HIV-1 genetic diversity in antenatal cohort, Canada.
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ABSTRACT:
SUBMITTER: Akouamba BS
PROVIDER: S-EPMC3320510 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Near full-length genomes of 4 unclassified HIV-1 variants infecting patients enrolled in an antenatal cohort in Canada were obtained by sequencing. All 4 variants showed original recombination profiles, including A1/A2/J, A1/D, and A1/G/J/CRF11_cpx structures. Identification of these variants highlights the growing prevalence of unique recombinant forms of HIV-1 in North America.
| S-EPMC3204757 | biostudies-literature
Project description:ObjectiveThis study was designed to provide information on the genetic diversity of HIV-1 and drug resistance mutations in Nigeria, as there is limited understanding of variants circulating in the country.MethodsWe used an advanced next-generation sequencing platform, Primer ID, to: investigate the presence of high and low abundance drug resistance mutations; characterize preexisting Integrase Strand Transfer Inhibitor (INSTI) mutations in antiretroviral therapy (ART)-experienced but dolutegravir-naive individuals; detect recent HIV-1 infections and characterize subtype diversity from a cohort of people with HIV-1 (PWH).ResultsHIV-1 subtype analysis revealed the predominance of CRF02_AG and subtype G in our study population. At detection sensitivity of 30% abundance, drug resistance mutations (DRMs) were identified in 3% of samples. At a sensitivity level of 10%, DRMs were identified in 27.3% of samples. We did not detect any major INSTI mutation associated with dolutegravir-resistance. Only one recent infection was detected in our study population.ConclusionOur study suggests that dolutegravir-containing antiretroviral regimens will be effective in Nigeria. Our study also further emphasizes the high genetic diversity of HIV-1 in Nigeria and that CRF02_AG and subtype G are the dominant circulating forms of HIV-1 in Nigeria. These two circulating forms of the virus are largely driving the epidemic in the country.
| S-EPMC8654252 | biostudies-literature
Project description:PURPOSE:The LHIV-Manitoba cohort was developed as a way to provide a comprehensive source of HIV-related health information in the central Canadian Prairie province of Manitoba. The cohort will provide important information as we aim to better understand local HIV epidemiology and address key knowledge and practice gaps in HIV prevention, treatment and care programming in the province. PARTICIPANTS:In total, 890 individuals, aged 18 or older and living or receiving HIV care in Manitoba are enrolled in the cohort. A complete clinical dataset exists for 725 participants, which includes variables on sociodemographic characteristics, comorbidities and co-infections, self-reported HIV exposure categories and HIV clinical indicators. A limited clinical dataset exists for an additional 165 individuals who were enrolled posthumously. 97.5% of cohort participants' clinical records are linked to provincial administrative health datasets. FINDINGS TO DATE:The average age of cohort participants is 49.7 years. Approximately three-quarters of participants are male, 42% self-identified as white and 42% as Indigenous. The majority of participants (64%) reported condomless vaginal sex as a risk exposure for HIV. Nearly one-fifth (18%) of participants have an active hepatitis C virus infection and the cohort's median CD4 count increased from 316 cells/mm3 to 518 cells/mm3 between time of entry into care and end of the first quarter in 2019. FUTURE PLANS:The LHIV-Manitoba cohort is an open cohort, and as such, participant enrolment, data collection and analyses will be continually ongoing. Future analyses will focus on the impact of provincial drug plans on clinical outcomes, determinants of mortality among cohort participants and deriving estimates for a local HIV care cascade.
| S-EPMC7259858 | biostudies-literature
Project description:Two genetically dissimilar sequence type 1 clades dominate the serotype VI group B Streptococcus population of strains causing invasive disease in Canada. Isolates of this rare serotype, recovered mainly from adult patients, were all susceptible to penicillin and vancomycin. However, we observed resistance to erythromycin and clindamycin.
| S-EPMC6154151 | biostudies-literature
Project description:Epstein-Barr virus (EBV) is associated with several types of cancers including Hodgkin's lymphoma (HL) and nasopharyngeal carcinoma (NPC). EBV-encoded latent membrane protein 1 (LMP1), a multifunctional oncoprotein, is a powerful activator of the transcription factor NF-κB, a property that is essential for EBV-transformed lymphoblastoid cell survival. Previous studies reported LMP1 sequence variations and induction of higher NF-κB activation levels compared to the prototype B95-8 LMP1 by some variants. Here we used biopsies of EBV-associated cancers and blood of individuals included in the Swiss HIV Cohort Study (SHCS) to analyze LMP1 genetic diversity and impact of sequence variations on LMP1-mediated NF-κB activation potential. We found that a number of variants mediate higher NF-κB activation levels when compared to B95-8 LMP1 and mapped three single polymorphisms responsible for this phenotype: F106Y, I124V and F144I. F106Y was present in all LMP1 isolated in this study and its effect was variant dependent, suggesting that it was modulated by other polymorphisms. The two polymorphisms I124V and F144I were present in distinct phylogenetic groups and were linked with other specific polymorphisms nearby, I152L and D150A/L151I, respectively. The two sets of polymorphisms, I124V/I152L and F144I/D150A/L151I, which were markers of increased NF-κB activation in vitro, were not associated with EBV-associated HL in the SHCS. Taken together these results highlighted the importance of single polymorphisms for the modulation of LMP1 signaling activity and demonstrated that several groups of LMP1 variants, through distinct mutational paths, mediated enhanced NF-κB activation levels compared to B95-8 LMP1.
| S-EPMC3285206 | biostudies-literature
Project description:PurposeThe Seek and Treat for Optimal Prevention of HIV/AIDS (STOP HIV/AIDS) Program Evaluation (SHAPE) study is a longitudinal cohort developed to monitor the progress of an HIV testing and treatment expansion programme across the province of British Columbia (BC). The study considers how sociostructural determinants such as gender, age, sexual identity, geography, income and ethnicity influence engagement in HIV care.ParticipantsBetween January 2016 and September 2018, 644 BC residents who were at least 19 years old and diagnosed with HIV were enrolled in the study and completed a baseline survey. Participants will complete two additional follow-up surveys (18 months apart) about their HIV care experiences, with clinical follow-up ongoing.Findings to dateAnalyses on baseline data have found high levels of HIV care engagement and treatment success among SHAPE participants, with 95% of participants receiving antiretroviral therapy and 90% having achieved viral suppression. However, persistent disparities in HIV treatment outcomes related to age, injection drug use and housing stability have been identified and require further attention when delivering services to marginalised groups.Future plansOur research will examine how engagement in HIV care evolves over time, continuing to identify barriers and facilitators for promoting equitable access to treatment and care among people living with HIV. A qualitative research project, currently in the formative phase, will compliment quantitative analyses by taking a strengths-based approach to exploring experiences of engagement and re-engagement in HIV treatment among individuals who have experienced delayed treatment initiation or treatment interruptions.
| S-EPMC7228510 | biostudies-literature
Project description:HIV-1 strain diversity in Bulgaria is extensive and includes contributions from nearly all major subtypes and the Circulating Recombinant Forms (CRF): 01_AE, 02_AG, and 05_DF. Prior to this study, HIV-1 sequence information from Bulgaria has been based solely on the pro-RT gene, which represent less than 15% of the viral genome. To further characterize HIV-1 in Bulgaria, assess participant risk behaviors, and strengthen knowledge of circulating strains in the region, the study "Genetic Subtypes of HIV-1 in Bulgaria (RV240)" was conducted. This study employed the real time-PCR based Multi-region Hybridization Assay (MHA) B/non-B and HIV-1 sequencing to survey 215 of the approximately 1100 known HIV-1 infected Bulgarian adults (2008-2009) and determine if they were infected with subtype B HIV-1. The results indicated a subtype B prevalence of 40% and demonstrate the application of the MHA B/non-B in an area containing broad HIV-1 strain diversity. Within the assessed risk behaviors, the proportion of subtype B infection was greatest in men who have sex with men and lowest among those with drug use risk factors. During this study, 15 near full-length genomes and 22 envelope sequences were isolated from study participants. Phylogenetic analysis shows the presence of subtypes A1, B, C, F1, and G, CRF01_AE, CRF02_AG, CRF05_DF, and one unique recombinant form (URF). These sequences also show the presence of two strain groups containing participants with similar risk factors. Previous studies in African and Asian cohorts have shown that co-circulation of multiple subtypes can lead to viral recombination within super-infected individuals and the emergence of new URFs. The low prevalence of URFs in the presence of high subtype diversity in this study, may be the result of successful infection prevention and control programs. Continued epidemiological monitoring and support of infection prevention programs will help maintain control of the HIV-1 epidemic in Bulgaria.
| S-EPMC6538145 | biostudies-literature
Project description:One of the factors determining a high degree of heterogeneity in the HIV population is recombination-based variation, which leads to the emergence of the virus variants with a mosaic genome. An example is CRF63_02A1, an HIV-1 variant currently spreading in the Siberian region of Russia. To prove that this HIV-1 variant is a new circulating recombinant form that had emerged as a result of repeated recombination between CRF02_AG and subtype A, we have isolated seven full-length HIV genomes and theoretically analyzed them, that is, reconstructed the phylogenetic relationships, determined recombination breakpoints and regions, and compared them with the regions known for CRF02_AG.
| S-EPMC4046202 | biostudies-literature
Project description:ImportanceWomen who experience imprisonment have high morbidity and an increased risk of adverse pregnancy outcomes. Antenatal care could modify pregnancy-related risks, but there is a lack of evidence regarding antenatal care in this population.ObjectivesTo examine antenatal care quality indicators for women who experience imprisonment and to compare these data with data for the general population.Design, setting, and participantsThis population-based, retrospective cohort study used linked correctional and health administrative data from women released from provincial prison in Ontario, Canada, in 2010 and women in the general population with deliveries at 20 weeks' gestation or greater from January 1, 2005, to December 31, 2015. Data analysis was performed from January 1, 2017, to May 4, 2020.ExposuresPregnancies in women with time in prison during pregnancy (prison pregnancies), pregnancies in women with time in prison but not while pregnant (prison control pregnancies), and pregnancies in women in the general population (general population pregnancies).Main outcomes and measuresAntenatal care quality indicators: first-trimester visit, first-trimester ultrasonography, and 8 or more antenatal care visits.ResultsA total of 626 prison pregnancies in 529 women (mean [SD] age, 26.6 [5.4] years), 2327 prison control pregnancies in 1570 women (mean [SD] age, 26.2 [5.4] years), and 1 308 879 general population pregnancies in 884 063 women (mean [SD] age, 30.3 [5.3] years) were studied. Of 626 prison pregnancies, 193 women (30.8%; 95% CI, 27.1%-34.6%) had a first-trimester visit, 272 (48.4%; 95% CI, 44.4%-52.4%) had at least 8 antenatal care visits, and 209 (34.6%; 95% CI, 31.0%-38.4%) received first-trimester ultrasonography. In 2327 prison control pregnancies, 1106 women (47.5%; 95% CI, 45.3%-49.8%) had a first-trimester visit, 1356 (59.2%; 95% CI, 56.9%-61.4%) had 8 or more antenatal care visits, and 893 (38.5%; 95% CI, 36.4%-40.6%) received first-trimester ultrasonography. Compared with 1 308 879 general population pregnancies, the odds of antenatal care were lower for the first-trimester visit (odds ratios [ORs], 0.11 [95% CI, 0.09-0.13] in prison pregnancies and 0.23 [95% CI, 0.21-0.25] in prison control pregnancies), 8 or more antenatal care visits (ORs, 0.16 [95% CI, 0.14-0.19] in prison pregnancies and 0.25 [95% CI, 0.23-0.28] in prison control pregnancies), and first-trimester ultrasonography (ORs, 0.43 [95% CI, 0.36-0.50] in prison pregnancies and 0.51 [95% CI, 0.46-0.55] in prison control pregnancies).Conclusions and relevanceThis study found that women who experienced imprisonment were substantially less likely to receive adequate antenatal care than were women in the general population whether or not they were in prison during pregnancy. Efforts are needed to improve antenatal care for this population both in prison and in the community.
| S-EPMC7411537 | biostudies-literature
Project description:BackgroundLate HIV diagnosis is associated with increased AIDS-related morbidity and mortality as well as an increased risk of HIV transmission. In this study, we quantified and characterized missed opportunities for earlier HIV diagnosis in British Columbia (BC), Canada.DesignRetrospective cohort.MethodsA missed opportunity was defined as a healthcare encounter due to a clinical manifestation which may be caused by HIV infection, or is frequently present among those with HIV infection, but no HIV diagnosis followed within 30 days. We developed an algorithm to identify missed opportunities within one, three, and five years prior to diagnosis. The algorithm was applied to the BC STOP HIV/AIDS population-based cohort. Eligible individuals were ≥18 years old, and diagnosed from 2001-2014. Multivariable logistic regression identified factors associated with missed opportunities.ResultsOf 2119 individuals, 7%, 12% and 14% had ≥1 missed opportunity during one, three and five years prior to HIV diagnosis, respectively. In all analyses, individuals aged ≥40 years, heterosexuals or people who ever injected drugs, and those residing in Northern health authority had increased odds of experiencing ≥1 missed opportunity. In the three and five-year analysis, individuals with a CD4 count <350 cells/mm3 were at higher odds of experiencing ≥1 missed opportunity. Prominent missed opportunities were related to recurrent pneumonia, herpes zoster/shingles among younger individuals, and anemia related to nutritional deficiencies or unspecified cause.ConclusionsBased on our newly-developed algorithm, this study demonstrated that HIV-diagnosed individuals in BC have experienced several missed opportunities for earlier diagnosis. Specific clinical indicator conditions and population sub-groups at increased risk of experiencing these missed opportunities were identified. Further work is required in order to validate the utility of this proposed algorithm by establishing the sensitivity, specificity, positive and negative predictive values corresponding to the incidence of the clinical indicator conditions among both HIV-diagnosed and HIV-negative populations.
| S-EPMC6428302 | biostudies-literature