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

Abstract

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.

Paleovirology of the DNA viruses of eukaryotes

“…In addition, some DNA virus EVEs appear to contribute to immune defence by RNA interference mechanisms. In the Ornithodoros soft ticks, small-interfering RNAs (siRNA) and PIWI-interacting RNAs (piRNAs) are produced from endogenous African swine fever virus-like integrations which may confer on these vectors some protection against infection by the virus [91]. In a study of arthropod genomes [40], piRNA clusters were found to be enriched in EVEs and 18.49% of these integrations resembled parvoviruses.…”

How relevant are in vitro culture models for study of tick-pathogen interactions?

“…In particular, ISE6 cells and I. scapularis ticks both contain many bunyaand orthomyxo-like NIRVS sequences, suggesting that ticks are a dominant host for these virus groups [101]. Furthermore, the genomes of OME/CTVM21 and other Ornithodoros moubata cell lines, as well as some populations of O. moubata ticks, harbor African swine fever virus (ASFV)-like integrated elements that may interfere with ASFV infection [102].…”

“…EVEs have been identified in genomes of both insects and ticks including sequences of viruses classified within several genera [191][192][193][194][195]. For example, the ASFV-related EVEs within the genomes of O. moubata ticks and cell lines are likely the origin of siRNA and piRNA interference responses against ASFV in ticks [102]. While infection of O. moubata and O. porcinus ticks resulted in detection of low levels of viral RNA transcripts, the cell lines OME/CTVM21, OME/CTVM22, OME/CTVM24, and OME/CTVM27 were resistant to infection with ASFV, with no detectable viral transcription.…”

Transcriptome Profiling Reveals Features of Immune Response and Metabolism of Acutely Infected, Dead and Asymptomatic Infection of African Swine Fever Virus in Pigs

“…However, in recent years, a novel way of analyzing virus evolution, which is the analysis of endogenous viral elements (EVEs)—ancient viral sequences integrated into the host genome revealed that a large and diverse population of sequences derived from nonretroviral viruses in animal genomes were identified and maintained in the host genome over many millions of year s ( 46 ). In a previous study, it was proven that ASFV and its hosts have undergone a long time of coevolution, and endogenous viral elements of ASFV might have been integrated into transmitted vector soft tick genomes ( 47 ). However, how did the viral genes integrate into the host genome?…”