Nanopore ReCappable sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs

The SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested subgenomic RNAsused to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5 ' cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs

StructuRly: A novel shiny app to produce comprehensive, detailed and interactive plots for population genetic analysis

Population genetics focuses on the analysis of genetic differences within and between-group of individuals and the inference of the populations’ structure. These analyses are usually carried out using Bayesian clustering or maximum likelihood estimation algorithms that assign individuals to a given population depending on specific genetic patterns. Although several tools were developed to perform population genetics analysis, their standard graphical outputs may not be sufficiently informative for users lacking interactivity and complete information. StructuRly aims to resolve this problem by offering a complete environment for population analysis. In particular, StructuRly combines the statistical power of the R language with the friendly interfaces implemented using the shiny libraries to provide a novel tool for performing population clustering, evaluating several genetic indexes, and comparing results. Moreover, graphical representations are interactive and can be easily personalized. StructuRly is available either as R package on GitHub, with detailed information for its installation and use and as shinyapps.io servers for those users who are not familiar with R and the RStudio IDE. The application has been tested on Linux, macOS and Windows operative systems and can be launched as a shiny app in every web browser.ISSN:1932-620

resistancebank.org, an open-access repository for surveys of antimicrobial resistance in animals

Antimicrobial resistance (AMR) is a growing threat to the health of humans and animals that requires global actions. In high-income countries, surveillance systems helped inform policies to curb AMR in animals. In low- and middle-income countries (LMICs), demand for meat is rising, and developing policies against AMR is urgent. However, surveillance of AMR is at best nascent, and the current evidence base to inform policymakers is geographically heterogeneous. We present resistancebank.org, an online platform that centralizes information on AMR in animals from 1,285 surveys from LMICs. Surveys were conducted between 2000 and 2019 and include 22,403 resistance rates for pathogens isolated from chickens, cattle, sheep, and pigs. The platform is built as a shiny application that provides access to individual surveys, country-level reports, and maps of AMR at 10 × 10 kilometers resolution. The platform is accessed via any internet browser and enables users to upload surveys to strengthen a global database. resistancebank.org aims to be a focal point for sharing AMR data in LMICs and to help international funders prioritize their actions.ISSN:2052-446

Socioeconomic position and the COVID-19 care cascade from testing to mortality in Switzerland: a population-based analysis

Background: The inverse care law states that disadvantaged populations need more health care than advantaged populations but receive less. Gaps in COVID-19-related health care and infection control are not well understood. We aimed to examine inequalities in health in the care cascade from testing for SARS-CoV-2 to COVID-19-related hospitalisation, intensive care unit (ICU) admission, and death in Switzerland, a wealthy country strongly affected by the pandemic. Methods: We analysed surveillance data reported to the Swiss Federal Office of Public Health from March 1, 2020, to April 16, 2021, and 2018 population data. We geocoded residential addresses of notifications to identify the Swiss neighbourhood index of socioeconomic position (Swiss-SEP). The index describes 1·27 million small neighbourhoods of approximately 50 households each on the basis of rent per m2, education and occupation of household heads, and crowding. We used negative binomial regression models to calculate incidence rate ratios (IRRs) with 95% credible intervals (CrIs) of the association between ten groups of the Swiss-SEP index defined by deciles (1=lowest, 10=highest) and outcomes. Models were adjusted for sex, age, canton, and wave of the epidemic (before or after June 8, 2020). We used three different denominators: the general population, the number of tests, and the number of positive tests. Findings: Analyses were based on 4 129 636 tests, 609 782 positive tests, 26 143 hospitalisations, 2432 ICU admissions, 9383 deaths, and 8 221 406 residents. Comparing the highest with the lowest Swiss-SEP group and using the general population as the denominator, more tests were done among people living in neighbourhoods of highest SEP compared with lowest SEP (adjusted IRR 1·18 [95% CrI 1·02–1·36]). Among tested people, test positivity was lower (0·75 [0·69–0·81]) in neighbourhoods of highest SEP than of lowest SEP. Among people testing positive, the adjusted IRR was 0·68 (0·62–0·74) for hospitalisation, was 0·54 (0·43–0·70) for ICU admission, and 0·86 (0·76–0·99) for death. The associations between neighbourhood SEP and outcomes were stronger in younger age groups and we found heterogeneity between areas. Interpretation: The inverse care law and socioeconomic inequalities were evident in Switzerland during the COVID-19 epidemic. People living in neighbourhoods of low SEP were less likely to be tested but more likely to test positive, be admitted to hospital, or die, compared with those in areas of high SEP. It is essential to continue to monitor testing for SARS-CoV-2, access and uptake of COVID-19 vaccination and outcomes of COVID-19. Governments and health-care systems should address this pandemic of inequality by taking measures to reduce health inequalities in response to the SARS-CoV-2 pandemic. Funding: Swiss Federal Office of Public Health, Swiss National Science Foundation, EU Horizon 2020, Branco Weiss Foundation.ISSN:2468-266

Human monoclonal antibody endowed with anti-HSV-1 and -2 activity strongly inhibits virus replication

BACKGROUND: Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens, infecting more than 500 million people worldwide. HSV-1 generally infects oral cavity, while HSV-2 the anogenital area. Both viruses undergo latency in the nervous system and are subjected to reactivation under different distress stimuli. HSV infection irresponsive to “classical” current antiviral therapy can be particularly severe among immunocompromised patients and new-borns, causing severe disseminated diseases characterized by high morbidity and mortality. Moreover, the antivirals currently used can be burdened by high toxicity not always allowing their use in therapy. New drugs effective against HSV isolates resistant to standard therapy are therefore clearly needed. METHODS: Human monoclonal antibodies (HuMabs) cross-reactive to both HSV-1 and 2 have been generated from a patient whose serum was able to recognise and neutralise both HSV-1 and -2 reference isolates. HuMabs have been characterised for their binding, neutralising activity and for their capability to inhibit virus replication after adsorption. RESULTS: A new human monoclonal antibody able to recognise both HSV-1 and -2 has been isolated. The antibody has been then characterised in different antibody formats (Fab and IgG). Both formats have been able to strongly inhibit HSV replication of reference isolates as well as clinical isolates featuring different susceptibility to first-line antiviral drug Acyclovir. CONCLUSIONS: The capability of our antibody to strongly inhibit HSV infection in vitro is the result of both its neutralising activity and its ability to inhibit HSV replication also after virus adsorption. These findings pave the way to the study of our antibody therapeutic activity in vivo

Geographically targeted surveillance of livestock could help prioritize intervention against antimicrobial resistance in China

The rise of antimicrobial resistance (AMR) in animals is being fuelled by the widespread use of veterinary antimicrobials. China is the largest global consumer of veterinary antimicrobials, and improving AMR surveillance strategies in this region could help prioritize intervention and preserve antimicrobial efficacy. Here we mapped AMR rates in pigs, chickens and cattle in China using 446 surveys of event-based surveillance between 2000 and 2019 for foodborne bacteria, in combination with geospatial models to identify locations where conducting new surveys could have the highest benefits. Using maps of uncertainty, we show that eastern China currently has the highest AMR rates, and southwestern and northeastern China would benefit the most from additional surveillance efforts. Instead of distributing new surveys evenly across administrative divisions, using geographically targeted surveillance could reduce AMR prediction uncertainty by two-fold. In a context of competing disease control priorities, our findings present a feasible option for optimizing surveillance efforts—and slowing the spread of AMR.ISSN:2662-135

Cloning of the first human anti-JCPyV/VP1 neutralizing monoclonal antibody: epitope definition and implications in risk stratification of patients under natalizumab therapy.

International audienceJC virus (JCPyV) has gained novel clinical importance as cause of progressive multifocal leukoencephalopathy (PML), a rare demyelinating disease recently associated to immunomodulatory drugs, such as natalizumab used in multiple sclerosis (MS) cases. Little is known about the mechanisms leading to PML, and this makes the need of PML risk stratification among natalizumab-treated patients very compelling. Clinical and laboratory-based risk-stratification markers have been proposed, one of these is represented by the JCPyV-seropositive status, which includes about 54% of MS patients. We recently proposed to investigate the possible protective role of neutralizing humoral immune response in preventing JCPyV reactivation. In this proof-of-concept study, by cloning the first human monoclonal antibody (GRE1) directed against a neutralizing epitope on JCPyV/VP1, we optimized a robust anti-JCPyV neutralization assay. This allowed us to evaluate the neutralizing activity in JCPyV-positive sera from MS patients, demonstrating the lack of correlation between the level of anti-JCPyV antibody and anti-JCPyV neutralizing activity. Relevant consequences may derive from future clinical studies induced by these findings; indeed the study of the serum anti-JCPyV neutralizing activity could allow not only a better risk stratification of the patients during natalizumab treatment, but also a better understanding of the pathophysiological mechanisms leading to PML, highlighting the contribution of peripheral versus central nervous system JCPyV reactivation. Noteworthy, the availability of GRE1 could allow the design of novel immunoprophylactic strategies during the immunomodulatory treatment

icumonitoring.ch: a platform for short-term forecasting of intensive care unit occupancy during the COVID-19 epidemic in Switzerland

In Switzerland, the COVID-19 epidemic is progressively slowing down owing to “social distancing” measures introduced by the Federal Council on 16 March 2020. However, the gradual ease of these measures may initiate a second epidemic wave, the length and intensity of which are difficult to anticipate. In this context, hospitals must prepare for a potential increase in intensive care unit (ICU) admissions of patients with acute respiratory distress syndrome. Here, we introduce icumonitoring.ch, a platform providing hospital-level projections for ICU occupancy. We combined current data on the number of beds and ventilators with canton-level projections of COVID-19 cases from two S-E-I-R models. We disaggregated epidemic projection in each hospital in Switzerland for the number of COVID-19 cases, hospitalisations, hospitalisations in ICU, and ventilators in use. The platform is updated every 3-4 days and can incorporate projections from other modelling teams to inform decision makers with a range of epidemic scenarios for future hospital occupancy.ISSN:1424-7860ISSN:1424-399

Mutation in the SYNJ1 gene associated with autosomal recessive, early-onset Parkinsonism.

Autosomal recessive, early-onset Parkinsonism is clinically and genetically heterogeneous. Here, we report the identification, by homozygosity mapping and exome sequencing, of a SYNJ1 homozygous mutation (p.Arg258Gln) segregating with disease in an Italian consanguineous family with Parkinsonism, dystonia, and cognitive deterioration. Response to levodopa was poor, and limited by side effects. Neuroimaging revealed brain atrophy, nigrostriatal dopaminergic defects, and cerebral hypometabolism. SYNJ1 encodes synaptojanin 1, a phosphoinositide phosphatase protein with essential roles in the postendocytic recycling of synaptic vesicles. The mutation is absent in variation databases and in ethnically matched controls, is damaging according to all prediction programs, and replaces an amino acid that is extremely conserved in the synaptojanin 1 homologues and in SAC1-like domains of other proteins. Sequencing the SYNJ1ORF in unrelated patients revealed another heterozygous mutation (p.Ser1422Arg), predicted as damaging, in a patient who also carries a heterozygous PINK1 truncating mutation. The SYNJ1 gene is a compelling candidate for Parkinsonism; mutations in the functionally linked protein auxilin cause a similar early-onset phenotype, and other findings implicate endosomal dysfunctions in the pathogenesis. Our data delineate a novel form of human Mendelian Parkinsonism, and provide further evidence for abnormal synaptic vesicle recycling as a central theme in the pathogenesis. (C) 2013 Wiley Periodicals, Inc