Prevalence of mixed genotype hepatitis C virus infections in the UK as determined by genotype‐specific PCR and deep sequencing

The incidence of mixed genotype hepatitis C virus infections in the UK is largely unknown. As the efficacy of direct acting antivirals is variable across different genotypes, treatment regimens are tailored to the infecting genotype, which may pose issues for the treatment of underlying genotypes within undiagnosed mixed genotype HCV infections. There is therefore a need to accurately diagnose mixed genotype infections prior to treatment. PCR-based diagnostic tools were developed to screen for the occurrence of mixed genotype infections caused by the most common UK genotypes, 1a and 3, in a cohort of 506 individuals diagnosed with either of these genotypes. The overall prevalence rate of mixed infection was 3.8% however this rate was unevenly distributed, with 6.7% of individuals diagnosed with genotype 3 harbouring genotype 1a strains and only 0.8% of samples from genotype 1a patients harbouring genotype 3 (p<0.05). Mixed infection samples consisted of a major and a minor genotype, with the latter constituting less than 21% of the total viral load and, in 67% of cases, less than 1% of the viral load. Analysis of a subset of the cohort by Illumina PCR-next generation sequencing resulted in a much greater incidence rate than obtained by PCR. This may have occurred due to the non-quantitative nature of the technique and despite the designation of false positive thresholds based on negative controls

Is India becoming a waste haven of metal scrap?

India is one of the largest importers of waste in the world with metallic scrap constituting the bulk of the waste imports. While relatively weak environmental standards in developing countries is often seen to be a key factor in the emergence of waste havens in cross-country studies, little attention has been given to examine the pattern of waste trade in a developing country over time. This paper analyzes factors determining metallic waste import in India from different source countries during 1996 through 2012. We empirically test the presence of waste haven effect in metallic scrap import by India after controlling for technology and home market demand. We find that the escalating domestic demand for metal and use of relatively labor-intensive technology are significant factors behind India’s import of metallic wastes from different source countries. We find no empirical evidence of waste haven effect

Post-mortem findings and causes of death of harbour porpoises (Phocoena phocoena) stranded from 1990 to 2000 along the coastlines of Belgium and northern France

peer reviewedBetween the,ears 1990 and 2000, an attempt was made to determine the causes of death of 55 harbour porpoises stranded along the Belgian and northern French coasts. From 1990 to 1996, only five carcasses were collected as against seven in 1997, eight in 1998, 27 in 1999 and eight in 2000. The sex ratio was normal and most of the animals were juvenile. The most common findings were emaciation, severe parasitosis and pneumonia. A few cases of fishing net entanglement were observed. The main microscopical lesions were acute pneumonia, massive lung oedema, enteritis, hepatitis and gastritis. Encephalitis was observed in six cases. No evidence of morbillivirus infection was detected. Pneumonia was associated with bacteria or parasites, or both. The causes of death and the lesions were similar to those previously reported in other countries bordering the North Sea. The cause of the increased numbers of carcasses in 1999 was unclear but did not include viral epizootics or net entanglement. A temporary increase in the porpoise populatiou in the southern North Sea may have been responsible. (C) 2002 Elsevier Science Ltd. All rights reserved

Viral Evolution in the Genomic Age

The remarkable increase in the number of viral genome sequences represents both opportunities and challenges for understanding disease ecology and evolution, and must stimulate researchers to address questions that were previously considered out of reach

Observational Study Design in Veterinary Pathology, Part 1: Study Design

Observational studies are the basis for much of our knowledge of veterinary pathology and are highly relevant to the daily practice of pathology. However, recommendations for conducting pathology-based observational studies are not readily available. In part 1 of this series, we offer advice on planning and conducting an observational study with examples from the veterinary pathology literature. Investigators should recognize the importance of creativity, insight, and innovation in devising studies that solve problems and fill important gaps in knowledge. Studies should focus on specific and testable hypotheses, questions, or objectives. The methodology is developed to support these goals. We consider the merits and limitations of different types of analytic and descriptive studies, as well as of prospective vs retrospective enrollment. Investigators should define clear inclusion and exclusion criteria and select adequate numbers of study subjects, including careful selection of the most appropriate controls. Studies of causality must consider the temporal relationships between variables and the advantages of measuring incident cases rather than prevalent cases. Investigators must consider unique aspects of studies based on archived laboratory case material and take particular care to consider and mitigate the potential for selection bias and information bias. We close by discussing approaches to adding value and impact to observational studies. Part 2 of the series focuses on methodology and validation of methods

An asymptotic treatment of the Elenbaas–Heller equation for a radiating wall‐stabilized high‐pressure gas‐discharge arc

An asymptotic analysis of the Elenbaas–Heller equation for a radiating wall-stabilized high-pressure gas-discharge arc is given. This analysis applies when the operating temperatures within the arc are lower than the ionization temperature by an order of magnitude. It is shown that for arcs that are radiating highly efficiently a further asymptotic treatment can be given. It is shown under what conditions, governed by a dimensionless parameter M, this limiting case prevails. Comparison with earlier results put forward by Zollweg [J. Appl. Phys. 49, 1077 (1978)] shows satisfactory agreement

Recombination rate and selection strength in HIV intra-patient evolution

The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the parameters governing genetic diversification and the strength of selection need to be known. While mutation rates can be measured in single replication cycles, the relevant effective recombination rate depends on the probability of coinfection of a cell with more than one virus and can only be inferred from population data. However, most population genetic estimators for recombination rates assume absence of selection and are hence of limited applicability to HIV, since positive and purifying selection are important in HIV evolution. Here, we estimate the rate of recombination and the distribution of selection coefficients from time-resolved sequence data tracking the evolution of HIV within single patients. By examining temporal changes in the genetic composition of the population, we estimate the effective recombination to be r=1.4e-5 recombinations per site and generation. Furthermore, we provide evidence that selection coefficients of at least 15% of the observed non-synonymous polymorphisms exceed 0.8% per generation. These results provide a basis for a more detailed understanding of the evolution of HIV. A particularly interesting case is evolution in response to drug treatment, where recombination can facilitate the rapid acquisition of multiple resistance mutations. With the methods developed here, more precise and more detailed studies will be possible, as soon as data with higher time resolution and greater sample sizes is available.Comment: to appear in PLoS Computational Biolog