A Standardized Pipeline for Assembly and Annotation of African Swine Fever Virus Genome.

Obtaining a complete good-quality sequence and annotation for the long double-stranded DNA genome of the African swine fever virus (ASFV) from next-generation sequencing (NGS) technology has proven difficult, despite the increasing availability of reference genome sequences and the increasing affordability of NGS. A gap analysis conducted by the global African swine fever research alliance (GARA) partners identified that a standardized, automatic pipeline for NGS analysis was urgently needed, particularly for new outbreak strains. Whilst there are several diagnostic and research labs worldwide that collect isolates of the ASFV from outbreaks, many do not have the capability to analyze, annotate, and format NGS data from outbreaks for submission to NCBI, and some publicly available ASFV genomes have missing or incorrect annotations.

Generation Pep - study protocol for an intersectoral community-wide physical activity and healthy eating habits initiative for children and young people in Sweden.

Background: There is overwhelming evidence for the preventive effects of regular physical activity and healthy eating habits on the risk for developing a non-communicable disease (NCD). Increasing attention has been paid to community-wide approaches in the battle against NCDs. Communities can create supportive policies, modify physical environments, and foster local stakeholder engagement through intersectoral collaboration to encourage communities to support healthy lifestyles.

Review of Play and Preisach Models for Hysteresis in Magnetic Materials.

This paper studies the properties of the Preisach model and the play model, and compare their similarities. Both are history-dependent hysteresis models that are used to model magnetic hysteresis. They are described as discrete sums of simple hysteresis operators but can easily be reformulated as integral equations of continuous distribution functions using either a Preisach weight distribution function or a play distribution function.

A Disease Outbreak in Beef Cattle Associated with and Infections.

An outbreak of disease in a Swedish beef cattle herd initiated an in-depth study to investigate the presence of bacteria and viruses in the blood of clinically healthy ( = 10) and clinically diseased cattle ( = 20) using whole-genome shotgun sequencing (WGSS). The occurrence of infectious agents was also investigated in ticks found attached to healthy cattle ( = 61) and wild deer (n = 23), and in spleen samples from wild deer ( = 30) and wild boars ( = 10). Moreover, blood samples from 84 clinically healthy young stock were analysed for antibodies against and The WGSS revealed the presence of at least three distinct variants that were most closely related to .

Characterization of a Novel Infectious Pancreatic Necrosis Virus (IPNV) from Genogroup 6 Identified in Sea Trout () from Lake Vänern, Sweden.

In November 2016, infectious pancreatic necrosis virus (IPNV) was isolated from a broodstock female of landlocked sea trout () in Lake Vänern in Sweden. VP2 gene sequencing placed the IPNV isolate in genogroup 6, for which pathogenicity is largely unknown. Lake Vänern hosts landlocked sea trout and salmon populations that are endangered, and thus the introduction of new pathogens poses a major threat.

Genetic Characterization of From Subclinical Mastitis Cases in Dairy Cows in Rwanda.

Whole-genome sequencing was carried out on 30 isolates from dairy cows with subclinical mastitis from all five provinces of Rwanda. Twenty-five of the isolates produced enough sequence to be analyzed using core genome multilocus sequence typing (cg-MLST). The isolates group into three main clusters.

Football and Ice Hockey Fans' Experience of a 12-Week Training and Weight-Loss Pilot Intervention (ViSiT) in Sweden-A Focus Group Study.

Excess weight is associated with an increased risk of poor health and premature mortality. This is more problematic for men than for women because men have a lower life expectancy and a higher prevalence of several lifestyle-related diseases. A concept whereby overweight male supporters of professional football clubs are recruited and offered a weight-loss intervention has been developed in Scotland.

Longitudinal study of Staphylococcus aureus genotypes isolated from bovine clinical mastitis.

Bovine clinical mastitis is an important problem for the dairy industry, and Staphylococcus aureus is a common mastitis-causing pathogen in many countries. Detailed knowledge on genetic variation of Staph. aureus strains within the bovine population, including changes over time, can be useful for mastitis control programs, because severity of disease and effects on milk production are at least partly strain-associated.

Screening of Eurasian Tundra Reindeer for Viral Sequences by Next-Generation Sequencing.

Reindeer husbandry is essential for the livelihood and culture of indigenous people in the Arctic. Parts of the herding areas are also used as pastures for farm animals, facilitating potential transmission of viruses between species. Following the Covid-19 pandemic, viruses circulating in the wild are receiving increased attention, since they might pose a potential threat to human health.

RT-qPCR assay for detection of mink astrovirus in outbreaks of diarrhea on Danish mink farms.

Diarrhea in mink kits is a major cause of disease and mortality in the mink production. The etiology remains unknown in most outbreaks due to a lack of diagnostic assays. In the current study we present an RT-qPCR method to detect mink astrovirus in fecal samples from mink kits with diarrhea.

Visualization of intestinal infections with astro- and sapovirus in mink () kits by hybridization.

Clarification of the infection microbiology remains a challenge in the pre-weaning diarrhea (PWD) syndrome in farmed mink (). Duodenal, jejunal and colon sections from 36 mink kits with PWD were systematically examined by chromogen hybridization targeting two incriminated viruses: mink astrovirus and mink sapovirus. Using the RNAscope 2.

Physical Activity in Relation to Wellbeing Among Newly Arrived Refugees in Sweden: A Quantitative Study.

Little is known about physical activity among newly arrived refugees and what impact physical activity might have on their health, as measured by mental wellbeing, vitality, stress and sleep quality. Thus, this study sought to investigate the relationship between physical activity and wellbeing among refugees who were newly arrived in Sweden. The present study was based on the results from a survey, conducted in 2015-2016 among newly arrived adult refugees who spoke Arabic, Pashto, Somali or Dari, participated in a mandatory public integration support programme in the Scania region of Sweden and agreed to participate in the survey.

Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset.

Metagenomics-based high-throughput sequencing (HTS) enables comprehensive detection of all species comprised in a sample with a single assay and is becoming a standard method for outbreak investigation. However, unlike real-time PCR or serological assays, HTS datasets generated for pathogen detection do not easily provide yes/no answers. Rather, results of the taxonomic read assignment need to be assessed by trained personnel to gain information thereof.

Detection and Genetic Characterization of Viruses Present in Free-Ranging Snow Leopards Using Next-Generation Sequencing.

Snow leopards inhabit the cold, arid environments of the high mountains of South and Central Asia. These living conditions likely affect the abundance and composition of microbes with the capacity to infect these animals. It is important to investigate the microbes that snow leopards are exposed to detect infectious disease threats and define a baseline for future changes that may impact the health of this endangered felid.

Identification and validation of internal reference genes for real-time quantitative polymerase chain reaction-based studies in Hyalomma anatolicum ticks.

Crimean-Congo hemorrhagic fever (CCHF) is an emerging tick-borne viral disease caused by the orthonairovirus CCHF virus (CCHFV). Ticks of the genus Hyalomma are the viral reservoir and they represent the main vector transmitting the virus to their hosts during blood feeding. However, how CCHFV replicates in its natural arthropod host cells and the nature of virus/host interactions are still largely unknown.

Seroprevalence of pestivirus in Eurasian tundra reindeer in Finland, Sweden, Norway, Iceland and Russian Federation.

Reindeer herding is of great importance for the indigenous people of the Fennoscandia peninsula and northern Russia. There are also free-ranging feral populations of reindeer in Finland, Iceland, Norway and Russian Federation. The genus contains several viral species that infect ungulates and often show capacity to transmit between different host species.

Comparing the treatment effect of narrow spectrum antimicrobial, probiotic and fluid with amoxicillin in mink kits (Neovison vison) with pre-weaning diarrhea.

Pre-weaning diarrhea in mink kits (PWD), also known as "sticky kits" is a multifactorial syndrome of considerable concern in the mink production. Evidence based treatment protocols are not available, and treatment is therefore empirical and often based on the use of antimicrobials. The purpose of the study was to test the effect of 3 alternative treatments to a standard antibiotic treatment, to characterize the study groups microbiologically, and finally to compare the intestinal microbiota of the different treatment groups at the age of 42 days.

Associated With an Outbreak of Infectious Keratoconjunctivitis in Semi-domesticated Reindeer in Sweden.

Infectious keratoconjunctivitis (IKC), the most common ocular disease in ruminants worldwide, has affected semi-domesticated Eurasian reindeer () for over 100 years, both as individual cases and in outbreaks affecting tens to hundreds of animals. Recurrent IKC outbreaks have been affecting a semi-domesticated reindeer herd in Östra Kikkejaure (Norrbotten county, Sweden) from 2014. The latest episode of these recurrent outbreaks, in winter 2016/2017, was investigated in this study.

Investigation of the viral and bacterial microbiota in intestinal samples from mink (Neovison vison) with pre-weaning diarrhea syndrome using next generation sequencing.

Pre-weaning diarrhea (PWD) in mink kits is a common multifactorial syndrome on commercial mink farms. Several potential pathogens such as astroviruses, caliciviruses, Escherichia coli and Staphylococcus delphini have been studied, but the etiology of the syndrome seems complex. In pooled samples from 38 diarrheic and 42 non-diarrheic litters, each comprising of intestinal contents from 2-3 mink kits from the same litter, the bacterial populations were studied using Illumina Next Generation Sequencing technology and targeted 16S amplicon sequencing.

A Text Message-Based Intervention Targeting Alcohol Consumption Among University Students: User Satisfaction and Acceptability Study.

Background: Heavy consumption of alcohol among university students is a global problem, with excessive drinking being the social norm. Students can be a difficult target group to reach, and only a minority seek alcohol-related support. It is important to develop interventions that can reach university students in a way that does not further stretch the resources of the health services.

Multiple pathogen biomarker detection using an encoded bead array in droplet PCR.

We present a droplet PCR workflow for detection of multiple pathogen DNA biomarkers using fluorescent color-coded Luminex® beads. This strategy enables encoding of multiple singleplex droplet PCRs using a commercially available bead set of several hundred distinguishable fluorescence codes. This workflow provides scalability beyond the limited number offered by fluorescent detection probes such as TaqMan probes, commonly used in current multiplex droplet PCRs.

Accurate Detection of Avian Respiratory Viruses by Use of Multiplex PCR-Based Luminex Suspension Microarray Assay.

A novel oligonucleotide suspension microarray (Luminex microsphere system) was developed for the rapid detection of avian respiratory viruses of major clinical importance. This test was optimized and validated with 70 clinical samples. The developed tool was accurate for high-throughput detection and differentiation of the most important avian respiratory viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious laryngotracheitis virus (ILTV) in single- and mixed-virus infections.