Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

The contribution of X-linked coding variation to severe developmental disorders

Abstract: Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders

Socializing One Health: an innovative strategy to investigate social and behavioral risks of emerging viral threats

In an effort to strengthen global capacity to prevent, detect, and control infectious diseases in animals and people, the United States Agency for International Development’s (USAID) Emerging Pandemic Threats (EPT) PREDICT project funded development of regional, national, and local One Health capacities for early disease detection, rapid response, disease control, and risk reduction. From the outset, the EPT approach was inclusive of social science research methods designed to understand the contexts and behaviors of communities living and working at human-animal-environment interfaces considered high-risk for virus emergence. Using qualitative and quantitative approaches, PREDICT behavioral research aimed to identify and assess a range of socio-cultural behaviors that could be influential in zoonotic disease emergence, amplification, and transmission. This broad approach to behavioral risk characterization enabled us to identify and characterize human activities that could be linked to the transmission dynamics of new and emerging viruses. This paper provides a discussion of implementation of a social science approach within a zoonotic surveillance framework. We conducted in-depth ethnographic interviews and focus groups to better understand the individual- and community-level knowledge, attitudes, and practices that potentially put participants at risk for zoonotic disease transmission from the animals they live and work with, across 6 interface domains. When we asked highly-exposed individuals (ie. bushmeat hunters, wildlife or guano farmers) about the risk they perceived in their occupational activities, most did not perceive it to be risky, whether because it was normalized by years (or generations) of doing such an activity, or due to lack of information about potential risks. Integrating the social sciences allows investigations of the specific human activities that are hypothesized to drive disease emergence, amplification, and transmission, in order to better substantiate behavioral disease drivers, along with the social dimensions of infection and transmission dynamics. Understanding these dynamics is critical to achieving health security--the protection from threats to health-- which requires investments in both collective and individual health security. Involving behavioral sciences into zoonotic disease surveillance allowed us to push toward fuller community integration and engagement and toward dialogue and implementation of recommendations for disease prevention and improved health security

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Annual and Durable HIV Retention in Care and Viral Suppression Among Patients of Peter Ho Clinic, 2013-2017

OBJECTIVES: To determine rates of annual and durable retention in medical care and viral suppression among patients enrolled in the Peter Ho Clinic, from 2013-2017. METHODS: This is a retrospective review of medical record data in an urban clinic, located in Newark, New Jersey, a high prevalence area of persons living with HIV. Viral load data were electronically downloaded, in rolling 1-year intervals, in two-month increments, from January 1, 2013 to December 31, 2019. Three teams were established, and every two months, they were provided with an updated list of patients with virologic failure. Retention and viral suppression rates were first calculated for each calendar-year. After patients were determined to be retained/suppressed annually, the proportion of patients with durable retention and viral suppression were calculated in two, three, four, five and six-year periods. Descriptive statistics were used to summarize sample characteristics by retention in care, virologic failure and viral suppression with Pearson Chi-square; p-value RESULTS: As of December 31, 2017, 1000 (57%) patients were retained in medical care of whom 870 (87%) were suppressed. Between 2013 and 2016, decreases in annual (85% to 77%) and durable retention in care were noted: two-year (72% to 70%) and three-year (63% to 59%) periods. However, increases were noted for 2017, in annual (89%) and durable retention in the two-year period (79%). In the adjusted model, when compared to current patients, retention in care was less likely among patients reengaging in medical care (adjusted Odds Ratio (aOR): 0.77, 95% CI: 0.61-0.98) but more likely among those newly diagnosed from 2014-2017 (aOR: 1.57, 95% CI: 1.08-2.29), compared to those in care since 2013. A higher proportion of patients re-engaging in medical care had virologic failure than current patients (56% vs. 47%, p \u3c 0.0001). As age decreased, virologic failure was more likely (p CONCLUSIONS: Restructuring clinical services at this urban clinic was associated with improved viral suppression. However, concurrent interventions to ensure retention in medical care were not implemented. Both retention in care and viral suppression interventions should be implemented in tandem to achieve an end to the epidemic. Retention in care and viral suppression should be measured longitudinally, instead of cross-sectional yearly evaluations, to capture dynamic changes in these indicators

Annual and durable HIV retention in care and viral suppression among patients of Peter Ho Clinic, 2013-2017.

ObjectivesTo determine rates of annual and durable retention in medical care and viral suppression among patients enrolled in the Peter Ho Clinic, from 2013-2017.MethodsThis is a retrospective review of medical record data in an urban clinic, located in Newark, New Jersey, a high prevalence area of persons living with HIV. Viral load data were electronically downloaded, in rolling 1-year intervals, in two-month increments, from January 1, 2013 to December 31, 2019. Three teams were established, and every two months, they were provided with an updated list of patients with virologic failure. Retention and viral suppression rates were first calculated for each calendar-year. After patients were determined to be retained/suppressed annually, the proportion of patients with durable retention and viral suppression were calculated in two, three, four, five and six-year periods. Descriptive statistics were used to summarize sample characteristics by retention in care, virologic failure and viral suppression with Pearson Chi-square; p-value ResultsAs of December 31, 2017, 1000 (57%) patients were retained in medical care of whom 870 (87%) were suppressed. Between 2013 and 2016, decreases in annual (85% to 77%) and durable retention in care were noted: two-year (72% to 70%) and three-year (63% to 59%) periods. However, increases were noted for 2017, in annual (89%) and durable retention in the two-year period (79%). In the adjusted model, when compared to current patients, retention in care was less likely among patients reengaging in medical care (adjusted Odds Ratio (aOR): 0.77, 95% CI: 0.61-0.98) but more likely among those newly diagnosed from 2014-2017 (aOR: 1.57, 95% CI: 1.08-2.29), compared to those in care since 2013. A higher proportion of patients re-engaging in medical care had virologic failure than current patients (56% vs. 47%, p ConclusionsRestructuring clinical services at this urban clinic was associated with improved viral suppression. However, concurrent interventions to ensure retention in medical care were not implemented. Both retention in care and viral suppression interventions should be implemented in tandem to achieve an end to the epidemic. Retention in care and viral suppression should be measured longitudinally, instead of cross-sectional yearly evaluations, to capture dynamic changes in these indicators

Correlates of Sexually Transmitted Infections among Adolescents Attending Public High Schools, Panama, 2015.

BACKGROUND:Sexually transmitted infections (STIs) are common in adolescents worldwide. Vulnerability to STIs increases with risky sexual practices. This study described the sexual practices, estimated the prevalence of STIs, and identified correlates associated with STIs among participants, enrolled in public high schools, in the District of Panama, Panama. METHODS:A cross sectional study, using multistage cluster sampling, was conducted among participants, aged 14-18 years, enrolled in public high schools, in the District of Panama, Panama City, Panama, from August to November, 2015. Participants completed a self-administered questionnaire and provided biological samples. The samples of those reporting sexual activity (oral, vaginal, and/or anal intercourse) were tested for STIs. Odds ratios were used to identify correlates of STIs in this population. RESULTS:A total of 592 participants were included, of whom, 60.8% reported a history of sexual activity, and 24.4% tested positive for least one STI. STIs were more common in female participants, (33.5%). Compared to those without STIs, higher proportions of those with at least one STI reported ≥3 sexual partners in their lifetime (60.0%) and current sexual activity (76.3%). In the multivariable model, correlates of STI included female participants (Adjusted Odds Ratio (AOR) = 5.8, 95% Confidence Interval (CI) 2.3-14.6) and those who engaged in sexual intercourse with casual partners (AOR = 3.0, 95% CI: 1.2-7.5). CONCLUSIONS:We report a high STI prevalence among adolescents attending public high schools, in the District of Panama. Reported risky sexual practices were common and correlated with STIs. Female participants and those reporting sexual intercourse with casual partners were more likely test positive for at least one STI. Our study identified a need for effective interventions to curb future infections in this population

Reported Sexual Practices Among Participants with a History of Sexual Activity, Panama, 2015.

<p>Reported Sexual Practices Among Participants with a History of Sexual Activity, Panama, 2015.</p