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Baltimore classification is a system used to classify
virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsk ...
es based on their manner of
messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the ...
(mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a distinct group. Seven Baltimore groups are described that take into consideration whether the viral genome is made of deoxyribonucleic acid (DNA) or
ribonucleic acid Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohyd ...
(RNA), whether the genome is single- or double-stranded, and whether the
sense A sense is a biological system used by an organism for sensation, the process of gathering information about the world through the detection of stimuli. (For example, in the human body, the brain which is part of the central nervous system re ...
of a single-stranded RNA genome is positive or negative. Baltimore classification also closely corresponds to the manner of replicating the genome, so Baltimore classification is useful for grouping viruses together for both transcription and replication. Certain subjects pertaining to viruses are associated with multiple, specific Baltimore groups, such as specific forms of
translation Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...
of mRNA and the host range of different types of viruses. Structural characteristics such as the shape of the viral
capsid A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or ma ...
, which stores the viral genome, and the evolutionary history of viruses are not necessarily related to Baltimore groups. Baltimore classification was created in 1971 by virologist
David Baltimore David Baltimore (born March 7, 1938) is an American biologist, university administrator, and 1975 Nobel laureate in Physiology or Medicine. He is President Emeritus and Distinguished Professor of Biology at the California Institute of Tec ...
. Since then, it has become common among virologists to use Baltimore classification alongside standard virus taxonomy, which is based on evolutionary history. In 2018 and 2019, Baltimore classification was partially integrated into virus taxonomy based on evidence that certain groups were descended from common ancestors. Various realms, kingdoms, and phyla now correspond to specific Baltimore groups.


Overview

Baltimore classification groups viruses together based on their manner of mRNA synthesis. Characteristics directly related to this include whether the genome is made of deoxyribonucleic acid (DNA) or
ribonucleic acid Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohyd ...
(RNA), the strandedness of the genome, which can be either single- or double-stranded, and the sense of a single-stranded genome, which is either positive or negative. The primary advantage of Baltimore classification is that by classifying viruses according to the aforementioned characteristics, viruses that behave in the same manner can be studied as distinct groups. There are seven Baltimore groups numbered with Roman numerals, listed hereafter. * Group I: double-stranded DNA viruses * Group II: single-stranded DNA viruses * Group III: double-stranded RNA viruses * Group IV: positive sense single-stranded RNA viruses * Group V: negative sense single-stranded RNA viruses * Group VI: single-stranded RNA viruses with a DNA intermediate in their life cycle * Group VII: double-stranded DNA viruses with a RNA intermediate in their life cycle Baltimore classification is chiefly based on the transcription of the viral genome, and viruses within each group typically share the manners by which the mRNA synthesis occurs. While not the direct focus of Baltimore classification, groups are organized in such a manner that viruses in each group also typically have the same mechanisms of replicating the viral genome. Because of this, Baltimore classification provides insights into both the transcription and replication parts of the viral life cycle. Structural characteristics of a virus particle, called a virion, such as the shape of the viral capsid and the presence of a
viral envelope A viral envelope is the outermost layer of many types of viruses. It protects the genetic material in their life cycle when traveling between host cells. Not all viruses have envelopes. Numerous human pathogenic viruses in circulation are encase ...
, a
lipid Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids in ...
membrane that surrounds the capsid, have no direct relation to Baltimore groups, nor do the groups necessarily show genetic relation based on evolutionary history.


Classification


DNA viruses

DNA viruses have genomes made of deoxyribonucleic acid (DNA) and are organized into two groups: double-stranded DNA (dsDNA) viruses, and single-stranded DNA (ssDNA) viruses. They are assigned to four separate realms: '' Adnaviria'', '' Duplodnaviria'', '' Monodnaviria'', and '' Varidnaviria''. Many have yet to be assigned to a realm.


Group I: double-stranded DNA viruses

The first Baltimore group contains viruses that have a double-stranded DNA (dsDNA) genome. All dsDNA viruses have their mRNA synthesized in a three-step process. First, a transcription preinitiation complex binds to the DNA upstream of the site where transcription begins, allowing for the recruitment of a host
RNA polymerase In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template. Using the enzyme helicase, RNAP locally opens th ...
. Second, once the RNA polymerase is recruited, it uses the negative strand as a template for synthesizing mRNA strands. Third, the RNA polymerase terminates transcription upon reaching a specific signal, such as a
polyadenylation Polyadenylation is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA). The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In euk ...
site. dsDNA viruses make use of several mechanisms to replicate their genome. Bidirectional replication, in which two replication forks are established at a replication origin site and move in opposite directions of each other, is widely used. A rolling circle mechanism that produces linear strands while progressing in a loop around the circular genome is also common. Some dsDNA viruses use a strand displacement method whereby one strand is synthesized from a template strand, and a complementary strand is then synthesized from the prior synthesized strand, forming a dsDNA genome. Lastly, some dsDNA viruses are replicated as part of a process called replicative transposition whereby a viral genome in a host cell's DNA is replicated to another part of a host genome. dsDNA viruses can be subdivided between those that replicate in the nucleus, and as such are relatively dependent on host cell machinery for transcription and replication, and those that replicate in the cytoplasm, in which case they have evolved or acquired their own means of executing transcription and replication. dsDNA viruses are also commonly divided between tailed dsDNA viruses, referring to members of the realm ''Duplodnaviria'', usually the tailed bacteriophages of the order ''Caudovirales'', and tailless or non-tailed dsDNA viruses of the realm ''Varidnaviria''. dsDNA viruses are classified into three of the four realms and include many taxa that are unassigned to a realm: *All viruses in ''Adnaviria'' are dsDNA viruses. Viruses in this realm infect
archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaeba ...
. *All viruses in ''Duplodnaviria'' are dsDNA viruses. Viruses in this realm belong to two groups: tailed bacteriophages in '' Caudovirales'' and herpesviruses in ''
Herpesvirales The ''Herpesvirales'' is an order of dsDNA viruses (Baltimore group I) with animal hosts, characterised by a common morphology consisting of an icosahedral capsid enclosed in a glycoprotein-containing lipid envelope. Common infections in humans ...
''. *In ''Monodnaviria'', members of the class '' Papovaviricetes'' are dsDNA viruses. Viruses in ''Papovaviricetes'' constitute two groups: papillomaviruses and
polyomavirus ''Polyomaviridae'' is a family of viruses whose natural hosts are primarily mammals and birds. As of 2020, there are six recognized genera and 117 species, five of which are unassigned to a genus. 14 species are known to infect humans, while othe ...
es. *All viruses in ''Varidnaviria'' are dsDNA viruses. Viruses in this realm include
adenovirus Adenoviruses (members of the family ''Adenoviridae'') are medium-sized (90–100 nm), nonenveloped (without an outer lipid bilayer) viruses with an icosahedral nucleocapsid containing a double-stranded DNA genome. Their name derives from ...
es, giant viruses, and poxviruses. *The following taxa that are unassigned to a realm exclusively contain dsDNA viruses: **Classes: ''
Naldaviricetes ''Naldaviricetes'' is a class of viruses, which infect arthropods. Members of ''Naldaviricetes'' are characterized by large enveloped rod-shaped virions, circular double-stranded DNA genomes, and replication in the nucleus of the host cell. All ...
'' **Families: ''
Ampullaviridae ''Ampullaviridae'' is a family of viruses that infect archaea of the genus '' Acidianus''. Only one genus in this family has been described, ''Bottigliavirus'', which contains three species. The name of the family and genus is derived from the L ...
'', ''
Bicaudaviridae ''Bicaudaviridae'' is a family of hyperthermophilic archaeal viruses. Members of the genus '' Acidianus'' serve as natural hosts. There is only one genus (''Bicaudavirus'') and one species in this family: ''Acidianus two-tailed virus''. However, ...
'', ''
Clavaviridae ''Clavaviridae'' is a family of double-stranded viruses that infect archaea. This family was first described by the team led by D. Prangishvili in 2010. There is one genus in this family (''Clavavirus''). Within this genus, a single species ha ...
'', '' Fuselloviridae'', '' Globuloviridae'', '' Guttaviridae'', ''
Halspiviridae ''Halspiviridae'' is a family of viruses that consists of a single genus, ''Salterprovirus'', which consists of a single recognised species; ''Salterprovirus His1'' (hereafter, 'His1'). This virus was isolated from hypersaline water in Australi ...
'', ''
Ovaliviridae ''Ovaliviridae'' is a family of viruses of archaea that is not assigned to any higher taxonomic ranks. The family contains a single genus, ''Alphaovalivirus'', which contains a single species, ''Sulfolobus ellipsoid virus 1''. The linear genome ...
'', '' Plasmaviridae'', '' Polydnaviridae'', '' Portogloboviridae'', ''
Thaspiviridae ''Thaspiviridae'' is a family of spindle-shaped viruses that is not assigned to any higher taxonomic ranks. The family contains a single genus, ''Nitmarvirus'', which contains a single species, ''Nitmarvirus NSV1''. Members of the family ''Thas ...
'' **Genera: '' Dinodnavirus'', ''
Rhizidiovirus ''Rhizidiovirus'' is a genus of viruses. StramenopilesDawe VH, Kuhn CW (1983) Isolation and characterization of a double-stranded DNA mycovirus infecting the aquatic fungus, ''Rhizidiomyces''. Virology 130(1):21–28 (fungi and hyphochytridiomy ...
''


Group II: single-stranded DNA viruses

The second Baltimore group contains viruses that have a single-stranded DNA (ssDNA) genome. ssDNA viruses have the same manner of transcription as dsDNA viruses. Because the genome is single-stranded, however, it is first made into a double-stranded form by a
DNA polymerase A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to crea ...
upon entering a host cell. mRNA is then synthesized from the double-stranded form. The double-stranded form of ssDNA viruses may be produced either directly after entry into a cell or as a consequence of replication of the viral genome. Eukaryotic ssDNA viruses are replicated in the nucleus. Most ssDNA viruses contain circular genomes that are replicated via rolling circle replication (RCR). ssDNA RCR is initiated by an
endonuclease Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonuclease ...
that bonds to and cleaves the positive strand, allowing a DNA polymerase to use the negative strand as a template for replication. Replication progresses in a loop around the genome by means of extending the 3′-end of the positive strand, displacing the prior positive strand, and the endonuclease cleaves the positive strand again to create a standalone genome that is ligated into a circular loop. The new ssDNA may be packaged into virions or replicated by a DNA polymerase to form a double-stranded form for transcription or continuation of the replication cycle. Parvoviruses contain linear ssDNA genomes that are replicated via
rolling hairpin replication Rolling hairpin replication (RHR) is a unidirectional, strand displacement form of DNA replication used by parvoviruses, a group of viruses that constitute the family '' Parvoviridae''. Parvoviruses have linear, single-stranded DNA (ssDNA) genomes ...
(RHR), which is similar to RCR. Parvovirus genomes have hairpin loops at each end of the genome that repeatedly unfold and refold during replication to change the direction of DNA synthesis to move back and forth along the genome, producing numerous copies of the genome in a continuous process. Individual genomes are then excised from this molecule by the viral endonuclease. For parvoviruses, either the positive or negative sense strand may be packaged into capsids, varying from virus to virus. Nearly all ssDNA viruses have positive sense genomes, but a few exceptions and peculiarities exist. The family '' Anelloviridae'' is the only ssDNA family whose members have negative sense genomes, which are circular. Parvoviruses, as previously mentioned, may package either the positive or negative sense strand into virions. Lastly, bidnaviruses package both the positive and negative linear strands. In any case, the sense of ssDNA viruses, unlike for ssRNA viruses, is not sufficient to separate ssDNA viruses into two groups since all ssDNA viral genomes are converted to dsDNA forms prior to transcription and replication. ssDNA viruses are classified into one of the four realms and include several families that are unassigned to a realm: *In ''Monodnaviria'', all members except viruses in ''Papovaviricetes'' are ssDNA viruses. *The unassigned families '' Anelloviridae'' and '' Spiraviridae'' are ssDNA virus families. *Viruses in the family '' Finnlakeviridae'' contain ssDNA genomes. ''Finnlakeviridae'' is unassigned to a realm but is a proposed member of ''Varidnaviria''.


RNA viruses

RNA viruses have genomes made of ribonucleic acid (RNA) and comprise three groups: double-stranded RNA (dsRNA) viruses, positive sense single-stranded RNA (+ssRNA) viruses, and negative sense single-stranded RNA (-ssRNA) viruses. The majority of RNA viruses are classified in the kingdom ''
Orthornavirae ''Orthornavirae'' is a kingdom of viruses that have genomes made of ribonucleic acid (RNA), those genomes encoding an RNA-dependent RNA polymerase (RdRp). The RdRp is used to transcribe the viral RNA genome into messenger RNA (mRNA) and to repli ...
'' in the realm ''
Riboviria ''Riboviria'' is a realm of viruses that includes all viruses that use a homologous RNA-dependent polymerase for replication. It includes RNA viruses that encode an RNA-dependent RNA polymerase, as well as reverse-transcribing viruses (with e ...
''. The exceptions are generally
viroid Viroids are small single-stranded, circular RNAs that are infectious pathogens. Unlike viruses, they have no protein coating. All known viroids are inhabitants of angiosperms (flowering plants), and most cause diseases, whose respective economi ...
s and other subviral agents. Some of the latter category, such as the hepatitis D virus, are classified in the realm '' Ribozyviria''.


Group III: double-stranded RNA viruses

The third Baltimore group contains viruses that have a double-stranded RNA (dsRNA) genome. After entering a host cell, the dsRNA genome is transcribed to mRNA from the negative strand by the viral RNA-dependent RNA polymerase (RdRp). The mRNA may be used for translation or replication. Single-stranded mRNA is replicated to form the dsRNA genome. The 5′-end of the genome may be naked, capped, or covalently bound to a viral protein. dsRNA is not a molecule made by cells, so cellular life has evolved antiviral systems to detect and inactivate viral dsRNA. To counteract this, many dsRNA genomes are constructed inside of capsids, thereby avoiding detection inside of the host cell's cytoplasm. mRNA is forced out from the capsid in order to be translated or to be translocated from a mature capsid to a progeny capsid. While dsRNA viruses typically have capsids, viruses in the families ''
Amalgaviridae ''Amalgaviridae'' is a family of double-stranded RNA viruses. Member viruses infect plants and are transmitted vertically via seeds. The name derives from ''amalgam'' (blend, mix) which refers to amalgaviruses possessing characteristics of both ...
'' and ''
Endornaviridae ''Endornaviridae'' is a family of viruses. Plants, fungi, and oomycetes serve as natural hosts. There are 31 species in this family, assigned to 2 genera (''Alphaendornavirus'' and ''Betaendornavirus''). Members of ''Alphaendornavirus'' infect ...
'' have not been observed to form virions and as such apparently lack capsids. Endornaviruses are also unusual in that unlike other RNA viruses, they possess a single, long
open reading frame In molecular biology, open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible readi ...
(ORF), or translatable portion, and a site-specific nick in the 5′ region of the positive strand. dsRNA viruses are classified into two phyla within the kingdom ''Orthornavirae'' of the realm ''Riboviria'': * All viruses in '' Duplornaviricota'' are dsRNA viruses. * In '' Pisuviricota'', all members of the class '' Duplopiviricetes'' are dsRNA viruses.


Group IV: positive sense single-stranded RNA viruses

The fourth Baltimore group contains viruses that have a positive sense single-stranded RNA (+ssRNA) genome. For +ssRNA viruses, the genome functions as mRNA, so no transcription is required for translation. +ssRNA viruses will also, however, produce positive sense copies of the genome from negative sense strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. The 5′-end may be naked, capped, or covalently bound to a viral protein, and the 3′-end may be naked or polyadenylated. Many +ssRNA viruses are able to have only a portion of their genome transcribed. Typically, subgenomic RNA (sgRNA) strands are used for translation of structural and movement proteins needed during intermediate and late stages of infection. sgRNA transcription may occur by commencing RNA synthesis within the genome rather than from the 5′-end, by stopping RNA synthesis at specific sequences in the genome, or by, as a part of both prior methods, synthesizing leader sequences from the viral RNA that are then attached to sgRNA strands. Because replication is required for sgRNA synthesis, RdRp is always translated first. Because the process of replicating the viral genome produces intermediate dsRNA molecules, +ssRNA viruses can be targeted by the host cell's immune system. To avoid detection, +ssRNA viruses replicate in membrane-associated vesicles that are used as replication factories. From there, only viral +ssRNA, which may be mRNA, enters the main cytoplasmic area of the cell. +ssRNA viruses can be subdivided between those that have polycistronic mRNA, which encodes a polyprotein that is cleaved to form multiple mature proteins, and those that produce subgenomic mRNAs and therefore undergo two or more rounds of translation. +ssRNA viruses are included in three phyla in the kingdom ''Orthornavirae'' in the realm ''Riboviria'': *All viruses in ''
Lenarviricota ''Lenarviricota'' is a phylum of RNA viruses that includes all positive-strand RNA viruses that infect prokaryotes. Some members also infect eukaryotes. Most of these viruses do not have capsids, except for the genus '' Ourmiavirus''. The name of ...
'' are +ssRNA viruses. *All viruses in '' Pisuviricota'' are +ssRNA viruses, excluding the class '' Duplopiviricetes'', whose members have dsRNA genomes. *All viruses in '' Kitrinoviricota'' are +ssRNA viruses.


Group V: negative sense single-stranded RNA viruses

The fifth Baltimore group contains viruses that have a negative sense, single-stranded RNA (-ssRNA) genome. mRNA, which is positive sense, is transcribed directly from the negative sense genome. The first process for -ssRNA transcription involves RdRp binding to a leader sequence on the 3′ end of the genome, transcribing a 5′ triphosphate-leader RNA that is capped, then stopping and restarting on a transcription signal which is capped, continuing until a stop signal is reached. The second manner is similar but instead of synthesizing a cap, RdRp may make use of
cap snatching The first step of transcription for some negative, single-stranded RNA viruses is cap snatching, in which the first 10 to 20 residues of a host cell RNA are removed (snatched) and used as the 5′ cap and primer to initiate the synthesis of the na ...
, whereby a short sequence of host cell mRNA is taken and used as the 5′ cap of the viral mRNA. Genomic -ssRNA is replicated from the positive sense antigenome in a similar manner as transcription, except in reverse using the antigenome as a template for the genome. RdRp moves from the 3′-end to the 5′-end of the antigenome and ignores all transcription signals when synthesizing genomic -ssRNA. Various -ssRNA viruses use special mechanisms for transcription. The manner of producing the polyA tail may be via polymerase stuttering, during which RdRp transcribes an
adenine Adenine () ( symbol A or Ade) is a nucleobase (a purine derivative). It is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The three others are guanine, cytosine and thymine. Its deriv ...
from
uracil Uracil () (symbol U or Ura) is one of the four nucleobases in the nucleic acid RNA. The others are adenine (A), cytosine (C), and guanine (G). In RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced b ...
and then moves back in the RNA sequence with the mRNA to transcribe it again, continuing this process numerous times until hundreds of adenines have been added to the 3′-end of the mRNA. Additionally, some -ssRNA viruses are ambisense, as both the positive and negative strands separately encode viral proteins, and these viruses produce two separate mRNA strands: one directly from the genome and one from a complementary strand. -ssRNA viruses can be subdivided informally between those that have nonsegmented and segmented genomes. Nonsegmented -ssRNA viruses replicate in the cytoplasm, and segmented -ssRNA viruses replicate in the nucleus. During transcription, the RdRp produces one monocistronic mRNA strand from each segment of the genome. All -ssRNA viruses are classified in the phylum '' Negarnaviricota'' in the kingdom ''Orthornavirae'' in the realm ''Riboviria''. ''Negarnaviricota'' only contains -ssRNA viruses, so "-ssRNA virus" is synonymous with ''Negarnaviricota''. ''Negarnaviricota'' is divided into two subphyla: ''Haploviricotina'', whose members synthesize a cap structure on viral mRNA required for protein synthesis, and ''Polyploviricotina'', whose members instead obtain caps on mRNA via cap snatching.


Reverse transcribing viruses

Reverse transcribing (RT) viruses have genomes made of either DNA or RNA and replicate via reverse transcription. Two groups of reverse transcribing viruses exist: single-stranded RNA-RT (ssRNA-RT) viruses, and double-stranded DNA-RT (dsDNA-RT) viruses. Reverse transcribing viruses are classified in the kingdom ''Pararnavirae'' in the realm ''Riboviria''.


Group VI: single-stranded RNA viruses with a DNA intermediate

The sixth Baltimore group contains viruses that have a (positive-sense) single-stranded RNA genome that has a DNA intermediate ((+)ssRNA-RT) in its replication cycle.ssRNA-RT viruses are often called retroviruses, although this term is also used to refer to any reverse transcribing virus as well as specifically to viruses in the ssRNA-RT family ''
Retroviridae A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptase ...
''.
ssRNA-RT viruses are transcribed in the same manner as DNA viruses, but their linear genomes are first converted to a dsDNA form through a process called
reverse transcription A reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genom ...
. The viral
reverse transcriptase A reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genom ...
enzyme synthesizes a DNA strand from the ssRNA strand, and the RNA strand is degraded and replaced with a DNA strand to create a dsDNA genome. The genome is then integrated into the DNA of the host cell, where it is now called a
provirus A provirus is a virus genome that is integrated into the DNA of a host cell. In the case of bacterial viruses (bacteriophages), proviruses are often referred to as prophages. However, proviruses are distinctly different from prophages and these te ...
. The host cell's
RNA polymerase II RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of euka ...
then transcribes RNA in the nucleus from the proviral DNA. Some of this RNA may become mRNA whereas other strands will become copies of the viral genome for replication. ssRNA-RT viruses are all included in the class '' Revtraviricetes'', phylum ''Arterviricota'', kingdom ''Pararnavirae'' of the realm ''Riboviria''. Excluding ''Caulimoviridae'', which belongs to Group VII, all members of the ''Revtraviricetes'' order ''
Ortervirales ''Ortervirales'' is an order that contains all accepted species of single-stranded RNA viruses that replicate through a DNA intermediate (Group VI) and all accepted species of double-stranded DNA viruses (except '' Hepadnaviridae'') that replic ...
'' are ssRNA-RT viruses.


Group VII: double-stranded DNA viruses with an RNA intermediate

The seventh Baltimore group contains viruses that have a double-stranded DNA genome that has an RNA intermediate (dsDNA-RT) in its replication cycle. dsDNA-RT viruses have a gap in one strand, which is repaired to create a complete dsDNA genome prior to transcription. dsDNA-RT viruses are transcribed in the same manner as dsDNA viruses, but make use of reverse transcription to replicate their circular genome while it is still in the capsid. The host cell's RNA polymerase II transcribes RNA strands from the genome in the cytoplasm, and the genome is replicated from these RNA strands. The dsDNA genome is produced from pregenomic RNA strands via the same general mechanism as ssRNA-RT viruses, but with replication occurring in a loop around the circular genome. After replication, the dsDNA genome may be packed or sent to the nucleus for further rounds of transcription. dsDNA-RT viruses are, like ssRNA-RT, all included in the class ''Revtraviricetes''. Two families of dsDNA-RT viruses are recognized: ''
Caulimoviridae ''Caulimoviridae'' is a family of viruses infecting plants. There are 94 species in this family, assigned to 11 genera. Viruses belonging to the family ''Caulimoviridae'' are termed double-stranded DNA (dsDNA) reverse-transcribing viruses (or pa ...
'', which belongs to the order ''Ortervirales'', and '' Hepadnaviridae'', which is the sole family in the order ''Blubervirales''.


Multi-group characteristics

A number of characteristics of viruses are not directly associated with Baltimore classification but nonetheless closely correspond to multiple, specific Baltimore groups. This includes alternative splicing during transcription, whether the viral genome is segmented, the host range of viruses, whether the genome is linear or circular, and different methods of translating viral mRNA.


Alternative splicing

Alternative splicing Alternative splicing, or alternative RNA splicing, or differential splicing, is an alternative splicing process during gene expression that allows a single gene to code for multiple proteins. In this process, particular exons of a gene may be i ...
is a mechanism by which different proteins can be produced from a single gene by means of using alternative splicing sites to produce different mRNAs. It is found in various DNA, -ssRNA, and reverse transcribing viruses. Viruses may make use of alternative splicing solely to produce multiple proteins from a single pre-mRNA strand or for other specific purposes. For certain viruses, including the families ''
Orthomyxoviridae ''Orthomyxoviridae'' (from Greek ὀρθός, ''orthós'' 'straight' + μύξα, ''mýxa'' 'mucus') is a family of negative-sense RNA viruses. It includes seven genera: ''Alphainfluenzavirus'', ''Betainfluenzavirus'', '' Gammainfluenzavirus'', ...
'' and '' Papillomaviridae'', alternative splicing acts as a way to regulate early and late
gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. T ...
during different stages of infection. Herpesviruses use it as a potential anti-host defense mechanism to prevent synthesis of specific antiviral proteins. Furthermore, in addition to alternative splicing, because cellular unspliced RNA cannot be transported out of the nucleus, hepadnaviruses and
retrovirus A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptas ...
es contain their own proteins for exporting their unspliced genomic RNA out of the nucleus.


Genome segmentation

Viral genomes can exist in a single, or monopartite, segment, or they may be split into more than one molecule, called multipartite. For monopartite viruses, all genes are on the single segment of the genome. Multipartite viruses typically package their genomes into a single virion so that the whole genome is in one virus particle, and the separate segments contain different genes. Monopartite viruses are found in all Baltimore groups, whereas multipartite viruses are usually RNA viruses. This is because most multipartite viruses infect plants or fungi, which are eukaryotes, and most eukaryotic viruses are RNA viruses. The family '' Pleolipoviridae'' varies as some viruses are monopartite ssDNA while others are bipartite with one segment being ssDNA and the other dsDNA. Viruses in the ssDNA
plant virus Plant viruses are viruses that affect plants. Like all other viruses, plant viruses are obligate intracellular parasites that do not have the molecular machinery to replicate without a host. Plant viruses can be pathogenic to higher plants. ...
family '' Geminiviridae'' likewise vary between being monopartite and bipartite.


Host range

Different Baltimore groups tend to be found within different branches of cellular life. In prokaryotes, the large majority of viruses are dsDNA viruses, and a significant minority are ssDNA viruses. Prokaryotic RNA viruses, in contrast, are relatively rare. Most eukaryotic viruses, including most animal and plant viruses, are RNA viruses, although eukaryotic DNA viruses are also common. By group, the vast majority of dsDNA viruses infect prokaryotes, ssDNA viruses are found in all three domains of life, dsRNA and +ssRNA viruses are primarily found in eukaryotes but also in bacteria, and -ssRNA and reverse transcribing viruses are only found in eukaryotes.


Linear vs circular genomes

Viral genomes may be either linear with ends or circular in a loop. Whether a virus has a linear or circular genome varies from group to group. A significant percentage of dsDNA viruses are both, ssDNA viruses are primarily circular, RNA viruses and ssRNA-RT viruses are typically linear, and dsDNA-RT viruses are typically circular.




In the dsDNA family ''
Sphaerolipoviridae This category is for articles about virus families (or redirects to such articles). There should be no subcategories. families Family (from la, familia) is a group of people related either by consanguinity (by recognized birth) or affinity (b ...
'', and in the family ''Pleolipoviridae'', viruses contain both linear and circular genomes, varying from genus to genus.


RNA editing

RNA editing is used by various ssRNA viruses to produce different proteins from a single gene. This can be done via polymerase slippage during transcription or by post-transcriptional editing. In polymerase slippage, the RNA polymerase slips one nucleotide back during transcription, inserting a nucleotide not included in the template strand. Editing of a genomic template would impair gene expression, so RNA editing is only done during and after transcription. For ebola viruses, RNA editing improves the ability to adapt to their hosts. Alternative splicing differs from RNA editing in that alternative splicing does not change the mRNA sequence like RNA editing but instead changes the coding capacity of an mRNA sequence as a result of alternative splicing sites. The two mechanisms otherwise have the same result: multiple proteins are expressed from a single gene.


Translation

Translation Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...
is the process by which
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
s are synthesized from mRNA by
ribosome Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to fo ...
s. Baltimore groups do not directly pertain to the translation of viral proteins, but various atypical types of translation used by viruses are usually found within specific Baltimore groups: *Non-canonical translation initiation: ** Viral initiation of translation: used primarily by +ssRNA and ssRNA-RT viruses, various viruses have evolved mechanisms to initiate translation, such as having internal ribosomal entry sites to allow for cap-independent translation, having downstream hairpin loops that allow for cap-dependent translation in the absence of an eIF2 initiation factor, and initiation at a CUG or other start codon with a
leucine Leucine (symbol Leu or L) is an essential amino acid that is used in the biosynthesis of proteins. Leucine is an α-amino acid, meaning it contains an α- amino group (which is in the protonated −NH3+ form under biological conditions), an α- ...
amino acid. ** Leaky scanning: used by various viruses in all Baltimore groups, the 40S ribosomal subunit may scan through a start codon, thereby skipping an ORF, only initiating translation with the 60S subunit at a subsequent start codon. **
Ribosomal shunting Ribosome shunting is a mechanism of translation initiation in which ribosomes bypass, or "shunt over", parts of the 5' untranslated region to reach the start codon. However, a benefit of ribosomal shunting is that it can translate backwards allowin ...
: used by various dsDNA, +ssRNA, -ssRNA, ssRNA-RT, a dsDNA-RT viruses, ribosomes will start scanning from a 5′-cap structure then bypass a leader structure in the mRNA, initiation translation downstream from the leader sequence. ** Termination-reinitiation: used by some dsRNA and +ssRNA viruses, ribosomes may translate an ORF, but following termination of translation of that ORF, a proportion of 40S subunits of the ribosome remain attached to the mRNA as a way to reinitiate translation of a subsequent ORF. *Non-canonical elongation and termination of translation: ** Ribosomal frameshifting: used by various dsDNA, dsRNA, +ssRNA, and ssRNA-RT viruses, produces merged proteins from overlapping ORFs. This is executed simply by ribosomes slipping one
nucleobase Nucleobases, also known as ''nitrogenous bases'' or often simply ''bases'', are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basi ...
forward or backward during translation. ** Suppression of termination: also called stop-codon readthrough, used by various dsRNA, +ssRNA, and ssRNA-RT viruses, certain viruses contain codons in their mRNA that would normally signal for termination of translation upon being recognized by a
release factor A release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence. They are named so because they release new peptides from the ribosome. Background During t ...
but are instead partially recognized by
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino ...
during translation, which allows for continued translation up to the next stop codon in order to produce an extended end of the viral protein. In viruses, this is often used to express replicase enzymes. ** Ribosomal skipping: also called stop-carry on, used by various dsRNA and +ssRNA viruses, a viral peptide, or amino acid sequence, may prevent a ribosome from covalently linking a new inserted amino acid, which blocks further translation. Consequently, the polyprotein is co-translationally cleaved, and a new amino acid sequence is started, leading to the production of two individual proteins from one ORF.


History

Baltimore classification was proposed in 1971 by virologist
David Baltimore David Baltimore (born March 7, 1938) is an American biologist, university administrator, and 1975 Nobel laureate in Physiology or Medicine. He is President Emeritus and Distinguished Professor of Biology at the California Institute of Tec ...
in a paper titled ''Expression of Animal Virus Genomes''. It initially contained the first six groups but was later expanded to include group VII. Because of the utility of Baltimore classification, it has come to be used alongside standard virus taxonomy, which is based on evolutionary relationships and governed by the
International Committee on Taxonomy of Viruses The International Committee on Taxonomy of Viruses (ICTV) authorizes and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to ap ...
(ICTV). From the 1990s to the 2010s, virus taxonomy used a 5-rank system ranging from order to species with Baltimore classification used in conjunction. Outside of the ICTV's official framework, various supergroups of viruses joining together different families and orders were created over time based on increasing evidence of deeper evolutionary relations. Consequently, in 2016, the ICTV began to consider establishing ranks higher than order as well as how the Baltimore groups would be treated among higher taxa. In two votes in 2018 and 2019, a 15-rank system ranging from
realm A realm is a community or territory over which a sovereign rules. The term is commonly used to describe a monarchical or dynastic state. A realm may also be a subdivision within an empire, if it has its own monarch, e.g. the German Empire. Et ...
to species was established by the ICTV. As part of this, the Baltimore groups for RNA viruses and RT viruses were incorporated into formal taxa. In 2018, the realm ''Riboviria'' was established and initially included the three RNA virus groups. A year later, ''Riboviria'' was expanded to also include both RT groups. Within the realm, RT viruses are included in the kingdom ''Pararnavirae'' and RNA viruses in the kingdom ''Orthornavirae''. Furthermore, the three Baltimore groups for RNA viruses are used as defining characteristics of the phyla in ''Orthornavirae''. Unlike RNA viruses and RT viruses, DNA viruses have not been united under a single realm but are instead dispersed across four realms and various taxa that are not assigned to a realm. The realms ''Adnaviria'' and ''Duplodnaviria'' exclusively contains dsDNA viruses, ''Monodnaviria'' primarily contains ssDNA viruses but also contains dsDNA viruses, and ''Varidnaviria'' exclusively contains dsDNA viruses, although some proposed members of ''Varidnaviria'', namely the family '' Finnlakeviridae'', are ssDNA viruses.


Explanatory notes


References


Citations


General bibliography

* * * * {{DEFAULTSORT:Baltimore Classification * Systems of virus taxonomy Viruses