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

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

The complete sequence of four major structural proteins of African horse sickness virus serotype 6: evolutionary relationships within and between the orbiviruses

The amino acid sequences of four major capsid proteins of African horse sickness virus (serotype 6, AHSV-6) have been determined from analyses of cDNA clones representing the L2, L3, M6 and S7 RNA segments. the AHSV-6 L3 RNA segment has an open reading frame of 2715 base pairs and encodes the inner capsid protein VP3 which comprises 905 amino acids. the VP3 layer forms the subcore of the virion and is surrounded by the VP7 protein which is encoded by the S7 gene. the AHSV-6 S7 gene was found to be 1047 nucleotides in length with a coding capacity for the VP7 protein of 349 amino acids. These core proteins are encapsulated by the outer capsid proteins VP5 and VP2 which are encoded by the M6 and L2 genes respectively. the M6 gene of AHSV-6 was determined to be 1564 nucleotides in length and encoded a protein product of 504 amino acids while the L2 gene comprised 3203 nucleotides which encoded a predicted protein product of 1051 amino acids. Comparison of these four sequences with the care protein sequences of other serotypes of African horse sickness virus, Bluetongue virus which infects sheep, and Epizootic haemorrhagic disease virus of deer, demonstrated that despite the pathobiological properties and host range of these distinct orbiviruses, extreme conservation is evident within the capsid genes. Sequence analyses also suggested that the similarity levels between serogroups depict the structure and function of the individual capsid proteins. the data indicated that the evolution of the capsid genes of gnat transmitted orbiviruses is strongly influenced by functional and structural constraints. (C) 1998 Elsevier Science B.V. All rights reserved.Univ Oxford, Dept Biochem, Oxford OX1 3SR, EnglandNERC, Inst Virol & Environm Microbiol, Oxford OX1 3SR, EnglandUniv Alabama, Dept Int Hlth, Birmingham, AL 35294 USAUniversidade Federal de São Paulo, UNIFESP, Escola Paulista Med, DIPA,Retrovirol Unit, BR-05508900 São Paulo, BrazilUniversidade Federal de São Paulo, UNIFESP, Escola Paulista Med, DIPA,Retrovirol Unit, BR-05508900 São Paulo, BrazilWeb of Scienc

Ultrarapid cerium(III)–NHC catalysts for high molar mass cyclic polylactide

Cyclic polyesters could improve the properties of degradable plastics, but routes to them that provide a product with faster rates, higher molar mass, and greater selectivity for cyclic vs linear polymer are needed. Here, homogeneous Ce(III)–N-heterocyclic carbene (NHC) catalysts show outstanding activities (turn-over-frequency (TOF) > 864 000 h–1), excellent control, and selectivity for cyclic polylactide (PLA) topology (>95%), yielding high molar mass PLA (60 < Mn < 250 kg mol–1). They efficiently produce cyclic PLA from rac-lactide or l-lactide and aliphatic cyclic polyesters from ε-caprolactone or β-butyrolactone. The enhanced performances are only achievable from combining cooperative Lewis acidic cerium(III) and hemilabile N-heterocyclic carbene functionalities