Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State.

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gravely affected societies around the world. Outbreaks in different parts of the globe have been shaped by repeated introductions of new viral lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State (USA) to characterize how the spread of SARS-CoV-2 in Washington State in early 2020 was shaped by differences in timing of mitigation strategies across counties and by repeated introductions of viral lineages into the state. In addition, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G but not the other variant (614D) into the state. At an individual level, we observed evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we did not find any evidence that the 614G variant affects clinical severity or patient outcomes. Overall, this suggests that with regard to D614G, the behavior of individuals has been more important in shaping the course of the pandemic in Washington State than this variant of the virus.

A clinically validated human capillary blood transcriptome test for global systems biology studies.

To prevent and treat chronic diseases, including cancer, a global application of systems biology is needed. We report here a whole blood transcriptome test that needs only 50 µl of capillary (fingerprick) blood. This test is suitable for global applications because the samples are preserved at ambient temperature for up to 4 weeks and the RNA preservative inactivates all pathogens, enabling safe transportation. Both the laboratory and bioinformatic steps are automated and performed in a clinical lab, which minimizes batch effects and creates unbiased datasets. Given its clinical testing performance and accessibility to traditionally underrepresented and diverse populations, this test offers a unique ability to reveal molecular mechanisms of disease and enable longitudinal, population-scale studies.

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State.

The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of SARS-CoV-2 in Washington State (USA) was shaped by differences in timing of mitigation strategies across counties, as well as by repeated introductions of viral lineages into the state. Additionally, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G, but not the other variant (614D) into the state. At an individual level, we see evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we do not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that at least to date, the behavior of individuals has been more important in shaping the course of the pandemic than changes in the virus.

High-throughput phenotyping of cell-to-cell interactions in gel microdroplet pico-cultures.

Microbiomes exert significant influence on our planet's ecology. Elucidating the identities of individual microbes within these communities and how they interact is a vital research imperative. Using traditional plating and culturing methods, it is impractical to assess even a small fraction of the interactions that exist within microbial communities. To address this technology gap, we integrated gel microdroplet technology with microfluidics to generate millions of microdroplet cultures (MDs) that sequester individual cells for phenotyping MDs, facilitating rapid analysis and viable recovery using flow cytometry. Herein, we describe a validated high-throughput phenotyping pipeline that elucidates cell-to-cell interactions for millions of combinations of microorganisms. Through iterative co-culturing of an algae and a pool of environmentally sourced microbes, we successfully isolated bacteria that improved algal growth.

Children's views on taking medicines and participating in clinical trials.

INTRODUCTION: Limited information is available on the views of children taking medicines and participating in clinical trials. These views may contribute to a better understanding of what can be improved on in the development of medicines from their perspective. OBJECTIVE: To collect children's views on taking medicines and participating in clinical trials. MATERIALS AND METHODS: A question-based survey was conducted among children living in European Union countries between January and August 2015. RESULTS: Almost 900 children aged 10-17 years from Finland, Germany, Sweden, Spain and Hungary responded. Almost 40% had a chronic health condition. The most commonly used pharmaceutical forms were solid or liquid medicines for oral use and injectable medicines. Bad taste and pain during administration were reported as common problems. Of 785 respondents, 17% had been taking part in a clinical trial. Most respondents would potentially agree to take part in a clinical trial because the investigational medicine might improve their own health or that of other children. Concern that the investigational medicine might be harmful was the main reason to refuse participation, if asked to. Over half of the respondents were willing to learn more about clinical trials, preferably online. CONCLUSIONS: It is necessary to involve children in the development of age-appropriate pharmaceutical forms and in the design of clinical trials. Children and their carers should be provided with age-appropriate medical information in the most suitable channels. We have identified some common problems that children experience when taking medicines, and we conclude that children are interested in learning more and giving their opinions on clinical trials.

A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health.

A functional readout of the gut microbiome is necessary to enable precise control of the gut microbiome's functions, which support human health and prevent or minimize a wide range of chronic diseases. Stool metatranscriptomic analysis offers a comprehensive functional view of the gut microbiome, but despite its usefulness, it has rarely been used in clinical studies due to its complexity, cost, and bioinformatic challenges. This method has also received criticism due to potential intrasample variability, rapid changes, and RNA degradation. Here, we describe a robust and automated stool metatranscriptomic method, called Viomega, which was specifically developed for population-scale studies. Viomega includes sample collection, ambient temperature sample preservation, total RNA extraction, physical removal of ribosomal RNAs (rRNAs), preparation of directional Illumina libraries, Illumina sequencing, taxonomic classification based on a database of >110,000 microbial genomes, and quantitative microbial gene expression analysis using a database of ~100 million microbial genes. We applied this method to 10,000 human stool samples and performed several small-scale studies to demonstrate sample stability and consistency. In summary, Viomega is an inexpensive, high-throughput, automated, and accurate sample-to-result stool metatranscriptomic technology platform for large-scale studies and a wide range of applications.

Usage of unpublished paediatric data.

The European Paediatric Regulation (EC No 1901/2006) has three main objectives: increasing the number of appropriate medicines for children, increasing information on these medicines and stimulating high-quality ethical research with children. To contribute to the information, pharmaceutical companies were required under article 45 of the Regulation to submit existing paediatric studies to regulatory authorities for review and update of the product information. Nearly, 19 000 study reports have been identified for a thousand active substances. The data are being assessed by member states' competent authorities in collaboration with European Medicines Agency (EMA). After 7 years, 262 active substances have been assessed, all of the 62 centrally approved and nearly 200 nationally approved medicines. The review so far has led to 16 new paediatric indications, of importance in addressing previously unmet needs, in particular, in younger age groups. The information is being made publicly available in an EMA database accessible directly or through the public face of the European Clinical Trials Register. This will increase awareness of existing data that are useful to researchers and other healthcare professionals, and contribute to avoiding unnecessary duplication of paediatric trials.

Enhanced Paediatric Pharmacovigilance at the European Medicines Agency: A Novel Query Applied to Adverse Drug Reaction Reports.

BACKGROUND: Databases of suspected adverse drug reactions (ADRs) are a cornerstone of pharmacovigilance. With increasing numbers of reports, additional statistical approaches are needed to better use the data. AIM: The present study was aimed at elucidating the European Medicines Agency's (EMA) use of a novel 'paediatric' query to analyse the data in its ADR database 'EudraVigilance'. METHODS: The proportional reporting ratio (PRR) is a measure of disproportionality for which the underlying principle is that a drug-event pair of interest is reported more often than expected relative to an independence model. The EMA's paediatric query, based on PRRs, was applied to the data in EudraVigilance to investigate the extent to which the known association between enalapril and renal toxicity was reflected in reported ADRs comparing children with adults and with adjustment for the effect of multiplicity. RESULTS: The comparison of PRRs for children (14.91, 95% confidence interval [CI] 13.05-17.04) versus adults (2.66, 95% CI 2.52-2.82) confirmed a higher risk of renal ADRs with enalapril when used in children compared with all other medicines and compared with adults. CONCLUSIONS: The EMA's paediatric query can be used to highlight an imbalance for a drug-event pair among ADRs for a medicine when used in children and as compared with adults. Applying the query in practice can help the EMA to decide on whether stand-alone paediatric medicine development is warranted, and which, if any, further studies are necessary. Ongoing evaluation of the query is contributing to the development of new methods and guidance.

Increase and change in pattern of hospital antimicrobial use, Denmark, 1997-2001.

OBJECTIVES: To analyse the changes and compare antimicrobial consumption in public hospitals in Denmark over the period 1997-2001. METHODS: Data on the number of WHO defined daily doses (DDD) were obtained from the Danish Medicines Agency. Data on the number of bed-days were obtained from the National Board of Health. We calculated antimicrobial consumption in hospitals as the number of DDD per 100 bed-days for all antibacterials for systemic use i.e. group J01 of the Anatomical Therapeutic Chemical (ATC) classification and for classes of this group. RESULTS: During 1997-2001, antimicrobial use in hospitals in Denmark significantly increased by 18%, from 38.0 to 44.8 DDD per 100 bed-days (P < 0.005). Most of this increase (55%) was attributed to an increase in consumption of commonly used classes of antimicrobials, mainly penicillins with extended spectrum (ATC group J01CA), beta-lactamase-sensitive penicillins (J01CE) and beta-lactamase-resistant penicillins (J01CF). The 'broad-spectrum' and newer antimicrobials, i.e. combinations of penicillins with beta-lactamase inhibitor (J01CR), cephalosporins (J01DA), carbapenems (J01DH) and fluoroquinolones (J01MA) contributed to 36% of the increase. Together, these amounted to 16% of total consumption in hospitals in Denmark in 1997, rising to 19% in 2001. CONCLUSIONS: Although antimicrobial consumption in public hospitals in Denmark is low compared with other countries, the steady increase and change in pattern of their use are causes of concern, deserving close monitoring and further investigations.