polymorphism at nucleotide position 28,144 , which results in amino acid substitution of Ser for Lys

at residue 84 of the ORF8 protein . Those variants with this muta tion make up a single subclade
labelled as ' clade S'33,34 . Currently , however , the available sequence data are not sufficient to
interpret the early global transmission his tory of the virus , and travel patterns , founder effects
and public health measures also strongly influence the spread of particular lineages , irrespective
of potential biological differences between different virus variants .
Animal host and spillover Bats are important natural hosts of alphacoronavi ruses and
betacoronaviruses . The closest relative to SARS - CoV - 2 known to date is a bat coronavirus
detected in Rhinolophus affinis from Yunnan province , China , named ' RaTG13 ' , whose full -
length genome sequence is 96.2 % identical to that of SARS - CoV - 2 ( REF.¹ ) . This bat virus
shares more than 90 % sequence identity with SARS - CoV - 2 in all ORFs throughout the genome
, including the highly variable S and ORF8 ( REF.¹ ) . Phylogenetic analysis confirms that SARS -
CoV - 2 closely clusters with RaTG13 ( FIG . 2 ) . The high genetic similarity between SARS - CoV
- 2 and RaTG13 supports the hypothesis that SARS - CoV - 2 likely originated from bats 35.
Another related coronavirus has been reported more recently in a Rhinolophus malayanus bat
sampled in Yunnan This novel bat virus denoted ' Rm YN02 '

To assess the genetic variation of different SARS CoV - 2 strains , the 2019 Novel Coronavirus
Resource of China National Center for Bioinformation aligned 77,801 genome sequences of SARS
- CoV - 2 detected glob ally and identified a total of 15,018 mutations , including 14,824 single -
nucleotide polymorphisms ( BIGD ) . In the S protein , four amino acid alterations , V483A , L4551
, F456V and G476S , are located near the binding interface in the RBD , but their effects on
binding to the host receptor are unknown . The alteration D614G in the S1 subunit was found far
more frequently than other S variant sites , and it is the marker of a major subclade of SARS - CoV
- 2 ( clade G ) . Since March 2020 , SARS - CoV - 2 variants with G614 in the S protein have
replaced the original D614 variants and become the dominant form circulating globally . Compared
with the D614 variant , higher viral loads were found in patients infected with the G614 variant , but
clinical data suggested no signif icant link between the D614G alteration and disease severity³2 .
Pseudotyped viruses carrying the S protein with G614 generated higher infectious titres than
viruses carrying the S protein with D614 , suggesting the altera tion may have increased the
infectivity of SARS - CoV - 2 ( REF . 32 ) . However , the results of in vitro experiments based on
pseudovirus models may not exactly reflect natural infection . This preliminary finding should be
validated more studies using wild - type SARS - CoV - 2 variants to infect different target cells and
animal models . Whether this amino acid change enhanced virus transmissibil ity is also to be
determined . Another marker mutation for SARS - CoV - 2 evolution is the single - nucleotide

a polybasic cleavage site ( RRAR ) , which enables effec tive cleavage by furin and other
proteases 27. Such an S1 - S2 cleavage site is not observed in all related viruses belonging to the
subgenus Sarbecovirus , except for a similar three amino acid insertion ( PAA ) in RmYN02 , a bat
- derived coronavirus newly reported from Rhinolophus malayanus in China²⁹ ( FIG . 3a ) .
Although the insertion in RmYN02 does not functionally represent a polybasic cleavage site , it
provides support for the notion that this characteristic , initially considered unique to SARS - CoV -
2 , has been acquired naturally28 . A structural study suggested that the furin - cleavage site can
reduce the stability of SARS - CoV - 2 S protein and facilitate the conformational adaption that is
required for the binding of the RBD to its receptor . Whether the higher trans missibility of SARS -
CoV - 2 compared with SARS - CoV is a gain of function associated with acquisition of the furin -
like cleavage site is yet to be demonstrated 26 . An additional distinction is the accessory gene
orf8 of SARS - CoV - 2 , which encodes a novel protein showing only 40 % amino acid identity to
ORF8 of SARS - CoV . Unlike in SARS - CoV , this new ORF8 protein does not contain a motif
that triggers intracellular stress pathways25 . Notably , a SARS - CoV - 2 variant with a 382 -
nucleotide deletion covering the whole of ORF8 has been discovered in a number of patients in
Singapore , which resembles the 29- or 415 - nucleotide deletions in the ORF8 region observed in
human SARS - CoV variants from the late phase of the 2002-2003 outbreak ³0 . Such ORF8
deletion may be indicative of human adaptation after cross - species transmission from an animal
host . To 2000 tin moniation of different SARS

and other SARSr - CoVs ( FIG . 2 ) . Using sequences of five conserved replicative domains in ppl
ab ( 3C - like protease ( 3CLpro ) , nidovirus RNA - dependent RNA polymerase ( RdRp ) -
associated nucleotidyltransferase ( NiRAN ) , RdRp , zinc - binding domain ( ZBD ) and HEL1 ) ,
the Coronaviridae Study Group of the International Committee on Taxonomy of Viruses estimated
the pairwise patristic distances between SARS - CoV - 2 and known coronaviruses , and assigned
SARS - CoV - 2 to the existing species SARSr - CoV¹7 . Although phyloge netically related , SARS
- CoV - 2 is distinct from all other coronaviruses from bats and pangolins in this species . The
SARS - CoV - 2 S protein has a full size of 1,273 amino acids , longer than that of SARS - CoV (
1,255 amino acids ) and known bat SARSr - CoVs ( 1,245–1,269 amino acids ) . It is distinct from
the S pro teins of most members in the subgenus Sarbecovirus , sharing amino acid sequence
similarities of 76.7 77.0 % with SARS - CoVs from civets and humans ,

length to the corresponding proteins in SARS - CoV . Of the four structural genes , SARS - CoV -
2 shares more than 90 % amino acid identity with SARS - CoV except for the S gene , which
diverges¹1.24 . The replicase gene covers two thirds of the 5 ' genome , and encodes a large
polyprotein ( pplab ) , which is proteolytically cleaved into 16 non - structural proteins that are
involved in transcrip tion and virus replication . Most of these SARS - CoV - 2 non - structural
proteins have greater than 85 % amino acid sequence identity with SARS - CoV²5 .
The phylogenetic analysis for the whole genome shows that SARS - CoV - 2 is clustered with
SARS - CoV and SARS - related coronaviruses ( SARSr - CoVs ) found in bats , placing it in the
subgenus Sarbecovirus of the genus Betacoronavirus . Within this clade , SARS - CoV - 2 is
grouped in a distinct lineage together with four horse shoe bat coronavirus isolates ( RaTG13 ,
RmYN02 , ZC45 and ZXC21 ) as well as novel coronaviruses recently iden tified in pangolins ,
which group parallel to SARS - CoV

216 countries and regions from all six continents had reported more than 20 million cases of
COVID - 19 , and more than 733,000 patients had died²¹ . High mortality occurred especially when
health - care resources were overwhelmed . The USA is the country with the largest number of
cases so far .
Although genetic evidence suggests that SARS - CoV - 2 is a natural virus that likely originated in
animals , there is no conclusion yet about when and where the virus first entered humans . As
some of the first reported cases in Wuhan had no epidemiological link to the seafood market22 , it
has been suggested that the market may not be the initial source of human infection with SARS -
CoV - 2 . One study from France detected SARS - CoV - 2 by PCR in a stored sample from a
patient who had pneumonia at the end of 2019 , suggesting SARS - CoV - 2 might have spread
there much earlier than the generally known starting time of the outbreak in France23 . However ,
this individual early report cannot give a solid answer to the origin of SARS - CoV - 2 and
contamination , and thus a false positive result cannot be excluded . To address this highly
controversial issue , further retrospective inves tigations involving a larger number of banked
samples from patients , animals and environments need to be conducted worldwide with well -
validated assays .
Genomics , phylogeny and taxonomy As a novel betacoronavirus , SARS - CoV - 2 shares 79 %
genome sequence identity with SARS - CoV and 50 % with MERS - CoV24 . Its genome
organization is shared with other betacoronaviruses . The six functional open reading frames (
ORFs ) are arranged in order from 5 ' to 3 ' : replicase ( ORF1a / ORF1b ) , spike ( S ) , envelope (
E ) , membrane ( M ) and nucleocapsid ( N ) . In addition , seven putative ORFs encoding
accessory proteins are interspersed between the structural genes 25. Most of the proteins
encoded by SARS - CoV - 2 have a similar

it had spread massively to all 34 provinces of China . The number of confirmed cases suddenly
increased , with thousands of new cases diagnosed daily during late January . On 30 January , the
WHO declared the novel coronavirus outbreak a public health emergency of inter national concern
. On 11 February , the International Committee on Taxonomy of Viruses named the novel
coronavirus ' SARS - CoV - 2 ' , and the WHO named the disease ' COVID - 19 ' ( REF.¹7 ) .
The outbreak of COVID - 19 in China reached an epidemic peak in February . According to the
National Health Commission of China , the total number of cases continued to rise sharply in early
February at an average rate of more than 3,000 newly confirmed cases per day . To control
COVID - 19 , China implemented unprecedentedly strict public health measures . The city of
Wuhan was shut down on 23 January , and all travel and transportation connecting the city was
blocked . In the following couple of weeks , all outdoor activities and gatherings were restricted ,
and public facilities were closed in most cities as well as in countryside ¹ . Owing to these
measures , the daily number of new cases in China started to decrease steadily¹⁹ .
However , despite the declining trend in China , the international spread of COVID - 19
accelerated from late February . Large clusters of infection have been reported from an increasing
number of countries¹8 . The high transmission efficiency of SARS - CoV - 2 and the abun dance of
international travel enabled rapid worldwide spread of COVID - 19 . On 11 March 2020 , the WHO
officially characterized the global COVID - 19 out break as a pandemic20 . Since March , while
COVID - 19 in China has become effectively controlled , the case numbers in Europe , the USA
and other regions have jumped sharply . According to the COVID - 19 dash board of the Center for
System Science and Engineering at Johns Hopkins University , as of 11 August 2020 ,

( 173 , 174 ) . Hence , knowledge and understanding of S protein - based vaccine development in
SARS - CoV will help to identify potential S protein vaccine candidates in SARS - CoV - 2 .
Therefore , vaccine strategies based on the whole S protein , S protein subunits , or specific
potential epitopes of S protein appear to be the most promising vaccine candidates against
coronaviruses . The RBD of the S1 subunit of S protein has a superior capacity to induce
neutralizing antibodies . This property of the RBD can be utilized for designing potential SARS -
CoV vaccines either by using RBD - containing recombinant proteins or recombinant vectors that
encode RBD ( 175 ) . Hence , the superior genetic similarity existing between SARS - CoV - 2 and
SARS CoV can be utilized to repurpose vaccines that have proven in vitro efficacy against SARS -
CoV to be utilized for SARS - CoV - 2 . The possibility of cross protection in COVID - 19 was
evaluated by comparing the S protein sequences of SARS - CoV - 2 with that of SARS - CoV . The
comparative analysis confirmed that the variable residues were found concentrated on the S1
subunit of S protein , an important vaccine target of the virus ( 150 ) . Hence , the possibility of
SARS - CoV - specific neutralizing antibodies providing cross - protection to COVID - 19 might be
lower . Further genetic analysis is required

viruses in nasal washes , saliva , urine and faeces for up to 8 days after infection , and a few naive
ferrets with only indirect contact were positive for viral RNA , suggest ing airborne transmission78 .
In addition , transmission of the virus through the ocular surface and prolonged presence of SARS
- CoV - 2 viral RNA in faecal samples were also documented 101,102 . Coronaviruses can persist
on inanimate surfaces for days , which could also be the case for SARS - CoV - 2 and could pose
a prolonged risk of infection 103. These findings explain the rapid geographic spread of COVID -
19 , and public health interventions to reduce transmission will provide benefit to mitigate the
epidemic , as has proved successful in China and several other countries , such as South Korea
89,104,105
Diagnosis Early diagnosis is crucial for controlling the spread of COVID - 19 . Molecular detection
of SARS - CoV - 2 nucleic acid is the gold standard . Many viral nucleic acid detec tion kits
targeting ORF1b ( including RdRp ) , N , E or S genes are commercially available1¹1,106-109 .
The detection time ranges from several minutes to hours depending on the
technology106,107,109-111 . The molecular detection can be affected by many factors . Although
SARS - CoV - 2 has been detected from a variety of respiratory sources , including throat swabs ,
posterior oropharyngeal saliva , nasopharyngeal swabs , sputum and bronchial fluid , the viral load
is higher in lower respiratory tract sam ples 11,96,112-115 . In addition , viral nucleic acid was also
found in samples from the intestinal tract or blood even when respiratory samples were
negative¹¹6 . Lastly , viral load may already drop from its peak level on disease onset 96 , 97.
Accordingly , false negatives can be common when oral swabs and used , and so multiple
detection methods should be adopted to confirm a COVID - 19 diagnosis 117,118 . Other
detection methods were there fore used to overcome this problem . Chest CT was used to quickly
identify a patient when the capacity of molecular detection was overloaded in Wuhan . Patients

No Text Found

or even die , whereas most young people and children have only mild diseases ( non - pneumonia
or mild pneumonia ) or are Notably , the risk asymptomatic , 81,82 . of disease was not higher for
pregnant women . However , evidence of transplacental transmission of SARS - CoV - 2 from an
infected mother to a neonate was reported , although it was an isolated case83,84 . On infection ,
the most common symptoms are fever , fatigue and dry cough13,60,80,81 . Less common
symptoms include sputum production , headache , haemoptysis , diarrhoea , anorexia , sore throat
, chest pain , chills and nausea and vomiting in studies of patients in China¹3,60,80,81 Self -
reported olfac tory and taste disorders were also reported by patients in Italy . Most people
showed signs of diseases after an incubation period of 1-14 days ( most commonly around 5 days
) , and dyspnoea and pneumonia developed within a median time of 8 days from illness onset . In
a report of 72,314 cases in China , 81 % of the cases were classified as mild , 14 % were severe
cases that required ventilation in an intensive care unit ( ICU ) and a 5 % were critical ( that is , the
patients had respiratory failure , septic shock and / or multiple organ dysfunction or failure ) 9,86 .
On admission , ground - glass opacity was the most common radiologic finding on chest computed
tomography ( CT ) 13,60,80,81 . Most patients also developed marked lymphopenia , similar to
what was observed in patients with SARS and MERS , and non - survivors devel oped severer
lymphopenia over time 13,60,80,81 . Compared with non - ICU patients , ICU patients had higher
levels
of plasma cytokines , which suggests an immunopatho logical process caused by a cytokine
storm60,86,87 . In this cohort of patient , around 2.3 % people died within a median time of 16
days from disease onset2,86 . Men older than 68 years had a higher risk of respiratory fail ure ,
acute cardiac injury and heart failure that led to death , regardless of a history of cardiovascular
disease86 ( FIG . 4 ) . Most patients recovered enough to be released from hospital in 2 weeks⁹ ,
80 ( FIG . 4 ) . Early transmission of SARS - CoV - 2 in Wuhan in December 2019 was initially
linked to the Huanan Seafood Wholesale Market , and it was suggested as the source of the
outbreak 9.22,60 . However , community transmission might have happened before that88 . Later ,
ongoing human - to - human transmission propagated the outbreak . It is generally accepted that
SARS - CoV - 2 is more transmissible than SARS - CoV and MERS - CoV ; however ,
determination of an accurate reproduction number ( RO ) for COVID - 19 is not possible yet , as
many asymptomatic infections cannot be accurately accounted for at this stage . An estimated R0
of 2.5 ( ranging from 1.8 to 3.6 ) has been proposed for SARS - CoV - 2 recently , compared with
2.0-3.0 for SARS - CoV . Notably , most of the SARS - CoV - 2 human - to - human transmission
early in China occurred in family clusters , and in other countries large outbreaks also happened in
other set tings , such as migrant worker communities , slaughter houses and meat packing plants ,
indicating the necessity of isolating infected people12,91-93 . Nosocomial transmis sion was not
the main source of transmission in China because of the implementation of infection control
measures in clinical settings . By contrast , a high risk of nosocomial transmission was reported in
some other

lower respiratory tracts . Acute viral interstitial pneu monia and humoral and cellular immune
responses were observed 48,75 . Moreover , prolonged virus shedding peaked early in the course
of infection in asymptomatic macaques , and old monkeys showed severer intersti tial pneumonia
than young monkeys , which is similar to what is seen in patients with COVID - 19 . In human
ACE2 - transgenic mice infected with SARS - CoV - 2 , typ ical interstitial pneumonia was present ,
and viral anti gens were observed mainly in the bronchial epithelial cells , macrophages and
alveolar epithelia . Some human ACE2 - transgenic mice even died after infection 70 , 71 , In wide
- type mice , a SARS - CoV - 2 mouse - adapted strain with the N501Y alteration in the RBD of the
S protein was generated at passage 6. Interstitial pneumonia and inflammatory responses were
found in both young and aged mice after infection with the mouse - adapted strain74 . Golden
hamsters also showed typical symptoms after being infected with SARS - CoV - 2 ( REF.77 ) . In
other animal models , including cats and ferrets , SARS - CoV - 2 could efficiently replicate in the
upper respiratory tract but did not induce severe clinical symptoms 43,78 . As trans mission by
direct contact and air was observed in infected ferrets and hamsters , these animals could be used
to model different transmission modes of COVID - 19 ( REFS77-79 ) . Animal models offer
important information for understanding the pathogenesis of SARS - CoV - 2 infection and the
transmission dynamics of SARS CoV - 2 , and are important to evaluate the efficacy of antiviral
therapeutics and vaccines .
Clinical and epidemiological features It appears that all ages of the population are susceptible to
SARS - CoV - 2 infection , and the median age of infection is around 50 years , 13.60,80,81 .
However , clinical manifesta tions differ with age . In general , older men ( > 60 years old ) with co
- morbidities are more likely to develop severe respiratory disease that requires hospitalization

The pathogenesis of SARS - CoV - 2 infection in humans manifests itself as mild symptoms to
severe respiratory failure . On binding to epithelial cells in the respiratory tract , SARS - CoV - 2
starts replicating and migrating down to the airways and enters alveo lar epithelial cells in the
lungs . The rapid replication of SARS - CoV - 2 in the lungs may trigger a strong immune response
. Cytokine storm syndrome causes acute res piratory distress syndrome and respiratory failure ,
which is considered the main cause of death in patients with COVID - 19 ( REFS60,61 ) . Patients
of older age ( > 60 years ) and with serious pre - existing diseases have a greater risk of
developing acute respiratory distress syndrome and death 62-64 ( FIG . 4 ) . Multiple organ failure
has also been reported in some COVID - 19 cases.13,65
Histopathological changes in patients with COVID - 19 occur mainly in the lungs . Histopathology
analyses showed bilateral diffused alveolar damage , hyaline membrane formation , desquamation
of pneumocytes and fibrin deposits in lungs of patients with severe COVID - 19 . Exudative
inflammation was also shown in some cases . Immunohistochemistry assays detected SARS -
CoV - 2 antigen in the upper airway , bronchiolar epithelium and submucosal gland epithelium , as
well as in type I and type II pneumocytes , alveolar macrophages and hyaline membranes in the
lungs 13,60,66,67 Animal models used for studying SARS - CoV - 2 infection pathogenesis
include non - human primates ( rhesus macaques , cynomolgus monkeys , marmosets and African
green monkeys ) , mice ( wild - type mice ( with mouse - adapted virus ) and human ACE2 -
transgenic or human ACE2 - knock - in mice ) , ferrets and golden hamsters 43,48,68-74 . In non -
human primate animal mod els , most species display clinical features similar to those of patients
with COVID - 19 , including virus shedding , virus replication and host responses to SARS - CoV -
2 infection 69,72,73 . For example , in the rhesus macaque model , high viral loads were detected
in the upper and

appeared asymptomatic 45. Another serological study detected SARS - CoV - 2 neutralizing
antibodies in cat serum samples collected in Wuhan after the COVID - 19 outbreak , providing
evidence for SARS - CoV - 2 infection in cat populations in Wuhan , although the potential of
SARS - CoV - 2 transmission from cats to humans is currently uncertain 46 .
Receptor use and pathogenesis SARS - CoV - 2 uses the same receptor as SARS - CoV ,
angiotensin - converting enzyme 2 ( ACE2 ) ¹147 . Besides human ACE2 ( hACE2 ) , SARS - CoV
- 2 also recognizes ACE2 from pig , ferret , rhesus monkey , civet , cat , pan golin , rabbit and
dog11,43,48,49 . The broad receptor usage of SARS - CoV - 2 implies that it may have a wide
host range , and the varied efficiency of ACE2 usage in differ ent animals may indicate their
different susceptibilities to SARS - CoV - 2 infection . The S1 subunit of a corona virus is further
divided into two functional domains , an N - terminal domain and a C - terminal domain . Structural
and biochemical analyses identified a 211 amino acid region ( amino acids 319-529 ) at the S1 C -
terminal domain of SARS - CoV - 2 as the RBD , which has a key role in virus entry and is the
target of neu tralizing antibodies5 ( FIG . 3a ) . The RBM mediates con tact with the ACE2 receptor
( amino acids 437-507 of SARS - CoV - 2 S protein ) , and this region in SARS - CoV - 2 differs
from that in SARS - CoV in the five residues crit 50,51

Currently , our knowledge on the animal origin of SARS - CoV - 2 remains incomplete to a large
part . The reservoir hosts of the virus have not been clearly proven . It is unknown whether SARS -
CoV - 2 was transmitted to humans through an intermediate host and which animals may act as its
intermediate host . Detection of RaTG13 , RmYN02 and pangolin coronaviruses implies that
diverse coronaviruses similar to SARS - CoV - 2 are circulating in wildlife . In addition , as previous
stud ies showed recombination as the potential origin of some sarbecoviruses such as SARS -
CoV , it cannot be excluded that viral RNA recombination among different related coronaviruses
was involved in the evolution of SARS - CoV - 2 . Extensive surveillance of SARS - CoV - 2 related
viruses in China , Southeast Asia and other regions targeting bats , wild and captured pangolins
and other wildlife species will help us to better understand the zoonotic origin of SARS - CoV - 2 .
Besides wildlife , researchers investigated the sus ceptibility of domesticated and laboratory
animals to SARS - CoV - 2 infection . The study demonstrated exper imentally that SARS - CoV -
2 replicates efficiently in cats and in the upper respiratory tract of ferrets , whereas dogs , pigs ,
chickens and ducks were not susceptible to SARS - CoV - 2 ( REF.43 ) . The susceptibility of
minks was documented by a report from the Netherlands on an outbreak of SARS - CoV - 2
infection in farmed minks . Although the symptoms in most infected minks were mild , some
developed severe respiratory distress and died of interstitial pneumonia44 . Both virologi cal and
serological testing found evidence for natural SARS - CoV - 2 infection in two dogs from
households with human cases of COVID - 19 in Hong Kong , but the dogs

residues for receptor binding40 ( FIG . 3b ) . In comparison with the Guangdong strains , pangolin
coronaviruses reported from Guangxi are less similar to SARS - CoV - 2 , with 85.5 % genome
sequence identity³9 . The repeated occurrence of SARS - CoV - 2 - related coronavirus infec tions
in pangolins from different smuggling events suggests that these animals are possible hosts of the
viruses . However , unlike bats , which carry coronaviruses healthily , the infected pangolins
showed clinical signs and histopathological changes , including interstitial pneumonia and
inflammatory cell infiltration in diverse organs40 . These abnormalities suggest that pangolins are
unlikely to be the reservoir of these coronaviruses but more likely acquired the viruses after
spillover from the natural hosts .
An intermediate host usually plays an important role in the outbreak of bat - derived emerging
coronaviruses ; for example , palm civets for SARS - CoV and dromedary camels for MERS - CoV
. The virus strains carried by these two intermediate hosts were almost genetically identi cal to the
corresponding viruses in humans ( more than 99 % genome sequence identity ) ¹ . Despise an
RBD that is virtually identical to that of SARS - CoV - 2 , the pangolin coronaviruses known to date
have no more than 92 % genome identity with SARS - CoV - 2 ( REF . 42 ) . The avail able data
are insufficient to interpret pangolins as the intermediate host of SARS - CoV - 2 . So far , no
evidence has shown that pangolins were directly involved in the emergence of SARS - CoV - 2 .

in Yunnan . This novel bat virus , denoted ' RmYN02 ' , is 93.3 % identical to SARS - CoV - 2
across the genome . In the long lab gene , it exhibits 97.2 % identity to SARS - CoV - 2 , which is
even higher than for RaTG13 ( REF . 28 ) . In addition to RaTG13 and RmYN02 , phyloge netic
analysis shows that bat coronaviruses ZC45 and ZXC21 previously detected in Rhinolophus
pusillus bats from eastern China also fall into the SARS - CoV - 2 lineage of the subgenus
Sarbecovirus 36 ( FIG . 2 ) . The dis covery of diverse bat coronaviruses closely related to SARS -
CoV - 2 suggests that bats are possible reservoirs of SARS - CoV - 2 ( REF.37 ) . Nevertheless ,
on the basis of current findings , the divergence between SARS - CoV - 2 and related bat
coronaviruses likely represents more than 20 years of sequence evolution , suggesting that these
bat coronaviruses can be regarded only as the likely evolu tionary precursor of SARS - CoV - 2 but
not as the direct progenitor of SARS - CoV - 2 ( REF.38 ) .
Beyond bats , pangolins are another wildlife host probably linked with SARS - CoV - 2 . Multiple
SARS - CoV - 2 related viruses have been identified in tissues of Malayan pangolins smuggled
from Southeast Asia into southern China from 2017 to 2019. These viruses from pangolins
independently seized by Guangxi and Guangdong pro vincial customs belong to two distinct
sublineages39-41 . The Guangdong strains , which were isolated or sequenced by different
research groups from smug gled pangolins , have 99.8 % sequence identity with each other . They
are very closely related to SARS - CoV - 2 , exhibiting 92.4 % sequence similarity . Notably , the
RBD of Guangdong pangolin coronaviruses is highly similar to that of SARS - CoV - 2 . The
receptor - binding motif ( RBM ; which is part of the RBD ) of these viruses has only one amino
acid variation from SARS - CoV - 2 , and it is identical to that of SARS - CoV - 2 in all five critical

differs from that in SARS - CoV in the five residues crit ical for ACE2 binding , namely Y455L ,
L486F , N493Q , D494S and T501N52 ( FIG . 3b , c ) . Owing to these residue changes ,
interaction of SARS - CoV - 2 with its receptor stabilizes the two virus - binding hotspots on the
surface of hACE2 ( REF 50 ) ( FIG . 3d ) . Moreover , a four - residue motif in the RBM of SARS -
CoV - 2 ( amino acids 482-485 : G - V - E - G ) results in a more compact conformation of its
hACE2 - binding ridge than in SARS - CoV and ena bles better contact with the N - terminal helix
of hACE2 ( REF . 50 ) . Biochemical data confirmed that the structural features of the SARS - CoV
- 2 RBD has strengthened its hACE2 binding affinity compared with that of SARS - CoV50,52,53
Similarly to other coronaviruses , SARS - CoV - 2 needs proteolytic processing of the S protein to
activate the endocytic route . It has been shown that host proteases participate in the cleavage of
the S protein and activate the entry of SARS - CoV - 2 , including transmembrane protease serine
protease 2 ( TMPRSS2 ) , cathepsin L and furin47,54,55 . Single - cell RNA sequencing data
showed that TMPRSS2 is highly expressed in several tissues and body sites and is co -
expressed with ACE2 in nasal epithelial cells , lungs and bronchial branches , which explains
some of the tissue tropism of SARS - CoV - 2 ( REFS56,57 ) . SARS - CoV - 2 pseudovirus entry
assays revealed that TMPRSS2 and cathepsin L have cumu lative effects with furin on activating
virus entry55 . Analysis of the cryo - electron microscopy structure of SARS - CoV - 2 S protein
revealed that its RBD is mostly in the lying - down state , whereas the SARS - CoV S protein
assumes equally standing - up and lying - down conforma tional states 50,51,58,59 . A lying -
down conformation of the SARS - CoV - 2 S protein may not be in favour of receptor binding but is
helpful for immune evasion 55 .

07:27 M.
infections clinically or through routine lab tests . Therefore travel history becomes important .
However , as the epidemic spreads , the travel history will become irrelevant .
Treatment [ 21 , 23 ] Treatment is essentially supportive and symptomatic .
The first step is to ensure adequate isolation ( discussed later ) to prevent transmission to other
contacts , patients and healthcare workers . Mild illness should be managed at home with
counseling about danger signs . The usual principles are maintaining hydration and nutrition and
controlling fever and cough . Routine use of antibiotics and antivirals such as oseltamivir should be
avoided in confirmed cases . In hypoxic patients , provision of oxygen through nasal prongs , face
mask , high flow nasal

07:27 M.
ncbi.nlm.nih.gov/pmc/arti 1 glass opacities and sub segmental consolidation . It is also abnormal in
asymptomatic patients / patients with no clinical evidence of lower respiratory tract involvement . In
fact , abnormal CT scans have been used to diagnose COVID - 19 in suspect cases with negative
molecular diagnosis ; many of these patients had positive molecular tests on repeat testing [ 22 ] .

Differential Diagnosis [ 21 ] The differential diagnosis includes all types of respiratory viral
infections [ influenza , parainfluenza , respiratory syncytial virus ( RSV ) , adenovirus , human
metapneumovirus , non COVID 19 coronavirus ] , atypical organisms ( mycoplasma , chlamydia )
and bacterial infections . It is not possible to differentiate COVID - 19 from these infections
clinically or through routine
07:25 M. consolidation .
It is also abnormal in asymptomatic patients / patients with no clinical evidence of lower respiratory
tract involvement . In fact , abnormal CT scans have been used to diagnose COVID - 19 in
suspect cases with negative molecular diagnosis ; many of these patients had positive molecular
tests on repeat testing [ 22 ] .
Differential Diagnosis [ 21 ] The differential diagnosis includes all types of respiratory viral
infections [ influenza , parainfluenza , respiratory syncytial virus ( RSV ) , adenovirus , human
metapneumovirus , non COVID 19 coronavirus ] , atypical organisms ( mycoplasma , chlamydia )
and bacterial infections . It is not possible to differentiate COVID - 19 from these infections
clinically or through routine lab tests . Therefore travel history becomes important . However , as
the epidemic spreads , the travel history

07:25 M.
epidemic progresses , commercial tests will become available .
Other laboratory investigations are usually non specific . The white cell count is usually normal or
low . There may be lymphopenia ; a lymphocyte count < 1000 has been associated with severe
disease . The platelet count is usually normal or mildly low . The CRP and ESR are generally
elevated but procalcitonin levels are usually normal . A high procalcitonin level may indicate a
bacterial co - infection . The ALT / AST , prothrombin time , creatinine , D - dimer , CPK and LDH
may be elevated and high levels are associated with severe disease .
The chest X - ray ( CXR ) usually shows bilateral infiltrates but may be normal in early disease .
The CT is more sensitive and specific . CT imaging generally shows infiltrates , ground glass
opacities and sub segmental

07:25 M
of persistent local transmission or contact with patients with similar travel history or those with
confirmed COVID - 19 infection . However cases may be asymptomatic or even without fever . A
confirmed case is a suspect case with a positive molecular test .
Specific diagnosis is by specific molecular tests on respiratory samples ( throat swab /
nasopharyngeal swab / sputum / endotracheal aspirates and bronchoalveolar lavage ) . Virus may
also be detected in the stool and in severe cases , the blood . It must be remembered that the
multiplex PCR panels currently available do not include the COVID - 19 . Commercial tests are
also not available at present . In a suspect case in India , the appropriate sample has to be sent to
designated reference labs in India or the National Institute of Virology in Pune . As the epidemic
progresses , commercial tests
07:25 M. was linked to a family member and 26 children had history of travel / residence to Hubei
province in China . All the patients were either asymptomatic ( 9 % ) or had mild disease . No
severe or critical cases were seen . The most common
symptoms were fever ( 50 % ) and cough ( 38 % ) . All patients recovered with symptomatic
therapy and there were no deaths . One case of severe pneumonia and multiorgan dysfunction in
a child has also been reported [ 19 ] . Similarly the neonatal cases that have been reported have
been mild [ 20 ] .
Diagnosis [ 21 ] A suspect case is defined as one with fever , sore throat and cough who has
history of travel to China or other areas of persistent local transmission or
contact with patients with similar travel history or those with confirmed

07:25 M
Interestingly , disease in patients outside Hubei province has been reported to be milder than
those from Wuhan [ 17 ] . Similarly , the severity and case fatality rate in patients outside China
has been reported to be milder [ 6 ] . This may either be due to selection bias wherein the cases
reporting from Wuhan included only the severe cases or due to predisposition of the Asian
population to the virus due to higher expression of ACE2 receptors on the respiratory mucosa [ 11
].
Disease in neonates , infants and children has been also reported to be significantly milder than
their adult counterparts . In a series of 34 children admitted to a hospital in Shenzhen , China
between January 19th and February 7th , there were 14 males and 20 females . The median age
was 8 y 11 mo and in 28 children the infection was linked to a family member and 26

07:25 M.
ncbi.nlm.nih.gov/pmc/arti 1 identified angiotensin receptor 2 ( ACE₂ ) as the receptor through

which the virus enters the respiratory mucosa [ 11 ] .

The basic case reproduction rate ( BCR ) is estimated to range from 2 to 6.47 in various

modelling studies [ 11 ] . In comparison , the BCR of SARS was 2 and 1.3 for pandemic flu

H1N1 2009 [ 2 ] .

Clinical Features [ 8 , 15-18 ] The clinical features of COVID - 19 are varied , ranging from

asymptomatic state to acute respiratory distress syndrome and multi organ dysfunction .

The common clinical features include fever ( not in all ) , cough , sore throat , headache ,

fatigue , headache , myalgia and breathlessness . Conjunctivitis has also been described .
Thus , they are indistinguishable from other respiratory infections . In a subcat

07:25 M. urupiets can spreau 1-4 m anu uepusn on surfaces . The virus can remain
viable on surfaces for days in favourable atmospheric conditions but are destroyed in less than a
minute by common disinfectants like sodium hypochlorite , hydrogen peroxide etc. [ 13 ] . Infection
is acquired either by inhalation of these droplets or touching surfaces contaminated by them and
then touching the nose , mouth and eyes . The virus is also present in the stool and contamination
of the water supply and subsequent transmission via aerosolization / feco oral route is also
hypothesized [ 6 ] . As per current information , transplacental transmission from pregnant women
to their fetus has not been described [ 14 ] . However , neonatal disease due to post natal
transmission is described [ 14 ] . The incubation period varies from 2 to 14 d [ median 5 d ] .
Studies have identified angiotensin receptor 2 ( ACE ) as the recentor through which

07:25 M
Epidemiology and Pathogenesis [ 10 , 11 ]
All ages are susceptible . Infection is transmitted through large droplets generated during coughing
and sneezing by symptomatic patients but can also occur from asymptomatic people and before
onset of symptoms [ 9 ] . Studies have shown higher viral loads in the nasal cavity as compared to
the throat with no difference in viral burden between symptomatic and asymptomatic people [ 12 ] .
Patients can be infectious for as long as the symptoms last and even on clinical recovery . Some
people may act as super spreaders ; a UK citizen who attended a conference in Singapore
infected 11 other people while staying in a resort in the French Alps and upon return to the UK [ 6 ]
. These infected droplets can spread 1-2 m and deposit

07:24 M.
ncbi.nlm.nih.gov/pmc/arti ( 1 exponentially in other countries including South Korea , Italy and Iran
. Of those infected , 20 % are in critical condition , 25 % have recovered , and 3310 ( 3013 in
China and 297 in other countries ) have died [ 2 ] . India , which had reported only 3 cases till
2/3/2020 , has also seen a sudden spurt in cases . By 5/3/2020 , 29 cases had been reported ;
mostly in Delhi , Jaipur and Agra in Italian tourists and their contacts . One case was reported in
an Indian who traveled back from Vienna and exposed a large number of school children in a
birthday party at a city hotel . Many of the contacts of these cases have been quarantined .

These numbers are possibly an underestimate of the infected and dead due to limitations of
surveillance and testing . Though the SARS - COV - 2 originated from bats , the intermediary
07:24 M.
ncbi.nlm.nih.gov/pmc/arti exponentially in other countries including South Korea , Italy and Iran .
Of those infected , 20 % are in critical condition , 25 % have recovered , and 3310 ( 3013 in China
and 297 in other countries ) have died [ 2 ] . India , which had reported only 3 cases till 2/3/2020 ,
has also seen a sudden spurt in cases . By 5/3/2020 , 29 cases had been reported ; mostly in
Delhi , Jaipur and Agra in Italian tourists and their contacts . One case was reported in an Indian
who traveled back from Vienna and exposed a large number of school children in a birthday party
at a city hotel . Many of the contacts of these cases have been quarantined .
These numbers are possibly an underestimate of the infected and dead due to limitations of
surveillance and testing . Though the SARS - CoV - 2 originated from bats , the intermediary

07:24 M.
Cases continued to increase exponentially and modelling studies reported an epidemic doubling
time of 1.8 d [ 10 ] . In fact on the 12th of February , China changed its definition of confirmed
cases to include patients with negative / pending molecular tests but with clinical , radiologic and
epidemiologic features of COVID - 19 leading to an increase in cases by 15,000 in a single day [ 6
] . As of 05/03/2020 96,000 cases worldwide ( 80,000 in China ) and 87 other countries and 1
international conveyance ( 696 , in the cruise ship Diamond Princess parked off the coast of Japan
) have been reported [ 2 ] . It is important to note that while the number of new cases has reduced
in China lately , they have increased exponentially in other countries including South Korea , Italy
and Iran . Of those infected , 20 % are in critical
and

07:24 M.
extended to other cities of Hupel province . Cases of COVID - 19 in countries outside China were
reported in those with no history of travel to China suggesting that local human - to human
transmission was occurring in these countries [ 9 ] . Airports in different countries including India
put in screening mechanisms to detect symptomatic people returning from China and placed them
in isolation and testing them for COVID - 19 . Soon it was apparent that the infection could be
transmitted from asymptomatic people and also before onset of symptoms . Therefore , countries
including India who evacuated their citizens from Wuhan through special flights or had travellers
returning from China , placed all people symptomatic or otherwise in isolation for 14 d and tested
them for the virus .
Cases continued to increase exponentially and modelling studies
14 ANTIVIRAL THERAPY COVID - 19 is an infectious disease caused by SARS - CoV - 2 , which
is also termed the novel coronavirus and is diligently associated with the SARS virus . The Ministry
of Science and Technology from the People's Republic of China declared three potential antiviral
medicines . suitable for treating COVID - 19 . Those three medicines are , namely , Favilavir ,
chloroquine phosphate and remdesivir . A clinical trial was conducted to test the efficacy of those
three drugs , and the results proved that out of the three medicines above only Favilavir is
effective in treating the patients with novel coronavirus . The remaining two drugs were effective in
treating malaria.62
Likewise a study carried out in the United States by the National Institute of Health proved that
remdesivir is effective in treating the Middle East respiratory syndrome coronavirus ( MERS CoV )
, which is also a type of coronavirus that was transmitted from monkeys . The drug remdesivir was
also used in the United States for treating the patients with COVID - 19 . There has been a
proposal to use the combination of protease inhibitors lopinavir - ritonavir for treating the patients
affected by COVID - 19.62

It is also evident that remdesivir was effective in treating the patients who were infected with Ebola
virus . Per this evidence , China has already started testing the efficacy of remdesivir in treating
the patients with COVID - 19 , especially in Wuhan , where the outbreak occurred . Chloroquine ,
which is an existing drug which is currently used in treating malaria cases , was given to more than
100 patients who were affected with novel coronavirus to test its efficacy.62
A multicentric study was conducted in China to test the effectiveness of remdesivir in treating the
patients with COVID - 19 . Thus , the results of the clinical trial proved that remdesivir has a
considerably acceptable level of efficacy for treating the patients with COVID - 19 . Therefore , the
National Health Commission of the People's Republic of China decided to include remdesivir in the
Guidelines for the Prevention , Diagnosis and Treatment of Pneumonia Caused by COVID 19,62
Chloroquine and hydroxychloroquine are existing anti - malaria drugs also given to more than 30
patients infected with COVID - 19 in Guangdong province and Hunan province to test their
effectiveness and efficacy . Thus , the results of the clinical trial showed that the

results of the clinical trial showed that the patients who were given chloroquine had a significant
reduction in their body temperature . The clinical trial also showed better recovery among the
patients who were given chloroquine and hydroxy chloroquine.63-65 Hydroxychloroquine
treatment is significantly associated with viral load reduction as well as disappearance in COVID -
19 patients . Further , the outcome is reinforced by azithromycin . The role of lopinavir and
ritonavir in the treatment of COVID - 19 is uncertain . A potential benefit was suggested by
preclinical data , but additional data has failed to confirm it . Tocilizumab is an immunomodulating
agent used as adjunct therapy in some protocols based on a theoretical mechanism and limited
preliminary data.66
15 HOME CARE Home management may be appropriate for patients with mild infection who can
be adequately isolated in the outpatient setting . Management of such patients should focus on
prevention of transmission to others , and monitoring for clinical deterioration , which should
prompt hospitalisation . Interim recommendations on home management of patients with COVID -
19 can be found on

patients with COVID - 19 can be found on the WHO and CDC websites.6 67 16 CONCLUSION
The corona virus ( COVID - 19 ) spreads at an alarming rate all over the world . The outbreak of
the virus has confronted the world's economic , medical and public health infrastructure . Elderly
and
immunocompromised patients also are susceptible to the virus's mortal impacts . Currently , there
is no documented cure for the virus and no vaccine has been created , although some treatment
protocols have been promising . Therefore , the virus can be controlled with the appropriate
prevention strategies . Also , attempts have to be made to formulate systematic strategies to
prevent such future zoonotic outbreaks .

07:25 M. including IL2 , IL7 , IL10 , GCSF , IP10 , MCP1 , MIP1A , and TNFa [ 15 ] . The median
time from onset of symptoms to dyspnea was 5 d , hospitalization 7 d and acute respiratory
distress syndrome ( ARDS ) 8 d . The need for intensive care admission was in 25 30 % of
affected patients in published series . Complications witnessed included acute lung injury , ARDS ,
shock and acute kidney injury . Recovery started in the 2nd or 3rd wk . The median duration of
hospital stay in those who recovered was 10 d . Adverse outcomes and death are more common
in the elderly and those with underlying co - morbidities ( 50-75 % of fatal cases ) . Fatality rate in
hospitalized adult patients ranged from 4 to 11 % . The overall case fatality rate is estimated to
range between 2 and 3 % [ 2 ] .
Interestingly , disease in patients outside Hubei province has been

07:29 M All clinicians should keep themselves updated about recent

developments including global spread of the disease .
Non - essential international travel should be avoided at this time .
People should stop spreading myths and false information about the disease and try to allay panic
and anxiety of the public .
Conclusions This new virus outbreak has challenged the economic , medical and public health
infrastructure of China and to some extent , of other countries especially , its neighbours . Time
alone will tell how the virus will impact our lives here in India . More so , future outbreaks of viruses
and pathogens of zoonotic origin are likely to continue . Therefore , apart from curbing this
outbreak . efforts should be made to

recovered patients and used for plasma transfusion twice in a volume of 200 to 250 ml on the day
of collection ( 310 ) . At present , treatment for sepsis and ARDS mainly involves antimicrobial
therapy , source control , and supportive care . Hence , the use of therapeutic plasma exchange
can be considered an option in managing such severe conditions . Further randomized trials can
be designed to investigate its efficacy ( 311 ) .
Potential Therapeutic Agents Potent therapeutics to combat SARS - CoV - 2 infection include virus
binding molecules , molecules or inhibitors targeting particular enzymes implicated in replication
and transcription process of the virus , helicase inhibitors , vital viral proteases and proteins ,
protease inhibitors of host cells , endocytosis inhibitors , short interfering RNA ( siRNA ) ,
neutralizing antibodies , MAbs against the host receptor , MAbs interfering with the S1 RBD ,
antiviral peptide aimed at S2 , and natural drugs / medicines ( 7 , 166 , 186 ) . The S protein acts
as the critical target for developing CoV antivirals , like inhibitors of S protein and S cleavage ,
neutralizing antibodies , RBD - ACE2 blockers , siRNAs , blockers of the fusion core , and
proteases ( 168 ) . All of these therapeutic approaches have revealed

All of these therapeutic approaches have revealed both in vitro and in vivo anti - CoV potential .
Although in vitro research carried out with these therapeutics showed efficacy , most need
appropriate support from randomized animal or human trials . Therefore , they might be of limited
applicability and require trials against SARS - CoV - 2 to gain practical usefulness . The binding of
SARS - CoV - 2 with ACE2 leads to the exacerbation of pneumonia as a consequence of the
imbalance in the renin angiotensin system ( RAS ) . The virus - induced pulmonary inflammatory
responses may be reduced by the administration of ACE inhibitors ( ACEI ) and angiotensin type -
1 receptor ( AT1R ) ( 207 ) . Several investigations have suggested the use of small - molecule
inhibitors for the potential control of SARS - CoV infections . Drugs of the FDA - approved
compound library were screened to identify four small - molecule inhibitors of MERS - CoV (
chlorpromazine , chloroquine , loperamide , and lopinavir ) that inhibited viral replication . These
compounds also hinder SARS - CoV and human CoVs ( 208 ) . Therapeutic strategies involving
the use of specific antibodies or compounds that neutralize cytokines and their receptors will help
to restrain the host inflammatory responses . Such drugs acting specifically in the respiratory tract
will help to

specifically in the respiratory tract will help to reduce virus - triggered immune pathologies in
COVID - 19 ( 209 ) . The later stages of coronavirus induced inflammatory cascades are
characterized by the release of proinflammatory interleukin - 1 ( IL - 1 ) family members , such as
IL - 1 and IL - 33 . Hence , there exists a possibility that the inflammation associated with
coronavirus can be inhibited by utilizing anti - inflammatory cytokines that belong to the IL - 1
family ( 92 ) . It has also been suggested that the actin protein is the host factor that is involved in
cell entry and pathogenesis of SARS - CoV - 2 . Hence , those drugs that modulate the biological
activity of this protein , like ibuprofen , might have some therapeutic application in managing the
disease ( 174 ) . The plasma angiotensin 2 level was found to be markedly elevated in COVID - 19
infection and was correlated with viral load and lung injury . Hence , drugs that block angiotensin
receptors may have potential for treating COVID - 19 infection ( 121 ) . A scientist from Germany ,
named Rolf Hilgenfeld , has been working on the identification of drugs for the treatment of
coronaviral infection since the time of the first SARS outbreak ( 19 ) . The SARS - CoV S2 subunit
has a significant function in mediating virus fusion that provides entry into the host cell . Heptad
repeat 1 ( HR1 ) and heptad

Animal Models and Cell Cultures For evaluating the potential of vaccines and therapeutics against
CoVs , including SARS - CoV , MERS - CoVs , and the presently emerging SARS CoV - 2 ,
suitable animal models that can mimic the clinical disease are needed ( 211 , 212 ) . Various
animal models were assessed for SARS - and MERS CoVs , such as mice , guinea pigs , golden
Syrian hamsters , ferrets , rabbits , nonhuman primates like rhesus macaques and marmosets ,
and cats ( 185 , 213-218 ) . The specificity of the virus to hACE2 ( receptor of SARS - CoV ) was
found to be a significant barrier in developing animal models . Consequently , a SARS - CoV
transgenic mouse model has been developed by inserting the hACE2 gene into the mouse
genome ( 219 ) . The inability of MERS - CoV to replicate in the respiratory tracts of animals ( mice
, hamsters , and ferrets ) is another limiting factor . However , with genetic engineering , a 288-330
++ MERS - CoV genetically modified mouse model was developed and now is in use for the
assessment of novel drugs and vaccines against MERS - CoV ( 220 ) . In the past , small animals
( mice or hamsters ) have been targeted for being closer to a humanized structure , such as
mouse DPP4 altered with human DPP4 ( hDPP4 ) , hDPP4 - transduced mice , and hDPP4 - Tg
mice ( transgenic for expressing

virological , radiological , and pathological observations indicated that the monkeys with
reexposure had no recurrence of COVID - 19 , like the SARS - CoV - 2 - infected monkeys without
rechallenge . These findings suggest that primary infection with SARS - CoV - 2 could protect from
later exposures to the virus , which could help in defining disease prognosis and crucial inferences
for designing and developing potent vaccines against COVID - 19 ( 274 ) .
PREVENTION , CONTROL , AND MANAGEMENT In contrast to their response to the 2002 SARS
outbreak , China has shown immense political openness in reporting the COVID - 19 outbreak
promptly . They have also performed rapid sequencing of COVID - 19 at multiple levels and
shared the findings globally within days of identifying the novel virus ( 225 ) . The move made by
China opened a new chapter in global health security and diplomacy . Even though complete
lockdown was declared following the COVID - 19 outbreak in Wuhan , the large - scale movement
of people has resulted in a radiating spread of infections in the surrounding provinces as well as to
several other countries . Large - scale screening programs might

countries . Large - scale screening programs might help us to control the spread of this virus .
However , this is both challenging as well as time - consuming due to the present extent of
infection ( 226 ) . The current scenario demands effective implementation of vigorous prevention
and control strategies owing to the prospect of COVID - 19 for nosocomial infections ( 68 ) . Follow
- ups of infected patients by telephone on day 7 and day 14 are advised to avoid any further
unintentional spread or nosocomial transmission ( 312 ) . The availability of public data sets
provided by independent analytical teams will act as robust evidence that would guide us in
designing interventions against the COVID - 19 outbreak . Newspaper reports and social media
can be used to analyze and reconstruct the progression of an outbreak . They can help us to
obtain detailed patient level data in the early stages of an outbreak ( 227 ) . Immediate travel
restrictions imposed by several countries might have contributed significantly to preventing the
spread of SARS - CoV - 2 globally ( 89 , 228 ) . Following the outbreak , a temporary ban was
imposed on the wildlife trade , keeping in mind the possible role played by wild animal species in
the origin of SARS - CoV - 2 / COVID - 19 ( 147 ) . Making a permanent and bold decision on the
trade of wild animal species is necessary to prevent the possibility

Princess , Celebrity Apex , and Ruby Princess . The number of confirmed COVID - 19 cases
around the world is on the rise . The success of preventive measures put forward by every country
is mainly dependent upon their ability to anticipate the approaching waves of patients . This will
help to properly prepare the health care workers and increase the intensive care unit ( ICU )
capacity ( 321 ) . Instead of entirely relying on lockdown protocols , countries should focus mainly
on alternative intervention strategies , such as large - scale testing , contract tracing , and
localized quarantine of suspected cases for limiting the spread of this pandemic virus . Such
intervention strategies will be useful either at the beginning of the pandemic or after lockdown
relaxation ( 322 ) . Lockdown should be imposed only to slow down disease progression among
the population so that the health care system is not overloaded .
The reproduction number ( Ro ) of COVID - 19 infection was earlier estimated to be in the range of
1.4 to 2.5 ( 70 ) ; recently , it was estimated to be 2.24 to 3.58 ( 76 ) . Compared to its coronavirus
predecessors , COVID - 19 has an Ro value that is greater than that of MERS ( Ro < 1 ) ( 108 )
but less than that of SARS ( Ro value of 2 to 5 ) ( 93 ) . Still , to prevent further spread of disease
at mass gatherings ,
involved in the COVID - 19 outbreak is of great importance , because the strain on their mental
well being will affect their attention , concentration , and decision - making capacity . Hence , for
control of the COVID - 19 outbreak , rapid steps should be taken to protect the mental health of
medical workers ( 229 ) . Since the living mammals sold in the wet market are suspected to be the
intermediate host of SARS CoV - 2 , there is a need for strengthening the regulatory mechanism
for wild animal trade ( 13 ) . The total number of COVID - 19 confirmed cases is on a continuous
rise and the cure rate is relatively low , making disease control very difficult to achieve . The
Chinese government is making continuous efforts to contain the disease by taking emergency
control and prevention measures . They have already built a hospital for patients affected by this
virus and are currently building several more for accommodating the continuously increasing
infected population ( 230 ) . The effective control of SARS CoV - 2 / COVID - 19 requires high -
level interventions like intensive contact tracing , as well as the quarantine of people with
suspected infection and the isolation of infected individuals . The implementation of rigorous
control and preventive measures together might control the Ro number and reduce the
transmission risk ( 228 ) . Considering the zoonotic

susceptible individuals . Hence , hand hygiene is equally as important as the use of appropriate
PPE , like face masks , to break the transmission cycle of the virus ; both hand hygiene and face
masks help to lessen the risk of COVID - 19 transmission ( 315 ) .
Medical staff are in the group of individuals most at risk of getting COVID - 19 infection . This is
because they are exposed directly to infected patients . Hence , proper training must be given to
all hospital staff on methods of prevention and protection so that they become competent enough
to protect themselves and others from this deadly disease ( 316 ) . As a preventive measure ,
health care workers caring for infected patients should take extreme precautions against both
contact and airborne transmission . They should use PPE such as face masks ( N95 or FFP3 ) ,
eye protection ( goggles ) , gowns , and gloves to nullify the risk of infection ( 299 ) .
The human - to - human transmission reported in SARS - CoV - 2 infection occurs mainly through
droplet or direct contact . Due to this finding , frontline health care workers should follow stringent
infection control and preventive measures , such as the use of PPE , to prevent infection ( 110 ) .
The mental health of the medical / health workers who are involved in the COVID - 19 outbreak is
of great

prevent further spread of disease at mass gatherings , functions remain canceled in the affected
cities , and persons are asked to work from home ( 232 ) . Hence , it is a relief that the current
outbreak of COVID - 19 infection can be brought under control with the adoption of strategic
preventive and control measures along with the early isolation of subsequent cases in the coming
days . Studies also report that since air traffic between China and African countries increased
many times over in the decade after the SARS outbreak , African countries need to be vigilant to
prevent the spread of novel coronavirus in Africa ( 225 ) . Due to fear of virus spread , Wuhan City
was completely shut down ( 233 ) . The immediate control of the ongoing COVID - 19 outbreaks
appears a mammoth task , especially for developing countries , due to their inability to allocate
quarantine stations that could screen infected individuals ' movements ( 234 ) . Such
underdeveloped countries should divert their resources and energy to enforcing the primary level
of preventive measures , like controlling the entry of individuals from China or countries where the
disease has flared up , isolating the infected individuals , and quarantining individuals with
suspected infection . Most of the sub - Saharan African countries have a fragile health system that
can be

countries have a fragile health system that can be crippled in the event of an outbreak . Effective
management of COVID - 19 would be difficult for low - income countries due to their inability to
respond rapidly due to the lack of an efficient health care system ( 65 ) . Controlling the imported
cases is critical in preventing the spread of COVID - 19 to other countries that have not reported
the disease until now . The possibility of an imported case of COVID - 19 leading to sustained
human - to - human transmission was estimated to be 0.41 . This can be reduced to a value of
0.012 by decreasing the mean time from the onset of symptoms to hospitalization and can only be
made possible by using intense disease surveillance systems ( 235 ) . The silent importations of
infected individuals ( before the manifestation of clinical signs ) also contributed significantly to the
spread of disease across the major cities of the world . Even though the travel ban was
implemented in Wuhan ( 89 ) , infected persons who traveled out of the city just before the
imposition of the ban might have remained undetected and resulted in local outbreaks ( 236 ) .
Emerging novel diseases like COVID - 19 are difficult to contain within the country of origin , since
globalization has led to a world without borders . Hence , international collaboration plays a vital
role

fatigue . Individuals with asymptomatic and atypical clinical manifestations were also identified
recently , further adding to the complexity of disease dynamics . Atypical clinical transmission
manifestations may only express symptoms such as fatigue instead of respiratory signs such as
fever , cough , and sputum . In such cases , the clinician must be vigilant for the possible
occurrence of asymptomatic and atypical clinical manifestations to avoid the possibility of missed
diagnoses . The present outbreak caused by SARS - CoV - 2 was , indeed , expected . Similar to
previous outbreaks , the current pandemic also will be contained shortly . However , the real
question is , how are we planning to counter the next zoonotic CoV epidemic that is likely to occur
within the next 5 to 10 years or perhaps sooner ? Our knowledge of most of the bat CoVs is
scarce , as these viruses have not been isolated and studied , and extensive studies on such
viruses are typically only conducted when they are associated with specific disease outbreaks .
The next step following the control of the COVID - 19 outbreak in China should be focused on
screening , identification , isolation , and characterization of CoVs present in wildlife species of
China , particularly in bats . Both in vitro and in vivo studies ( using suitable animal models )
should be conducted

( using suitable animal models ) should be conducted to evaluate the risk of future epidemics .
Presently , licensed antiviral drugs or vaccines against SARS CoV , MERS - CoV , and SARS -
CoV - 2 are lacking . However , advances in designing antiviral drugs and vaccines against
several other emerging diseases will help develop suitable therapeutic agents against COVID - 19
in a short time . Until then , we must rely exclusively on various control and prevention measures
to prevent this new disease from becoming a pandemic .

4 VIROLOGY Coronaviruses , a family of viruses within the nidoviruses superfamily , are further
classified according to their genera , alpha- , beta- , gamma and deltacoronaviruses ( a- , B- , y-
and 8- ) . Among those , alpha and beta species are capable of contaminating only mammals ,
whereas the other two genera can infect birds and could also infect mammals . 13 , 14 Two of
these genera belong to human coronaviruses ( HCOVS ) : a - coronaviruses , which comprise
human coronavirus 229E ( hcov229E ) and human coronavirus NL63 ( hcovNL63 ) , and B
coronaviruses , which are human coronavirus HKU1 , human coronavirus OC43 , MERS - COV (
known as Middle East respiratory syndrome coronavirus ) and SARS - CoV ( referred to as severe
acute respiratory syndrome coronavirus ) . 1 15
The severe acute respiratory syndrome CoV - 2 ( SARS - CoV - 2 ) is now named novel COVID -
19 ( coronavirus disease 2019 ) .16 Genome sequencing and phylogenetic research revealed that
the COVID - 19 - causing coronavirus is a beta - coronavirus that belongs to the same subtypes as
SARS virus , but still exists in a variant group . The receptor - binding gene region

No Text Found

4.2 Viral replication Usually replication of coronavirus occurs within the cytoplasm and is closely
associated with endoplasmic reticulum and other cellular membrane organelles . Human
coronaviruses are thought to invade cells , primarily through different receptors . For 229E and
OC43 , amino peptidase - N ( AP - N ) and a sialic acid containing receptor , respectively , were
known to function in this role . After the virus enters the host cell and uncoating process occurs ,
the genome is transcribed , and then , translated . A characteristic feature of replication is that all
mRNAs form an enclosed group of typical 3 ' ends ; only the special portions of the 5 ' ends are
translated . In total , about 7 mRNAs are produced . The shortest mRNA codes and the others can
express the synthesis of another genome segment for nucleoprotein . At the cell membrane ,
these proteins are collected and genomic RNA is initiated as a mature particle type by burgeoning
from internal cell membranes . 22 , 23
5 PATHOGENESIS Coronaviruses are tremendously precise and mature in most of the airway
epithelial cells as observed through both in vivo and in vitro

there , there is an increase in the outbreak of this virus through human - to - human transmission ,
with the fact that it has become widespread around the globe . This confirms the fact similar to the
previous epidemics , including SARS and MERS , that this coronavirus exhibited potential human -
to - human transmission , as it was recently declared a pandemic by WHO.26
Respiratory droplets are the major carrier for coronavirus transmission . Such droplets can either
stay in the nose or mouth or enter the lungs via the inhaled air . Currently , it is known that COVID
- 19's transmission from one person to another also occurs through touching either an infected
surface or even an object . With the current scant awareness of the transmission systems however
, airborne safety measures with a high - risk procedure have been proposed in many countries .
Transmission levels , or the rates from one person to another , reported differ by both location and
interaction with involvement in infection control . It is stated that even asymptomatic individuals or
those individuals in their incubation period can act as carrier of SARS - CoV2.27 , 28 With the data
and evidence provided by the CDC , the usual incubation period is probably 3 to 7 days ,
sometimes being prolonged up to even 2 weeks , and the typical symptom occurrence

6.1 Laboratory testing for coronavirus disease 2019 ( COVID 19 ) in suspected human cases
The assessment of the patients with COVID - 19 should be based on the clinical features and also
epidemiological factors . The screening protocols must be prepared and followed per the native
context.31 Collecting and testing of specimen samples from the suspected individual is considered
to be one of the main principles for controlling and managing the outbreak of the disease in a
country . The suspected cases must be screened thoroughly in order to detect the virus with the
help of nucleic acid amplification tests such as reverse transcription polymerase chain reaction (
RT PCR ) . If a country or a particular region does not have the facility to test the specimens , the
specimens of the suspected individual should be sent to the nearest reference laboratories per the
list provided by WHO.32
It is also recommended that the suspected patients be tested for the other respiratory pathogens
by performing the routine laboratory investigation per the local guidelines , mainly to differentiate
from other viruses that include influenza virus , parainfluenza virus , adenovirus , respiratory
syncytial virus , rhinovirus , human
weeks , and the typical symptom occurrence from incubation period to infection takes an average
of 12.5 days.² 29 6 CLINICAL DIAGNOSIS The symptoms of COVID - 19 remain very similar to
those of the other respiratory epidemics in the past , which include SARS and MERS , but here the
range of symptoms includes mild rhinitis to septic shock . Some intestinal disturbances were
reported with the other epidemics , but COVID - 19 was devoid of such symptoms . When
examined , unilateral or bilateral involvement compatible with viral pneumonia is observed in the
patients , and bilateral multiple lobular and sub - segmental consolidation areas were observed in
patients hospitalised in the intensive care unit . Comorbid patients showed a more severe clinical
course than predicted from previous epidemics . Diagnosis of COVID - 19 includes the complete
history of travel and touch , with laboratory testing . It is more preferable to choose serological
screening , which can help to analyse even the asymptomatic infections ; several serological tests
are in progress for SARS - COV - 2.14 , 30

observed through both in vivo and in vitro experiments . There is an enhanced nasal secretion
observed along with local oedema because of the damage of the host cell , which further
stimulates the synthesis of inflammatory mediators . In addition , these reactions can induce
sneezing , difficulty breathing by causing airway inhibition and elevate mucosal temperature .
These viruses , when released , chiefly affect the lower respiratory tract , with the signs and
symptoms existing clinically . Also , the virus further affects the intestinal lymphocytes , renal cells
, liver cells and T - lymphocytes . Furthermore , the virus induces T - cell apoptosis , causing the
reaction of the T - cell to be erratic , resulting in the immune system's complete collapse . 24 , 25
5.1 Mode of transmission In fact it was accepted that the original transmission originated from a
seafood market , which had a tradition of selling live animals , where the majority of the patients
had either worked or visited , although up to now the understanding of the COVID - 19
transmission risk remains incomplete . 16 In addition , while the newer patients had no exposure
to the market and still got the virus from the humans present there , there is an increase in the
outbreak of

variant group . The receptor - binding gene region appears to be very similar to that of the SARS
CoV and it is believed that the same receptor would be used for cell entry.17 4.1 Virion structure
and its genome Coronaviruses are structurally enveloped , belonging to the positive - strand RNA
viruses category that has the largest known genomes of RNA . The structures of the coronavirus
are more spherical in shape , but their structure has the potential to modify their morphology in
response to environmental conditions , being pleomorphic . The capsular membrane which
represents the outer envelope usually has glycoprotein projection and covers the nucleus ,
comprising a matrix protein containing a positive - strand RNA . Since the structure possesses 5 ' -
capped and 3 ' - polyadenylated ends , it remains identical to the cellular mRNAs . 18 The
structure is comprised of hemagglutinin esterase ( HE ) ( present only in some beta -
coronaviruses ) , spike ( S ) , small membrane ( E ) , membrane ( M ) and nucleocapsid ( N ) , as
shown ( Figure 1 ) . The envelope containing glycoprotein is responsible for attachment to the host
cell , which possesses the primary anti - genic epitopes mainly those

CONCLUDING REMARKS Several years after the global SARS epidemic , the current SARS -
CoV - 2 / COVID - 19 pandemic has served as a reminder of how novel pathogens can rapidly
emerge and spread through the human population and eventually cause severe public health
crises . Further research should be conducted to establish animal models for SARS - CoV - 2 to
investigate replication , transmission dynamics , and pathogenesis in humans . This may help
develop and evaluate potential therapeutic strategies against zoonotic CoV epidemics . Present
trends suggest the occurrence of future outbreaks of CoVs due to changes in the climate , and
ecological conditions may be associated with human - animal contact . Live animal markets , such
as the Huanan South China Seafood Market , represent ideal conditions for interspecies contact of
wildlife with domestic birds , pigs , and mammals , which substantially increases the probability of
interspecies transmission of CoV infections and could result in high risks to humans due to
adaptive genetic recombination in these viruses ( 323-325 ) .
The COVID - 19 - associated symptoms are fever , cough , expectoration , headache , and
myalgia or fatigue . Individuals with asymptomatic and atypical

We also predict the possibility of another outbreak , as predicted by Fan et al . ( 6 ) . Indeed , the
present outbreak caused by SARS - CoV - 2 ( COVID 19 ) was expected . Similar to previous
outbreaks , the current outbreak also will be contained shortly . However , the real issue is how we
are planning to counter the next zoonotic CoV epidemic that is likely to occur within the next 5 to
10 years or even sooner ( Fig . 7 ) .

transmission risk ( 228 ) . Considering the zoonotic links associated with SARS - CoV - 2 , the One
Health approach may play a vital role in the prevention and control measures being followed to
restrain this pandemic virus ( 317-319 ) . The substantial importation of COVID - 19
presymptomatic cases from Wuhan has resulted in independent , self sustaining outbreaks across
major cities both within the country and across the globe . The majority of Chinese cities are now
facing localized outbreaks of COVID - 19 ( 231 ) . Hence , deploying efficient public health
interventions might help to cut the spread of this virus globally . The occurrence of COVID - 19
infection on several cruise ships gave us a preliminary idea regarding the transmission pattern of
the disease . Cruise ships act as a closed environment and provide an ideal setting for the
occurrence of respiratory disease outbreaks . Such a situation poses a significant threat to
travelers , since people from different countries are on board , which favors the introduction of the
pathogen ( 320 ) . Although nearly 30 cruise ships from different countries have been found
harboring COVID - 19 infection , the major cruise ships that were involved in the COVID - 19
outbreaks are the Diamond Princess , Grand Princess , Celebrity Apex , and Ruby Princess . The

animal species is necessary to prevent the possibility of virus spread and initiation of an outbreak
due to zoonotic spillover ( 1 ) .
Personal protective equipment ( PPE ) , like face masks , will help to prevent the spread of
respiratory infections like COVID - 19 . Face masks not only protect from infectious aerosols but
also prevent the transmission of disease to other susceptible individuals while traveling through
public transport systems ( 313 ) . Another critical practice that can reduce the transmission of
respiratory diseases is the maintenance of hand hygiene . However , the efficacy of this practice in
reducing the transmission of respiratory viruses like SARS - CoV - 2 is much dependent upon the
size of droplets produced . Hand hygiene will reduce disease transmission only if the virus is
transmitted through the formation of large droplets ( 314 ) . Hence , it is better not to
overemphasize that hand hygiene will prevent the transmission of SARS - CoV - 2 , since it may
produce a false sense of safety among the general public that further contributes to the spread of
COVID - 19 . Even though airborne spread has not been reported in SARS - CoV - 2 infection ,
transmission can occur through droplets and fomites , especially when there is close , unprotected
contact between infected and susceptible individuals . Hence , hand hygiene is

mice , and hDPP4 - Tg mice ( transgenic for expressing hDPP4 ) for MERS - CoV infection ( 221 )
. The CRISPR - Cas9 gene - editing tool has been used for inserting genomic alterations in mice ,
making them susceptible to MERS - CoV infection ( 222 ) . Efforts are under way to recognize
suitable animal models for SARS - CoV2 / COVID - 19 , identify the receptor affinity of this virus ,
study pathology in experimental animal models , and explore virus - specific immune responses
and protection studies , which together would increase the pace of efforts being made for
developing potent vaccines and drugs to counter this emerging virus . Cell lines , such as monkey
epithelial cell lines ( LLC - MK2 and Vero - B4 ) , goat lung cells , alpaca kidney cells , dromedary
umbilical cord cells , and advanced ex vivo three - dimensional tracheobronchial tissue , have
been explored to study human CoVs ( MERS - CoV ) ( 223 , 224 ) . Vero and Huh - 7 cells (
human liver cancer cells ) have been used for isolating SARS - CoV - 2 ( 194 ) . Recently , an
experimental study with rhesus monkeys as animal models revealed the absence of any viral
loads in nasopharyngeal and anal swabs , and no viral replication was recorded in the primary
tissues at a time interval of 5 days post - reinfection in reexposed monkeys ( 274 ) . The
subsequent virological , radiological , and pathological
into the host cell . Heptad repeat 1 ( HR1 ) and heptad repeat 2 ( HR2 ) can interact and form a six
- helix bundle that brings the viral and cellular membranes in close proximity , facilitating its fusion
. The sequence alignment study conducted between COVID - 19 and SARS - CoV identified that
the S2 subunits are highly conserved in these CoVs . The HR1 and HR2 domains showed 92.6 %
and 100 % overall identity , respectively ( 210 ) . From these findings , we can confirm the
significance of COVID - 19 HR1 and HR2 and their vital role in host cell entry . Hence , fusion
inhibitors target the HR1 domain of S protein , thereby preventing viral fusion and entry into the
host cell . This is another potential therapeutic strategy that can be used in the management of
COVID - 19 . Other than the specific therapy directed against COVID - 19 , general treatments
play a vital role in the enhancement of host immune responses against the viral agent .
Inadequate nutrition is linked to the weakening of the host immune response , making the
individual more susceptible . The role played by nutrition in disease susceptibility should be
measured by evaluating the nutritional status of patients with COVID - 19 ( 205 ) .

The exploration of fully human antibodies ( human single - chain antibodies ; HuscFvs ) or
humanized nanobodies ( single - domain antibodies ; sdAb , VH / VHH ) could aid in blocking virus
replication , as these agents can traverse the virus infected cell membranes ( transbodies ) and
can interfere with the biological characteristics of the replicating virus proteins . Such examples
include transbodies to the influenza virus , hepatitis C virus , Ebola virus , and dengue virus ( 206 )
. Producing similar transbodies against intracellular proteins of coronaviruses , such as papain -
like proteases ( PLpro ) , cysteine - like protease ( 3CLpro ) , or other nsps , which are essential
for replication and transcription of the virus , might formulate a practical move forward for a safer
and potent passive immunization approach for virus - exposed persons and rendering therapy to
infected patients . In a case study on five grimly sick patients having symptoms of severe
pneumonia due to COVID - 19 , convalescent plasma administration was found to be helpful in
patients recovering successfully . The convalescent plasma containing a SARS - CoV - 2 - specific
ELISA ( serum ) antibody titer higher than 1 : 1,000 and neutralizing antibody titer more significant
than 40 was collected from the recovered patients and used for plasma transfusion

RBD , indicating its potential as a therapeutic agent in the management of COVID - 19 . It can be
used alone or in combination with other effective neutralizing antibodies for the treatment and
prevention of COVID - 19 ( 202 ) . Furthermore , SARS CoV - specific neutralizing antibodies , like
m396 and CR3014 , failed to bind the S protein of SARS - CoV 2 , indicating that a particular level
of similarity is mandatory between the RBDs of SARS - CoV and SARS - CoV - 2 for the cross -
reactivity to occur .
Further assessment is necessary before confirming the effectiveness of such combination therapy
. In addition , to prevent further community and nosocomial spread of COVID - 19 , the
postprocedure risk management program should not be neglected ( 309 ) . Development of broad
- spectrum inhibitors against the human coronaviral pathogens will help to facilitate clinical trials on
the effectiveness of such inhibitors against endemic and emerging coronaviruses ( 203 ) . A
promising animal study revealed the protective effect of passive immunotherapy with immune
serum from MERS immune camels on mice infected with MERS - CoV ( 204 ) . Passive
immunotherapy using convalescent plasma is another strategy that can be used for treating
COVID - 19 - infected , critically ill patients ( 205 ) .

considerable protection in mice against a MERS CoV lethal challenge . Such antibodies may play
a crucial role in enhancing protective humoral responses against the emerging CoVs by aiming
appropriate epitopes and functions of the S protein . The cross - neutralization ability of SARS -
CoV RBD specific neutralizing MAbs considerably relies on the resemblance between their RBDs ;
therefore , SARS - CoV RBD - specific antibodies could cross neutralized SL CoVs , i.e. , bat - SL
- CoV strain WIV1 ( RBD with eight amino acid differences from SARS CoV ) but not bat - SL -
CoV strain SHC014 ( 24 amino acid differences ) ( 200 ) .
Appropriate RBD - specific MAbs can be recognized by a relative analysis of RBD of SARS CoV -
2 to that of SARS - CoV , and cross - neutralizing SARS - CoV RBD - specific MAbs could be
explored for their effectiveness against COVID - 19 and further need to be assessed clinically .
The U.S. biotechnology company Regeneron is attempting to recognize potent and specific MAbs
to combat COVID - 19 . An ideal therapeutic option suggested for SARS - CoV - 2 ( COVID - 19 )
is the combination therapy comprised of MAbs and the drug remdesivir ( COVID - 19 ) ( 201 ) .
The SARS - CoV - specific human MAb CR3022 is found to bind with SARS - CoV - 2 RBD ,
indicating its potential as a therapeutic agent