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. However, analyses into this virus’ evolution are aggravated by the absence of any closely related viruses. Even ancient endogenous viral elements, viral sequences integrated into a host’s genome many thousand years ago that have proven extremely valuable to analyse virus evolution, remain to be identified. Therefore, the evolution of ASFV, the only known DNA virus transmitted by arthropods, remains a mystery. - RESULTS: For the identification of ASFV-like sequences, we sequenced DNA from different recent Ornithodoros tick species, e.g. O. moubata and O. porcinus, O. moubata tick cells and also 100-year-old O. moubata and O. porcinus ticks using high-throughput sequencing. We used BLAST analyses for the identification of ASFV-like sequences and further analysed the data through phylogenetic reconstruction and molecular clock analyses. In addition, we performed tick infection experiments as well as additional small RNA sequencing of O. moubata and O. porcinus soft ticks. - CONCLUSION: Here, we show that soft ticks of the Ornithodoros moubata group, the natural arthropod vector of ASFV, harbour African swine fever virus-like integrated (ASFLI) elements corresponding to up to 10% (over 20 kb) of the ASFV genome. Through orthologous dating and molecular clock analyses, we provide data suggesting that integration could have occurred over 1.47 million years ago. Furthermore, we provide data showing ASFLI-element specific siRNA and piRNA in ticks and tick cells allowing for speculations on a possible role of ASFLI-elements in RNA interference-based protection against ASFV in ticks. We suggest that these elements, shaped through many years of co-evolution, could be part of an evolutionary virus-vector ‘arms race’, a finding that has not only high impact on our understanding of the co-evolution of viruses with their hosts but also provides a glimpse into the evolution of ASFV.Background Results - Evidence of ASFLI-elements in the O. moubata tick cell genome - Phylogenetic analysis shows ASFLI-elements are close relatives of ASFV sequences - ASFLI-elements are present in recently sampled O.moubata, O. porcinus and approx. 100-year-old O.moubata and O. porcinus field-collected ticks from Africa - Phylogenetic reconstruction using full-length mitochondrial genomes of soft ticks reveals a possible integration of an ASFLI-element might have occurred over 1.46–1.47 million years ago (mya) - Molecular clock analyses using ASFLI-elements from different Ornithodoros species provide an estimate for a time to the most recent common ancestor consistent with orthologous dating - Ornithodoros tick species and tick cell lines show differences in the infectability with various ASFV genotype isolates - RNA sequencing demonstrates ASFLI-element-specific mRNA—small-interfering and piwi-interacting RNAs in tick cells - The reconstructed ASFLI-A104R protein is highly similar to its ASFV homologue but is not expressed in tick cell lines Discussion Conclusion Methods - Virus strains - Tick rearing, tick infection and tick cell cultures - Nucleic acid extraction - Oligonucleotide design - PCR - qPCR - RT-qPCR - Sanger sequencing - Next-generation sequencing - Amplicon sequencing for assembly validation - Data analysis - Phylogenetic analysis - Clock rate estimates and Bayesian time-scaled trees - Protein expression and purification in E. coli and rabbit immunisation - Transfection - SDS-PAGE and immunoblotting - Statistical analysi

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: Campylobacter spp., Shiga toxin-producing Escherichia coli, Listeria monocytogenes, and Salmonella enterica. The participants, ranging from German federal research institutes, federal state laboratories to universities and companies, were asked to follow their routine in-house protocols for short-read sequencing of 10 cultures and one isolated bacterial DNA per species. Sequence and assembly quality were then analyzed centrally. Variations within isolate samples were detected with SNP and cgMLST calling. Overall, we found that the quality of Illumina raw sequence data was high with little overall variability, with one exception, attributed to a specific library preparation kit. The variability of Ion Torrent data was higher, independent of the investigated species. For cgMLST and SNP analysis results, we found that technological sequencing artefacts could be reduced by the use of filters, and that SNP analysis was more suited than cgMLST to compare data of different contributors. Regarding the four species, a minority of Campylobacter isolate data showed the in comparison highest divergence with regard to sequence type and cgMLST analysis. We additionally compared the assembler SPAdes and SKESA for their performance on the Illumina data sets of the different species and library preparation methods and found overall similar assembly quality metrics and cgMLST statistics

2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.

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 deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV

Improved diagnostic metagenomics for virus discovery

The advances in high-throughput sequencing technologies have revolutionized the possibilities for pathogen identification in cases of unknown disease origin. Diagnostic metagenomics allows the unbiased and simultaneous detection of almost all nucleic acids in a clinical sample, with the potential to provide pivotal insights into otherwise undeterminable causes of human or animal disease. In this thesis, possibilities, pitfalls and the suitability of Ion Torrent and Illumina sequencing platforms for comprehensive use in diagnostic metagenomics were assessed and optimized procedures developed. Clinical field samples, undiagnosable by standard diagnostics, were taken as real-life examples for the investigations. The results show that cross-contamination due to index swapping and run-to-run-carryover constitute a major issue on Illumina platforms, severely compromising the correct interpretation of results for clinical specimens. In contrast, Ion Torrent platforms did not display any form of cross-contamination, however, the commercial library preparation method is less efficient. Combining the advantages of both platforms, customized Y adapters, facilitating highly efficient library preparation, were developed for Ion Torrent sequencing and applied in further experiments. The obstacles of strongly degraded RNA in formalin-fixed paraffin-embedded samples were identified and the workflow adapted to meet the requirements of smaller fragments. Additionally, it was shown that adequate sampling is a very important step, if not the most important step, in the workflow, as well as subsequent validation of the obtained results in terms of causation. The achievements in this study allow other researchers the application of a sensitive and optimized diagnostic metagenomics workflow. Furthermore, the investigations on the clinical samples resulted in the discovery of a novel respirovirus with putative zoonotic potential, the first description of Borna disease virus 1 in human organ transplant recipients, and the discovery of a very distantly related novel ovine picornavirus. These discoveries build a basis for further research and expand the knowledge regarding new and emerging viruses.Die Möglichkeiten der Identifizierung von Pathogenen in Krankheitsfällen unbekannter Ursache wurden durch den technischen Fortschritt im Bereich der Hochdurchsatz-Sequenzierung enorm erweitert. Die diagnostische Metagenomanalyse ermöglicht mit der Erfassung nahezu aller Nukleinsäuren einer klinischen Probe eine ergebnisoffene Untersuchung und bietet damit zentrale Erkenntnisgewinne in Fällen, die mit etablierter Standard-Diagnostik nicht aufgeklärt werden können. In dieser Arbeit wurden die Möglichkeiten und Schwierigkeiten sowie die Eignung der Sequenzierplattformen Illumina und Ion Torrent im Hinblick auf einen breiten Einsatz der Metagenomanalyse in der Diagnostik untersucht und optimierte Ansätze entwickelt. Für die Untersuchungen wurden echte Feldproben herangezogen, bei denen die Ursache der Erkrankung mit Standard-Diagnostik nicht aufklärbar war. Kreuz-Kontaminationen aufgrund von Index-Austauschen und Verschleppungen zwischen den Läufen stellten bei der getesteten Illumina-Plattform ein bedeutendes Problem dar, wodurch die korrekte Interpretation der Ergebnisse im Hinblick auf das potentielle Pathogen erheblich erschwert wurde. Bei den getesteten Ion Torrent-Plattformen trat diese Art der Kontaminationen nicht auf, allerdings ist die kommerzielle Methode zur Vorbereitung der Sequenz-Bibliothek weniger effizient. Daher wurden individuell zugeschnittene Y-Adapter für Ion Torrent-Sequenzierungen aufwändig entwickelt und in weiteren Versuchen angewandt. Weiterhin wurden Hürden bei der Untersuchung stark degradierter RNA von formalinfixiertem und in Paraffin eingebettetem Gewebe identifiziert und der Workflow entsprechend der Anforderungen angepasst. Die Bedeutung einer adäquaten Probennahme als wesentlicher Schritt des Workflows und die Validierung der erhaltenen Ergebnisse im Hinblick auf die Ursache wurden verdeutlicht. Die Ergebnisse dieser Studie ermöglichen die Anwendung eines optimierten, sehr sensitiven und verlässlichen Workflows für die diagnostische Metagenomanalyse. Des Weiteren resultierten die Untersuchungen der klinischen Proben in der Entdeckung eines neuen Respirovirus mit putativem zoonotischen Potential, der ersten Beschreibung des Borna disease virus 1 in humanen Organtransplantat-Empfängern und der Entdeckung eines neuen ovinen Picornavirus, das phylogenetisch sehr weit von bekannten Picornaviren entfernt ist. Damit leisten diese Entdeckungen einen wichtigen Beitrag zur Identifizierung bisher unbekannter Viren und bilden eine Grundlage für weitere Forschungsansätze

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. Here, we present a deep sequencing approach for polyvalent inactivated FMD vaccines that can identify all component strains by their genome sequences. The genomes of all strains of a commercial pentavalent FMD vaccine were de novo assembled and the vaccine composition determined semi-quantitatively. The genome assembly required high stringency parameters to prevent misassemblies caused by conserved regions of the genome shared by related strains. In contrast, reference-guided assembly is only recommended in cases where the number of strains is previously known and appropriate reference sequences are available. The presented approach can be applied not only to any inactivated whole-virus FMD vaccine but also to vaccine quality testing in general and allows for better decision-making for vaccines with an unknown composition

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 Paramyxoviridae, was isolated from a Sri Lankan Giant squirrel (Ratufa macroura), 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. Congruently, phylogenetic analyses showed a solitary position of GSqRV between known murine and human respiroviruses, implicating a putative zoonotic potential. A tailored real-time reverse transcription-polymerase chain reaction (RT-qPCR) for specific detection of GSqRV confirmed a very high viral load in the lung, and, to a lesser extent, in the brain of the deceased animal. A pilot study on indigenous and exotic squirrels did not reveal additional cases in Germany. Therefore, further research is essential to assess the geographic distribution, host range, and zoonotic potential of this novel viral pathogen