Assay validation is an essential component of disease surveillance testing, but can be problematic in settings where access to positive control material is limited and a safety risk for handlers. ...Here we describe a single non-infectious synthetic control that can help develop and validate the PCR based detection of the viral causes of Crimean-Congo hemorrhagic fever, Ebola virus disease, Lassa fever, Marburg virus disease and Rift Valley fever. We designed non-infectious synthetic DNA oligonucleotide sequences incorporating primer binding sites suitable for five assays, and a T7 promotor site which was used to transcribe the sequence. Transcribed RNA was used as template in a dilution series, extracted and amplified with RT-PCR and RT-qPCR to demonstrate successful recovery and determine limits of detection in a range of laboratory settings. Our results show this approach is adaptable to any diagnostic assay requiring validation of nucleic acid extraction and/or amplification, particularly where sourcing reliable, safe material for positive controls is infeasible.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Group-2 innate lymphoid cells (ILC2), type-2 cytokines, and eosinophils have all been implicated in sustaining adipose tissue homeostasis. However, the interplay between the stroma and ...adipose-resident immune cells is less well understood. We identify that white adipose tissue-resident multipotent stromal cells (WAT-MSCs) can act as a reservoir for IL-33, especially after cell stress, but also provide additional signals for sustaining ILC2. Indeed, we demonstrate that WAT-MSCs also support ICAM-1-mediated proliferation and activation of LFA-1-expressing ILC2s. Consequently, ILC2-derived IL-4 and IL-13 feed back to induce eotaxin secretion from WAT-MSCs, supporting eosinophil recruitment. Thus, MSCs provide a niche for multifaceted dialogue with ILC2 to sustain a type-2 immune environment in WAT.
Six Felis catus papillomavirus (FcaPV) types have been fully sequenceed from domestic cats including some that have been associated with the development of neoplasia. A sequence from a novel FcaPV ...type was amplified from a basal cell carcinoma that contained unusual histological evidence of PV infection and intense p16CDKN2A protein (p16) immunostaining. The entire 7467 bp genome was amplified using ‘outward facing’ primers. The PV was designated FcaPV7 and contained putative coding regions that were predicted to produce five early proteins and two late ones. The ORF L1 showed 77% similarity to that of FcaPV6. As the novel PV also showed greater than 60% similarity to three other feline Tau-PV types, FcaPV7 is proposed to be classified within this genus. Specific primers were designed but did not amplify FcaPV7 DNA from any of 60 samples from the mouth and skin of cats. FcaPV7 appears to rarely infect cats. However, FcaPV7 may be associated with skin cancer in this species.
•The complete genetic sequence of the seventh papillomavirus from domestic cats is reported.•FcaPV7 is classified within the Taupapillomavirus genus.•FcaPV7 was detected in a skin cancer.•The cancer containing FcaPV7 DNA had unusual histological features.•Cats are rarely infected by FcaPV7.
Genetic variation in Cryptosporidium, a common protozoan gut parasite in humans, is often based on marker genes containing trinucleotide repeats, which differentiate subtypes and track outbreaks. ...However, repeat regions have high replication slippage rates, making it difficult to discern biological diversity from error. Here, we synthesised Cryptosporidium DNA in clonal plasmid vectors, amplified them in different mock community ratios and sequenced them using next generation sequencing to determine the rate of replication slippage with dada2. Our results indicate that slippage rates increase with the length of the repeat region and can contribute to error rates of up to 20%.
Viruses of the subfamily Orthocoronavirinae can cause mild to severe disease in people, including COVID-19, MERS and SARS. Their most common natural hosts are bat and bird species, which are mostly ...split across four virus genera. Molecular clock analyses of orthocoronaviruses suggested the most recent common ancestor of these viruses might have emerged either around 10,000 years ago or, using models accounting for selection, many millions of years. Here, we reassess the evolutionary history of these viruses. We present time-aware phylogenetic analyses of a RNA-dependent RNA polymerase locus from 123 orthocoronaviruses isolated from birds and bats, including those in New Zealand, which were geographically isolated from other bats around 35 million years ago. We used this age, as well as the age of the avian-mammals split, to calibrate the molecular clocks, under the assumption that these ages are applicable to the analyzed viruses. We found that the time to the most recent ancestor common for all orthocoronaviruses is likely 150 or more million years, supporting clock analyses that account for selection.
•New Zealand and Australian bat orthocoronaviruses share a common ancestor.•We analyzed four Orthocoronavirinae genera RdRp gene fragments from bats and birds.•Calibrated molecular clocks included a 35 million year New Zealand bat virus origin.•Analyses suggest orthocoronaviruses are over 150 million years old.•Orthocoronaviruses may have co-evolved with amniote hosts over millions of years.
Domestic dogs are currently recognized as being infected by 25 different canine papillomavirus (CPV) types classified into three genera. A short sequence from a novel CPV type was amplified, along ...with CPV1, from a papilloma (wart) from the mouth of a dog. The entire 7499 bp genome was amplified, and CPV26 contained putative coding regions that were predicted to produce four early proteins and two late ones. The ORF L1 showed less than 62% similarity for all previously sequenced CPV types but over 69% similarity to multiple
types from a variety of Caniform species including the giant panda, Weddel seal, and polar bear. Phylogenetic analysis confirmed CPV26 clusters within the
genus. Specific primers were used to investigate the presence of CPV26 DNA within a series of 37 canine proliferative lesions. CPV26 DNA was amplified from one lesion, a cutaneous papilloma that also contained CPV6. This is the first time a PV type within the
genus has been detected in a non-domestic species and this provides evidence that the omegapapillomaviruses infected a common ancestor of, and then co-evolved with, the Caniform species. Whether CPV26 causes disease is uncertain, but the absence of an E7 protein may suggest low pathogenicity.
Numerous large dark plaques developed over the ventrum, legs and head of a 9-year-old pug dog over a 4-year-period. Histology confirmed a diagnosis of viral pigmented plaque and a short section of a ...novel papillomavirus (PV) type was amplified using consensus PCR primers. Taking advantage of the circular nature of PV DNA, 'outward facing' PCR primers allowed amplification of the full sequence. As this is the 24th PV known to infect dogs, the novel PV was designated canine papillomavirus (CPV) type 24. The CPV24 genome contained putative coding regions for 5 early proteins and 2 late ones. The CPV24 open reading frame
showed the highest (78.2%) similarity to CPV4 and phylogenetic analysis showed that CPV24 clustered with CPV4 and CPV16 suggesting CPV24 is the third species 2
type identified in dogs. This is the third report of extensive pigmented plaques covering a high proportion of the skin. Both previous cases were caused CPV4 and, considering the high genetic similarity between CPV4 and CP24, infection by these CPV types may predispose to more severe clinical disease. In addition, as plaques caused by CPV16 appear more likely to progress to neoplasia, the detection of a species 2
within a pigmented plaque may indicate the potential for more severe disease.
Abstract Objectives The aim of this study was to determine the correlation between coronary artery calcium (CAC) scores on 3 mm electrocardiography (ECG)-gated computed tomography (CT) scans and ...standard 6 mm chest CT scans, and to compare relative strength of associations of CAC on each scan type with mortality risk. Background Coronary artery calcification predicts cardiovascular disease (CVD) and all-cause mortality, and is typically measured on ECG-gated 3 mm CT scans. Patients undergo standard 6 mm chest CTs for various clinical indications much more frequently, but CAC is not usually quantified. To better understand the usefulness of standard chest CTs to quantify CAC, we conducted a case-control study among persons who had both scan types. Methods Between 2000 and 2003, 4,544 community-living individuals self- or physician-referred for “whole-body” CT scans, had 3 mm ECG-gated CTs and standard 6 mm chest CTs, and were followed for mortality through 2009. In this nested case-control study, we identified 157 deaths and 494 controls frequency matched (1:3) on age and sex. The Agatston method quantified CAC on both scan types. Unconditional logistic regression determined associations with mortality, accounting for CVD risk factors. Results Participants were 68 ± 11 years of age and 63% male. The Spearman correlation of CAC scores between the 2 scan types was 0.93 (p < 0.001); median CAC scores were lower on 6 mm CTs compared to 3 mm CTs (22 vs.104 Agatston units, p < 0.001). Adjusted for traditional CVD risk factors, each standard deviation higher CAC score on 6 mm CTs was associated with 50% higher odds of death (odds ratio: 1.5; 95% confidence interval: 1.2 to 1.9), similar to 50% higher odds on the 3 mm ECG-gated CTs (odds ratio: 1.5; 95% confidence interval: 1.1 to 1.9). Conclusions CAC scores on standard 6 mm chest CTs are strongly correlated with 3 mm ECG-gated CTs and similarly predict mortality in community-living individuals. Chest CTs performed for other clinical indications may provide an untapped resource to garner CVD risk information without additional radiation exposure or expense.
Cross-species transmission of pathogens is intimately linked to human and environmental health. With limited healthcare and challenging living conditions, people living in poverty may be particularly ...susceptible to endemic and emerging diseases. Similarly, wildlife is impacted by human influences, including pathogen sharing, especially for species in close contact with people and domesticated animals. Here we investigate human and animal contacts and human health in a community living around the Bwindi Impenetrable National Park (BINP), Uganda. We used contact and health survey data to identify opportunities for cross-species pathogen transmission, focusing mostly on people and the endangered mountain gorilla. We conducted a survey with background questions and self-reported diaries to investigate 100 participants' health, such as symptoms and behaviours, and contact patterns, including direct contacts and sightings over a week. Contacts were revealed through networks, including humans, domestic, peri-domestic, and wild animal groups for 1) contacts seen in the week of background questionnaire completion, and 2) contacts seen during the diary week. Participants frequently felt unwell during the study, reporting from one to 10 disease symptoms at different intensity levels, with severe symptoms comprising 6.4% of the diary records and tiredness and headaches the most common symptoms. After human-human contacts, direct contact with livestock and peri-domestic animals were the most common. The contact networks were moderately connected and revealed a preference in contacts within the same taxon and within their taxa groups. Sightings of wildlife were much more common than touching. However, despite contact with wildlife being the rarest of all contact types, one direct contact with a gorilla with a timeline including concerning participant health symptoms was reported. When considering all interaction types, gorillas mostly exhibited intra-species contact, but were found to interact with five other species, including people and domestic animals. Our findings reveal a local human population with recurrent symptoms of illness in a location with intense exposure to factors that can increase pathogen transmission, such as direct contact with domestic and wild animals and proximity among animal species. Despite significant biases and study limitations, the information generated here can guide future studies, such as models for disease spread and One Health interventions.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Social and medical scientists are often concerned that the external validity of experimental results may be compromised because of heterogeneous treatment effects. If a treatment has different ...effects on those who would choose to take it and those who would not, the average treatment effect estimated in a standard randomized controlled trial (RCT) may give a misleading picture of its impact outside of the study sample. Patient preference trials (PPTs), where participants' preferences over treatment options are incorporated in the study design, provide a possible solution. In this paper, we provide a systematic analysis of PPTs based on the potential outcomes framework of causal inference. We propose a general design for PPTs with multi-valued treatments, where participants state their preferred treatments and are then randomized into either a standard RCT or a self-selection condition. We derive nonparametric sharp bounds on the average causal effects among each choice-based subpopulation of participants under the proposed design. We also propose a sensitivity analysis for the violation of the key ignorability assumption sufficient for identifying the target causal quantity. The proposed design and methodology are illustrated with an original study of partisan news media and its behavioral impact.
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