Identification of constrained sequence elements across 239 primate genomes.

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.

Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation.

Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.

Ten Years of Improving Acute Stroke Management in a Metropolitan Area: A Population-Based Quantification of Quality Indicators.

BACKGROUND AND PURPOSE: Rapid access to acute stroke treatment improves clinical outcomes in patients with ischemic stroke. We aimed to shorten the time to admission and to acute stroke treatment for patients with acute stroke in the Hamburg metropolitan area by collaborative multilevel measures involving all hospitals with stroke units, the Emergency Medical Services (EMS), and health-care authorities. METHODS: In 2007, an area-wide stroke care quality project was initiated. The project included mandatory admission of all stroke patients in Hamburg exclusively to hospitals with stroke units, harmonized acute treatment algorithms among all hospitals, repeated training of the EMS staff, a multimedia educational campaign, and a mandatory stroke care quality monitoring system based on structured data assessment and quality indicators for procedural measures. We analyzed data of all patients with acute stroke who received inhospital treatment in the city of Hamburg during the evaluation period from the quality assurance database data and evaluated trends of key quality indicators over time. RESULTS: From 2007 to 2016, a total of 83,395 patients with acute stroke were registered. During this period, the proportion of patients admitted within ≤3 h from symptom onset increased over time from 27.8% in 2007 to 35.2% in 2016 (p < 0.001). The proportion of patients who received rapid thrombolysis (within ≤30 min after admission) increased from 7.7 to 54.1% (p < 0.001). CONCLUSIONS: Collaborative stroke care quality projects are suitable and effective to improve acute stroke care.

Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish.

The use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

Screening for TB by sputum culture in high-risk groups in Copenhagen, Denmark: a novel and promising approach.

INTRODUCTION: Evidence on screening high-risk groups for TB by mobile X-ray in low-incidence countries is building, but knowledge on other possible screening methods is limited. In this retrospective study we report results from a community based programme screening for TB by spot sputum culture. METHODS: On seven occasions, from September 2012 through June 2014, we offered TB screening to all persons present at 11 locations where socially marginalised people gather in Copenhagen. Spot sputum samples from participants were examined by smear microscopy and culture. Genotype, nucleic acid amplification test and chest X-ray were done if TB was found. RESULTS: Among 1075 participants, we identified 36 cases of TB. Twenty-four cases (66.7%) were identified at the first screening of each participant, that is, the prevalence of TB was 2233/100 000. Thirty-five (97%) of the TB cases were culture-positive and seven (19.4%) were smear-positive. Twelve out of 21 (57.1%) cases tested were nucleic acid amplification test positive. Twenty-eight (77.8%) had chest X-ray suggestive of TB. All patients with TB started treatment, 30 (83.3%) had a successful outcome. DISCUSSION: Screening for TB by spot sputum culture is possible and a promising alternative to mobile X-ray in a community based screening programme. 22.2% did not have chest X-ray suggestive of TB and would not have been identified using mobile X-ray. Most of the TB cases were smear-negative, suggesting that they were identified at an early, less infectious stage, which is essential in order to prevent transmission and gain infection control.

Comparative genomic analyses provide new insights into evolutionary history and conservation genomics of gorillas.

Genome sequencing is a powerful tool to understand species evolutionary history, uncover genes under selection, which could be informative of local adaptation, and infer measures of genetic diversity, inbreeding and mutational load that could be used to inform conservation efforts. Gorillas, critically endangered primates, have received considerable attention and with the recently sequenced Bwindi mountain gorilla population, genomic data is now available from all gorilla subspecies and both mountain gorilla populations. Here, we reanalysed this rich dataset with a focus on evolutionary history, local adaptation and genomic parameters relevant for conservation. We estimate a recent split between western and eastern gorillas of 150,000-180,000 years ago, with gene flow around 20,000 years ago, primarily between the Cross River and Grauer's gorilla subspecies. This gene flow event likely obscures evolutionary relationships within eastern gorillas: after excluding putatively introgressed genomic regions, we uncover a sister relationship between Virunga mountain gorillas and Grauer's gorillas to the exclusion of Bwindi mountain gorillas. This makes mountain gorillas paraphyletic. Eastern gorillas are less genetically diverse and more inbred than western gorillas, yet we detected lower genetic load in the eastern species. Analyses of indels fit remarkably well with differences in genetic diversity across gorilla taxa as recovered with nucleotide diversity measures. We also identified genes under selection and unique gene variants specific for each gorilla subspecies, encoding, among others, traits involved in immunity, diet, muscular development, hair morphology and behavior. The presence of this functional variation suggests that the subspecies may be locally adapted. In conclusion, using extensive genomic resources we provide a comprehensive overview of gorilla genomic diversity, including a so-far understudied Bwindi mountain gorilla population, identify putative genes involved in local adaptation, and detect population-specific gene flow across gorilla species.

The landscape of tolerated genetic variation in humans and primates.

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence Summary: Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.

A global catalog of whole-genome diversity from 233 primate species.

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.

The landscape of tolerated genetic variation in humans and primates.

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

Migrant tuberculosis: the extent of transmission in a low burden country.

BACKGROUND: Human migration caused by political unrest, wars and poverty is a major topic in international health. Infectious diseases like tuberculosis follow their host, with potential impact on both the migrants and the population in the recipient countries. In this study, we evaluate Mycobacterium tuberculosis transmission between the national population and migrants in Denmark. METHODS: Register study based on IS6110-RFLP results from nationwide genotyping of tuberculosis cases during 1992 through 2004. Cases with 100% identical genotypes were defined as clustered and part of a transmission chain. Origin of clusters involving both Danes and migrants was defined as Danish/migrant/uncertain. Subsequently, the proportion of cases likely infected by the "opposite" ethnic group was estimated. RESULTS: 4,631 cases were included, representing 99% of culture confirmed cases during 1992 through 2004. Migrants contributed 61.6% of cases. Up to 7.9% (95% CI 7.0-8.9) of migrants were infected by Danes. The corresponding figure was 5.8% (95% CI 4.8-7.0) for Danes. Thus, transmission from Danes to migrants occurred up to 2.5 (95% CI 1.8-3.5) times more frequent than vice versa (OR = 1). A dominant strain, Cluster-2, was almost exclusively found in Danes, particular younger-middle-aged males. CONCLUSIONS: Transmission between Danes and migrants is limited, and risk of being infected by the "opposite" ethnic group is highest for migrants. TB-control efforts should focus on continues micro-epidemics, e.g. with Cluster-2 in Danes, prevention of reactivation TB in high-risk migrants, and outbreaks in socially marginalized migrants, such as Somalis and Greenlanders. Fears that TB in migrants poses a threat for resident Danes seem exaggerated and unjustified. We believe this to be true for other low incidence countries as well.

New helicase-primase inhibitors as drug candidates for the treatment of herpes simplex disease.

The vast majority of the world population is infected with at least one member of the human herpesvirus family. Herpes simplex virus (HSV) infections are the cause of cold sores and genital herpes as well as life-threatening or sight-impairing disease mainly in immunocompromized patients, pregnant women and newborns. Since the milestone development in the late 1970s of acyclovir (Zovirax), a nucleosidic inhibitor of the herpes DNA polymerase, no new non-nucleosidic anti-herpes drugs have been introduced. Here we report new inhibitors of the HSV helicase-primase with potent in vitro anti-herpes activity, a novel mechanism of action, a low resistance rate and superior efficacy against HSV in animal models. BAY 57-1293 (N-[5-(aminosulfonyl)-4-methyl-1,3-thiazol-2-yl]-N-methyl-2-[4-(2-pyridinyl)phenyl]acetamide), a well-tolerated member of this class of compounds, significantly reduces time to healing, prevents rebound of disease after cessation of treatment and, most importantly, reduces frequency and severity of recurrent disease. Thus, this class of drugs has significant potential for the treatment of HSV disease in humans, including those resistant to current medications.

Clinical outcome and imaging follow-up in acute stroke patients with normal perfusion CT and normal CT angiography.

INTRODUCTION: Acute stroke multimodal CT imaging (MMCT: non-enhanced CT, CT angiography, and CT perfusion (CTP)) may show normal results despite persistent clinical stroke. We prospectively evaluated the sensitivity/specificity of MMCT infarct detection and the clinical outcome in patients with normal MMCT findings. METHODS: From April 2007 to April 2008, all patients with acute hemispheric stroke within 6 h of symptom onset who underwent complete MMCT and MRI follow-up imaging were included. MMCT analysis included occlusion type, early infarct hypodensities (EIH), mean transit time (MTT), and cerebral blood volume (CBV) maps according to Alberta Stroke Program Early CT Score (ASPECTS). Clinical assessment included symptom onset to CT scan (≤3 h/>3 h), the National Institute of Health Stroke Scale score (admission/discharge), and the modified Rankin scale (mRS) 90 days after stroke onset. RESULTS: One hundred seven were included (mean age, 68.4 years; ≤3 h, n = 84; >3 h, n = 23; intravenous thrombolysis (IVT), n = 51; ≤3 h, n = 40; >3 h, n = 11). In patients with normal MMCT on admission (n = 54), follow-up MRT detected brain infarctions in 23 patients (lacunar strokes, n = 16; infratentorial strokes, n = 4; territorial infarction, n = 3). Sensitivity/specificity/positive predictive value/negative predictive value of any infarct detection was 69.5%/99.8%/99.9%/57.2% and of a any territorial infarct detection was 93.9%/99.9%/99.9%/93.6%, respectively. In univariate regression analysis (time to CT scan, ≤3 h/>3 h; IVT: yes/no; ASPECTS EIH/CBV/MTT, 10/<10), only the evidence of normal CTP (ASPECTS MTT = 10) had a statistically significant impact (p = 0.02) on a good outcome (mRS 0.1). CONCLUSION: MMCT sensitivity in acute lacunar or infratentorial stroke was poor. But, we found a high specifity and a fairly good sensitivity in territorial infarct detection. In acute stroke patients with normal MMCT findings on admission, a good clinical prognosis can be expected.

Endovascular treatment in proximal and intracranial carotid occlusion 9 hours after symptom onset.

INTRODUCTION: A debate is emerging over whether the treatment time window in acute stroke can be extended beyond 6 h if penumbral tissue can be identified. Treatment decisions are very difficult in cases of tandem proximal carotid occlusion with arterioarterial intracranial embolism. We enter this debate with the present report on a case of atherosclerotic proximal carotid occlusion and resulting periocclusional carotid T embolism that was successfully treated 9 h after symptom onset. METHODS: The case of a 68-year-old man with fluctuating symptoms of right-hemispheric stroke is presented (NIHSS score 12-20 on admission). CT angiography demonstrated proximal carotid occlusion and periocclusional embolism of the entire internal carotid artery (ICA) including the carotid T segment. Penumbral tissue was diagnosed by nonenhanced and perfusion CT imaging 7.5 h after symptom onset. Treatment was initiated 9 h after symptom onset by passing the proximal occlusion with a microcatheter and local administration of recombinant tissue plasminogen activator (rt-PA) into the carotid T segment at the level of posterior communicating artery (PCoA) origin. RESULTS: Recanalization of the ICA and middle cerebral artery was accomplished within 1 h by flow establishment via the PCoA. The atherosclerotic proximal ICA occlusion was not stented due to the risk of embolism from remnant thrombi in the petrous and cavernous ICA segments. Follow-up MRI showed only mild haemorrhagic infarct transformation of the initial infarct core. The patient was discharged from hospital 18 days after treatment with NIHSS score 5. CONCLUSION: If penumbral tissue can be conclusively identified, endovascular treatment in proximal and intracranial tandem occlusion can be successful, even in treatments initiated 6-9 h after stroke onset. If the intracranial flow after recanalization can be established via the circle of Willis, the underlying proximal ICA occlusion may not require treatment.

Bacillarity at autopsy in pulmonary tuberculosis. Mycobacterium tuberculosis is often disseminated.

The aim of this investigation was to quantify dissemination of Mycobacterium tuberculosis infection in patients with pulmonary tuberculosis and to show the pattern of eradication during treatment. The study is based on 98 out of the 113 patients with pulmonary tuberculosis who died during their admission to hospital in the Municipality of Copenhagen from 1963 to 1971. These patients had cultures for M. tuberculosis performed from different organs at autopsy: 78% treated <=100 days had dissemination of bacteria, cultured with decreasing frequency in the lungs, spleen, liver, and kidneys, respectively. In comparison, 23% treated >100 days had dissemination of bacteria, among which 50% occurred in patients with records of poor treatment compliance, 14% in patients with good treatment compliance. 81% of all patients had at least one chest x-ray judged to be without a miliary pattern. This study emphasizes that M. tuberculosis is often disseminated to organs other than the lungs in severe pulmonary tuberculosis. Eradication of bacteria in these organs can take several months. This observation adds to our understanding of the natural history of tuberculosis: M. tuberculosis is a resilient organism that can adapt to a wide variety of environmental conditions.

Characteristics of non-clustered tuberculosis in a low burden country.

Molecular genotyping studies often focus on clustered tuberculosis and recent transmission. Less attention has been paid to non-clustered tuberculosis. However, non-clustered cases also contribute significantly to the tuberculosis burden, especially in low-incidence countries. The objective of this study is to characterize non-clustered tuberculosis cases in Denmark and point out potential implications for tuberculosis control. The study is based on nationwide IS6110-RFLP genotyping of tuberculosis cases from 1992 through 2004, corresponding to 98% of culture verified cases. Of 3988 cases, 45% were non-clustered. Both Danes and immigrants had a peak incidence of non-clustered tuberculosis at older ages, 80-89 years (4.3 cases/10(5) population/year) and 60-69 years (28.8 cases/10(5) population/year), respectively. In addition, immigrants had a peak at 20-29 years (43.2 cases/10(5) inhabitants/year). In Danes, the incidence of non-clustered tuberculosis decreased during the study period and was predominantly found in elderly persons, presumably reactivating infection acquired during 1910-40, when tuberculosis incidence was high. In immigrants, the incidence was high at all ages, presumably reflecting reactivation of imported infections. In the future, the number of non-clustered tuberculosis cases will decrease, as older Danes die, and as time since primary infection increases for immigrants residing in Denmark. TB control should include focus on non-clustered cases.

Prospective evaluation of a whole-blood test using Mycobacterium tuberculosis-specific antigens ESAT-6 and CFP-10 for diagnosis of active tuberculosis.

A new immunodiagnostic test based on the Mycobacterium tuberculosis-specific antigens CFP-10/ESAT-6(QFT-RD1) has been launched as an aid in the diagnosis of latent tuberculosis (TB) infection (LTBI). The aim of this study was to evaluate this test for the diagnosis of active TB. Eighty-two patients with suspicion of TB and 39 healthy BCG-vaccinated persons were enrolled. Forty-eight had active TB, 25 did not, and 9 were excluded. Sensitivity and specificity of the test for active TB were evaluated in a prospective blinded manner in patients suspected of TB. The sensitivity of the QFT-RD1 was 85% (40/48; confidence interval [CI], 75 to 96), and it was higher than the sensitivity of microscopy, 42% (20/48; CI, 27 to 56; P = 0.001), and culture, 59% (27/46; CI, 44 to 73; P = 0.009). Of patients with extrapulmonary TB, 92% (12/13) were QFT-RD1 positive, whereas only 31% (4/13) were positive by microscopy and 42% (5/12) by culture (P < 0.05), and 87% (13/15) of those who were negative by both microscopy and culture were QFT-RD1 positive. By combining microscopy and culture with the QFT-RD1 test, sensitivity increased to 96% (CI, 90 to 102). Ten of 25 (40%) non-TB patients were QFT-RD1 positive, resulting in a specificity of 60%. However, 80% (8/10) of these had risk-factors for TB, indicating latent infection in this group. In healthy controls, only 3% (1/39) were QFT-RD1 positive. In conclusion, the QFT-RD1 test is sensitive for diagnosis of TB, especially in patients with negative microscopy and culture. The accuracy of the QFT-RD1 test will vary with the prevalence of LTBI. We suggest that the QFT-RD1 test could be a very useful supplementary tool for the diagnosis of TB.

Natural resistance-associated macrophage protein 1 polymorphisms are associated with microscopy-positive tuberculosis.

The natural resistance-associated macrophage protein 1 (NRAMP1) is implicated in the pathophysiology of mycobacterial infections. We investigated by polymerase chain reaction previously published Nramp1 genotypes at 4 loci-INT4, N543D, 3'UTR, and 5'(CA)(n) microsatellite markers-in 104 human immunodeficiency virus-negative patients with tuberculosis and 176 healthy control subjects living in Denmark. No significant difference in genotype frequency was found between white patients with tuberculosis and control subjects (P>.16), but carriage of Nramp1 variant alleles at loci INT4 and 5'(CA)(n) conferred a significantly increased risk of having microscopy-positive compared with microscopy-negative tuberculosis (65% vs. 35% [P=.0004] and 63% vs. 38% [P=.047], respectively). The Nramp1 alleles were not associated with increased risk for the development of cavities seen on chest radiographs, or with extrapulmonary tuberculosis. These results indicate that variant alleles in the Nramp1 gene are associated with increased mycobacterial replication rather than susceptibility for tuberculosis and may thus confer increased risk of severe disease.