The Long Noncoding RNA HEAL Regulates HIV-1 Replication through Epigenetic Regulation of the HIV-1 Promoter.

A major challenge in finding a cure for HIV-1/AIDS is the difficulty in identifying and eradicating persistent reservoirs of replication-competent provirus. Long noncoding RNAs (lncRNAs, >200 nucleotides) are increasingly recognized to play important roles in pathophysiology. Here, we report the first genome-wide expression analysis of lncRNAs in HIV-1-infected primary monocyte-derived macrophages (MDMs). We identified an lncRNA, which we named HIV-1-enhanced lncRNA (HEAL), that is upregulated by HIV-1 infection of MDMs, microglia, and T lymphocytes. Peripheral blood mononuclear cells of HIV-1-infected individuals show elevated levels of HEAL Importantly, HEAL is a broad enhancer of multiple HIV-1 strains because depletion of HEAL inhibited X4, R5, and dual-tropic HIV replications and the inhibition was rescued by HEAL overexpression. HEAL forms a complex with the RNA-binding protein FUS, which facilitates HIV replication through at least two mechanisms: (i) HEAL-FUS complex binds the HIV promoter and enhances recruitment of the histone acetyltransferase p300, which positively regulates HIV transcription by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin-dependent kinase 2 gene, CDK2, to enhance CDK2 expression. Notably, HEAL knockdown and knockout mediated by RNA interference (RNAi) and CRISPR-Cas9, respectively, prevent HIV-1 recrudescence in T cells and microglia upon cessation of azidothymidine treatment in vitro Our results suggest that silencing of HEAL or perturbation of the HEAL-FUS ribonucleoprotein complex could provide a new epigenetic silencing strategy to eradicate viral reservoirs and effect a cure for HIV-1/AIDS.IMPORTANCE Despite our increased understanding of the functions of lncRNAs, their potential to develop HIV/AIDS cure strategies remains unexplored. A genome-wide analysis of lncRNAs in HIV-1-infected primary monocyte-derived macrophages (MDMs) was performed, and 1,145 differentially expressed lncRNAs were identified. An lncRNA named HIV-1-enhanced lncRNA (HEAL) is upregulated by HIV-1 infection and promotes HIV replication in T cells and macrophages. HEAL forms a complex with the RNA-binding protein FUS to enhance transcriptional coactivator p300 recruitment to the HIV promoter. Furthermore, HEAL knockdown and knockout prevent HIV-1 recrudescence in T cells and microglia upon cessation of azidothymidine treatment, suggesting HEAL as a potential therapeutic target to cure HIV-1/AIDS

Accelerated avian invasion into the Mediterranean region endangers biodiversity and mandates international collaboration

Policy DirectionDespite posing a serious threat to global biodiversity, national and international management efforts have not been able to limit the spread of most invasive species. In highly dispersive species, local invasions may be followed by regional range expansion that crosses international borders. In such cases, independent management efforts of the invading population may be futile unless international collaboration is practiced. 2. We focus on the ongoing human-mediated invasion of the common myna Acridotheres tristis into the Mediterranean basin, a region rich in overall numbers of species and endemic species, where common mynas have been introduced into a handful of countries. Some introductions were followed by subsequent range expansions into neighbouring countries. This species poses major threats to the biodiversity of the Mediterranean which is already susceptible to biodiversity loss as the result of ongoing land use and climate changes. Without action, this species and possibly others similar to it, could have severe consequences for native ecosystems. 3. Policy implications. Given the regional scope of its invasion in the Mediterranean basin, common myna management requires an international collaboration to successfully prevent additional introductions and range expansions and to avoid accelerating threats to Mediterranean biodiversity, already at risk as a result of ongoing changes in land use and climate. We argue that international reciprocal transfer of information and the development of regional mitigation are essential for the successful management of the invasion of the common myna and other species into the Mediterraneaninfo:eu-repo/semantics/publishedVersio

Factors Associated with Severity of COVID-19 Disease in a Multicenter Cohort of People with HIV in the United States, March-December 2020

Background: Understanding the spectrum of COVID-19 in people with HIV (PWH) is critical to provide clinical guidance and risk reduction strategies.Setting:Centers for AIDS Research Network of Integrated Clinic System, a US multisite clinical cohort of PWH in care.Methods:We identified COVID-19 cases and severity (hospitalization, intensive care, and death) in a large, diverse HIV cohort during March 1, 2020-December 31, 2020. We determined predictors and relative risks of hospitalization among PWH with COVID-19, adjusted for disease risk scores. Results: Of 16,056 PWH in care, 649 were diagnosed with COVID-19 between March and December 2020. Case fatality was 2%; 106 (16.3%) were hospitalized, and 12 died. PWH with current CD4 count <350 cells/mm3[aRR 2.68; 95% confidence interval (CI): 1.93 to 3.71; P < 0.001] or lowest recorded CD4 count <200 cells/mm3(aRR 1.67; 95% CI: 1.18 to 2.36; P < 0.005) had greater risks of hospitalization. HIV viral load and antiretroviral therapy status were not associated with hospitalization, although most of the PWH were suppressed (86%). Black PWH were 51% more likely to be hospitalized with COVID-19 compared with other racial/ethnic groups (aRR 1.51; 95% CI: 1.04 to 2.19; P = 0.03). Chronic kidney disease, chronic obstructive pulmonary disease, diabetes, hypertension, obesity, and increased cardiovascular and hepatic fibrosis risk scores were associated with higher hospitalization risk. PWH who were older, not on antiretroviral therapy, and with current CD4 count <350 cells/mm3, diabetes, and chronic kidney disease were overrepresented among PWH who required intubation or died. Conclusions: PWH with CD4 count <350 cells/mm3, and a history of CD4 count <200 cells/mm3, have a clear excess risk of severe COVID-19, accounting for comorbidities associated with severe outcomes. PWH with these risk factors should be prioritized for COVID-19 vaccination and early treatment and monitored closely for worsening illness

Racial and ethnic disparities in coronavirus disease 2019 disease incidence independent of comorbidities, among people with HIV in the United States

Objectives: To define the incidence of clinically detected coronavirus disease 2019 (COVID-19) in people with HIV (PWH) in the United States and evaluate how racial and ethnic disparities, comorbidities, and HIV-related factors contribute to risk of COVID-19. Design: Observational study within the CFAR Network of Integrated Clinical Systems cohort in seven cities during 2020. Methods: We calculated cumulative incidence rates of COVID-19 diagnosis among PWH in routine care by key characteristics including race/ethnicity, current and lowest CD4þ cell count, and geographic area. We evaluated risk factors for COVID-19 among PWH using relative risk regression models adjusted with disease risk scores. Results: Among 16 056 PWH in care, of whom 44.5% were black, 12.5% were Hispanic, with a median age of 52 years (IQR 40 - 59), 18% had a current CD4þ cell count less than 350 cells/ml, including 7% less than 200; 95.5% were on antiretroviral therapy (ART), and 85.6% were virologically suppressed. Overall in 2020, 649 PWH were diagnosed with COVID-19 for a rate of 4.94 cases per 100 person-years. The cumulative incidence of COVID-19 was 2.4-fold and 1.7-fold higher in Hispanic and black PWH respectively, than non-Hispanic white PWH. In adjusted analyses, factors associated with COVID-19 included female sex, Hispanic or black identity, lowest historical CD4þ cell count less than 350 cells/ml (proxy for CD4þ nadir), current low CD4þ : CD8þ ratio, diabetes, and obesity. Conclusion: Our results suggest that the presence of structural racial inequities above and beyond medical comorbidities increased the risk of COVID-19 among PWH. PWH with immune exhaustion as evidenced by lowest historical CD4þ cell count or current low CD4þ : CD8þ ratio had greater risk of COVID-19

Methods to detect spatial biases in tracking studies caused by differential representativeness of individuals, populations and time

Este artículo contiene 20 páginas, 6 figuras, 4 tablas.Aim: Over the last decades, the study of movement through tracking data has grown exceeding the expectations of movement ecologists. This has posed new challenges, specifically when using individual tracking data to infer higher- level distributions (e.g. population and species). Sources of variability such as individual site fidelity (ISF), en-vironmental stochasticity over time, and space-use variability across species ranges must be considered, and their effects identified and corrected, to produce accurate estimates of spatial distribution using tracking data. Innovation: We developed R functions to detect the effect of these sources of vari-ability in the distribution of animal groups when inferred from individual tracking data. These procedures can be adapted for their use in most tracking datasets and tracking techniques. We demonstrated our procedures with simulated datasets and showed their applicability on a real-world dataset containing 1346 year- round migratory trips from 805 individuals of three closely related seabird species breeding in 34 colonies in the Mediterranean Sea and the Atlantic Ocean, spanning 10 years. We detected an effect of ISF in one of the colonies, but no effect of the environmental stochasticity on the distribution of birds for any of the species. We also identified among-colony variability in nonbreeding space use for one species, with significant effects of popu-lation size and longitude. Main conclusions: This work provides a useful, much- needed tool for researchers using animal tracking data to model species distributions or establish conservation measures. This methodology may be applied in studies using individual tracking data to accurately infer the distribution of a population or species and support the deline-ation of important areas for conservation based on tracking data. This step, designed to precede any analysis, has become increasingly relevant with the proliferation of studies using large tracking datasets that has accompanied the globalization process in science driving collaborations and tracking data sharing initiatives.We thank the following institutions for funding: EU H2020 pro-gramme through grant 634495; Seventh Framework Programme (Research Executive Agency) through Marie Curie Career Integration Grant 618841 (FP7-PEOPLE-2013- CIG); ESFRI LifeWatch Project; LIFE programme of the European Commission through projects LIFE10 NAT/MT090 and LIFE11 NAT/IT/000093; Ministerio de Ciencia e Innovación/Ministerio de Economia y Competitividad (Spain) through projects CGL2009- 11278/BOS, CGL2013-42585-P, C G L 2 0 1 3 - 4 2 2 0 3 - R , C G L 2 0 16 - 7 8 5 3 0 - R a n d C G L 2 0 17- 8 52 10 - P ; Organismo Autónomo de Parques Nacionales (Spain) through pro-ject 1248/2014; Fundação para a Ciência e a Tecnologia (MCTES, Portugal) through projects MARE-UID/MAR/04292/2019; IF/00502/2013/CP1186/CT0003, PTDC/BIA-ANM/3743/2014, PTDC/MAR-PRO/0929/2014, UID/AMB/50017/2019 and UIDP/50017/2020 + UIDB/50017/2020 (to CESAM); Office Français de la Biodiversité (France), through the Programme PACOMM, Natura2000 en mer; Hellenic Bird Ringing Centre; MSDEC (Malta). VMP was supported by pre-doctoral contract BES-2014- 068025 of the Spanish Ministerio de Industria, Economía y Competitividad; MM by grant SFRH/BPD/47047/2008 from the Portuguese Foundation for Science and Technology; JMRG by Ph.D. grant AP2009-2163 from the Spanish Ministerio de Educación; GDO and MMü by Ornis italica and by the Regione Siciliana and Assessorato Risorse Agricole e Alimentari thoriugh a grant to the Ringing Unit of Palermo; VHP by grant SFRH/BPD/85024/2012 from the Portuguese Foundation for Science and Technology; VN by grant SFRH/BPD/88914/2012 from the Portuguese Foundation for Science and Technology; and JN by the Spanish National Programme Ramón y Cajal (RYC-2015- 17809); GK and SX were partially funded by the Operational Program “Environment and Sustainable Development” (EPPERAA) of the National Strategic Reference Framework (NSRF) 2007-2013, co- financed by the ERDF and Greek EDP; FdF by a Ph.D. grant from the Coordination for the Improvement of Higher Education Personnel (CAPES—Brazilian government agency; Bex Process 1307/13-4); ZZ by a PhD grant from the University of Barcelona (APIF/2012); MCF by a PhD grant from the University of Barcelona; and RR by post-doctoral contracts of the PLEAMAR programme from MINECO and Fundación Biodiversidad (2017/2349), and Ministerio de Ciencia, in-novación y Universidades (RYC-2017- 22055). This publication is part of the project I+D+i/PID2020-117155GB-I00, funded by MCIN/ AEI/10.13039/501100011033.Peer reviewe

HIV and Aging Reconsidering the Approach to Management of Comorbidities

Health care for older adults with human immunodeficiency virus can be highly complex, resource intensive, and carry a high administrative burden. Data from aging longitudinal cohorts and feedback from the human immunodeficiency virus community suggest that the current model is not meeting the needs of these older adults. We introduce the 6 Ms approach, which acknowledges the multicomplexity of older adults with human immunodeficiency virus, simplifies geriatric principles for non-geriatrics-trained providers, and minimizes extensive training and specialized screening tests or tools. Implementing novel approaches to care requires support at local/national levels

Investigating the Role of Vaccinia Virus Protein A34 in Viral Morphogenesis and Its Interaction with B5 and A33

Thesis (Ph.D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Microbiology and Immunology, 2010.Vaccinia virus, the most studied member of Poxviridae family, is well known as the live vaccine used in the global eradication of smallpox. This large complex DNA virus, which replicates in the cytoplasm of cells, produces three forms of virus; intracellular mature virus (IMV) which accounts for a large majority of the progeny virions, intracellular enveloped virus (IEV), and extracellular virus (EV). EV is further defined into two groups. Virions that remain on the cell surface are cell-associated enveloped virus (CEV) and those released from the cell surface are extracellular enveloped virus (EEV). CEV are responsible for cell-to-cell spread and EEV are responsible for long-range dissemination of the virus. A34, A33, and B5 are proteins found specifically on the enveloped form of the virus (IEV, CEV and EEV) and A36 is found exclusively on IEV. Deletion of any one of these genes attenuates the virus and the mutants display reduced plaque size on cell monolayer cultures. While interactions between A33-A36, A33-B5, A34-A36, and A34-B5 have been reported, only the A33-A36 interaction has been shown to have a specific function. In addition, while there have been a fair number of studies on A33, A36 and B5, less information is known about A34. The overall goal of this research project was to determine the role of A34 in viral morphogenesis and how it interacts with other enveloped viral proteins. A recombinant virus that expresses B5-GFP in place of B5 and had the A34 gene deleted (vB5R-GFP/ΔA34R) was created to look at viral morphogenesis in the absence of A34. Fluorescent microscopy and subcellular fractionation of cells infected with vB5R-GFP/ΔA34R revealed that in the absence of A34, B5-GFP was mislocalized in the endoplasmic reticulum and failed to traffic to the site of wrapping compared to cells infected with a normal B5-GFP expressing virus (vB5R-GFP). Trans-complementation assays in cells infected with vB5R-GFP/ΔA34 showed that the luminal domain of A34 was responsible for the proper trafficking of B5-GFP and correlated with co-immunoprecipitation studies in which an interaction between A34 and B5-GFP was only detected when the luminal domain of A34 was present. Next EEV from vB5R-GFP/ΔA34 infected cells were analyzed and found to contain greatly diminished levels of B5-GFP compared to the levels found in EEV from vB5R-GFP infected cells. These results show that during infection, A34 is required for the proper targeting of B5-GFP to the site of wrapping and incorporation into enveloped virions. In addition, we show that A34 and B5 interact through their luminal domains. The next objective was to further define the region within the luminal domain of A34 required for interaction. Several mutants of A34 were created and co-expressed with B5 to test for interaction by co-immunoprecipitation. Results from the luminal domain deletion mutants and truncation mutants revealed that A34 residues 1-80 were sufficient for interaction and residues 1-120 were required for full interaction. When small A34 regions were tested for interaction, we found two separate regions that were able to interact with B5. We hypothesized that A34 localized to the site of wrapping through targeting signals in its transmembrane or cytoplasmic domain and that expressing soluble A34 or an interacting A34 region during normal infection would act as a dominant negative displacing endogenous A34 and mislocalizing B5. Immunofluorescence studies of cells expressing the small A34 regions during infection showed that only full length soluble A34, which contains both regions, mislocalized B5. This set of data demonstrates that there are two sites of interaction between A34 and B5. A33 has also been reported to require A34 for proper localization and incorporation into enveloped virions and this is thought to be through A33’s interaction with B5. Co-expression of A34 and A33 followed by co-immunoprecipitation revealed that the two proteins interact through their luminal domains. Using recombinant epitope-tagged A34 viruses we were also able to detect this interaction during normal infection. This body of work shows that the interaction between A34 and B5 is required for the proper localization of B5 and its efficient incorporation into enveloped virions. We also show that A34 and B5 have two sites of interaction and that A34 interacts with A33. Taken together we show that A34’s interactions with other enveloped virion proteins are important for viral morphogenesis by determining the composition of the enveloped virion membrane