First Dating of a Recombination Event in Mammalian Tick-Borne Flaviviruses

The mammalian tick-borne flavivirus group (MTBFG) contains viruses associated with important human and animal diseases such as encephalitis and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where recombination events are frequent, the evolutionary dynamic within the MTBFG was believed to be essentially clonal. This assumption was challenged with the recent report of several homologous recombinations within the Tick-borne encephalitis virus (TBEV). We performed a thorough analysis of publicly available genomes in this group and found no compelling evidence for the previously identified recombinations. However, our results show for the first time that demonstrable recombination (i.e., with large statistical support and strong phylogenetic evidences) has occurred in the MTBFG, more specifically within the Louping ill virus lineage. Putative parents, recombinant strains and breakpoints were further tested for statistical significance using phylogenetic methods. We investigated the time of divergence between the recombinant and parental strains in a Bayesian framework. The recombination was estimated to have occurred during a window of 282 to 76 years before the present. By unravelling the temporal setting of the event, we adduce hypotheses about the ecological conditions that could account for the observed recombination

Prioritisation of Anti-SARS-Cov-2 Drug Repurposing Opportunities Based on Plasma and Target Site Concentrations Derived from their Established Human Pharmacokinetics.

There is a rapidly expanding literature on the in vitro antiviral activity of drugs that may be repurposed for therapy or chemoprophylaxis against SARS-CoV-2. However, this has not been accompanied by a comprehensive evaluation of the target plasma and lung concentrations of these drugs following approved dosing in humans. Accordingly, EC90 values recalculated from in vitro anti-SARS-CoV-2 activity data was expressed as a ratio to the achievable maximum plasma concentrations (Cmax) at an approved dose in humans (Cmax/EC90 ratio). Only 14 of the 56 analysed drugs achieved a Cmax/EC90 ratio above 1. A more in-depth assessment demonstrated that only nitazoxanide, nelfinavir, tipranavir (ritonavir-boosted) and sulfadoxine achieved plasma concentrations above their reported anti-SARS-CoV-2 activity across their entire approved dosing interval. An unbound lung to plasma tissue partition coefficient (Kp Ulung ) was also simulated to derive a lung Cmax/EC50 as a better indicator of potential human efficacy. Hydroxychloroquine, chloroquine, mefloquine, atazanavir (ritonavir-boosted), tipranavir (ritonavir-boosted), ivermectin, azithromycin and lopinavir (ritonavir-boosted) were all predicted to achieve lung concentrations over 10-fold higher than their reported EC50 . Nitazoxanide and sulfadoxine also exceeded their reported EC50 by 7.8- and 1.5-fold in lung, respectively. This analysis may be used to select potential candidates for further clinical testing, while deprioritising compounds unlikely to attain target concentrations for antiviral activity. Future studies should focus on EC90 values and discuss findings in the context of achievable exposures in humans, especially within target compartments such as the lung, in order to maximise the potential for success of proposed human clinical trials

Design, statistical analysis and sample size calculation of a phase IIb/III study of linagliptin versus voglibose and placebo

<p>Abstract</p> <p>Background</p> <p>Many patients with diabetes mellitus (DM) require a combination of antidiabetic drugs with complementary mechanisms of action to lower their hemoglobin A_1clevels to achieve therapeutic targets and reduce the risk of cardiovascular complications. Linagliptin is a novel member of the dipeptidyl peptidase-4 (DPP-4) inhibitor class of antidiabetic drugs. DPP-4 inhibitors increase incretin (glucagon-like peptide-1 and gastric inhibitory polypeptide) levels, inhibit glucagon release and, more importantly, increase insulin secretion and inhibit gastric emptying. Currently, phase III clinical studies with linagliptin are underway to evaluate its clinical efficacy and safety. Linagliptin is expected to be one of the most appropriate therapies for Japanese patients with DM, as deficient insulin secretion is a greater concern than insulin resistance in this population. The number of patients with DM in Japan is increasing and this trend is predicted to continue. Several antidiabetic drugs are currently marketed in Japan; however there is no information describing the effective dose of linagliptin for Japanese patients with DM.</p> <p>Methods</p> <p>This prospective, randomized, double-blind study will compare linagliptin with placebo over a 12-week period. The study has also been designed to evaluate the safety and efficacy of linagliptin by comparing it with another antidiabetic, voglibose, over a 26-week treatment period. Four treatment groups have been established for these comparisons. A phase IIb/III combined study design has been utilized for this purpose and the approach for calculating sample size is described.</p> <p>Discussion</p> <p>This is the first phase IIb/III study to examine the long-term safety and efficacy of linagliptin in diabetes patients in the Japanese population.</p> <p>Trial registration</p> <p>Clinicaltrials.gov (NCT00654381).</p

The large grey area between ‘bona fide’ and ‘rogue’ stem cell interventions — ethical acceptability and the need to include local variability

This article aims to put into perspective the binary opposition between ‘scientific’ clinical research trials and ‘rogue’ experimental stem cell therapies, and to show why the ethics criteria used by the dominant science community are not suitable for distinguishing between adequate and inadequate treatments. By focusing on the grey area between clinical stem cell trials and stem cell experimentation, the experimental space where patients, medical professionals and life scientists negotiate for diverging reasons and aims, I show why idealised notions of ethics are not feasible for many stem cell scientists in low- and middle-income countries. Drawing on fieldwork in China from 2012 to 2013, the article asks why ‘the unethical’ according to some is acceptable to Chinese life scientists. The case study of stem cell service provider Beike Biotech illustrates how stem cell interventions take place in a large grey area, where narrow notions of ethics are blurred with and supplanted by broader notions of ethics, co-determined by estimations of socio-economic, political and cultural understandings of risk, opportunity and benefit. I borrow the term ‘bionetworking’, understood as the entrepreneurial aspects of scientific networks that engage in creating biomedical products, to analyse various forms of medical experimentation. I speak of the ‘externalisation’ and ‘internalisation’ of local factors to elucidate how features of patient populations and their environments are subsumed in clinical research applications. Compared to polarised views of stem cell therapy, this approach increases the transparency of clinical interventions and broadens our understanding of why ‘stem cell tourism’ to some is ‘stem cell therapy’ to others

Comparing national home-keeping and the regulation of translational stem cell applications: an international perspective

A very large grey area exists between translational stem cell research and applications that comply with the ideals of randomised control trials and good laboratory and clinical practice and what is often referred to as snake-oil trade. We identify a discrepancy between international research and ethics regulation and the ways in which regulatory instruments in the stem cell field are developed in practice. We examine this discrepancy using the notion of ‘national home-keeping’, referring to the way governments articulate international standards and regulation with conflicting demands on local players at home. Identifying particular dimensions of regulatory tools – authority, permissions, space and acceleration – as crucial to national home-keeping in Asia, Europe and the USA, we show how local regulation works to enable development of the field, notwithstanding international (i.e. principally ‘western’) regulation. Triangulating regulation with empirical data and archival research between 2012 and 2015 has helped us to shed light on how countries and organisations adapt and resist internationally dominant regulation through the manipulation of regulatory tools (contingent upon country size, the state's ability to accumulate resources, healthcare demands, established traditions of scientific governance, and economic and scientific ambitions)

Maximum likelihood methods for detecting adaptive evolution after gene duplication

The rapid accumulation of genomic sequences in public databases will finally allow large scale studies of gene family evolution, including evaluation of the role of positive Darwinian selection following a duplication event. This will be possible because recent statistical methods of comparing synonymous and nonsynonymous substitution rates permit reliable detection of positive selection at individual amino acid sites and along evolutionary lineages. Here, we summarize maximum-likelihood based methods, and present a framework for their application to analysis of gene families. Using these methods, we investigated the role of positive Darwinian selection in the ECP-EDN gene family of primates and the Troponin C gene family of vertebrates. We also comment on the limitations of these methods and discuss directions for further improvements