10 research outputs found
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A case for a negative-strand coding sequence in a group of positive-sense RNA viruses.
Get PDFPositive-sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-sense RNA viruses are generally accepted to encode proteins solely on the positive strand. However, we previously identified a surprisingly long (∼1,000-codon) open reading frame (ORF) on the negative strand of some members of the family Narnaviridae which, together with RNA bacteriophages of the family Leviviridae, form a sister group to all other positive-sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungal, and plant transcriptomic data sets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95 per cent of the genome. The reverse-frame ORFs correspond to a specific avoidance of CUA, UUA, and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a positive-sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution and de novo origin of genes
The International Virus Bioinformatics Meeting 2020.
Get PDFThe International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting
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Mining Diverse and Novel RNA Viruses in Transcriptomic Datasets
No full textIn my project, I analysed multiple various transcriptomic data with a goal to identify novel and diverse RNA viruses. For this, I developed a workflow and applied various methods to accommodate and characterize the (un)expected viral diversity.
I analysed multiple RNA-sequencing datasets of ants and I searched for viruses in various National Center for Biotechnology Information (NCBI) databases. The analysed NCBI databases are: viruses (non redundant) nucleotide database (nt/nt GenBank) and Transcriptome Shotgun Assembly (TSA) database. With this approach, data generated for one goal was analysed with a completely different purpose. The search was performed using multiple methods ( de-novo assemblies, sequence-sequence (BLAST) or sequence-profile (HMMER) comparisons). For the HMMER tools based search, I created and manually curated profile Hidden Markov Models (pHMMs) for viral RNA dependent RNA polymerase, which was the main protein of interest of this project. The pHMMs represented various viral families as well as genera.
The analysis resulted in finding a novel polycistronic picorna-like RNA virus family: Polycipiviridae . This is a unique genome organisation having arthropods infecting RNA viruses. My and my colleagues hypothesise these viruses employ novel molecular mechanisms to express their structural (re-initiation) and replication (possibly novel IRES) proteins.
The pHMMs-based search was evaluated, resulting in a selection of various thresholds and insights into current viral diversity and taxonomy. Finally, using this optimized pHMMs-based search, I identified over 15,000 viral RdRp-encoding sequences. A downstream analysis of these sequences resulted in better explanation of taxonomic relationships between various RNA virus groups, helped to improve knowledge of RNA dependent RNA polymerase diversity and expanded current understanding of host specificity, as well as uncovered novel molecular mechanisms of divergent and novel RNA viruses. European Research Council grant [646891] to Andrew Firt
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Identification of RNA virus-derived RdRp sequences in publicly available transcriptomic datasets.
No full textRNA viruses are abundant, highly diverse, and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost effectively expand the diversity of known RNA virus sequences we mined publicly available transcriptomic datasets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA dependent RNA polymerase - the only universal "hall-mark" gene of RNA viruses. By using these to search the NCBI Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analysed their diversity, taxonomic classification, phylogeny and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp pHMMs provide a useful resource for the virus discovery community
ICTV Virus Taxonomy Profile:PolycipiviridaeIngrida
Get PDFPolycipiviridae is a family of picorna-like viruses with non-segmented, linear, positive-sense RNA genomes of approximately 10-12 kb. Unusually for viruses within the order Picornavirales, their genomes are polycistronic, with four (or more) consecutive 5' -proximal open reading frames (ORFs) encoding structural (and possibly other) proteins and a long 3' ORF encoding the replication polyprotein. Members of species within the family have all been detected in ants or via arthropod transcriptomic datasets. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the Polycipiviridae, which is available at www.ictv.global/report/polycipiviridae.Production of this summary, the online chapter, and associated resources was funded by a grant from the Wellcome Trust (WT108418AIA). DMAG is supported by BFU2012-36241 and Elkartek KK-2017/00008 grants, Spain
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The International Virus Bioinformatics Meeting 2020.
No full textThe International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting
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Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities
No full textPeer reviewed: TrueAcknowledgements: We would like to thank Amy Heather Fitzpatrick, Anastasia Gulyaeva, Chien-Fu Wu, Heli Mönttinen, Liubov Chuprikova, Fabiana Neves, Nikolay Simankov, Noriko Cassman, Nuria Fontdevila Pareta, Rebecca Grimwood, Stephanie Waller, Zivile Buivydaite, Alexander Allman, Artem Baidaliuk, Benjamin Lee, Cadhla Firth, Chuan Cao, Clarence Le, Luca Nishimura, Dehan Cai, Manja Marz, Elizabeth Fahsbender, Gabriel Lencioni Lovate, Hassan Z. A. Ishag, Isa de Vries, Janelle Wierenga, Javier Rodriguez-Grille, Jordan Taylor, Katarina Bačnik, Katrina Kalantar, Lauren Lim, Mark Paul S. Rivarez, Nina A. H. Madsen, Nolwenn Dheilly, Olve Peersen, Robert Edgar, Sandra Triebel, Satyabrata Satapathy, Sung won Lim, Xubo Tang and Yuanyuan Zhang for their precious contribution to the RdRp summit and the fruitful exchanges. We are also thankful to the sponsors of the first RdRp summit, the Chan-Zuckerberg Initiative (CZI) and Frontiers in Virology, for their support.Improved RNA virus understanding is critical to studying animal and plant health, and environmental processes. However, the continuous and rapid RNA virus evolution makes their identification and characterization challenging. While recent sequence-based advances have led to extensive RNA virus discovery, there is growing variation in how RNA viruses are identified, analyzed, characterized, and reported. To this end, an RdRp Summit was organized and a hybrid meeting took place in Valencia, Spain in May 2023 to convene leading experts with emphasis on early career researchers (ECRs) across diverse scientific communities. Here we synthesize key insights and recommendations and offer these as a first effort to establish a consensus framework for advancing RNA virus discovery. First, we need interoperability through standardized methodologies, data-sharing protocols, metadata provision and interdisciplinary collaborations and offer specific examples as starting points. Second, as an emergent field, we recognize the need to incorporate cutting-edge technologies and knowledge early and often to improve omic-based viral detection and annotation as novel capabilities reveal new biology. Third, we underscore the significance of ECRs in fostering international partnerships to promote inclusivity and equity in virus discovery efforts. The proposed consensus framework serves as a roadmap for the scientific community to collectively contribute to the tremendous challenge of unveiling the RNA virosphere
