Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

SARS-CoV-2-specific immune responses and clinical outcomes after COVID-19 vaccination in patients with immune-suppressive disease

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune responses and infection outcomes were evaluated in 2,686 patients with varying immune-suppressive disease states after administration of two Coronavirus Disease 2019 (COVID-19) vaccines. Overall, 255 of 2,204 (12%) patients failed to develop anti-spike antibodies, with an additional 600 of 2,204 (27%) patients generating low levels (<380 AU ml−1). Vaccine failure rates were highest in ANCA-associated vasculitis on rituximab (21/29, 72%), hemodialysis on immunosuppressive therapy (6/30, 20%) and solid organ transplant recipients (20/81, 25% and 141/458, 31%). SARS-CoV-2-specific T cell responses were detected in 513 of 580 (88%) patients, with lower T cell magnitude or proportion in hemodialysis, allogeneic hematopoietic stem cell transplantation and liver transplant recipients (versus healthy controls). Humoral responses against Omicron (BA.1) were reduced, although cross-reactive T cell responses were sustained in all participants for whom these data were available. BNT162b2 was associated with higher antibody but lower cellular responses compared to ChAdOx1 nCoV-19 vaccination. We report 474 SARS-CoV-2 infection episodes, including 48 individuals with hospitalization or death from COVID-19. Decreased magnitude of both the serological and the T cell response was associated with severe COVID-19. Overall, we identified clinical phenotypes that may benefit from targeted COVID-19 therapeutic strategies

The Biological Diversity and Production of Volatile Organic Compounds by Stem-Inhabiting Endophytic Fungi of Ecuador

Fungal endophytes colonize every major lineage of land plants without causing apparent harm to their hosts. Despite their production of interesting and potentially novel compounds, endophytes—particularly those inhabiting stem tissues—are still a vastly underexplored component of microbial diversity. In this study, we explored the diversity of over 1500 fungal endophyte isolates collected from three Ecuadorian ecosystems: lowland tropical forest, cloud forest, and coastal dry forest. We sought to determine whether Ecuador’s fungal endophytes are hyperdiverse, and whether that biological diversity is reflected in the endophytes’ chemical diversity. To assess this chemical diversity, we analyzed a subset of isolates for their production of volatile organic compounds (VOCs), a representative class of natural products. This study yielded a total of 1526 fungal ITS sequences comprising some 315 operational taxonomic units (OTUs), resulting in a non-asymptotic OTU accumulation curve and characterized by a Fisher’s α of 120 and a Shannon Diversity score of 7.56. These figures suggest that the Ecuadorian endophytes are hyperdiverse. Furthermore, the 113 isolates screened for VOCs produced more than 140 unique compounds. These results present a mere snapshot of the remarkable biological and chemical diversity of stem-inhabiting endophytic fungi from a single neotropical country

Undeclared baggage: Do tourists act as vectors for seed dispersal in fynbos protected areas?

Encroachment by alien species is the second greatest threat to biodiversity worldwide. As South Africa’s Cape Floristic Region has a botanical endemism of nearly 70%, conservation efforts are a high priority. Estimates suggest that alien species cost the country over R6.5 billion per year. Despite significant research on alien species dispersal, the role of tourists as seed dispersers requires further exploration. To investigate the potential role tourists play in introducing alien seeds into protected areas, long-bristle brushes were used to scrape seeds off the shoes of hikers, dog walkers and cyclists, as well as the wheels of mountain bikes and dogs themselves, upon entering the Silvermine Nature Reserve section of the Table Mountain National Park in the Western Cape province, South Africa. In addition, a vegetation survey was conducted. This comprised 18 transects at various distances from the recreational paths in the park, and used a prioritisation ranking system that identified the alien species of greatest concern. It was concluded that the greatest number of alien plant species could be found along dog paths, in comparison to the hiking trails and cycling trails. This corresponded to the findings that dog walkers had the highest incidence of seeds on their shoes, suggesting that tourists were possibly dispersing seeds from their gardens. Alien species significantly covered more of the vegetation transects closer to the trails than they did in transects further into the matrix. Because more alien species were present in areas susceptible to human disturbance, the data suggest that tourists can act as vectors for alien seed dispersal. These findings emphasise the need for active tourism management in line with the South African National Parks Biodiversity Monitoring Programme in order to prevent the introduction and spread of alien species into South Africa’s protected areas. Conservation implications: Tourism is the main source of revenue for South African National Parks, and one of the organisation’s principal goals is to create a tourism management policy conducive to conservation. This research explores the potential role that tourists may play in the introduction of non-native species into a protected area, thereby providing novel information that could assist managers in the sustainable management of protected areas

Lifetime suicidal ideation and attempt are common among HIV+ individuals

BackgroundEstimates of the prevalence of lifetime suicidal ideation and attempt, and risks for new-onset suicidality, among HIV-infected (HIV+) individuals are not widely available in the era of modern combined antiretroviral treatment (cART).MethodParticipants (n=1560) were evaluated with a comprehensive battery of tests that included the depression and substance use modules of the Composite International Diagnostic Interview (CIDI) and the Beck Depression Inventory-II (BDI-II) as part of a large prospective cohort study at six U.S. academic medical centers. Participants with possible lifetime depression (n=981) were classified into five categories: 1) no thoughts of death or suicide (n=352); 2) thoughts of death (n=224); 3) thoughts of suicide (n=99); 4) made a suicide plan (n=102); and 5) attempted suicide (n=204).ResultsTwenty-six percent (405/1560) of participants reported lifetime suicidal ideation and 13% (204/1560) reported lifetime suicide attempt. Participants who reported suicidal thoughts or plans, or attempted suicide, reported higher scores on the BDI-II (p<0.0001), and higher rates of current major depressive disorder (p=0.01), than those who did not. Attempters reported higher rates of lifetime substance abuse (p=0.02) and current use of psychotropic medications (p=0.01) than non-attempters.LimitationsStudy assessments focused on lifetime, rather than current, suicide. Data was not collected on the timing of ideation or attempt, frequency, or nature of suicide attempt.ConclusionsHigh rates of lifetime suicidal ideation and attempt, and the relationship of past report with current depressed mood, suggest that mood disruption is still prevalent in HIV. Findings emphasize the importance of properly diagnosing and treating psychiatric comorbidities among HIV persons in the cART era