Detection of squirrel poxvirus by nested and real-time PCR from red (Sciurus vulgaris) and grey (Sciurus carolinensis) squirrels

<p>Abstract</p> <p>Background</p> <p>Squirrel poxvirus (SQPV) is highly pathogenic to red squirrels (<it>Sciurus vulgaris</it>), and is a significant contributing factor to the local extinction of the species in most parts of England and Wales, where infection is endemic in Eastern grey squirrel (<it>Sciurus carolinensis</it>) populations. Although a nested PCR assay has been used successfully to study the epidemiology of SQPV, samples have a long processing time and the assay is not quantifiable.</p> <p>Results</p> <p>This project describes the design and optimization of a real-time PCR for SQPV. Comparison with the nested PCR showed the real-time assay to be more sensitive by one log and able to detect approximately 144 genome copies per mg of tissue.</p> <p>Conclusions</p> <p>The real-time PCR has been used to quantify viral genome load in tissues from diseased and apparently healthy red and grey squirrels, and suggests that the titre of virus in tissues from diseased red squirrels is considerably higher than that found even in a grey squirrel with cutaneous lesions.</p

Application of next-generation sequencing technologies in virology

The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance knowledge. Following on from electron microscopy, cell culture and PCR, next-generation sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. Possibilities for these methodologies are only limited by our scientific imagination and, to some extent, by their cost, which has restricted their use to relatively small numbers of samples. Challenges remain, including the storage and analysis of the large amounts of data generated. As the chemistries employed mature, costs will decrease. In addition, improved methods for analysis will become available, opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. An exciting era of viral exploration has begun, and will set us new challenges to understand the role of newly discovered viral diversity in both disease and health

A multi-national European cross-sectional study of feline calicivirus epidemiology, diversity and vaccine cross-reactivity

Background Feline calicivirus (FCV) is an important pathogen of cats for which vaccination is regularly practised. Long-term use of established vaccine antigens raises the theoretical possibility that field viruses could become resistant. This study aimed to assess the current ability of the FCV-F9 vaccine strain to neutralise a randomly collected contemporary panel of FCV field strains collected prospectively in six European countries. Methods Veterinary practices (64) were randomly selected from six countries (UK, Sweden, Netherlands, Germany, France and Italy). Oropharyngeal swabs were requested from 30 (UK) and 40 (other countries) cats attending each practice. Presence of FCV was determined by virus isolation, and risk factors for FCV shedding assessed by multivariable logistic regression. Phylogenetic analyses were used to describe the FCV population structure. In vitro virus neutralisation assays were performed to evaluate FCV-F9 cross-reactivity using plasma from four vaccinated cats. Results The overall prevalence of FCV was 9.2%. Risk factors positively associated with FCV shedding included multi-cat households, chronic gingivostomatitis, younger age, not being neutered, as well as residing in certain countries. Phylogenetic analysis showed extensive variability and no countrywide clusters. Despite being first isolated in the 1950s, FCV-F9 clustered with contemporary field isolates. Plasma raised to FCV-F9 neutralized 97% of tested isolates (titres 1:4 to 1:5792), with 26.5%, 35.7% and 50% of isolates being neutralized by 5, 10 and 20 antibody units respectively. Conclusions This study represents the largest prospective analysis of FCV diversity and antigenic cross-reactivity at a European level. The scale and random nature of sampling used gives confidence that the FCV isolates used are broadly representative of FCVs that cats are exposed to in these countries. The in vitro neutralisation results suggest that antibodies raised to FCV-F9 remain broadly cross-reactive to contemporary FCV isolates across the European countries sampled

Visualising spatio-temporal health data: the importance of capturing the 4th dimension

Confronted by a rapidly evolving health threat, such as an infectious disease outbreak, it is essential that decision-makers are able to comprehend the complex dynamics not just in space but also in the 4th dimension, time. In this paper this is addressed by a novel visualisation tool, referred to as the Dynamic Health Atlas web app, which is designed specifically for displaying the spatial evolution of data over time while simultaneously acknowledging its uncertainty. It is an interactive and open-source web app, coded predominantly in JavaScript, in which the geospatial and temporal data are displayed side-by-side. The first of two case studies of this visualisation tool relates to an outbreak of canine gastroenteric disease in the United Kingdom, where many veterinary practices experienced an unusually high case incidence. The second study concerns the predicted COVID-19 reproduction number along with incidence and prevalence forecasts in each local authority district in the United Kingdom. These studies demonstrate the effectiveness of the Dynamic Health Atlas web app at conveying geospatial and temporal dynamics along with their corresponding uncertainties.Comment: 4 Figures, 27 page

Stakeholder opinion-led study to identify canine priority diseases for surveillance and control in the UK

BackgroundMany pathogens cause disease in dogs; however, meaningful surveillance in small companion animals is often only possible for the most impactful diseases. We describe the first stakeholder opinion-led approach to identify which canine infectious diseases should be prioritised for inclusion in surveillance and control strategies in the UK.MethodsParticipants were identified through a stakeholder analysis. A multicriteria decision analysis was undertaken to establish and weight epidemiological criteria for evaluating diseases, and a Delphi technique was employed to achieve a consensus among participants on the top-priority canine diseases.ResultsNineteen stakeholders from multiple backgrounds participated in this study. Leptospirosis and parvovirus were identified as the top two endemic diseases of concern, while leishmaniosis and babesiosis were the top two exotic diseases. Respiratory and gastrointestinal diseases were identified as the top two syndromes of concern.LimitationsDue to the COVID-19 pandemic, the number of participants was reduced. Despite this, a representative multidisciplinary sample of relevant stakeholders contributed to the present study.ConclusionsFindings from this study are being used to inform the development of a future UK-wide epidemic response strategy. This methodology could provide a blueprint for other countries

Factors Associated with Prescription of Antimicrobial Drugs for Dogs and Cats, United Kingdom, 2014–2016

Antimicrobial stewardship is a cornerstone of efforts to curtail antimicrobial resistance. To determine factors potentially influencing likelihood of prescribing antimicrobials for animals, we analyzed electronic health records for unwell dogs (n = 155,732 unique dogs, 281,543 consultations) and cats (n = 69,236 unique cats, 111,139 consultations) voluntarily contributed by 173 UK veterinary practices. Using multivariable mixed effects logistic regression, we found that factors associated with decreased odds of systemic antimicrobial prescription were client decisions focused on preventive health: vaccination (dogs, odds ratio [OR] 0.93, 95% CI, 0.90-0.95; cats, OR 0.92, 95% CI 0.89-0.95), insurance (dogs, OR 0.87, 95% CI 0.84-0.90; cats, OR 0.82, 95% CI 0.79-0.86), neutering of dogs (OR 0.90, 95% CI 0.88-0.92), and practices accredited by the Royal College of Veterinary Surgeons (OR 0.79, 95% 95% CI 0.68-0.92). This large multicenter companion animal study demonstrates the potential of preventive healthcare and client engagement to encourage responsible antimicrobial drug use

Canine babesiosis and tick activity monitored using companion animal electronic health records in the UK

Recent publications highlighting autochthonous Babesia canis infection in dogs from Essex that have not travelled outside the UK are a powerful reminder of the potential for pathogen emergence in new populations. Here the authors use electronic health data collected from two diagnostic laboratories and a network of 392 veterinary premises to describe canine Babesia cases and levels of Babesia concern from January 2015 to March 2016, and the activity of ticks during December 2015–March 2016. In most areas of the UK, Babesia diagnosis in this population was rare and sporadic. In addition, there was a clear focus of Babesia cases in the affected area in Essex. Until February 2016, analysis of health records indicated only sporadic interest in Babesia largely in animals coming from overseas. Following media coverage in March 2016, there was a spike in owner concern that was geographically dispersed beyond the at-risk area. Tick activity (identified as ticks being removed from animals in veterinary consultations) was consistent but low during the period preceding the infections (<5 ticks/10,000 consultations), but increased in March. This highlights the use of electronic health data to describe rapidly evolving risk and concern that follows the emergence of a pathogen

Molecular characterization of the uncultivatable hemotropic bacterium Mycoplasma haemofelis

Mycoplasma haemofelis is a pathogenic feline hemoplasma. Despite its importance, little is known about its metabolic pathways or mechanism of pathogenicity due to it being uncultivatable. The recently sequenced M. haemofelis str. Langford 1 genome was analysed and compared to those of other available hemoplasma genomes

GP coding behaviour for non-specific clinical presentations: a pilot study.

Clinical coding is an integral part of primary care. Disease incidence studies based on primary care electronic health records (EHRs) rely on the accuracy of these codes. Current code validation methods are not appropriate for non-specific conditions and provide limited information about GPs' decision-making behaviour around coding. Qualitative methods could offer insight into decision-making behaviour around coding of patients with non-specific conditions. To investigate the decision-making behaviour of GPs when applying Read codes to non-specific clinical presentations, using Lyme disease as a case example. A pilot study was undertaken, involving masked semi-structured interviews of eight GPs in the North West of England. Semi-structured interviews were carried out based on 11 clinical cases representative of Lyme disease presentations. Discrete answers were described descriptively. Interview transcripts were analysed using a thematic approach. Themes underpinning GPs' coding behaviour included: GP personal and professional experience; clinical evidence; diagnostic uncertainty; professional integrity and defensive practice; and patient-sourced health information and beliefs. GPs placed Lyme disease on their differential diagnosis list for five cases; in only two cases would GPs select a Lyme disease related Read code. GPs were reluctant to code with specific diagnostic Read codes when they were presented with patients with vague or unfamiliar symptomology. This masked questionnaire methodology offers a new approach to validate incidence figures, based on Read codes of non-specific conditions. The reluctance to code poses many problems for primary care EHRs research. Further research is needed to understand what drives GPs' coding behaviour