Leonie F. Forth
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View article: An inter-laboratory study characterizes the impact of bioinformatic approaches on genome-based cluster detection for foodborne bacterial pathogens
An inter-laboratory study characterizes the impact of bioinformatic approaches on genome-based cluster detection for foodborne bacterial pathogens Open
Accurate assignment of whole-genome sequences to clusters in foodborne outbreak investigations remains challenging. Variability in bioinformatics tools and quality metrics significantly impacts clustering outcomes. This study assessed inte…
View article: Distinct mutations emerge in the genome of serotype O foot-and-mouth disease virus during persistence in cattle
Distinct mutations emerge in the genome of serotype O foot-and-mouth disease virus during persistence in cattle Open
Like other RNA viruses, foot-and-mouth disease virus (FMDV) has a high mutation rate. After the acute phase of infection, about half of infected cattle develop a persistent FMDV infection that can last for weeks or months. During this pers…
View article: Impact of wet-lab protocols on quality of whole-genome short-read sequences from foodborne microbial pathogens
Impact of wet-lab protocols on quality of whole-genome short-read sequences from foodborne microbial pathogens Open
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…
View article: Whole-Genome Sequence of an African Swine Fever Virus Isolate from the Czech Republic
Whole-Genome Sequence of an African Swine Fever Virus Isolate from the Czech Republic Open
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 show…
View article: Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
View article: Sequence Analysis of Egyptian Foot-and-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus
Sequence Analysis of Egyptian Foot-and-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus Open
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 incursi…
View article: 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales Open
In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were d…
View article: African swine fever whole-genome sequencing—Quantity wanted but quality needed
African swine fever whole-genome sequencing—Quantity wanted but quality needed Open
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…
View article: Sequence Analysis of Egyptian Foot-And-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus
Sequence Analysis of Egyptian Foot-And-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus Open
In addition to the risk of vaccine failure caused by strain mismatch, the production of inactivated FMD vaccines is dangerous if adequate biosafety cannot be maintained. Using a high-throughput sequencing protocol optimized for short nucle…
View article: Borna disease outbreak with high mortality in an alpaca herd in a previously unreported endemic area in Germany
Borna disease outbreak with high mortality in an alpaca herd in a previously unreported endemic area in Germany Open
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…
View article: African swine fever virus-like integrated elements in a soft tick genome – an ancient virus vector arms race?
African swine fever virus-like integrated elements in a soft tick genome – an ancient virus vector arms race? Open
Background African swine fever virus (ASFV) is the only known DNA-arbovirus and a most devastating suid pathogen that, originating from a sylvatic cycle in Africa, has spread to eastern Europe and recently reached western Europe and Asia, …
View article: High-Resolution Composition Analysis of an Inactivated Polyvalent Foot-and-Mouth Disease Vaccine
High-Resolution Composition Analysis of an Inactivated Polyvalent Foot-and-Mouth Disease Vaccine Open
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 sub…
View article: Additional file 2 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 2 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 2: Table S2. ASFV-like transcripts detected in data from six Ornithodoros moubata cell lines and O.moubata ticks by mRNA-sequencing and data analysis from published sequences ASFV-like sequences from tick cell libraries lib…
View article: Additional file 6 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 6 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 6: Table S5. Results of tick and tick cell line screening for ASFLI-elements by qPCR. DNA from single ticks and every tick cell line (n=1) was extracted and analysed by qPCR for six ASFV-like genes as described in the ‘Mate…
View article: Additional file 15 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 15 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 15: Table S9. Results of small RNA sequencing and mapping against ASFV and ASFLI-elements. Small RNA was sequenced from Ornithodoros porcinus and Ornithodoros moubata nymphal stage ticks. After deduplication using BBMap, 22…
View article: Additional file 1 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 1 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 1: Table S1. Overview of NGS experiments conducted in this study and data obtained from the literature. Ornithodoros moubata cell line names have been abbreviated by removal of “/CTVM” and Ornithodoros porcinus and Ornithod…
View article: Additional file 16 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 16 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 16: Table S10. O. moubata piRNA ping-pong signature analysed by PingPongPro v1.0 with default parameters and -b option (creates additional browser track files, which are suitable for display in common genome browsers). The …
View article: Additional file 19 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 19 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 19: Table S12.Primer and probe sequences used in this study.
View article: Additional file 7 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 7 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 7: Table S6. BLASTn results of SPAdes-assembled contigs from Ornithodoro porcinus France and Kenya17 containing ASFLI-elements. Shown are hits with the lowest e-value for ASFV-genes as obtained by Blastn against the entire …
View article: Additional file 10 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 10 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 10: Table S8. qRT-PCR results of Ornithodoros ticks experimentally infected with different ASFV-genotype isolate. Shown are ASFV-P72 transcript-specific Cq-values of third nymphal stage ticks fed with defibrinated pig blood…
View article: Additional file 17 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 17 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 17: Table S11. O. porcinus piRNA ping-pong signature analysed by PingPongPro v1.0 with default parameters and -b option (creates additional browser track files, which are suitable for display in common genome browsers). The…
View article: Additional file 3 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 3 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 3: Table S3. BLASTn results of SPAdes-assembled contigs containing ASFLI- and other endogenous viral elements detected in the OME/CTVM21 genome. Shown are hits with the lowest e-value for viral, tick and mobile genetic elem…
View article: Additional file 9 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 9 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 9: Table S7. SPAdes-assembled contigs from deep sequencing data from libraries AGL001 and MPA001, as generated from museum-stored ticks. Data from libraries from museum-stored tick were mapped against ASFLI-element-containi…
View article: Additional file 4 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution
Additional file 4 of Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution Open
Additional file 4: Table S4. BLASTp results of all ORFs >500 bp on SPAdes-assembled contigs containing ASFLI- and other endogenous viral elements detected in the OME/CTVM21 genome Shown are hits with the lowest e-value for viral-, tick and…
View article: Unbiased High-Resolution Composition Analysis of an Inactivated Polyvalent Foot-and-Mouth Disease Vaccine
Unbiased High-Resolution Composition Analysis of an Inactivated Polyvalent Foot-and-Mouth Disease Vaccine Open
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 sub…
View article: Highly Efficient Library Preparation for Ion Torrent Sequencing Using Y-Adapters
Highly Efficient Library Preparation for Ion Torrent Sequencing Using Y-Adapters Open
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 librar…
View article: A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences
A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences Open
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-gen…
View article: Comparative Analysis of Whole-Genome Sequence of African Swine Fever Virus Belgium 2018/1
Comparative Analysis of Whole-Genome Sequence of African Swine Fever Virus Belgium 2018/1 Open
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). The high-coverage sequence revealed 15 differences compared with an improved African swine…
View article: Novel Picornavirus in Lambs with Severe Encephalomyelitis
Novel Picornavirus in Lambs with Severe Encephalomyelitis Open
Using metagenomic analysis, we identified a novel picornavirus in young preweaned lambs with neurologic signs associated with severe nonsuppurative encephalitis and sensory ganglionitis in 2016 and 2017 in the United Kingdom. In situ hybri…
View article: A Novel Squirrel Respirovirus with Putative Zoonotic Potential
A Novel Squirrel Respirovirus with Putative Zoonotic Potential Open
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 Paramyxoviridae, was isolated from a Sri Lankan Giant squirrel…