Virus Nomenclature and Classification PDF

(nomenclature) ‫نامگذاری ویروس ها‬ :‫فواید رده بندی ویروس ها‬ ‫ یادگیری آسان‬-1...

(nomenclature) ‫نامگذاری ویروس ها‬ :‫فواید رده بندی ویروس ها‬ ‫ یادگیری آسان‬-1 ‫ کمک به ارتباطات علمی بین افراد‬-2 ‫ خصوصیات ویروس های جدید قابل پیش بینی خواهد بود‬-3 ‫ آشکار کردن روابط خویشاوندی و تبارزائی‬-4 :‫روش نامگذاری‬  Smith (1937): known viruses or virus diseases were divided into 51 groups.  Viruses were grouped according to the generic name of the host in which they were first found. For example, Nicotiana virus group with15 viruses, including Nicotiana virus 1 (now named as TMV).  Holmes (1939): classified based on host reactions and methods of transmission, used a Latin binomial–trinomial system of naming.  TMV became Marmor tabaci H., Tobacco necrosis virus became Marmor lethale H. ‫ نام انگلیسی میزبان‬+‫ عالئم بارز بیماری در میزبان‬+ virus.‫ که نام یک گونه ویروس گیاهی به نام ویروس موزائیک توتون می باشد‬Tobacco mosaic virus :‫مثال‬.‫آرایه های مورد تایید برای رده بندی ویروس ها در اسالیدهای بعدی آمده است‬ https://ictv.global/taxonomy.‫ نام تمام آرایه ها باید بصورت علمی (ایتالیک) نوشته شود‬:‫نکته مهم‬.‫ وجود دارد‬acronym ‫برای هرگونه ویروس نام مخفف یا اکرونیم‬.‫ می باشد‬TMV ‫ بصورت‬Tobacco mosaic virus ‫مثال اکرونیم‬ Gibbs, A. Binomial nomenclature for virus species: a long view. ‫تغییر روش نامگذاری گونه ویروسی به روش دونامی‬ Arch Virol 165, 3079–3083 (2020). ‫ نام جنس ویروس‬+‫نام میزبان‬ https://doi.org/10.1007/s00705-020-04828-8 :‫مثال‬ Barley yellow striate mosaic virus :‫نام قبلی‬ Cytorhabdovirus hordei :‫نام جدید‬.‫ وجود دارد‬acronym ‫برای هرگونه ویروس نام مخفف یا اکرونیم‬.‫ می باشد‬TMV ‫ بصورت‬Tobacco mosaic virus ‫مثال اکرونیم‬ Example: :‫اکرونیم برای کلمات زیر در روبروی آن امده‬ Grapevine leafroll-associated virus 1 GLRaV-1 Grapevine leafroll-associated virus 7 GLRaV-7 virus V Cucumber green mottle mosaic virus CGMMV viroid Vd Tomato yellow leaf curl China virus TYLCCNV mosaic M Tomato mosaic virus ToMV mottle Mo Maize Iranian mosaic nucleorhabdovirus MIMV ringspot RS Beet curly top Iran virus BCTIV Old name New name Host name Eggplant mottled dwarf alphanucleorhabdovirus (EMDV) Alphanucleorhabdovirus melongenae Solanum melongena Maize Iranian mosaic alphanucleorhabdovirus (MIMV) Alphanucleorhabdovirus zeairanense Zea mays Maize mosaic alphanucleorhabdovirus (MMV) Alphanucleorhabdovirus maydis Peach alphanucleorhabdovirus (PeV1) Alphanucleorhabdovirus pruni Prunus persica Potato yellow dwarf alphanucleorhabdovirus (PYDV) Alphanucleorhabdovirus tuberosum Rice yellow stunt alphanucleorhabdovirus (RYSV) Alphanucleorhabdovirus oryzae Wheat yellow striate alphanucleorhabdovirus (WYSV) Alphanucleorhabdovirus tritici Alfalfa betanucleorhabdovirus Betanucleorhabdovirus medicagonis Apple betanucleorhabdovirus Betanucleorhabdovirus mali Alfalfa dwarf cytorhabdovirus Cytorhabdovirus medicagonis Barley yellow striate mosaic cytorhabdovirus Cytorhabdovirus hordei Lettuce necrotic yellows cytorhabdovirus Cytorhabdovirus lactucanecante Lactuca sativa necante= killing Lettuce yellow mottle cytorhabdovirus Cytorhabdovirus lactucamaculante Lmaculante = spotting Maize-associated cytorhabdovirus Cytorhabdovirus maydis Maize yellow striate cytorhabdovirus Cytorhabdovirus maysflavostriatis Kuhn, J.H., Adkins, S., Alkhovsky, S.V. et al. 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 167, 2857–2906 (2022). https://doi.org/10.1007/s00705-022-05546-z  CLASSIFICATION OF VIRUSES  1966: At the International Congress for Microbiology (in Moscow), the first meeting of the International Committee on Nomenclature of Viruses (ICNV) was held.  1971: Then the first report was published.  1973: ICNV change to International Committee for Taxonomy of Viruses (ICTV).  Web site: http://talk.ictvonline.org  Systems for classification: Monothetic hierarchial (Linnaeus) Polythetic (Adanson, 1763)  Polythetic denotes a taxonomic group classified on the basis of several characters, as opposed to a monothetic group.  Baltimore classes of viruses, 1971 By classification of viruses by the routes of genome expression Fig. The amended scheme of the seven Baltimore classes of viruses. Shown is the transfer of genetic information between genomes and mRNA. (The Baltimore Classification of Viruses 50 Years Later: How Does It Stand in the Light of Virus Evolution? doi: 10.1128/MMBR.00053-21) 5 Hierarchical virus classification system In 1962 Lwoff, R. W. Horne, and P. Tournier Distinction between polythetic and monothetic classes in the case of 8 individuals (1–8) and 8 properties (A–H). The possession of a property is indicated by a plus sign. Individuals 1–4 constitute a polythetic class, each member possessing 3 out of 4 properties with no common property being present in all the members. Individuals 5–6, 7–8 and 5–6–7–8 form three monothetic classes with respectively 3, 3 and 2 properties present in all the members  Descriptors used in virus taxonomy I. Virion properties A. Morphology properties of virions 1. Size 2. Shape 8. Presence or absence of 5' terminal 3. Presence or absence of an envelope covalently-linked polypeptide 4. Capsomeric symmetry and structure 9. Presence or absence of 3' terminal poly(A) tract (or other specific tract) B. Physical properties of virions 10. Nucleotide sequence comparisons 1. Molecular mass 2. Buoyant density D. Properties of proteins 1. Number C. Properties of the genome 2. Size 1. Type of nucleic acid, DNA or RNA 3. Functional activities 2. Strandedness: single-stranded or double- 4. Amino acid sequence comparisons stranded 3. Linear or circular E. Lipids 4. Sense: positive, negative or ambisense 1. Presence or absence 5. Number of segments 2. Nature 6. Size of genome or genome segments 7. Presence or absence and type of 5' terminal F. Carbohydrates cap 1. Presence or absence 2. Nature II. Genome organization and replication 1. Genome organization 2. Strategy of replication of nucleic acid 3. Characteristics of transcription 4. Characteristics of translation 5. Sites of accumulation of virion proteins, site of assembly, site of maturation and release 6. Cytopathology, inclusion body formation III. Antigenic properties 1. Serological relationships 2. Mapping epitopes IV. Biological properties 1. Host range, natural and experimental 2. Pathogenicity 3. histopathology 4. Mode of transmission in nature 5. Vector relationships 6. Geographic distribution  In the third Report (Matthews, 1979):  the viruses were listed on the basis of the kind and strandedness of the viral genome  and the presence or absence of an envelope.  ICTV had approved families and genera.  By the time of the Sixth Report (Murphy et al., 1995) ICTV had finally accepted the controversial category of virus species based on a proposal made in 1990 (van Regenmortel, 1990).  King et al. 2012a: A species is a monophyletic group of viruses whose properties can be distinguished from those of other species by multiple criteria.  A virus species is not a uniform population because in each infected cell, a wide range of variants is present. This situation is termed a quasi-species A quasi-species is a population structure in which collections of closely related genomes are subjected to a continuous process of genetic variation, competition, and selection. Usually, the distribution of mutants or variants is centered on one or several master sequences.  CRITERIA FOR THE RECOGNITION OF STRAINS AND SPECIES  Structural criteria (structural, non-structural proteins, NA)  Serological relationship  Biological criteria (symptoms, ….)  http://ictvonline.org/ International Committee on Taxonomy of Viruses VIRUS TAXONOMY 2023 Ebola. Kuhn et al., 2019 Covid-19  The host range distribution in the seven Baltimore classes of viruses. (A) Distribution of the BCs in the three cellular domains. The panel illustrates the dominance of dsDNA viruses in Bacteria and Archaea, which contrasts the dominance of viruses with RNA genomes in Eukarya. (B) Distribution of the BCs in eukaryotes. Each circle represents the breakdown of the virus genera (according to the ICTV taxonomy release number 35 [https://talk.ictvonline.org/files/maste r-species-lists/m/msl/9601]) associated with the indicated group DNA-RT of hosts. The number of virus genera (n) is indicated inside each circle. The BCs are denoted by the virion nucleic acid and are color coded. doi: 10.1128/MMBR.0005 3-21 Published in 2021 15  (2022) 10434 84 2606 168 233 8 65 0 39 2 17 0 10 0 6 https://www.nature.com/articles/s41564-020-0709-x/figures/1 17 18 ‫* توصیف و فهرست کردن ویروس ها‬ ‫جهت استفاده از مزایا و شناخت تهدیدهای ویروس ها برای انسان‬ ‫* تهیه نقشه روابط تکاملی آنها‬ 20 21  The Baltimore classes and monophyletic realms of viruses. The connections between the BCs and the virus realms are shown by colored edges. doi: 10.1128/MMBR.00053-21 Published in 2021 25  realm: Riboviria: RNA viruses *RNA-dependent RNA polymerases (RdRps) for replication *RNA virus *infect a wide range of prokaryotic and eukaryotic hosts membership of this taxon, it is named Riboviria realm: Monodnaviria: a virus is a member of this realm if it has a ssDNA genome encoding a rolling-circle replication endonuclease of the HUH superfamily realm: Adnaviria: filamentous archaeal viruses with linear double-stranded DNA (dsDNA) genomes. No infection on Plants realm: Duplodnaviria: a virus is a member of this realm if it has a dsDNA genome encoding a major capsid protein containing the HK97 fold (HK97-MCP), HK97-type major capsid proteins. No infection on Plants realm: Varidnaviria: a virus is a member of this realm if it has a DNA genome encoding a major capsid protein containing the vertical jelly- roll fold and forming pseudohexameric capsomers. No infection on Plants realm: Ribozyviria: specific for Hepatitis D virus (HDV) and its relatives. HDV has a ribozyme-containing negative-sense single-stranded circular RNA genome. No infection on Plants Global Organization and Proposed Megataxonomy of the Virus World. 2020. DOI: 10.1128/MMBR.00061- 19  1 1 1 Luteovirus (satellite viruses) Subphylum 1: two classes Subphylum 2: four classes 33 Riboviria › Orthornavirae › Pisuviricota › Stelpaviricetes › Patatavirales › Potyviridae *monopartite/ bipartite genome Riboviria › Orthornavirae › Kitrinoviricota › Tolucaviricetes › Tolivirales › Tombusviridae › Luteovirus ssRNA(+) 35 Riboviria › Orthornavirae › Pisuviricota › Pisoniviricetes › Sobelivirales › Solemoviridae › Polerovirus Riboviria › Orthornavirae › Kitrinoviricota › Alsuviricetes › Tymovirales Flexiviridae and Tymoviridae * positive sense ssRNA *replication proteins *A common evolutionary ancestor: polyadenylated genome filamentous virions triple gene block of movement proteins 37  * Linear ssRNA(+) * potexvirus-like replication proteins *All the plant infecting members possess a TGB module 38 Riboviria › Orthornavirae › Kitrinoviricota › Alsuviricetes › Tymovirales 39 40  Riboviria › Orthornavirae › Kitrinoviricota › Alsuviricetes › Hepelivirales › Benyviridae ssRNA(+) Riboviria › Orthornavirae › Kitrinoviricota › Alsuviricetes › Martellivirales › Bromoviridae * Spherical or bacilliform * Genomic RNAs in separate virions 41 ssRNA(+) Very large genome, ssRNA(+)  Riboviria › Orthornavirae › Pisuviricota › Pisoniviricetes › Picornavirales › Secoviridae * positive-sense, mono- or bipartite RNA 43 Riboviria › Orthornavirae › Kitrinoviricota › Tolucaviricetes › Tolivirales › Tombusviridae 44  Riboviria › Orthornavirae › Duplornaviricota › Resentoviricetes › Reovirales dsRNA * genome segments (usually 9, 10, 11 or 12) * RdRp or inner capsid shell proteins * wide range of Host: mammals, birds, reptiles, fish, crustaceans, marine protists, insects, ticks, arachnids, plants and fungi 45 Riboviria › Orthornavirae › Kitrinoviricota › Alsuviricetes › Martellivirales › Virgaviridae 46  Riboviria › Orthornavirae › Negarnaviricota Phylum:Negarnaviricota Negative-sense RNA viruses 47  Haploviricotina: simple 48 Serpentovirales: serpent-like ‫مار‬ appearance of virions Aspiviridae: snake”, morphology of virions Serpentovirales: serpent-like ‫مار‬ appearance of virions Aspiviridae: snake”, morphology of virions  Monjiviricetes: contraction of Mononega and Jingchu ‫کوتاه شده‬ 51  ‫› ‪Riboviria › Orthornavirae › Negarnaviricota › Haploviricotina‬‬ ‫*پیکره باسیلی فرم یا فشنگی‬ ‫‪Monjiviricetes › Mononegavirales › Rhabdoviridae‬‬ ‫*پوشش لیپیدی و زوائد گلیکوپروتئینی‬ ‫‪https://doi.org/10.1007/s00705-022-05546-z‬‬ ‫*در سطح درونی پوشش لیپیدی‪ :‬پروتئین ماتریکس‬ ‫*پروتئین ماتریکس‪ :‬دور تا دور نوکلئوپروتئین‬ ‫*دارای پنج پروتئین ساختاری‬ ‫‪52‬‬  ‫*میزبان‪ :‬مهره داران‪ ،‬بی مهرگان و گیاهان‬ ‫‪53‬‬  Ellioviricetes: a contraction of Elliott (Richard), the late pioneer of bunyavirus molecular virology 54  S, M, and L segments 55  (Tomato spotted wilt orthotospovirus) 56  ‫*تقارن‪T=12 :‬‬ ‫‪57‬‬  Caulimoviridae Genome is dsDNA, but, as are reverse transcribing viruses, so, belonged to Riboviria isometric virions (members of the genera Caulimovirus, Cavemovirus, Petuvirus, Rosadnavirus, Solendovirus and Soymovirus) or bacilliform-shaped virions (members of the genera Badnavirus and Tungrovirus) 58 Monodnaviria › Shotokuvirae › Cressdnaviricota ssDNA 59 Monodnaviria › Shotokuvirae › Cressdnaviricota › Repensiviric * Twinned incomplete icosahedra etes › Geplafuvirales › Geminiviridae ssDNA 60 Monodnaviria › Shotokuvirae › Cressdnaviricota › Arfiviricetes › Mulpavirales › Nanoviridae ssDNA Alphasatellitidae 62  Associated with the newly described coconut foliar decay virus (genus Cofodevirus) and Babuviruses 63  Alphasatellitidae *nanovirus genome share two regions of sequence similarity: common region stem-loop (CR-SL) and the common region major (CRM). *The DNA-R component of nanoviruses encodes a replication-associated protein (Rep). Viruses of the family Nanoviridae, and some begomoviruses and mastreviruses may be associated with additional ssDNA components that resemble the DNA-R of nanoviruses; these will be referred to as alphasatellites. However, alphasatellites associated with nanoviruses, lack the CR-SL and CRM of their helper viruses and are unable to trans-replicate genome. 64 Tolecusatellitidae The name Tolecusatellitidae is based on the first DNA satellite shown to be associated with geminiviruses - Tomato leaf curl virus – satellite. the true satellites that associate with geminiviruses. Betasatellites They have a highly conserved structure: a sequence rich in adenine (A-rich), the satellite conserved region (SCR), a single product (known as betaC1). in association with begomoviruses and mastreviruses. *The betaC1 protein: *The interactions with betasatellites: -symptom determinant fully dependent (the virus cannot infect a particular plant -in overcoming plant host defences by species without the satellite) suppressing both post-transcriptional facultative (some virus isolates associate with the and transcriptional gene silencing. betasatellites but others do not). 65 Tolecusatellitidae Deltasatellites: *an A-rich sequence, *a sequence derived from the betasatellite SCR, but are non-coding. Deltasatellites: (interactions) *fully dependent on the begomoviruses, *the helper viruses do not seem to depend on them a helper begomovirus of the deltasatellite: -reduce virus damage -extend the life of the plant, -greater period for transmission of the virus 66 Avsunviroidae *Genome: a single-stranded, circular RNA rod-like or a branched conformation *lack the central conserved region hammerhead ribozymes: *the conserved sequence and structural motifs *in the strands of either polarity, *involved in their replication in plastids, symmetric RNA-RNA rolling-circle mechanism. 67 Avsunviroidae self-cleavage sites hammerhead structures Oligomeric RNAs of both polarities are synthesized by a nuclear-encoded plastid RNA polymerase (NEP) generating linear monomeric RNAs that, are ligated into circular forms by a tRNA ligase tRNA ligase & NEP, is encoded in the nucleus and translocated into plastids. 68 Pospiviroidae *Circular ssRNAs *rod-like or quasi-rod-like conformation *a central conserved region (CCR) *with five domains: central conserved region (CCR), terminal conserved region (TCR) P (pathogenic), V (variable) Replication: in the nucleus asymmetric rolling-circle mechanism 70 VIRUSES OF GYMNOSPERMS )‫(بازدانگان‬, PTERIDOPHYTES )‫(سرخس تباران‬, ALGAE, AND FUNGI A disease of Cycas revoluta (Gymnosperms) has been shown to be due to a Nepovirus No viruses have been reported from bryophytes )‫ (خزه‬but several viruses have been reported from ferns )‫ (سرخس‬. An increasing number of viruses (termed virioplankton). Almost of studied viruses have very large particles, double- stranded DNA genomes, and are placed in the family Phycodnaviridae Viruses of Fungi (Also Known as Mycoviruses) Representatives of 16 genera in 14 viral families infect fungi  A virus species is not a uniform population because in each infected cell, a wide range of variants is present. This situation is termed a quasi-species A quasi-species is a population structure in which collections of closely related genomes are subjected to a continuous process of genetic variation, competition, and selection. Usually, the distribution of mutants or variants is centered on one or several master sequences. FIGURE 2.9 Differentiation of taxa by pairwise identities of sequences of variants of amino acid sequences of CPs of potyviruses. Example: Potyviridae: Genus demarcation criteria, for the entire open reading frame, are