The document summarizes the structure and replication of COVID-19. It discusses that COVID-19 is caused by SARS-CoV-2, a novel coronavirus first identified in Wuhan, China in late 2019. SARS-CoV-2 has a single-stranded RNA genome and spike proteins that give it a crown-like appearance. The virus likely originated in bats and enters cells by binding to ACE2 receptors, using its spike proteins to fuse with and enter the cell membrane. It then expresses replicase proteins and uses its RNA-dependent RNA polymerase to make copies of its genome and structural proteins, assembling new virus particles that exit the cell.

1. STRUCTUREANDREPLICATIONOFCOVID-19
– DHANSHRI ANIL PATIL

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1| INTRODUCTION
 The Chinese governmentand researchers took rapid measuresto control the epidemic
and carried out etiological research. On 12 January2020, (WHO)tentativelynamed
this new virusas the 2019 novel corona virus(2019-nCoV).
 On 11 February2020, the International Committeeon Taxonomyof Viruses named
2019-nCoV assevere acute respiratory syndrome CoVs 2 (SARS-CoV 2). On 23
February2020, 77,041confirmed cases of SARS-CoV 2 infection in China.
 COVID -19 is an important pathogens for human and vertebrates. They can infect
respiratory, gastrointestinal, hepatic, and central nervous system of human, livestock,
birds, bat, mouse, and manyother wildanimals.
OUTLINE:
Since December 2019, a series of unexplained pneumonia cases have been reported in Wuhan,
China. On 12 January 2020, the World Health Organization (WHO) temporarily named this
new virus as the 2019 novel corona virus (2019-nCoV). On 11 February 2020, the WHO
officially named the disease caused by the 2019-nCoV as corona virus disease (COVID-19).
The COVID-19 epidemicis spreading allover the world, especially in China.
Figure 1.1 the images have been captured using the transmission electron microscope
imaging. They have been published in the Indian Journal of Medical Research.

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 The outbreaks of the severe acute respiratory syndrome (SARS) in 2002/2003 and
(MERS) in 2012 have demonstrated the possibility of animal to human and human to
human transmissionof newlyemerging.
 The causative agent of the mystery pneumonia has been identified as a novel
coronovirus by deep sequencing and etiological investigations by at least five
independentlaboratories of China.
 As with other respiratory pathogens, the transmission is believed to occur through
respiratory droplets from coughing and sneezing.
 Aerosol transmission is also possible in case of protracted exposure to elevated aerosol
concentrations in closed spaces.
Figure 1.2 Animal to human and human to human mode of transmission
1.1| SOURCE OF SARS –Cov-2
 SARS-CoV-2 is a corona virus and belongs to the α-corona virus cluster. COVID-19 is
the third known zoometric corona virus disease after SARS and (MERS), belonging to

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the subgenusbotulinum of Coronaviridae.
 A study by JI and ZHU showed that the SARS-CoV-2 was a chimerical virus between a
bat corona virusand a corona virusof unknown origin.
 By comparing with other animals, they found that snakes are the most likely wildlife
repository for the SARS-CoV-2.
 The research by Benevento showed that the SARS-CoV-2 was only closely related to
the corona virusIsolated from Chinese chrysanthemum, headed batsin 2015.
 Their research supported the theory that the transmission chain started from bats to
humans.
 Recently, found that the sequence homology between SARS-CoV-2 and SARS-CoV was
79.5%. They also found that the SARS-CoV-2 had high homology with bat corona
viruses.
 Therefore, the current evidence strongly supports that the SARS-CoV-2 was derived
from bats, although the hosts of SARS-CoV-2remainto be undetermined.
2| CORONAVIRAL STRUCTURE
DETAILS
FIGURE 1.2 The genomic structure and phylogenetic tree of CoVs. A, phylogenetic tree of
representative CoVs, with the new corona virus 2019-nCoV. B, The genome structure of four genera
of corona viruses.
(B)

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 CoVs are positive-stranded RNA viruses with a crown-like appearance under
an electron microscope, due to the
presence of spike glycoprotein’s on
the envelope. Within the envelope of
the virion is the nucleocapsid.
 Corona viruses have helically
symmetrical nucleocapsids, which is
uncommon among positive-sense RNA
viruses, but far more common for
negative-sense RNA viruses.
A) Spike (S) protein (PDB code –
6CRV)
 The S protein (~150 kDa), utilizes an N-terminal signal sequence to gain
access to the ER, and is heavily N-linked glycosylated.
B) Envelope (E) protein (PDB code – 5X29)
 The E protein (~8–12 kDa) is found in small quantities within the virion. E
protein from corona viruses is highly divergent but has a common
architecture.
 The E protein has an N-terminal ectodomain and a C-terminal endodomain
and has ion channel activity. As, recombinant viruses lacking the E protein
are not always lethal although this is virus type dependent.
C) Membrane (M) protein (PDB code – 3I6G)

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 The M protein is the most abundant structural protein in the virion. It is a
small (~25–30 kDa) protein with 3 transmembrane domains and is thought to
give the virion its shape.
 It has a small N-terminal glycosylated ectodomain and a much larger C-
terminal endodomain that extends 6–8 nm into the viral particle.
D) Nucleoplasmid (N) Protein
 The N protein constitutes the only protein present in the nucleocapsid. It is
composed of two separate domains, an N-terminal domain (NTD) and a C-
terminal domain (CTD), both capable of binding RNA in vitro, but each
domain uses different mechanisms to bind RNA.
 Genomic characterization has shown that probably bats and rodents are the
gene sources of α CoVs and β CoVs. On the contrary, avian species seem to
represent the gene sources of δ CoVs and γ CoVs. viruses can cause:
 respiratory, enteric, hepatic, and neurological diseases in different
animal species, including camels, cattle, cats, and bats.
(* note that the M protein shown is complexed with HLA-A *02 (human leukocyte
antigen serotype).

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The subfamily Orthocoronavirinae of the Coronaviridae family (order Nidovirales)
classifies into four genera of CoVs: Alpha coronavirus (alphaCoV), Beta
coronavirus (betaCoV), Delta coronavirus (deltaCoV), and Gammacoronavirus
(gammaCoV) as shown below in the figure 2.4
 The CoV genome is much larger ~ 30kb in length, the largest known RNA
virus, contains several RNA processing enzymes such as the 3′‐ 5′
exoribonuclease of nsp14.
 The 3′‐ 5′ exoribonuclease is unique to CoVs among all RNA viruses, probably
providing a proofreading function of the RTC.
Figure 2.3 The crystal complex
structure of the main proteases. By
PDB (protein data base)
Figure 2.2 Transmission electron microscope
image shows SARS-Cov-2, the virus that
causes COVID-19. The spikes on the outer
edge of the virus particles gives corona virus
their name, crown like.

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Figure 2.1 showing the genomic structure of SARS-COV-2. On both protein (translation)
genomic level.
Figure 2.4
Taxonomy of
HCoVs:
classification of
corona virus.
Alphacoronaviru
s(alpaca), Beta
coronavirus(bet
aCoV), Delta
coronavirus
(deltaCoV), and
Gamma
coronavirus
(gammaCoV)

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# GENOMIC ANALYSIS OF SARS-COV-2
 In genetic terms, Chan have proven that the genome of the new HCoV,
isolated from a cluster-patient with atypical pneumonia after visiting Wuhan,
had 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with
that of human SARS-CoV.
 This new virus was called SARS-CoV-2. Its single-stranded RNA genome
contains 29891 nucleotides, encoding for 9860 amino acids. Although its
origins are not entirely understood.
 These genomic analyses suggest that SARS-CoV-2 probably evolved from a
strain found in bats. The potential amplifying mammalian host, intermediate
between bats and humans, is, however, not known.
Genomeorganization ofRo-BatCoV GCCDC: 1. Nonstructural genes and putative
mature nonstructuralproteins, structural genes, and 5’- and 3’-UTR are illustrated with
yellow, dark blue and lightblue colors, respectively. 2. The potential origin of the p10 gene
is indicated by a dotted arrow and a question mark. Theleader sequence and leader
transcription regulatory sequence (TRS) are directly shown with nucleobases.3. The
bat, Rousettus leschenaulti, is used to show the host species that Ro-BatCoV GCCDC1
discovered.

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3| LIFECYCLE OF SARS-Cov-2
STEP 1 --- Attachment and Entry
 The initial attachment of the virion to the host cell is initiated by interactions between
the S protein and its receptor.
 The sites of receptor binding domains (RBD) within the S1 region of a corona virus S
protein vary depending on the virus, with some having the RBD at the N-terminus of
S1 (MHV) whileothers (SARS-CoV)havethe RBD at the C-terminusof S1 .
 The S-
protein/receptor
interaction is the
primary determinant
for a CoVs to infect a
host species and also
governs the tissue
tropism of the virus.
 Many CoVs
utilize peptidases as
their cellular receptor.
It is unclear why
peptidases are used,
as entry occurs even
in the absence of the
enzymatic domain of
these proteins.
 Many αCoVs
utilize amino peptidase N (APN) as their receptor, SARS-CoV and HCoV-NL63 use
angiotensin-converting enzyme 2 (ACE2) as their receptor, MHV enters through
CEACAM1, to gain entry into human cells.
 It gain access to host cytosol. This is generally accomplished by acid-dependent
proteolytic cleavageof S protein by a cathepsin.

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 Cleavage at S2, exposes a fusion peptide that inserts into the membrane, in S2 forming
an ant parallel six-helixbundle.
 The formation of this bundle allows for the mixing of viral and cellular membranes,
resulting in fusion and ultimatelyrelease of the viral genomeintothe cytoplasm.
STEP 2--- REPLICASE PROTEIN EXPRESSION
 The next step in the corona virus lifecycle is the translation of the replicase gene from
the virion genomic RNA. The replicase gene encodes two large ORFS, rep1a and
rep1b.
 In order to express both polyproteins, the virusutilizesa slipperysequence (5’-
UUUAAAC-3’)and an RNA pseudo knot that cause ribosomal frameshifting from the
rep1a reading frameintothe rep1b ORF.
 The ribosomeunwindsthe pseudoknot structure, and continuestranslation untilit
encounters the rep1a stop cordon.
 −1 frameshift, before the ribosomeis ableto meltthe pseudoknot structure and
extend translate on into rep1b, resulting in the translation.
 These polyproteinsare subsequentlycleaved intothe individualnsps. CoVsencode
either two or three proteases that cleave the replicasepolyproteins.
 They are the (PLpro), encoded withinnsp3, and a serine type protease, the or Mpro,
encoded by nsp5.
 Many of the nsps assembleintothe (RTC)to create an environmentsuitablefor RNA
synthesis, and ultimatelyare responsiblefor RNA replication and transcription of the
sub-genomicRNAs.
STEP 3---REPLICATION AND TRANSCRITION
 Viral RNA synthesis followsthe translation andassemblyof the viral replicase
complexes. Viral RNA synthesis produces both genomicand sub-genomicRNAs.
 Sub-genomicRNAs serve as mRNAsfor the structural and accessory genes which
reside downstream of the replicasepolyproteins.Bothgenomicand sub-genomicRNAs

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are produced through negative-strandintermediates.
 These negative-strand intermediates contain both poly-uridylateand anti-leader
sequences.
 Within the 5’ UTR of the genomeare seven stem-loop structures that mayextend into
the replicase1a gene . The 3’ UTR containsa bulged stem-loop, a pseudoknot, and a
hyper variableregion.
 Therefore, these different structures are proposed to regulatealternatestages of RNA
synthesis.
 TRS segmentsfuse during production of sub-genomicRNAs. This wasoriginally
thought to occur during positive-strandsynthesis, believed to occur during the
discontinuousextension of negative-strand RNA.
 The current model proposes that the RdRp pausesat any one of the body TRS
sequences (TRS-B); it switches to amplifyingthe leader sequence at the 5’ end of the
TRS-B to the leader TRS (TRS-L).

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`
STEP4 ---ASSEMBLY AND RELEASE
 The viral structural proteins, S, E, and M are translated and inserted into the
endoplasmicreticulum (ER). These proteinsmove along the secretory pathwayintothe
endoplasmicreticulum-Golgi intermediatecompartment (ERGIC).
 The M protein directs most protein-protein interactionsrequired for assemblyof CoVs.
M protein is expressed along withE protein VLPs are formed, suggesting these two
proteins function together to produce CoVs envelopes
 N protein enhances VLP formation, suggestingthat fusion of encapsulated genomes
into the ERGIC enhances viral envelopment.
 The S protein but is not required for assembly. The abilityof the S protein to traffic to
the ERGIC and interactwiththe M protein is critical for its incorporation intovirions.
Working model of
transcription.1) Proteins
binding the5’ - and 3’-
end TGEV sequences. (B)
Negative-strand RNA is
in a lighter color than
positive-strand RNA. The
transcription complex is
represented by the
hexagon. Vertical dotted
bars represent the base-
pairing scanning bythe
TRS-L sequence in the
transcription process.

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 M protein interactionsprovidethe impetusfor envelopematuration.E protein prevents
the aggregation of M protein. The E protein altering the host secretory pathway.
 The M protein alsobindsto the nucleocapsid, andthis interaction promotes the
completion of virion assembly.A packagingsignal for MHV has been identifiedin the
nsp15 coding sequence.
 Virionsare transported to the cell surface in vesicles and released by exocytosis. S -
protein that does not get assembled intovirionstransitsto the cell surface where it
mediatescell-cell fusion between infected cells and adjacent cells.
 Leadsto the formation of giant, multinucleated cells, whichallowsthe virusto spread
within an infected organism withoutbeingdetected or neutralized byvirus-specific
antibodies.

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# REFERENCES
Web pages
 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291385/
 https://www.researchgate.net/figure/Three-step-working-model-of-coronavirus-
transcription-A-The-5-J-3-J-complex-formation_fig12_8943697
 https://www.researchgate.net/figure/b-Systematic-Assembly-of-Coronavirus-
Genomes_fig4_38000020
 https://www.ncbi.nlm.nih.gov/books/NBK554776/
 http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=F2D7EDC8
ARTICLES
 Tropical Medicine andInternational Health : Editorial The COVID-19
epidemic
 Journal of medicinal virology WILLEY: Emerging corona viruses: Genome
structure ,replication, and pathogenesis.

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