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

Forth, J. H., Forth, L. F., Lycett, S., Bell-Sakyi, L., Keil, G. M., Blome, S., et al. (2020). Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution. BMC Biology, 18(1): 136. doi:10.1186/s12915-020-00865-6.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0007-4E1B-5 Version Permalink: http://hdl.handle.net/21.11116/0000-0007-4E1E-2
Genre: Journal Article

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https://www.ebi.ac.uk/ena/data/search?query=PRJEB26739 (Supplementary material)
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The datasets supporting the conclusions of this article are available from the International Nucleotide Sequence Database Collaboration (INSDC) under study accession number PRJEB26739.

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 Creators:
Forth, Jan H., Author
Forth, Leonie F., Author
Lycett, Samantha, Author
Bell-Sakyi, Lesley, Author
Keil, Günther M., Author
Blome, Sandra, Author
Calvignac-Spencer, Sébastien, Author
Wissgott, Antje1, Author              
Krause, Johannes1, 2, Author              
Höper, Dirk, Author
Kampen, Helge, Author
Beer, Martin, Author
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              
2MHAAM, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2541699              

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Free keywords: African swine fever virus, Coevolution, Endogenous viral element, Tick cell line, RNA interference, ASFLI-element
 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.

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Language(s): eng - English
 Dates: 2020-10-08
 Publication Status: Published online
 Pages: 18
 Publishing info: -
 Table of Contents: 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 analysis
 Rev. Type: Peer
 Identifiers: DOI: 10.1186/s12915-020-00865-6
Other: shh2743
 Degree: -

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Title: BMC Biology
Source Genre: Journal
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Publ. Info: Berlin ; Heidelberg : Springer
Pages: - Volume / Issue: 18 (1) Sequence Number: 136 Start / End Page: - Identifier: ISSN: 1741-7007
CoNE: https://pure.mpg.de/cone/journals/resource/111071069889000