Reverse transcriptase (RNA-dependent DNA polymerase)
Crystallographic structure of HIV-1
reverse transcriptase where the two subunits p51 and p66 are colored
and the active sites of polymerase and nuclease are highlighted.
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 genomes, by retrotransposon mobile genetic elements to proliferate within the host genome, and by eukaryotic cells to extend the telomeres at the ends of their linear chromosomes. Contrary to a widely held belief, the process does not violate the flows of genetic information as described by the classical central dogma, as transfers of information from RNA to DNA are explicitly held possible.
Retroviral RT has three sequential biochemical activities: RNA-dependent DNA polymerase activity, ribonuclease H
(RNase H), and DNA-dependent DNA polymerase activity. Collectively,
these activities enable the enzyme to convert single-stranded RNA into
double-stranded cDNA. In retroviruses and retrotransposons, this cDNA
can then integrate into the host genome, from which new RNA copies can
be made via host-cell transcription. The same sequence of reactions is widely used in the laboratory to convert RNA to DNA for use in molecular cloning, RNA sequencing, polymerase chain reaction (PCR), or genome analysis.
HIV-1 reverse transcriptase from human immunodeficiency virus type 1 (PDB: 1HMV) has two subunits, which have respective molecular weights of 66 and 51 kDas.
Reverse transcriptase is shown with its finger, palm, and thumb regions. The catalytic amino acids of the RNase H active site and the polymerase active site are shown in ball-and-stick form.
The enzymes are encoded and used by viruses that use reverse
transcription as a step in the process of replication.
Reverse-transcribing RNA viruses, such as retroviruses, use the enzyme to reverse-transcribe their RNA genomes into DNA, which is then integrated into the host genome and replicated along with it. Reverse-transcribing DNA viruses, such as the hepadnaviruses,
can allow RNA to serve as a template in assembling and making DNA
strands. HIV infects humans with the use of this enzyme. Without reverse
transcriptase, the viral genome would not be able to incorporate into
the host cell, resulting in failure to replicate.
Process of reverse transcription or retrotranscription
Reverse transcriptase creates double-stranded DNA from an RNA template.
In virus species with reverse transcriptase lacking DNA-dependent
DNA polymerase activity, creation of double-stranded DNA can possibly
be done by host-encoded DNA polymerase δ, mistaking the viral DNA-RNA for a primer and synthesizing a double-stranded DNA by a similar mechanism as in primer removal, where the newly synthesized DNA displaces the original RNA template.
The process of reverse transcription, also called
retrotranscription or retrotras, is extremely error-prone, and it is
during this step that mutations may occur. Such mutations may cause drug resistance.
Retroviral reverse transcription
Mechanism of reverse transcription in HIV. Step numbers will not match up.
Retroviruses, also referred to as class VI ssRNA-RT viruses, are RNA reverse-transcribing viruses with a DNA intermediate. Their genomes consist of two molecules of positive-sense single-stranded RNA with a 5' cap and 3' polyadenylated tail. Examples of retroviruses include the human immunodeficiency virus (HIV) and the human T-lymphotropic virus (HTLV). Creation of double-stranded DNA occurs in the cytosol as a series of these steps:
LysyltRNA acts as a primer and hybridizes to a complementary part of the virus RNA genome called the primer binding site or PBS.
Reverse transcriptase then adds DNA nucleotides onto the 3' end of the primer, synthesizing DNA complementary to the U5 (non-coding region) and R region (a direct repeat found at both ends of the RNA molecule) of the viral RNA.
A domain on the reverse transcriptase enzyme called RNAse H degrades the U5 and R regions on the 5’ end of the RNA.
The tRNA primer then "jumps" to the 3’ end of the viral genome, and
the newly synthesised DNA strands hybridizes to the complementary R
region on the RNA.
The complementary DNA (cDNA) added in (2) is further extended.
The majority of viral RNA is degraded by RNAse H, leaving only the PP sequence.
Synthesis of the second DNA strand begins, using the remaining PP fragment of viral RNA as a primer.
The tRNA primer leaves and a "jump" happens. The PBS from the second
strand hybridizes with the complementary PBS on the first strand.
Both strands are extended to form a complete double-stranded DNA
copy of the original viral RNA genome, which can then be incorporated
into the host's genome by the enzyme integrase.
Creation of double-stranded DNA also involves strand transfer,
in which there is a translocation of short DNA product from initial
RNA-dependent DNA synthesis to acceptor template regions at the other
end of the genome, which are later reached and processed by the reverse
transcriptase for its DNA-dependent DNA activity.
Retroviral RNA is arranged in 5’ terminus to 3’ terminus. The site where the primer
is annealed to viral RNA is called the primer-binding site (PBS). The
RNA 5’end to the PBS site is called U5, and the RNA 3’ end to the PBS is
called the leader. The tRNA primer is unwound between 14 and 22 nucleotides
and forms a base-paired duplex with the viral RNA at PBS. The fact that
the PBS is located near the 5’ terminus of viral RNA is unusual because
reverse transcriptase synthesize DNA from 3’ end of the primer in the
5’ to 3’ direction (with respect to the newly synthesized DNA strand).
Therefore, the primer and reverse transcriptase must be relocated to 3’
end of viral RNA. In order to accomplish this reposition, multiple steps
and various enzymes including DNA polymerase, ribonuclease H(RNase H) and polynucleotide unwinding are needed.
The HIV reverse transcriptase also has ribonuclease activity that degrades the viral RNA during the synthesis of cDNA, as well as DNA-dependent DNA polymerase activity that copies the sense cDNA strand into an antisense DNA to form a double-stranded viral DNA intermediate (vDNA).
In cellular life
Self-replicating stretches of eukaryotic genomes known as retrotransposons
utilize reverse transcriptase to move from one position in the genome
to another via an RNA intermediate. They are found abundantly in the
genomes of plants and animals. Telomerase is another reverse transcriptase found in many eukaryotes, including humans, which carries its own RNA template; this RNA is used as a template for DNA replication.
Initial reports of reverse transcriptase in prokaryotes came as far back as 1971 in France (Beljanski et al., 1971a, 1972) and a few years later in the USSR (Romashchenko 1977). These have since been broadly described as part of bacterial Retrons, distinct sequences that code for reverse transcriptase, and are used in the synthesis of msDNA. In order to initiate synthesis of DNA, a primer is needed. In bacteria, the primer is synthesized during replication.
Valerian Dolja of Oregon State argues that viruses, due to their
diversity, have played an evolutionary role in the development of
cellular life, with reverse transcriptase playing a central role.
Structure
The reverse transcriptase employs a "right hand" structure similar to that found in other viral nucleic acid polymerases. In addition to the transcription function, retroviral reverse transcriptases have a domain belonging to the RNase H
family, which is vital to their replication. By degrading the RNA
template, it allows the other strand of DNA to be synthesized. Some fragments from the digestion also serve as the primer for the DNA polymerase (either the same enzyme or a host protein), responsible for making the other (plus) strand.
Replication fidelity
There
are three different replication systems during the life cycle of a
retrovirus. The first process is the reverse transcriptase synthesis of
viral DNA from viral RNA, which then forms newly made complementary DNA
strands. The second replication process occurs when host cellular DNA
polymerase replicates the integrated viral DNA. Lastly, RNA polymerase
II transcribes the proviral DNA into RNA, which will be packed into
virions. Mutation can occur during one or all of these replication
steps.
Reverse transcriptase has a high error rate when transcribing RNA into DNA since, unlike most other DNA polymerases, it has no proofreading ability. This high error rate allows mutations
to accumulate at an accelerated rate relative to proofread forms of
replication. The commercially available reverse transcriptases produced
by Promega are quoted by their manuals as having error rates in the range of 1 in 17,000 bases for AMV and 1 in 30,000 bases for M-MLV.
Other than creating single-nucleotide polymorphisms, reverse transcriptases have also been shown to be involved in processes such as transcript fusions, exon shuffling and creating artificial antisense transcripts. It has been speculated that this template switching activity of reverse transcriptase, which can be demonstrated completely in vivo, may have been one of the causes for finding several thousand unannotated transcripts in the genomes of model organisms.
Template switching
Two RNAgenomes are packaged into each retrovirus particle, but, after an infection, each virus generates only one provirus.
After infection, reverse transcription is accompanied by template
switching between the two genome copies (copy choice recombination).
There are two models that suggest why RNA transcriptase switches
templates. The first, the forced copy-choice model, proposes that
reverse transcriptase changes the RNA template when it encounters a
nick, implying that recombination is obligatory to maintaining virus
genome integrity. The second, the dynamic choice model, suggests that
reverse transcriptase changes templates when the RNAse function and the
polymerase function are not in sync rate-wise, implying that
recombination occurs at random and is not in response to genomic damage.
A study by Rawson et al. supported both models of recombination. From 5 to 14 recombination events per genome occur at each replication cycle.
Template switching (recombination) appears to be necessary for
maintaining genome integrity and as a repair mechanism for salvaging
damaged genomes.
Applications
The molecular structure of zidovudine (AZT), a drug used to inhibit reverse transcriptase
As HIV
uses reverse transcriptase to copy its genetic material and generate new
viruses (part of a retrovirus proliferation circle), specific drugs
have been designed to disrupt the process and thereby suppress its
growth. Collectively, these drugs are known as reverse-transcriptase inhibitors and include the nucleoside and nucleotide analogues zidovudine (trade name Retrovir), lamivudine (Epivir) and tenofovir (Viread), as well as non-nucleoside inhibitors, such as nevirapine (Viramune).
Reverse transcriptase is commonly used in research to apply the polymerase chain reaction technique to RNA in a technique called reverse transcription polymerase chain reaction (RT-PCR). The classical PCR technique can be applied only to DNA strands, but, with the help of reverse transcriptase, RNA can be transcribed into DNA, thus making PCR analysis of RNA molecules possible. Reverse transcriptase is used also to create cDNA libraries from mRNA.
The commercial availability of reverse transcriptase greatly improved
knowledge in the area of molecular biology, as, along with other enzymes, it allowed scientists to clone, sequence, and characterise RNA.
Reverse transcriptase has also been employed in insulin
production. By inserting eukaryotic mRNA for insulin production along
with reverse transcriptase into bacteria, the mRNA could be inserted
into the prokaryote's genome. Large amounts of insulin can then be
created, sidestepping the need to harvest pig pancreas and other such
traditional sources. Directly inserting eukaryotic DNA into bacteria
would not work because it carries introns,
so would not translate successfully using the bacterial ribosomes.
Processing in the eukaryotic cell during mRNA production removes these
introns to provide a suitable template. Reverse transcriptase converts
this edited RNA back into DNA so it could be incorporated in the genome.
The name "coronavirus" is derived from Latin corona, meaning "crown" or "wreath", itself a borrowing from Greekκορώνηkorṓnē, "garland, wreath". The name was coined by June Almeida and David Tyrrell who first observed and studied human coronaviruses. The word was first used in print in 1968 by an informal group of virologists in the journal Nature to designate the new family of viruses. The name refers to the characteristic appearance of virions (the infective form of the virus) by electron microscopy, which have a fringe of large, bulbous surface projections creating an image reminiscent of the solar corona or halo. This morphology is created by the viral spike peplomers, which are proteins on the surface of the virus.
The scientific name Coronavirus was accepted as a genus name by the International Committee for the Nomenclature of Viruses (later renamed International Committee on Taxonomy of Viruses) in 1971. As the number of new species increased, the genus was split into four genera, namely Alphacoronavirus, Betacoronavirus, Deltacoronavirus, and Gammacoronavirus in 2009. The common name coronavirus is used to refer to any member of the subfamily Orthocoronavirinae. As of 2020, 45 species are officially recognised.
The earliest reports of a coronavirus infection in animals occurred
in the late 1920s, when an acute respiratory infection of domesticated
chickens emerged in North America. Arthur Schalk and M.C. Hawn in 1931 made the first detailed report which described a new respiratory infection of chickens in North Dakota. The infection of new-born chicks was characterized by gasping and listlessness with high mortality rates of 40–90%. Leland David Bushnell and Carl Alfred Brandly isolated the virus that caused the infection in 1933. The virus was then known as infectious bronchitis virus (IBV). Charles D. Hudson and Fred Robert Beaudette cultivated the virus for the first time in 1937.
The specimen came to be known as the Beaudette strain. In the late
1940s, two more animal coronaviruses, JHM that causes brain disease
(murine encephalitis) and mouse hepatitis virus (MHV) that causes hepatitis in mice were discovered. It was not realized at the time that these three different viruses were related.
Human coronaviruses were discovered in the 1960s using two different methods in the United Kingdom and the United States. E.C. Kendall, Malcolm Bynoe, and David Tyrrell working at the Common Cold Unit of the British Medical Research Council collected a unique common cold virus designated B814 in 1961. The virus could not be cultivated using standard techniques which had successfully cultivated rhinoviruses, adenoviruses and other known common cold viruses. In 1965, Tyrrell and Bynoe successfully cultivated the novel virus by serially passing it through organ culture of human embryonictrachea. The new cultivating method was introduced to the lab by Bertil Hoorn. The isolated virus when intranasally inoculated into volunteers caused a cold and was inactivated by ether which indicated it had a lipid envelope. Dorothy Hamre and John Procknow at the University of Chicago isolated a novel cold from medical students in 1962. They isolated and grew the virus in kidney tissue culture, designating it 229E. The novel virus caused a cold in volunteers and, like B814, was inactivated by ether.
Transmission electron micrograph of organ cultured coronavirus OC43
Scottish virologist June Almeida at St Thomas' Hospital in London, collaborating with Tyrrell, compared the structures of IBV, B814 and 229E in 1967. Using electron microscopy the three viruses were shown to be morphologically related by their general shape and distinctive club-like spikes. A research group at the National Institute of Health
the same year was able to isolate another member of this new group of
viruses using organ culture and named one of the samples OC43 (OC for
organ culture).
Like B814, 229E, and IBV, the novel cold virus OC43 had distinctive
club-like spikes when observed with the electron microscope.
The IBV-like novel cold viruses were soon shown to be also morphologically related to the mouse hepatitis virus. This new group of viruses were named coronaviruses after their distinctive morphological appearance. Human coronavirus 229E and human coronavirus OC43 continued to be studied in subsequent decades. The coronavirus strain B814 was lost. It is not known which present human coronavirus it was. Other human coronaviruses have since been identified, including SARS-CoV in 2003, HCoV NL63 in 2003, HCoV HKU1 in 2004, MERS-CoV in 2013, and SARS-CoV-2 in 2019. There have also been a large number of animal coronaviruses identified since the 1960s.
Microbiology
Structure
Structure of a coronavirus
Coronaviruses are large, roughly spherical particles with unique surface projections. Their size is highly variable with average diameters of 80 to 120 nm. Extreme sizes are known from 50 to 200 nm in diameter. The total molecular mass is on average 40,000 kDa. They are enclosed in an envelope embedded with a number of protein molecules. The lipid bilayer envelope, membrane proteins, and nucleocapsid protect the virus when it is outside the host cell.
The viral envelope is made up of a lipid bilayer in which the membrane (M), envelope (E) and spike (S) structural proteins are anchored. The molar ratio of E:S:M in the lipid bilayer is approximately 1:20:300.
The E and M protein are the structural proteins that combined with the
lipid bilayer to shape the viral envelope and maintain its size. S proteins are needed for interaction with the host cells. But human coronavirus NL63 is peculiar in that its M protein has the binding site for the host cell, and not its S protein.
The diameter of the envelope is 85 nm. The envelope of the virus in
electron micrographs appears as a distinct pair of electron-dense shells
(shells that are relatively opaque to the electron beam used to scan
the virus particle).
The M protein is the main structural protein of the envelope that provides the overall shape and is a type III membrane protein. It consists of 218 to 263 amino acid residues and forms a layer 7.8 nm thick. It has three domains, a short N-terminalectodomain, a triple-spanning transmembrane domain, and a C-terminalendodomain.
The C-terminal domain forms a matrix-like lattice that adds to the
extra-thickness of the envelope. Different species can have either N- or O-linked glycans in their protein amino-terminal domain. The M protein is crucial during the assembly, budding, envelope formation, and pathogenesis stages of the virus lifecycle.
The E proteins are minor structural proteins and highly variable in different species. There are only about 20 copies of the E protein molecule in a coronavirus particle. They are 8.4 to 12 kDa in size and are composed of 76 to 109 amino acids.
They are integral proteins (i.e. embedded in the lipid layer) and have
two domains namely a transmembrane domain and an extramembrane
C-terminal domain. They are almost fully α-helical, with a single
α-helical transmembrane domain, and form pentameric (five-molecular) ion channels in the lipid bilayer. They are responsible for virion assembly, intracellular trafficking and morphogenesis (budding).
Diagram of the genome and functional domains of the Sprotein for SARS-CoV and MERS-CoV
The spikes are the most distinguishing feature of coronaviruses and
are responsible for the corona- or halo-like surface. On average a
coronavirus particle has 74 surface spikes. Each spike is about 20 nm long and is composed of a trimer of the Sprotein. The S protein is in turn composed of an S1 and S2 subunit. The homotrimeric Sprotein is a class I fusion protein which mediates the receptor binding and membrane fusion
between the virus and host cell. The S1 subunit forms the head of the
spike and has the receptor-binding domain (RBD). The S2 subunit forms
the stem which anchors the spike in the viral envelope and on protease
activation enables fusion. The two subunits remain noncovalently linked
as they are exposed on the viral surface until they attach to the host
cell membrane.
In a functionally active state, three S1 are attached to two S2
subunits. The subunit complex is split into individual subunits when the
virus binds and fuses with the host cell under the action of proteases such as cathepsin family and transmembrane protease serine 2 (TMPRSS2) of the host cell.
After binding of the ACE2 receptor, SARS-CoV spike is activated and cleaved at the S1/S2 level
S1 proteins are the most critical components in terms of infection.
They are also the most variable components as they are responsible for
host cell specificity. They possess two major domains named N-terminal
domain (S1-NTD) and C-terminal domain (S1-CTD), both of which serve as
the receptor-binding domains. The NTDs recognize and bind sugars on the
surface of the host cell. An exception is the MHV NTD that binds to a protein receptor carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1). S1-CTDs are responsible for recognizing different protein receptors such as angiotensin-converting enzyme 2 (ACE2), aminopeptidase N (APN), and dipeptidyl peptidase 4 (DPP4).
A subset of coronaviruses (specifically the members of betacoronavirussubgroup A) also has a shorter spike-like surface protein called hemagglutinin esterase (HE).
The HE proteins occur as homodimers composed of about 400 amino acid
residues and are 40 to 50 kDa in size. They appear as tiny surface
projections of 5 to 7 nm long embedded in between the spikes. They help
in the attachment to and detachment from the host cell.
Inside the envelope, there is the nucleocapsid, which is formed from multiple copies of the nucleocapsid (N) protein, which are bound to the positive-sense single-stranded RNA genome in a continuous beads-on-a-string type conformation. N protein is a phosphoprotein
of 43 to 50 kDa in size, and is divided into three conserved domains.
The majority of the protein is made up of domains 1 and 2, which are
typically rich in arginines and lysines.
Domain 3 has a short carboxy terminal end and has a net negative charge
due to excess of acidic over basic amino acid residues.
The genome organization for a coronavirus is 5′-leader-UTR-replicase (ORF1ab)-spike (S)-envelope (E)-membrane (M)-nucleocapsid (N)-3′UTR-poly (A) tail. The open reading frames
1a and 1b, which occupy the first two-thirds of the genome, encode the
replicase polyprotein (pp1ab). The replicase polyprotein self cleaves to
form 16 nonstructural proteins (nsp1–nsp16).
The later reading frames encode the four major structural proteins: spike, envelope, membrane, and nucleocapsid.
Interspersed between these reading frames are the reading frames for
the accessory proteins. The number of accessory proteins and their
function is unique depending on the specific coronavirus.
Replication cycle
Cell entry
The life cycle of a coronavirus
Infection begins when the viral spike protein attaches to its complementary host cell receptor. After attachment, a protease of the host cell cleaves
and activates the receptor-attached spike protein. Depending on the
host cell protease available, cleavage and activation allows the virus to enter the host cell by endocytosis or direct fusion of the viral envelope with the host membrane.
Genome translation
On entry into the host cell, the virus particle is uncoated, and its genome enters the cell cytoplasm. The coronavirus RNA genome has a 5′ methylated cap and a 3′ polyadenylated tail, which allows it to act like a messenger RNA and be directly translated by the host cell's ribosomes. The host ribosomes translate the initial overlapping open reading framesORF1a and ORF1b of the virus genome into two large overlapping polyproteins, pp1a and pp1ab.
The larger polyprotein pp1ab is a result of a -1 ribosomal frameshift caused by a slippery sequence (UUUAAAC) and a downstream RNA pseudoknot at the end of open reading frame ORF1a. The ribosomal frameshift allows for the continuous translation of ORF1a followed by ORF1b.
The polyproteins have their own proteases, PLpro (nsp3) and 3CLpro
(nsp5), which cleave the polyproteins at different specific sites. The
cleavage of polyprotein pp1ab yields 16 nonstructural proteins (nsp1 to
nsp16). Product proteins include various replication proteins such as RNA-dependent RNA polymerase (nsp12), RNA helicase (nsp13), and exoribonuclease (nsp14).
Replicase-transcriptase
Replicase-transcriptase complex
A number of the nonstructural proteins coalesce to form a multi-protein replicase-transcriptase complex (RTC). The main replicase-transcriptase protein is the RNA-dependent RNA polymerase (RdRp). It is directly involved in the replication and transcription
of RNA from an RNA strand. The other nonstructural proteins in the
complex assist in the replication and transcription process. The exoribonuclease nonstructural protein, for instance, provides extra fidelity to replication by providing a proofreading function which the RNA-dependent RNA polymerase lacks.
Replication – One of the main functions of the complex is to replicate the viral genome. RdRp directly mediates the synthesis
of negative-sense genomic RNA from the positive-sense genomic RNA. This
is followed by the replication of positive-sense genomic RNA from the
negative-sense genomic RNA.
Transcription of nested mRNAs
Nested set of subgenomic mRNAs
Transcription – The other important function of the complex is to transcribe the viral genome. RdRp directly mediates the synthesis
of negative-sense subgenomic RNA molecules from the positive-sense
genomic RNA. This process is followed by the transcription of these
negative-sense subgenomic RNA molecules to their corresponding
positive-sense mRNAs. The subgenomic mRNAs form a "nested set" which have a common 5'-head and partially duplicate 3'-end.
Recombination – The replicase-transcriptase complex is also capable of genetic recombination when at least two viral genomes are present in the same infected cell.
RNA recombination appears to be a major driving force in determining
genetic variability within a coronavirus species, the capability of a
coronavirus species to jump from one host to another and, infrequently,
in determining the emergence of novel coronaviruses.
The exact mechanism of recombination in coronaviruses is unclear, but
likely involves template switching during genome replication.
Assembly and release
The replicated positive-sense genomic RNA becomes the genome of the progeny viruses.
The mRNAs are gene transcripts of the last third of the virus genome
after the initial overlapping reading frame. These mRNAs are translated
by the host's ribosomes into the structural proteins and many accessory
proteins. RNA translation occurs inside the endoplasmic reticulum. The viral structural proteins S, E, and M move along the secretory pathway into the Golgi intermediate compartment. There, the Mproteins direct most protein-protein interactions required for the assembly of viruses following its binding to the nucleocapsid. Progeny viruses are then released from the host cell by exocytosis through secretory vesicles. Once released the viruses can infect other host cells.
Transmission
Infected carriers are able to shed viruses into the environment. The interaction of the coronavirus spike protein with its complementary cell receptor is central in determining the tissue tropism, infectivity, and species range of the released virus. Coronaviruses mainly target epithelial cells. They are transmitted from one host to another host, depending on the coronavirus species, by either an aerosol, fomite, or fecal-oral route.
For a more detailed list of members, see Coronaviridae.
Phylogenetic tree of coronaviruses
Coronaviruses form the subfamily Orthocoronavirinae, which is one of two sub-families in the family Coronaviridae, order Nidovirales, and realm Riboviria. They are divided into the four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus.
Alphacoronaviruses and betacoronaviruses infect mammals, while
gammacoronaviruses and deltacoronaviruses primarily infect birds.
Origins of human coronaviruses with possible intermediate hosts
The most recent common ancestor (MRCA) of all coronaviruses is estimated to have existed as recently as 8000 BCE,
although some models place the common ancestor as far back as
55 million years or more, implying long term coevolution with bat and
avian species.
The most recent common ancestor of the alphacoronavirus line has been
placed at about 2400 BCE, of the betacoronavirus line at 3300 BCE, of
the gammacoronavirus line at 2800 BCE, and the deltacoronavirus line at
about 3000 BCE. Bats and birds, as warm-blooded flying vertebrates, are an ideal natural reservoir for the coronavirus gene pool (with bats the reservoir
for alphacoronaviruses and betacoronavirus – and birds the reservoir
for gammacoronaviruses and deltacoronaviruses). The large number and
global range of bat and avian species that host viruses have enabled
extensive evolution and dissemination of coronaviruses.
Many human coronaviruses have their origin in bats. The human coronavirus NL63 shared a common ancestor with a bat coronavirus (ARCoV.2) between 1190 and 1449 CE. The human coronavirus 229E shared a common ancestor with a bat coronavirus (GhanaGrp1 Bt CoV) between 1686 and 1800 CE. More recently, alpaca coronavirus and human coronavirus 229E diverged sometime before 1960. MERS-CoV emerged in humans from bats through the intermediate host of camels. MERS-CoV, although related to several bat coronavirus species, appears to have diverged from these several centuries ago. The most closely related bat coronavirus and SARS-CoV diverged in 1986. The ancestors of SARS-CoV first infected leaf-nose bats of the genus Hipposideridae; subsequently, they spread to horseshoe bats in the species Rhinolophidae, then to Asian palm civets, and finally to humans.
Unlike other betacoronaviruses, bovine coronavirus of the species Betacoronavirus 1 and subgenus Embecovirus is thought to have originated in rodents and not in bats. In the 1790s, equine coronavirus diverged from the bovine coronavirus after a cross-species jump. Later in the 1890s, human coronavirus OC43 diverged from bovine coronavirus after another cross-species spillover event. It is speculated that the flu pandemic of 1890 may have been caused by this spillover event, and not by the influenza virus, because of the related timing, neurological symptoms, and unknown causative agent of the pandemic. Besides causing respiratory infections, human coronavirus OC43 is also suspected of playing a role in neurological diseases. In the 1950s, the human coronavirus OC43 began to diverge into its present genotypes. Phylogenetically, mouse hepatitis virus (Murine coronavirus), which infects the mouse's liver and central nervous system,
is related to human coronavirus OC43 and bovine coronavirus. Human
coronavirus HKU1, like the aforementioned viruses, also has its origins
in rodents.
Infection in humans
Transmission and life-cycle of SARS-CoV-2 causing COVID-19
Coronaviruses vary significantly in risk factor. Some can kill more than 30% of those infected, such as MERS-CoV, and some are relatively harmless, such as the common cold. Coronaviruses can cause colds with major symptoms, such as fever, and a sore throat from swollen adenoids. Coronaviruses can cause pneumonia (either direct viral pneumonia or secondary bacterial pneumonia) and bronchitis (either direct viral bronchitis or secondary bacterial bronchitis). The human coronavirus discovered in 2003, SARS-CoV, which causes severe acute respiratory syndrome (SARS), has a unique pathogenesis because it causes both upper and lower respiratory tract infections.
Six species of human coronaviruses are known, with one species
subdivided into two different strains, making seven strains of human
coronaviruses altogether.
Seasonal distribution of HCoV-NL63 in Germany shows a preferential detection from November to March
Four human coronaviruses produce symptoms that are generally mild,
even though it is contended they might have been more aggressive in the
past:
Although the common cold is usually caused by rhinoviruses, in about 15% of cases the cause is a coronavirus.
The human coronaviruses HCoV-OC43, HCoV-HKU1, HCoV-229E, and HCoV-NL63
continually circulate in the human population in adults and children
worldwide and produce the generally mild symptoms of the common cold. The four mild coronaviruses have a seasonal incidence occurring in the winter months in temperate climates. There is no preponderance in any season in tropical climates.
In 2003, following the outbreak of severe acute respiratory syndrome
(SARS) which had begun the prior year in Asia, and secondary cases
elsewhere in the world, the World Health Organization
(WHO) issued a press release stating that a novel coronavirus
identified by several laboratories was the causative agent for SARS. The
virus was officially named the SARS coronavirus (SARS-CoV). More than
8,000 people from 29 different countries and territories were infected,
and at least 774 died.
In September 2012, a new type of coronavirus was identified,
initially called Novel Coronavirus 2012, and now officially named Middle
East respiratory syndrome coronavirus (MERS-CoV). The World Health Organization issued a global alert soon after. The WHO update on 28 September 2012 said the virus did not seem to pass easily from person to person. However, on 12 May 2013, a case of human-to-human transmission in France was confirmed by the French Ministry of Social Affairs and Health. In addition, cases of human-to-human transmission were reported by the Ministry of Health in Tunisia.
Two confirmed cases involved people who seemed to have caught the
disease from their late father, who became ill after a visit to Qatar
and Saudi Arabia. Despite this, it appears the virus had trouble
spreading from human to human, as most individuals who are infected do
not transmit the virus. By 30 October 2013, there were 124 cases and 52 deaths in Saudi Arabia.
After the Dutch Erasmus Medical Centre
sequenced the virus, the virus was given a new name, Human
Coronavirus–Erasmus Medical Centre (HCoV-EMC). The final name for the
virus is Middle East respiratory syndrome coronavirus (MERS-CoV). The
only U.S. cases (both survived) were recorded in May 2014.
In May 2015, an outbreak of MERS-CoV occurred in the Republic of Korea,
when a man who had traveled to the Middle East, visited four hospitals
in the Seoul area to treat his illness. This caused one of the largest
outbreaks of MERS-CoV outside the Middle East. As of December 2019, 2,468 cases of MERS-CoV infection had been confirmed by laboratory tests, 851 of which were fatal, a mortality rate of approximately 34.5%.
In December 2019, a pneumonia outbreak was reported in Wuhan, China. On 31 December 2019, the outbreak was traced to a novel strain of coronavirus, which was given the interim name 2019-nCoV by the World Health Organization, later renamed SARS-CoV-2 by the International Committee on Taxonomy of Viruses.
As of 15 December 2021, there have been at least 5,321,328 confirmed deaths and more than 271,501,910 confirmed cases in the COVID-19 pandemic. The Wuhan strain has been identified as a new strain of Betacoronavirus from group 2B with approximately 70% genetic similarity to the SARS-CoV. The virus has a 96% similarity to a bat coronavirus, so it is widely suspected to originate from bats as well.
During a surveillance study of archived samples of Malaysian viral pneumonia patients, virologists identified a strain of canine coronavirus which has infected humans in 2018.
Infection in animals
Coronaviruses have been recognized as causing pathological conditions in veterinary medicine since the 1930s. They infect a range of animals including swine, cattle, horses, camels, cats, dogs, rodents, birds and bats. The majority of animal related coronaviruses infect the intestinal tract and are transmitted by a fecal-oral route. Significant research efforts have been focused on elucidating the viral pathogenesis of these animal coronaviruses, especially by virologists interested in veterinary and zoonotic diseases.
Farm animals
Coronaviruses infect domesticated birds. Infectious bronchitis virus (IBV), a type of coronavirus, causes avian infectious bronchitis. The virus is of concern to the poultry industry because of the high mortality from infection, its rapid spread, and its effect on production. The virus affects both meat production and egg production and causes substantial economic loss. In chickens, infectious bronchitis virus targets not only the respiratory tract but also the urogenital tract. The virus can spread to different organs throughout the chicken. The virus is transmitted by aerosol and food contaminated by feces. Different vaccines against IBV exist and have helped to limit the spread of the virus and its variants. Infectious bronchitis virus is one of a number of strains of the species Avian coronavirus. Another strain of avian coronavirus is turkey coronavirus (TCV) which causes enteritis in turkeys.
Coronaviruses infect domestic pets such as cats, dogs, and ferrets. There are two forms of feline coronavirus which are both members of the species Alphacoronavirus 1. Feline enteric coronavirus is a pathogen of minor clinical significance, but spontaneous mutation of this virus can result in feline infectious peritonitis (FIP), a disease with high mortality. There are two different coronaviruses that infect dogs. Canine coronavirus (CCoV), which is a member of the species Alphacoronavirus 1, causes mild gastrointestinal disease. Canine respiratory coronavirus (CRCoV), which is a member of the species Betacoronavirus 1 and related to HCoV-OC43, cause respiratory disease. Similarly, there are two types of coronavirus that infect ferrets. Ferret enteric coronavirus
causes a gastrointestinal syndrome known as epizootic catarrhal
enteritis (ECE), and a more lethal systemic version of the virus (like
FIP in cats) known as ferret systemic coronavirus (FSC).
Laboratory animals
Coronaviruses infect laboratory animals. Mouse hepatitis virus (MHV), which is a member of the species Murine coronavirus, causes an epidemic murine illness with high mortality, especially among colonies of laboratory mice. Prior to the discovery of SARS-CoV, MHV was the best-studied coronavirus both in vivo and in vitro as well as at the molecular level. Some strains of MHV cause a progressive demyelinating encephalitis in mice which has been used as a murine model for multiple sclerosis. Sialodacryoadenitis virus (SDAV), which is a strain of the species Murine coronavirus,
is highly infectious coronavirus of laboratory rats, which can be
transmitted between individuals by direct contact and indirectly by
aerosol. Rabbit enteric coronavirus causes acute gastrointestinal
disease and diarrhea in young European rabbits. Mortality rates are high.
Prevention and treatment
A number of vaccines using different methods have been developed against human coronavirus SARS-CoV-2. Antiviral targets against human coronaviruses have also been identified such as viral proteases, polymerases, and entry proteins. Drugs are in development which target these proteins and the different steps of viral replication.
Vaccines are available for animal coronaviruses IBV, TGEV, and
Canine CoV, although their effectiveness is limited. In the case of
outbreaks of highly contagious animal coronaviruses, such as PEDV,
measures such as destruction of entire herds of pigs may be used to prevent transmission to other herds.
