Impact of wet-lab protocols on quality of whole-genome short-read sequences from foodborne microbial pathogens.

For successful elucidation of a food-borne infection chain, the availability of high-quality sequencing data from suspected microbial contaminants is a prerequisite. Commonly, those investigations are a joint effort undertaken by different laboratories and institutes. To analyze the extent of variability introduced by differing wet-lab procedures on the quality of the sequence data we conducted an interlaboratory study, involving four bacterial pathogens, which account for the majority of food-related bacterial infections: spp.

Whole-Genome Sequence of an African Swine Fever Virus Isolate from the Czech Republic.

Between June 2017 and April 2018, an outbreak of African swine fever (ASF) affected wild boar in the southeast of the Czech Republic. Here, we present the whole-genome sequence of the causative ASF virus. It belongs to genotype II and shows very high identity with other strains from Eastern Europe.

Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution.

Background: African swine fever virus (ASFV) is a most devastating pathogen affecting swine. In 2007, ASFV was introduced into Eastern Europe where it continuously circulates and recently reached Western Europe and Asia, leading to a socio-economic crisis of global proportion. In Africa, where ASFV was first described in 1921, it is transmitted between warthogs and soft ticks of the genus Ornithodoros in a so-called sylvatic cycle.

Sequence Analysis of Egyptian Foot-and-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus.

In spite of annual mass vaccination programs with polyvalent inactivated vaccines, the incidence and economic impact of foot-and-mouth disease (FMD) in Egypt is high. Viruses of the A, O and SAT 2 serotypes are endemic and repeated incursions of new lineages from other countries lead to an unstable situation that makes the selection of appropriate vaccine antigens very difficult. In this study, whole genome sequencing of a 2016 serotype A isolate from Egypt revealed a recombination event with an African serotype O virus.

African swine fever whole-genome sequencing-Quantity wanted but quality needed.

The pandemic spread of African swine fever virus (ASFV) genotype II (GTII) has led to a global crisis. Since the circulating strains are almost identical, time and money have been mis-invested in whole-genome sequencing the last years. New methods, harmonised protocols for sample selection, sequencing, and bioinformatics are therefore urgently needed.

Borna disease outbreak with high mortality in an alpaca herd in a previously unreported endemic area in Germany.

Borna disease virus 1 (BoDV-1) is the causative agent of Borna disease, an often fatal neurologic condition of domestic mammals, including New World camelids, in endemic areas in Central Europe. Recently, BoDV-1 gained further attention by the confirmation of fatal zoonotic infections in humans. Although Borna disease and BoDV-1 have been described already over the past decades, comprehensive reports of Borna disease outbreaks in domestic animals employing state-of-the-art diagnostic methods are missing.

High-Resolution Composition Analysis of an Inactivated Polyvalent Foot-and-Mouth Disease Vaccine.

Appropriate vaccine selection is crucial in the control of foot-and-mouth disease (FMD). Vaccination can prevent clinical disease and reduces viral shedding, but there is a lack of cross-protection between the seven serotypes and their sublineages, making the selection of an adequately protective vaccine difficult. Since the exact composition of their vaccines is not consistently disclosed by all manufacturers, incompatibility of the strains used for vaccination with regionally circulating strains can cause vaccination campaigns to fail.

Zoonotic spillover infections with Borna disease virus 1 leading to fatal human encephalitis, 1999-2019: an epidemiological investigation.

Background: In 2018-19, Borna disease virus 1 (BoDV-1), the causative agent of Borna disease in horses, sheep, and other domestic mammals, was reported in five human patients with severe to fatal encephalitis in Germany. However, information on case frequencies, clinical courses, and detailed epidemiological analyses are still lacking. We report the occurrence of BoDV-1-associated encephalitis in cases submitted to the Institute of Clinical Microbiology and Hygiene, Regensburg University Hospital, Regensburg, Germany, and provide a detailed description of newly identified cases of BoDV-1-induced encephalitis.

Highly efficient library preparation for Ion Torrent sequencing using Y-adapters.

Library preparation is a crucial step in next-generation sequencing workflows. Key determinants of successful library preparation are the available amount of input DNA and the efficiency of the conversion of this DNA into functional library molecules. While the standard blunt-end ligation protocol for Ion Torrent libraries has a theoretical maximum efficiency of 25%, Y-adapters enable highly efficient library preparation by (i) sticky-end ligation and (ii) rendering both DNA strands functional for sequencing, hence resulting in a theoretical efficiency of up to 100%.

A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences.

African swine fever (ASF) is a severe disease of suids caused by African swine fever virus (ASFV). Its dsDNA genome (170-194 kbp) is scattered with homopolymers and repeats as well as inverted-terminal-repeats (ITR), which hamper whole-genome sequencing. To date, only a few genome sequences have been published and only for some are data on sequence quality available enabling in-depth investigations.

Comparative Analysis of Whole-Genome Sequence of African Swine Fever Virus Belgium 2018/1.

We analyzed the whole-genome sequence of African swine fever virus Belgium 2018/1. The strain fits into the European genotype II (>99.98% identity).

A Novel Squirrel Respirovirus with Putative Zoonotic Potential.

In a globalized world, the threat of emerging pathogens plays an increasing role, especially if their zoonotic potential is unknown. In this study, a novel respirovirus, family , was isolated from a Sri Lankan Giant squirrel (), which originated in Sri Lanka and deceased with severe pneumonia in a German zoo. The full-genome characterization of this novel virus, tentatively named Giant squirrel respirovirus (GSqRV), revealed similarities to murine (71%), as well as human respiroviruses (68%) with unique features, for example, a different genome length and a putative additional accessory protein.

Presence of two different bovine hepacivirus clusters in Germany.

During the last years, genetic information of hepaciviruses (family Flaviviridae), whose type species is the human hepatitis C virus, was detected in a wide range of primates and non-primate vertebrates. Here, samples collected from 263 German cattle kept in 22 different holdings were analysed for the presence of hepacivirus N (syn. bovine hepacivirus; BovHepV).

From low to high pathogenicity-Characterization of H7N7 avian influenza viruses in two epidemiologically linked outbreaks.

The ability of low pathogenic (LP) avian influenza viruses (AIV) of the subtypes H5 and H7 to mutate spontaneously to highly pathogenic (HP) variants is the main reason for their stringent control. On-the-spot evidence from the field of mutations in LPAIV to render the virus into nascent HP variants is scarce. Epidemiological investigations and molecular characterization of two spatiotemporally linked outbreaks caused by LP, and subsequently, HPAIV H7N7 in two-layer farms in Germany yielded such evidence.

Deletion at the 5'-end of Estonian ASFV strains associated with an attenuated phenotype.

African swine fever (ASF) was introduced into the Eastern European Union in 2014 and led to considerable mortality among wild boar. In contrast, unexpected high antibody prevalence was reported in hunted wild boar in north-eastern Estonia. One of the causative virus strains was recently characterized.