI) resistance. Single class TDR was 10.0%, 5.1%, and 1.6% to NRTIs, NNRTIs, and PIs. Dual TDR to PI and NRTI was seen in 1.6%, NRTI and NNRTI in 3.4%, and triple class TDR in 0.9%. TDR frequency decreased from 1994-2006 (27.1%) to 2007-2013 (19.4%; P = .02). Only 6/79 (7.6%) individuals within transmission clusters had evidence of TDR. DISCUSSIONS: We identified high prevalence of TDR among HIV-infected individuals in metropolitan Washington, DC, regardless of gender. Active surveillance for TDR is needed to guide ART usage and analyses of risk group contributions to HIV transmission and resistance.


Subject(s)
Anti-HIV Agents/pharmacology , Drug Resistance, Viral/genetics , HIV Infections/epidemiology , HIV Infections/virology , HIV-1 , Adult , Anti-HIV Agents/therapeutic use , Bayes Theorem , District of Columbia/epidemiology , Female , HIV Infections/drug therapy , HIV-1/classification , HIV-1/drug effects , HIV-1/genetics , Humans , Male , Phylogeny , Retrospective Studies
2.
J Infect Dis ; 211(11): 1735-44, 2015 Jun 01.
Article in English | MEDLINE | ID: mdl-25512631

ABSTRACT

BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) subtype CRF01_AE originated in Africa and then passed to Thailand, where it established a major epidemic. Despite the global presence of CRF01_AE, little is known about its subsequent dispersal pattern. METHODS: We assembled a global data set of 2736 CRF01_AE sequences by pooling sequences from public databases and patient-cohort studies. We estimated viral dispersal patterns, using statistical phylogeographic analysis run over bootstrap trees estimated by the maximum likelihood method. RESULTS: We show that Thailand has been the source of viral dispersal to most areas worldwide, including 17 of 20 sampled countries in Europe. Japan, Singapore, Vietnam, and other Asian countries have played a secondary role in the viral dissemination. In contrast, China and Taiwan have mainly imported strains from neighboring Asian countries, North America, and Africa without any significant viral exportation. DISCUSSION: The central role of Thailand in the global spread of CRF01_AE can be probably explained by the popularity of Thailand as a vacation destination characterized by sex tourism and by Thai emigration to the Western world. Our study highlights the unique case of CRF01_AE, the only globally distributed non-B clade whose global dispersal did not originate in Africa.


Subject(s)
HIV Infections/transmission , HIV Infections/virology , HIV-1/classification , HIV-1/genetics , Heterosexuality , Phylogeography , Population Dynamics , Asia, Southeastern , Cluster Analysis , Databases, Factual , Europe , Humans , Phylogeny
3.
Bioinformatics ; 29(11): 1477-80, 2013 Jun 01.
Article in English | MEDLINE | ID: mdl-23645815

ABSTRACT

SUMMARY: RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyse patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface. AVAILABILITY AND IMPLEMENTATION: Source code, binaries and documentation are available on http://rega.kuleuven.be/cev/regadb. RegaDB is written in the Java programming language, using a web-service-oriented architecture.


Subject(s)
Databases, Factual , Software , Virus Diseases , Database Management Systems , Humans , Virus Diseases/diagnosis , Virus Diseases/therapy , Virus Diseases/virology
4.
BMC Infect Dis ; 14: 407, 2014 Jul 21.
Article in English | MEDLINE | ID: mdl-25047543

ABSTRACT

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.


Subject(s)
Anti-HIV Agents/therapeutic use , Drug Resistance, Viral , HIV Infections/drug therapy , HIV Infections/virology , HIV-1/genetics , Adult , Europe/epidemiology , Female , Genotype , HIV Infections/epidemiology , HIV Infections/transmission , HIV-1/classification , HIV-1/drug effects , HIV-1/isolation & purification , Humans , Male , Mutation , Phylogeny , Prevalence
5.
Retrovirology ; 10: 7, 2013 Jan 14.
Article in English | MEDLINE | ID: mdl-23317093

ABSTRACT

BACKGROUND: Understanding HIV-1 subtype distribution and epidemiology can assist preventive measures and clinical decisions. Sequence variation may affect antiviral drug resistance development, disease progression, evolutionary rates and transmission routes. RESULTS: We investigated the subtype distribution of HIV-1 in Europe and Israel in a representative sample of patients diagnosed between 2002 and 2005 and related it to the demographic data available. 2793 PRO-RT sequences were subtyped either with the REGA Subtyping tool or by a manual procedure that included phylogenetic tree and recombination analysis. The most prevalent subtypes/CRFs in our dataset were subtype B (66.1%), followed by sub-subtype A1 (6.9%), subtype C (6.8%) and CRF02_AG (4.7%). Substantial differences in the proportion of new diagnoses with distinct subtypes were found between European countries: the lowest proportion of subtype B was found in Israel (27.9%) and Portugal (39.2%), while the highest was observed in Poland (96.2%) and Slovenia (93.6%). Other subtypes were significantly more diagnosed in immigrant populations. Subtype B was significantly more diagnosed in men than in women and in MSM > IDUs > heterosexuals. Furthermore, the subtype distribution according to continent of origin of the patients suggests they acquired their infection there or in Europe from compatriots. CONCLUSIONS: The association of subtype with demographic parameters suggests highly compartmentalized epidemics, determined by social and behavioural characteristics of the patients.


Subject(s)
Epidemics , HIV Infections/epidemiology , HIV-1/genetics , Bayes Theorem , Europe/epidemiology , Female , HIV Infections/virology , HIV-1/classification , Humans , Male , Risk Factors , Risk-Taking , Social Behavior , Socioeconomic Factors
6.
Retrovirology ; 10: 36, 2013 Apr 03.
Article in English | MEDLINE | ID: mdl-23551870

ABSTRACT

BACKGROUND: International travel plays a role in the spread of HIV-1 across Europe. It is, however, not known whether international travel is more important for spread of the epidemic as compared to endogenous infections within single countries. In this study, phylogenetic associations among HIV of newly diagnosed patients were determined across Europe. RESULTS: Data came from the SPREAD programme which collects samples of newly diagnosed patients that are representative for national HIV epidemics. 4260 pol sequences from 25 European countries and Israel collected in 2002-2007 were included.We identified 457 clusters including 1330 persons (31.2% of all patients). The cluster size ranged between 2 and 28. A number of 987 patients (74.2%) were part of a cluster that consisted only of patients originating from the same country. In addition, 135 patients (10.2%) were in a cluster including only individuals from neighboring countries. Finally, 208 patients (15.6%) clustered with individuals from countries without a common border. Clustering with patients from the same country was less prevalent in patients being infected with B subtype (P-value <0.0001), in men who have sex with men (P-value <0.0001), and in recently infected patients (P-value =0.045). CONCLUSIONS: Our findings indicate that the transmission of HIV-1 in Europe is predominantly occurring between patients from the same country. This could have implications for HIV-1 transmission prevention programmes. Because infections through travelling between countries is not frequently observed it is important to have good surveillance of the national HIV-1 epidemics.


Subject(s)
HIV Infections/epidemiology , HIV Infections/virology , HIV-1/classification , HIV-1/genetics , RNA, Viral/genetics , Adult , Cluster Analysis , Europe/epidemiology , HIV Infections/transmission , HIV-1/isolation & purification , Humans , Male , Molecular Epidemiology , Molecular Sequence Data , Phylogeny , Sequence Analysis, DNA , Travel
7.
Harefuah ; 152(8): 477-80, 498, 2013 Aug.
Article in Hebrew | MEDLINE | ID: mdl-24167934

ABSTRACT

Diagnosis of HIV infection is performed via enzyme immunoassay (EIA), an assay based on screening for antibodies against HIV. Confirmation of diagnosis is performed by Western-Blot, a more specific assay directed at a number of viral proteins for which antibodies exist. Routine follow-up of HIV-infected individuals includes measurement of CD4 cell count to evaluate the immune status, of viral load to assess virus replication, and of changes in the viral genome to characterize resistance to drugs and tropism. In addition, absence of the HLA B*57:01 allele is verified before prescription of abacavir, and drug levels of protease-inhibitors are determined in treatment-failing individuals after ruling out other causes of failure. Rapid diagnosis and regular follow-up improve the quality of life of patients and extend their life expectancy, also helping to control the spread of the epidemic at the national level.


Subject(s)
CD4 Lymphocyte Count/methods , HIV Infections/diagnosis , Immunoenzyme Techniques/methods , Anti-HIV Agents/therapeutic use , Blotting, Western , Genome, Viral , HIV Infections/drug therapy , HIV Infections/virology , Humans , Quality of Life , Viral Load , Virus Replication
8.
Harefuah ; 152(4): 230-4, 245-6, 2013 Apr.
Article in Hebrew | MEDLINE | ID: mdl-23844526

ABSTRACT

Resistance testing is part of the routine checkup for HIV carriers in Israel and in most of the developed world. Viruses with mutations which confer resistance to antiretroviral therapy in treated patients and in new HIV carriers are identified. The results of these tests form the basis for updating the HIV treatment guidelines and contribute to the epidemiological and phylogenetic understanding of the HIV epidemic. The viral reverse transcriptase and protease are the targets for most of the antiretroviral drugs in use today and are included in the standard resistance testing. Recently, genotypic examination of the integrase and tropism test to verify use of the HIV CCR5 co-receptor have been introduced to better support treatment decisions and to enable effective use of all available drug combinations. New and more sensitive molecular tests, such as ultra-deep sequencing, are expected to broaden our knowledge of rare mutations not detected by the currently used methodologies. Consequently, we will be able to improve treatment strategy and life quality and increase Life expectancy of HIV carriers.


Subject(s)
Anti-HIV Agents/pharmacology , Drug Resistance, Viral/genetics , HIV Infections , HIV-1 , Antiretroviral Therapy, Highly Active/trends , Genetic Techniques/trends , HIV Infections/diagnosis , HIV Infections/drug therapy , HIV Infections/virology , HIV Reverse Transcriptase/genetics , HIV-1/drug effects , HIV-1/genetics , Humans , Mutagenesis/drug effects , Peptide Hydrolases/genetics , Polymorphism, Genetic/drug effects , Receptors, CCR5/metabolism
9.
iScience ; 26(10): 107986, 2023 Oct 20.
Article in English | MEDLINE | ID: mdl-37854696

ABSTRACT

Ongoing HIV transmission is a public health priority in Indonesia. We developed a new multiassay algorithm (MAA) to identify recent HIV infection. The MAA is a sequential decision tree based on multiple biomarkers, starting with CD4+ T cells >200/µL, followed by plasma viral load (pVL) > 1,000 copies/ml, avidity index (AI) < 0 · 7, and pol ambiguity <0 · 47%. Plasma from 140 HIV-infected adults from 19 hospitals across Indonesia (January 2018 - June 2020) was studied, consisting of a training set (N = 60) of longstanding infection (>12-month) and a test set (N = 80) of newly diagnosed (≤1-month) antiretroviral (ARV) drug naive individuals. Ten of eighty (12 · 5%) newly diagnosed individuals were classified as recent infections. Drug resistance mutations (DRMs) against reverse transcriptase inhibitors were identified in two individuals: one infected with HIV subtype C (K219Q, V179T) and the other with CRF01_AE (V179D). Ongoing HIV transmission, including infections with DRMs, is substantial in Indonesia.

10.
Retrovirology ; 9: 81, 2012 Oct 03.
Article in English | MEDLINE | ID: mdl-23031662

ABSTRACT

BACKGROUND: The effect of drug resistance transmission on disease progression in the newly infected patient is not well understood. Major drug resistance mutations severely impair viral fitness in a drug free environment, and therefore are expected to revert quickly. Compensatory mutations, often already polymorphic in wild-type viruses, do not tend to revert after transmission. While compensatory mutations increase fitness during treatment, their presence may also modulate viral fitness and virulence in absence of therapy and major resistance mutations. We previously designed a modeling technique that quantifies genotypic footprints of in vivo treatment selective pressure, including both drug resistance mutations and polymorphic compensatory mutations, through the quantitative description of a fitness landscape from virus genetic sequences. RESULTS: Genotypic correlates of viral load and CD4 cell count were evaluated in subtype B sequences from recently diagnosed treatment-naive patients enrolled in the SPREAD programme. The association of surveillance drug resistance mutations, reported compensatory mutations and fitness estimated from drug selective pressure fitness landscapes with baseline viral load and CD4 cell count was evaluated using regression techniques. Protease genotypic variability estimated to increase fitness during treatment was associated with higher viral load and lower CD4 cell counts also in treatment-naive patients, which could primarily be attributed to well-known compensatory mutations at highly polymorphic positions. By contrast, treatment-related mutations in reverse transcriptase could not explain viral load or CD4 cell count variability. CONCLUSIONS: These results suggest that polymorphic compensatory mutations in protease, reported to be selected during treatment, may improve the replicative capacity of HIV-1 even in absence of drug selective pressure or major resistance mutations. The presence of this polymorphic variation may either reflect a history of drug selective pressure, i.e. transmission from a treated patient, or merely be a result of diversity in wild-type virus. Our findings suggest that transmitted drug resistance has the potential to contribute to faster disease progression in the newly infected host and to shape the HIV-1 epidemic at a population level.


Subject(s)
Anti-HIV Agents/therapeutic use , CD4 Lymphocyte Count , HIV Infections/drug therapy , HIV-1/enzymology , Peptide Hydrolases/genetics , Polymorphism, Genetic , Viral Load , Viral Proteins/genetics , Adult , Drug Resistance, Viral , Female , HIV Infections/immunology , HIV Infections/virology , HIV-1/drug effects , HIV-1/genetics , HIV-1/physiology , Humans , Male , Peptide Hydrolases/metabolism , Prospective Studies , Viral Proteins/metabolism
11.
J Antimicrob Chemother ; 67(4): 988-94, 2012 Apr.
Article in English | MEDLINE | ID: mdl-22315096

ABSTRACT

OBJECTIVES: Relatively little is known about the development of resistance to protease inhibitors (PIs) in non-B subtypes. In subtype B viruses, L89 is commonly found at position 89 in the HIV protease (PR) gene, whereas M89 is commonly observed as a polymorphism in other subtypes. We compared the frequencies of substitutions at position 89 in PR in tissue culture selections and in clinical databases of PI-naive and PI-experienced populations. METHODS: Representative subtype A/CRF01_AE (n = 2 and 3) and subtype C (n = 5) isolates were cultured in MT-2 cells and cord blood mononuclear cells (CBMCs), respectively, under increasing drug pressure with PIs, and drug resistance mutations were identified. RESULTS: The M89 natural polymorphism in non-B subtypes commonly led to the appearance of an M89T mutation in selections with atazanavir in subtypes A/AE and C, and was accompanied by other previously recognized atazanavir mutations. The M89T mutation contributed to phenotypic resistance to atazanavir and cross-resistance to lopinavir and nelfinavir, but not to other PIs. A shift from a L89 natural polymorphism to L89I/M arose in two of five subtype C selections with PIs. M89I/V/T mutations were acquired by 10%-11% of individuals harbouring non-B subtypes who were failing PI-based regimens, but were rarely observed in drug-naive persons and in patients failing non-PI-based regimens. CONCLUSIONS: The M/L89 natural polymorphism present in non-B subtypes may lead to the M89T mutational pathway conferring resistance to atazanavir, lopinavir and nelfinavir.


Subject(s)
Anti-HIV Agents/pharmacology , Drug Resistance, Viral , HIV Infections/virology , HIV Protease Inhibitors/pharmacology , HIV Protease/genetics , HIV-1/genetics , Polymorphism, Genetic , Amino Acid Substitution , Atazanavir Sulfate , Cells, Cultured , Genotype , HIV-1/classification , HIV-1/isolation & purification , Humans , Leukocytes, Mononuclear/virology , Lopinavir/pharmacology , Nelfinavir/pharmacology , Oligopeptides/pharmacology , Pyridines/pharmacology , Virus Cultivation
12.
J Med Virol ; 84(2): 183-7, 2012 Feb.
Article in English | MEDLINE | ID: mdl-22170535

ABSTRACT

Detection of HIV-1 RNA in semen is used commonly to determine the safety of semen processing procedures before assisted reproductive technology (ART). Using two panels of prepared semen samples containing HIV-1 the performances of protocols from 14 centers have been compared. No false-positive results were detected but false-negative results were frequent when the concentration was below 500 HIV-1 RNA copies/ml of seminal plasma. Frequency of HIV-1 RNA detection was higher on seminal cells than on seminal plasma. Assays (or protocols) for quantifying HIV-1 RNA in semen performed less well than standardized blood plasma assays. The HIV load in seminal plasma could be a useful marker of the risk of sexual transmission of the virus. Its use as a marker of global HAART efficiency in the HIV reservoir needs further study. Standardized assays are required for detection and measurement of HIV-1 RNA in semen samples.


Subject(s)
HIV-1/genetics , RNA, Viral/analysis , Semen/virology , HIV Infections/transmission , HIV Infections/virology , HIV Seropositivity/virology , Humans , Male , Quality Control , Reproductive Techniques, Assisted , Sensitivity and Specificity , Viral Load
13.
Scand J Infect Dis ; 44(1): 65-9, 2012 Jan.
Article in English | MEDLINE | ID: mdl-21923627

ABSTRACT

The diagnosis of HIV, quality of follow-up, and treatment among immigrants are greatly influenced by cultural factors and access to the healthcare system. Israel, an immigrant-based society, features 3 cardinal HIV-positive patient groups, namely non-immigrant Israelis, legal immigrants (mainly from Ethiopia), and illegal African work-immigrants. While the first 2 groups are covered by a national health insurance, the latter group depends on an unstructured system of antiretroviral therapy (ART) supply. In the early 1990s, a national mentoring programme was implemented for legal immigrants. The programme involves community-based Ethiopian mentors who follow HIV-positive Ethiopians. In this retrospective cohort study we reviewed the files of HIV-positive patients diagnosed between 1995 and 2007, focusing on comparison between HIV-positive non-immigrant populations with both legal Ethiopian immigrants and the often overlooked illegal immigrants. Our results point to a substantial rate of loss to follow-up among the illegal immigrants. When comparing non-immigrants to legal immigrants, both feature similar adherence to follow-up, exposure and response to ART, despite profound cultural differences. Our results suggest that ethnic-related obstacles in HIV diagnosis and treatment may be overcome by 'cultural mediators', yet, addressing the silent mass of HIV-positive illegal work-immigrants, who are deprived of such programme benefits, poses a major challenge to Western health authorities.


Subject(s)
Anti-Retroviral Agents/supply & distribution , HIV Infections/ethnology , Healthcare Disparities/ethnology , Adult , Anti-Retroviral Agents/therapeutic use , Cohort Studies , Drug Resistance, Viral , Emigrants and Immigrants/statistics & numerical data , Ethiopia/ethnology , Female , HIV Infections/therapy , Health Services Accessibility , Humans , Israel , Lost to Follow-Up , Male , Middle Aged , Retrospective Studies , Treatment Outcome
14.
AIDS ; 36(13): 1835-1840, 2022 11 01.
Article in English | MEDLINE | ID: mdl-35848510

ABSTRACT

The integrase strand transfer inhibitor (INSTI) dolutegravir is commonly used in combination antiretroviral therapy regimens and retains strong potency even with primary resistance mutations to some other INSTIs. Acquisition of accessory mutations to primary mutations results in significant increases in dolutegravir resistance. Previously, we reported that addition of the secondary mutation T97A can result in rapid treatment failure in individuals with INSTI mutations at positions 140 and 148. Here, we conducted a detailed case study of one of these individuals and find that T97A-containing HIV emerged from a large replicating population from only a few (≤4) viral lineages. When combined with primary INSTI resistance mutations, T97A provides a strong selective advantage; the finding that T97A-containing variants spread by replication and recombination, and persisted for months after discontinuing dolutegravir, has important implications as dolutegravir is rolled out worldwide.


Subject(s)
HIV Infections , HIV Integrase Inhibitors , HIV Integrase , HIV-1 , Quinolones , Drug Resistance, Viral/genetics , HIV Infections/drug therapy , HIV Integrase/genetics , HIV Integrase Inhibitors/pharmacology , HIV Integrase Inhibitors/therapeutic use , HIV-1/genetics , Heterocyclic Compounds, 3-Ring/pharmacology , Heterocyclic Compounds, 3-Ring/therapeutic use , Humans , Mutation , Oxazines , Piperazines , Pyridones/therapeutic use , Quinolones/pharmacology , Recombination, Genetic , Salvage Therapy
15.
Viruses ; 15(1)2022 12 25.
Article in English | MEDLINE | ID: mdl-36680108

ABSTRACT

Background: Molecular epidemiological approaches provide opportunities to characterize HIV transmission dynamics. We analyzed HIV sequences and virus load (VL) results obtained during routine clinical care, and individual's zip-code location to determine utility of this approach. Methods: HIV-1 pol sequences aligned using ClustalW were subtyped using REGA. A maximum likelihood (ML) tree was generated using IQTree. Transmission clusters with ≤3% genetic distance (GD) and ≥90% bootstrap support were identified using ClusterPicker. We conducted Bayesian analysis using BEAST to confirm transmission clusters. The proportion of nucleotides with ambiguity ≤0.5% was considered indicative of early infection. Descriptive statistics were applied to characterize clusters and group comparisons were performed using chi-square or t-test. Results: Among 2775 adults with data from 2014−2015, 2589 (93%) had subtype B HIV-1, mean age was 44 years (SD 12.7), 66.4% were male, and 25% had nucleotide ambiguity ≤0.5. There were 456 individuals in 193 clusters: 149 dyads, 32 triads, and 12 groups with ≥ four individuals per cluster. More commonly in clusters were males than females, 349 (76.5%) vs. 107 (23.5%), p < 0.0001; younger individuals, 35.3 years (SD 12.1) vs. 44.7 (SD 12.3), p < 0.0001; and those with early HIV-1 infection by nucleotide ambiguity, 202/456 (44.3%) vs. 442/2133 (20.7%), p < 0.0001. Members of 43/193 (22.3%) of clusters included individuals in different jurisdictions. Clusters ≥ four individuals were similarly found using BEAST. HIV-1 viral load (VL) ≥3.0 log10 c/mL was most common among individuals in clusters ≥ four, 18/21, (85.7%) compared to 137/208 (65.8%) in clusters sized 2−3, and 927/1169 (79.3%) who were not in a cluster (p < 0.0001). Discussion: HIV sequence data obtained for HIV clinical management provide insights into regional transmission dynamics. Our findings demonstrate the additional utility of HIV-1 VL data in combination with phylogenetic inferences as an enhanced contact tracing tool to direct HIV treatment and prevention services. Trans-jurisdictional approaches are needed to optimize efforts to end the HIV epidemic.


Subject(s)
HIV Infections , HIV Seropositivity , HIV-1 , Adult , Male , Female , Humans , United States , HIV-1/genetics , Phylogeny , Routinely Collected Health Data , Bayes Theorem , Cluster Analysis , Molecular Epidemiology , Genotype
16.
Front Med (Lausanne) ; 9: 979756, 2022.
Article in English | MEDLINE | ID: mdl-36072945

ABSTRACT

Background: HIV persistence during antiretroviral therapy (ART) is the principal obstacle to cure. Lymphoid tissue is a compartment for HIV, but mechanisms of persistence during ART and viral rebound when ART is interrupted are inadequately understood. Metabolic activity in lymphoid tissue of patients on long-term ART is relatively low, and increases when ART is stopped. Increases in metabolic activity can be detected by 18F-fluorodeoxyglucose Positron Emission Tomography (FDG-PET) and may represent sites of HIV replication or immune activation in response to HIV replication. Methods: FDG-PET imaging will be used to identify areas of high and low metabolic uptake in lymphoid tissue of individuals undergoing long-term ART. Baseline tissue samples will be collected. Participants will then be randomized 1:1 to continue or interrupt ART via analytic treatment interruption (ATI). Image-guided biopsy will be repeated 10 days after ATI initiation. After ART restart criteria are met, image-guided biopsy will be repeated once viral suppression is re-achieved. Participants who continued ART will have a second FDG-PET and biopsies 12-16 weeks after the first. Genetic characteristics of HIV populations in areas of high and low FDG uptake will be assesed. Optional assessments of non-lymphoid anatomic compartments may be performed to evaluate HIV populations in distinct anatomic compartments. Anticipated results: We anticipate that PET standardized uptake values (SUV) will correlate with HIV viral RNA in biopsies of those regions and that lymph nodes with high SUV will have more viral RNA than those with low SUV within a patient. Individuals who undergo ATI are expected to have diverse viral populations upon viral rebound in lymphoid tissue. HIV populations in tissues may initially be phylogenetically diverse after ATI, with emergence of dominant viral species (clone) over time in plasma. Dominant viral species may represent the same HIV population seen before ATI. Discussion: This study will allow us to explore utility of PET for identification of HIV infected cells and determine whether high FDG uptake respresents areas of HIV replication, immune activation or both. We will also characterize HIV infected cell populations in different anatomic locations. The protocol will represent a platform to investigate persistence and agents that may target HIV populations. Study protocol registration: Identifier: NCT05419024.

17.
Clin Infect Dis ; 52(11): 1363-70, 2011 Jun.
Article in English | MEDLINE | ID: mdl-21596678

ABSTRACT

BACKGROUND: Centralized data collection and analytic tools facilitate tracing HIV transmission trends at the patient-population level with increasing resolution, complementing behavioral studies while avoiding sampling biases. By several measures, the rate of HIV infection among men who have sex with men (MSM) in Israel increased in the past several years more rapidly than was expected. We describe features of the data that connect this increase to behavioral changes. METHODS: We retrospectively analyzed data from the national HIV reference laboratory and the national HIV and sexually transmitted infections registries. We examined changes in selected epidemiologic and clinical parameters and in the pattern of drug-resistant virus transmission among MSM in Israel. In particular, virus isolates from 296 MSM (23.8% of all MSM who received a diagnosis) were genotyped, drug-resistance conferring mutations were characterized, and phylogenetic trees were constructed. RESULTS: Compared with earlier years, during 2007-2009 MSM were more often infected with drug-resistant virus before treatment initiation, were coinfected with syphilis, and received a diagnosis during acute retroviral syndrome. Phylogenetic analysis suggested frequent transmission of drug-resistant HIV by drug-treated individuals to >1 partner. Secondary transmission of resistant virus by drug-naive patients is also consistent with the phylogenetic patterns. In addition, non-B HIV subtypes began to appear among MSM. CONCLUSIONS: Together, our findings suggest that the sexual behavior of MSM, both HIV-infected and uninfected, has become riskier, contributing to the number of those seeking early clarification of status, to syphilis comorbidity, and to the spread of drug resistance. These findings call for action by public health planners and community-based organizations aimed at increasing awareness of the risks, bringing a change in attitude and establishing safe sex norms.


Subject(s)
HIV Infections/epidemiology , Homosexuality, Male , Risk-Taking , Adolescent , Adult , Amino Acid Substitution/genetics , Anti-HIV Agents/pharmacology , Anti-HIV Agents/therapeutic use , Drug Resistance, Viral , Genotype , HIV/drug effects , HIV/genetics , HIV/isolation & purification , HIV Infections/drug therapy , HIV Infections/pathology , HIV Infections/virology , Humans , Incidence , Israel/epidemiology , Male , Molecular Epidemiology , Mutation, Missense , Phylogeny , Retrospective Studies , Young Adult
18.
J Clin Microbiol ; 49(7): 2480-4, 2011 Jul.
Article in English | MEDLINE | ID: mdl-21562110

ABSTRACT

Rapid detection of drug-resistant bacteria in clinical samples plays an instrumental role in patients' infection management and in implementing effective infection control policies. In the study described in this report, we validated a multiplex TaqMan real-time quantitative PCR (qPCR) assay for the detection of bla(KPC) genes and the human RNase P gene in Bactec blood culture bottles. The MagNA Pure LC (version 2.0) instrument was utilized to extract nucleic acids from the inoculated broth, while bovine serum albumin (BSA) was utilized as the PCR inhibitor reliever. The multiplex assay, which was specific for the detection of bla(KPC) genes, had a limit of detection of 19 CFU per reaction mixture with human blood-spiked Bactec bottles. Of the 323 Bactec blood culture sets evaluated, the same 55 (17%) blood cultures positive for carbapenem-resistant bacteria by culture were also positive by the validated qPCR assay. Thus, the sensitivity, specificity, positive predictive value, and negative predictive value of the qPCR assay compared to the results of culture were all 100%. bla(KPC) genes were also detected from the same Bactec bottle broth after manual extraction with a QIAamp DNA minikit; however, there was an average 3-threshold-cycle delay in the qPCR readings. With the limited therapeutic options available, the accurate and rapid detection of bla(KPC)-possessing bacteria by the described bla(KPC)/RNase P assay will be a crucial first step in ensuring optimal clinical outcomes and infection control.


Subject(s)
Bacterial Proteins/genetics , Bacteriological Techniques/methods , Enterobacteriaceae/enzymology , Enterobacteriaceae/genetics , Polymerase Chain Reaction/methods , beta-Lactamases/genetics , Blood/microbiology , Enterobacteriaceae/growth & development , Humans , Predictive Value of Tests , Sensitivity and Specificity , Time Factors
19.
J Obstet Gynaecol Can ; 33(7): 720-724, 2011 Jul.
Article in English | MEDLINE | ID: mdl-21749748

ABSTRACT

OBJECTIVE: To evaluate the outcome of infants born to mothers with varicella zoster virus (VZV) infection in pregnancy who had second trimester amniocentesis for detection of placental transfer. METHODS: We interviewed women who had had VZV infection in pregnancy and who underwent diagnostic amniocentesis to detect transplacental infection using both polymerase chain reaction (PCR) and cell culture methods to characterize their children's clinical and psychomotor development. RESULTS: Twenty women who had a diagnosis of primary VZV during pregnancy were available for interview. The mean gestational age at which primary VZV was acquired was 11±3.5 weeks. One infant had hypospadias and developmental delay. He was born to an epileptic mother who had been treated during pregnancy with sodium valproate and clonazepam. Another infant had abnormal brainstem auditory-evoked potentials. All other infants were reported to have normal clinical and psychomotor development. CONCLUSION: In cases of varicella infection during pregnancy, negative studies of amniotic fluid using PCR may contribute to decision making.


Subject(s)
Amniocentesis , Chickenpox/complications , Chickenpox/transmission , Pregnancy Complications, Infectious/virology , Pregnancy Outcome , Adult , Chickenpox/diagnosis , Female , Gestational Age , Humans , Infant, Newborn , Infectious Disease Transmission, Vertical , Middle Aged , Pregnancy , Pregnancy Complications, Infectious/diagnosis , Retrospective Studies
20.
Harefuah ; 150(3): 246-50, 304, 303, 2011 Mar.
Article in Hebrew | MEDLINE | ID: mdl-21574358

ABSTRACT

More than ten years have eLapsed since highly active antiretroviral therapy [HAART] was introduced to treat people living with HIV. Unfortunately, there is still no light at the end of the road leading to complete eradication of the virus and full recovery, or to the development of immunization that will be safe and effective in the long run. Nevertheless, in recent years with the introduction of more effective and safer drugs, that also have a high genetic barrier, and a more comfortable pharmacological profile and better tolerance, HIV has become a manageable chronic disease and patients can live many years with a good quality of life. These developments have significantly influenced epidemiological, therapeutic, psychological and social aspects of the AIDS epidemic.


Subject(s)
Acquired Immunodeficiency Syndrome/epidemiology , Antiretroviral Therapy, Highly Active/methods , HIV Infections/epidemiology , Acquired Immunodeficiency Syndrome/drug therapy , Acquired Immunodeficiency Syndrome/physiopathology , Anti-HIV Agents/adverse effects , Anti-HIV Agents/therapeutic use , Antiretroviral Therapy, Highly Active/adverse effects , Drug Design , HIV Infections/drug therapy , HIV Infections/physiopathology , Humans , Quality of Life
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