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2020 Taxonomic Update for Phylum Negarnaviricota (Riboviria: Orthornavirae), Including the Large Orders Bunyavirales and Mononegavirales
Archives of Virology https://doi.org/10.1007/s00705-020-04731-2 VIROLOGY DIVISION NEWS 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales Jens H. Kuhn1 · Scott Adkins2 · Daniela Alioto3 · Sergey V. Alkhovsky4 · Gaya K. Amarasinghe5 · Simon J. Anthony6,7 · Tatjana Avšič‑Županc8 · María A. Ayllón9,10 · Justin Bahl11 · Anne Balkema‑Buschmann12 · Matthew J. Ballinger13 · Tomáš Bartonička14 · Christopher Basler15 · Sina Bavari16 · Martin Beer17 · Dennis A. Bente18 · Éric Bergeron19 · Brian H. Bird20 · Carol Blair21 · Kim R. Blasdell22 · Steven B. Bradfute23 · Rachel Breyta24 · Thomas Briese25 · Paul A. Brown26 · Ursula J. Buchholz27 · Michael J. Buchmeier28 · Alexander Bukreyev18,29 · Felicity Burt30 · Nihal Buzkan31 · Charles H. Calisher32 · Mengji Cao33,34 · Inmaculada Casas35 · John Chamberlain36 · Kartik Chandran37 · Rémi N. Charrel38 · Biao Chen39 · Michela Chiumenti40 · Il‑Ryong Choi41 · J. Christopher S. Clegg42 · Ian Crozier43 · John V. da Graça44 · Elena Dal Bó45 · Alberto M. R. Dávila46 · Juan Carlos de la Torre47 · Xavier de Lamballerie38 · Rik L. de Swart48 · Patrick L. Di Bello49 · Nicholas Di Paola50 · Francesco Di Serio40 · Ralf G. Dietzgen51 · Michele Digiaro52 · Valerian V. Dolja53 · Olga Dolnik54 · Michael A. Drebot55 · Jan Felix Drexler56 · Ralf Dürrwald57 · Lucie Dufkova58 · William G. Dundon59 · W. Paul Duprex60 · John M. Dye50 · Andrew J. Easton61 · Hideki Ebihara62 · Toufc Elbeaino63 · Koray Ergünay64 · Jorlan Fernandes195 · Anthony R. Fooks65 · Pierre B. H. Formenty66 · Leonie F. Forth17 · Ron A. M. Fouchier48 · Juliana Freitas‑Astúa67 · Selma Gago‑Zachert68,69 · George Fú Gāo70 · María Laura García71 · Adolfo García‑Sastre72 · Aura R. Garrison50 · Aiah Gbakima73 · Tracey Goldstein74 · Jean‑Paul J. Gonzalez75,76 · Anthony Grifths77 · Martin H. Groschup12 · Stephan Günther78 · Alexandro Guterres195 · Roy A. -
The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V
PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA. -
Virology Is That the Study of Viruses ? Submicroscopic, Parasitic Particles
Current research in Virology & Retrovirology 2021, Vol.4, Issue 3 Editorial Bahman Khalilidehkordi Shahrekord University of Medical Sciences, Iran mobile genetic elements of cells (such as transposons, Editorial retrotransposons or plasmids) that became encapsulated in protein capsids, acquired the power to “break free” from Virology is that the study of viruses – submicroscopic, the host cell and infect other cells. Of particular interest parasitic particles of genetic material contained during a here is mimivirus, a huge virus that infects amoebae and protein coat – and virus-like agents. It focuses on the sub- encodes much of the molecular machinery traditionally sequent aspects of viruses: their structure, classification associated with bacteria. Two possibilities are that it’s a and evolution, their ways to infect and exploit host cells for simplified version of a parasitic prokaryote or it originated copy , their interaction with host organism physiology and as an easier virus that acquired genes from its host. The immunity, the diseases they cause, the techniques to iso- evolution of viruses, which frequently occurs together with late and culture them, and their use in research and ther- the evolution of their hosts, is studied within the field of apy. Virology is a subfield of microbiology.Structure and viral evolution. While viruses reproduce and evolve, they’re classification of Virus: A major branch of virology is virus doing not engage in metabolism, don’t move, and depend classification. Viruses are often classified consistent with on variety cell for copy . The often-debated question of the host cell they infect: animal viruses, plant viruses, fun- whether or not they’re alive or not could also be a matter gal viruses, and bacteriophages (viruses infecting bacte- of definition that does not affect the biological reality of vi- ria, which include the foremost complex viruses). -
Coronavirus: Detailed Taxonomy
Coronavirus: Detailed taxonomy Coronaviruses are in the realm: Riboviria; phylum: Incertae sedis; and order: Nidovirales. The Coronaviridae family gets its name, in part, because the virus surface is surrounded by a ring of projections that appear like a solar corona when viewed through an electron microscope. Taxonomically, the main Coronaviridae subfamily – Orthocoronavirinae – is subdivided into alpha (formerly referred to as type 1 or phylogroup 1), beta (formerly referred to as type 2 or phylogroup 2), delta, and gamma coronavirus genera. Using molecular clock analysis, investigators have estimated the most common ancestor of all coronaviruses appeared in about 8,100 BC, and those of alphacoronavirus, betacoronavirus, gammacoronavirus, and deltacoronavirus appeared in approximately 2,400 BC, 3,300 BC, 2,800 BC, and 3,000 BC, respectively. These investigators posit that bats and birds are ideal hosts for the coronavirus gene source, bats for alphacoronavirus and betacoronavirus, and birds for gammacoronavirus and deltacoronavirus. Coronaviruses are usually associated with enteric or respiratory diseases in their hosts, although hepatic, neurologic, and other organ systems may be affected with certain coronaviruses. Genomic and amino acid sequence phylogenetic trees do not offer clear lines of demarcation among corona virus genus, lineage (subgroup), host, and organ system affected by disease, so information is provided below in rough descending order of the phylogenetic length of the reported genome. Subgroup/ Genus Lineage Abbreviation -
A Tool for Hierarchical Clustering, Core Gene Detection and Annotation of (Prokaryotic) Viruses Cristina Moraru
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.14.448304; this version posted June 14, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. VirClust – a tool for hierarchical clustering, core gene detection and annotation of (prokaryotic) viruses Cristina Moraru Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky –Str. 9 -11, D-26111 Oldenburg, Germany; [email protected] Abstract Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called “megataxonomy of viruses”, recognizes five different viral realms, defined based on the presence of viral hallmark genes. Within the realms, viruses are classified into hierarchical taxons, ideally defined by their shared genes. Therefore, there is currently a need for virus classification tools based on such shared genes / proteins. Here, VirClust is presented – a novel tool capable of performing i) hierarchical clustering of viruses based on intergenomic distances calculated from their protein cluster content, ii) identification of core proteins and iii) annotation of viral proteins. VirClust groups proteins into clusters both based on BLASTP sequence similarity, which identifies more related proteins, and also based on hidden markow models (HMM), which identifies more distantly related proteins. Furthermore, VirClust provides an integrated visualization of the hierarchical clustering tree and of the distribution of the protein content, which allows the identification of the genomic features responsible for the respective clustering. By using different intergenomic distances, the hierarchical trees produced by VirClust can be split into viral genome clusters of different taxonomic ranks. -
Phylogeny of the COVID-19 Virus SARS-Cov-2 by Compression
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.22.216242; this version posted July 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Phylogeny of the COVID-19 Virus SARS-CoV-2 by Compression Rudi L. Cilibrasi Paul M.B. Vitanyi´ Abstract We analyze the phylogeny and taxonomy of the SARS-CoV-2 virus using compression. This is a new alignment-free method called the “normalized compression distance” (NCD) method. It discovers all effective similarities based on Kolmogorov complexity. The latter being incomputable we approximate it by a good compressor such as the modern zpaq. The results comprise that the SARS-CoV-2 virus is closest to the RaTG13 virus and similar to two bat SARS-like coronaviruses bat-SL-CoVZXC21 and bat-SL-CoVZC4. The similarity is quantified and compared with the same quantified similarities among the mtDNA of certain species. We treat the question whether Pangolins are involved in the SARS-CoV-2 virus. I. INTRODUCTION In the 2019 and 2020 pandemic of the COVID-19 illness many studies use essentially two methods, alignment-based phylogenetic analyses e.g. [19], and an alignment-free machine learning approach [23]. These pointed to the origin of the SARS-CoV-2 virus which causes the COVID-19 pandemic as being from bats. It is thought to belong to lineage B (Sarbecovirus) of Betacoronavirus. From phylogenetic analysis and genome organization it was identified as a SARS-like coronavirus, and to have the highest similarity to the SARS bat coronavirus RaTG13 [19] and similar to two bat SARS-like coronaviruses bat-SL-CoVZXC21 and bat- SL-CoVZC45. -
Structure Unveils Relationships Between RNA Virus Polymerases
viruses Article Structure Unveils Relationships between RNA Virus Polymerases Heli A. M. Mönttinen † , Janne J. Ravantti * and Minna M. Poranen * Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 1, P.O. Box 56 (Viikinkaari 9), 00014 Helsinki, Finland; heli.monttinen@helsinki.fi * Correspondence: janne.ravantti@helsinki.fi (J.J.R.); minna.poranen@helsinki.fi (M.M.P.); Tel.: +358-2941-59110 (M.M.P.) † Present address: Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Viikki Biocenter 2, P.O. Box 56 (Viikinkaari 5), 00014 Helsinki, Finland. Abstract: RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure- based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. -
Transcriptome and Coronavirus: New Hope and Therapy
Review Volume 11, Issue 2, 2021, 9541 - 9552 https://doi.org/10.33263/BRIAC112.95419552 Transcriptome and Coronavirus: New Hope and Therapy Khaled Mohamed Mohamed Koriem 1,* 1 Department of Medical Physiology, Medical Research Division, National Research Centre, 33 El-Buhouth Street, Dokki, Cairo, 12622, Egypt * Correspondence: [email protected]; Scopus Author ID 24477156100 Received: 20.08.2020; Revised: 7.09.2020; Accepted: 9.09.2020; Published: 13.09.2020 Abstract: Transcriptome refers to all RNA particles occur inside one cell or inside numerous cells in one organ. Coronaviruses are a family of correlated viruses that induce viral infection. In humans, coronaviruses induce respiratory viral infections that may be mild or dangerous. The coronavirus shape is large circular elements that have round tip outbreaks - the virus diameter particles=120 nm. The RNA viral genome occurs in coronavirus. The coronavirus genome size = 27-34 kilobases, and this size is the largest RNA genome size. The Life cycle of coronavirus includes viral entry, replication, and release. Coronavirus transmission was done through the connection of its protein with host cell receptors in a specific process. There are 4 types of coronavirus genus: (1) Alphacoronavirus, (2) Betacoronavirus, (3) Gammacoronavirus, and (4) Deltacoronavirus. Viral replication, immune evasion, and virion biogenesis correlated with host cell transformation mechanism. Viral molecular mechanism hijacks the host cell protein production mechanism. There is an important host factor (CPSF6) that connects with nuclear protein (NP1). The CPSF6 increases the nuclear production of NP1 in the same time, CPSF6 possesses an important role in the progress of capsid mRNAs inside the nucleus. -
The Incredible Diversity of Viruses
Feature ACANTHAMOEBA ACANTHAMOEBA BOTTLE-SHAPED VIRUS; VIRUS; BOTTLE-SHAPED ACIDIANUS ; FREDERICK A. MURPHY/CDC GLOBAL ; FREDERICK A. MURPHY/CDC PLOS PATHOG. PLOS / ET AL. ; E. GHIGO J. VIROL. J. / ET AL. MIMIVIRUS. CENTRE ROW L–R: RABIES VIRUS; T4 BACTERIOPHAGE; ROTAVIRUS. BOTTOM ROW L–R: EBOLA VIRUS; TOBACCO RATTLE VIRUS; VIRUS; RATTLE TOBACCO EBOLA VIRUS; L–R: ROW BOTTOM ROTAVIRUS. T4 BACTERIOPHAGE; RABIES VIRUS; L–R: ROW CENTRE MIMIVIRUS. FALSE-COLOUR ELECTRON MICROGRAPHS (NOT TO SAME SCALE). TOP ROW L–R: SMALLPOX VIRUS; VIRUS; SMALLPOX L–R: ROW SCALE). TOP SAME TO (NOT MICROGRAPHS ELECTRON FALSE-COLOUR POLYPHAGA SPL; M. HÄRING HIV-2. Viruses come in all shapes and sizes, such as the giant mimivirus (top right) and the lunar-lander-shaped bacteriophage (centre). The incredible diversity of viruses They’re everywhere virologists look, and they’re not all bad. Scientists are beginning to identify and classify the nonillions of viruses on the planet and their contributions to global ecosystems. By Amber Dance 22 | Nature | Vol 595 | 1 July 2021 ©2021 Spri nger Nature Li mited. All rights reserved. ©2021 Spri nger Nature Li mited. All rights reserved. ya Breitbart has hunted novel time to be doing this kind of research, says part of a group whose members are large in viruses in African termite Breitbart. “I think, in many ways, now is the terms of both genome size and absolute size mounds, Antarctic seals and time of the virome.” (typically, 200 nanometres or more across). water from the Red Sea. But to In 2020 alone, the ICTV added 1,044 species These viruses infect amoebae, algae and other hit pay dirt, she has only to step to its official list, and thousands more await protists, putting them in a position to influ- into her back garden in Florida. -
Metagenomic Insights Into the Sewage RNA Virosphere of a Large City
viruses Article Metagenomic Insights into the Sewage RNA Virosphere of a Large City Sergio Guajardo-Leiva 1 , Jonás Chnaiderman 2 , Aldo Gaggero 2,* and Beatriz Díez 1,3,* 1 Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; [email protected] 2 Programa de Virología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile; [email protected] 3 Center for Climate and Resilience Research (CR)2, Santiago 8370449, Chile * Correspondence: [email protected] (A.G.); [email protected] (B.D.) Received: 4 August 2020; Accepted: 14 September 2020; Published: 21 September 2020 Abstract: Sewage-associated viruses can cause several human and animal diseases, such as gastroenteritis, hepatitis, and respiratory infections. Therefore, their detection in wastewater can reflect current infections within the source population. To date, no viral study has been performed using the sewage of any large South American city. In this study, we used viral metagenomics to obtain a single sample snapshot of the RNA virosphere in the wastewater from Santiago de Chile, the seventh largest city in the Americas. Despite the overrepresentation of dsRNA viruses, our results show that Santiago’s sewage RNA virosphere was composed mostly of unknown sequences (88%), while known viral sequences were dominated by viruses that infect bacteria (60%), invertebrates (37%) and humans (2.4%). Interestingly, we discovered three novel genogroups within the Picobirnaviridae family that can fill major gaps in this taxa’s evolutionary history. We also demonstrated the dominance of emerging Rotavirus genotypes, such as G8 and G6, that have displaced other classical genotypes, which is consistent with recent clinical reports. -
2021 Taxonomic Update of Phylum Negarnaviricota (Riboviria: Orthornavirae), Including the Large Orders Bunyavirales and Mononegavirales
Archives of Virology https://doi.org/10.1007/s00705-021-05143-6 VIROLOGY DIVISION NEWS 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales Jens H. Kuhn1 · Scott Adkins2 · Bernard R. Agwanda211,212 · Rim Al Kubrusli3 · Sergey V. Alkhovsky (Aльxoвcкий Cepгeй Bлaдимиpoвич)4 · Gaya K. Amarasinghe5 · Tatjana Avšič‑Županc6 · María A. Ayllón7,197 · Justin Bahl8 · Anne Balkema‑Buschmann9 · Matthew J. Ballinger10 · Christopher F. Basler11 · Sina Bavari12 · Martin Beer13 · Nicolas Bejerman14 · Andrew J. Bennett15 · Dennis A. Bente16 · Éric Bergeron17 · Brian H. Bird18 · Carol D. Blair19 · Kim R. Blasdell20 · Dag‑Ragnar Blystad21 · Jamie Bojko22,198 · Wayne B. Borth23 · Steven Bradfute24 · Rachel Breyta25,199 · Thomas Briese26 · Paul A. Brown27 · Judith K. Brown28 · Ursula J. Buchholz29 · Michael J. Buchmeier30 · Alexander Bukreyev31 · Felicity Burt32 · Carmen Büttner3 · Charles H. Calisher33 · Mengji Cao (曹孟籍)34 · Inmaculada Casas35 · Kartik Chandran36 · Rémi N. Charrel37 · Qi Cheng38 · Yuya Chiaki (千秋祐也)39 · Marco Chiapello40 · Il‑Ryong Choi41 · Marina Ciufo40 · J. Christopher S. Clegg42 · Ian Crozier43 · Elena Dal Bó44 · Juan Carlos de la Torre45 · Xavier de Lamballerie37 · Rik L. de Swart46 · Humberto Debat47,200 · Nolwenn M. Dheilly48 · Emiliano Di Cicco49 · Nicholas Di Paola50 · Francesco Di Serio51 · Ralf G. Dietzgen52 · Michele Digiaro53 · Olga Dolnik54 · Michael A. Drebot55 · J. Felix Drexler56 · William G. Dundon57 · W. Paul Duprex58 · Ralf Dürrwald59 · John M. Dye50 · Andrew J. Easton60 · Hideki Ebihara (海老原秀喜)61 · Toufc Elbeaino62 · Koray Ergünay63 · Hugh W. Ferguson213 · Anthony R. Fooks64 · Marco Forgia65 · Pierre B. H. Formenty66 · Jana Fránová67 · Juliana Freitas‑Astúa68 · Jingjing Fu (付晶晶)69 · Stephanie Fürl70 · Selma Gago‑Zachert71 · George Fú Gāo (高福)214 · María Laura García72 · Adolfo García‑Sastre73 · Aura R. -
Porcine Rotavirus Strain JL94 Inner Capsid Protein VP6 (VP6) Mrna, Complete Cds Genbank: AY538664.1 FASTA Graphics
Porcine rotavirus strain JL94 inner capsid protein VP6 (VP6) mRNA, complete cds GenBank: AY538664.1 FASTA Graphics Go to: LOCUS AY538664 1356 bp mRNA linear VRL 25-OCT-2004 DEFINITION Porcine rotavirus strain JL94 inner capsid protein VP6 (VP6) mRNA, complete cds. ACCESSION AY538664 VERSION AY538664.1 KEYWORDS . SOURCE Porcine rotavirus ORGANISM Porcine rotavirus Viruses; Riboviria; Orthornavirae; Duplornaviricota; Resentoviricetes; Reovirales; Reoviridae; Sedoreovirinae; Rotavirus. REFERENCE 1 (bases 1 to 1356) AUTHORS Chen,S., Li,Y. and Song,Y. TITLE Porcine rotavirus JL94 inner capsid protein VP6 mRNA JOURNAL Unpublished REFERENCE 2 (bases 1 to 1356) AUTHORS Chen,S., Li,Y., Shi,D. and Song,Y. TITLE Direct Submission JOURNAL Submitted (02-FEB-2004) Molecular Virology & Microbiology, Veterinary Medicine College, Northeast Agricultural University, Mucai Street, Harbin, Heilongjiang 150030, ChinaFEATURES Location/Qualifiers source 1..1356 /organism="Porcine rotavirus" /mol_type="mRNA" /strain="JL94" /db_xref="taxon:10913" gene 1..1356 /gene="VP6" CDS 24..1217 /gene="VP6" /codon_start=1 /product="inner capsid protein VP6" /protein_id="AAS46764.1" /translation="MEVLYSLSKTLKDARDKIVEGTLYSNISDLIQQFNQMIVTMNGN DFQTGGIGNLPIRNWNFDFGLLGTTLLNIDANYVENARTTIEYFIDFIDNVCMDEMAR ESQRNGIAPQSEALRKLSGIKFKGINFDNSSDYIENWNLQNRRQRTGFVFHKPNILPY SASFTLNRSQPAHDNLMGTMWINAGSEIQVAGFDYSCAFNAPANIQQFEHVVPLRRAL TTATITLLPDAERFSFPRVINSADGATTWYFNPVIIRPSNVEVEFLLNGQIINTYQAR FGTIIARNFDTIRLSFQLVRPPNMTPAVANLFPQAPPFIFHATVGLTLRIESAVCESV LADASETLLANVTAVRQEYAIPVGPVFPPGMNWTELITNYSPSREDNLQRVFTVASIR