[12/22, 3:36 AM] ......

: 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

[12/22, 3:37 AM] ......: by the University of Oxford. In a randomized controlled phase I/II trial, it induced
neutralizing antibodies against SARS-COV-2 in all 1,077 participants after a second vaccine dose, while its
safety profile was acceptable as well 163. The NIAID and Moderna co-manufactured mRNA-1273, a lipid
nanoparticle-formulated mRNA vaccine candidate that encodes the stabilized prefusion SARS-CoV-2 S
protein. Its immunogenicity has been confirmed by a phase I trial in which robust neutralizing antibody
responses were induced in a dose-dependent manner and increased after a second dose 164. .
Regarding inactivated vaccines, a successful phase I/II trial involv- ing 320 participants has been reported
in China. The whole-virus COVID-19 vaccine had a low rate of adverse reactions and effectively induced
neutralizing antibody production 165. The verified safety and immunogenicity support advancement of
these vaccine candidates to phase III clinical trials, which will evaluate their efficacy in protecting healthy
populations from SARS-CoV-2 infection.

Future perspectives

COVID-19 is the third highly pathogenic human coro- navirus disease to date. Although less deadly than
SARS and MERS, the rapid spreading of this highly conta- gious disease has posed the severest threat to
global health in this century. The SARS-CoV-2 outbreak has lasted for more than half a year now, and it is
likely that

[12/22, 3:37 AM] ......: 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).

[12/22, 3:37 AM] ......: Initially, the epicenter of the SARS-CoV-2 pandemic was China, which reported a
significant number of deaths associated with COVID-19, with 84,458 laboratory-confirmed cases and
4,644 deaths as of 13 May 2020 (Fig. 4). As of 13 May 2020, SARS-CoV-2 confirmed cases have been
reported in more than 210 countries apart from China (Fig. 3 and 4) (WHO Situation Report 114) (25,
64). COVID-19 has been reported on all continents except Antarctica. For many weeks, Italy was the
focus of concerns regarding the large number of cases, with 221,216 cases and 30,911 deaths, but now,
the United States is the country with the largest number of cases, 1,322,054, and 79,634 deaths. Now,
the United Kingdom has even more cases (226,4671) and deaths (32,692) than Italy. A John Hopkins
University web platform has provided daily updates on the basic epidemiology of the COVID-19
outbreak

[12/22, 3:37 AM] ......: 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

[12/22, 3:38 AM] ......: Based on molecular characterization, SARS- CoV-2 is considered a new
Betacoronavirus belonging to the subgenus Sarbecovirus (3). A few other critical zoonotic viruses (MERS-
related COV and SARS-related CoV) belong to the same genus. However, SARS-CoV-2 was identified as a
distinct virus based on the percent identity with other Betacoronavirus; conserved open reading frame
1a/b (ORF1a/b) is below 90% identity (3). An overall 80% nucleotide identity was observed between
SARS-CoV-2 and the original SARS-CoV, along with 89% identity with ZC45 and ZXC21 SARS- related CoVs
of bats (2, 31, 36). In addition, 82% identity has been observed between SARS-CoV-2 and human SARS-
CoV Tor2 and human SARS-CoV BJ01 2003 (31). A sequence identity of only 51.8% was observed
between MERS-related CoV and the recently emerged SARS-CoV-2 (37). Phylogenetic analysis of the
structural genes also revealed that SARS-CoV-2 is closer to bat SARS-related CoV. Therefore, SARS-CoV-2
might have originated from bats, while other amplifier hosts might have played a role in disease
transmission to humans (31). Of note, the other two zoonotic CoVs (MERS-related CoV and SARS-related
CoV) also originated from bats (38, 39). Nevertheless, for SARS and MERS, civet

[12/22, 3:38 AM] ......: areas. For example, a cohort study in London revea 44% of the frontline health-
care workers from a hosp were infected with SARS-CoV-2 (REF.94).
The high transmissibility of SARS-CoV-2 may be attributed to the unique virological features of SARS-
CoV-2. Transmission of SARS-CoV occurred mainly after illness onset and peaked following dis- ease
severity⁹5. However, the SARS-CoV-2 viral load in upper respiratory tract samples was already high- est
during the first week of symptoms, and thus the risk of pharyngeal virus shedding was very high at the
beginning of infection 96,97. It was postulated that undocumented infections might account for 79% of
documented cases owing to the high transmissibility of the virus during mild disease or the
asymptomatic period. A patient with COVID-19 spreads viruses in liquid droplets during speech.
However, smaller and much more numerous particles known as aerosol parti- cles can also be visualized,
which could linger in the air for a long time and then penetrate deep into the lungs when inhaled by
someone else98-100. Airborne trans- mission was also observed in the ferret experiments mentioned
above. SARS-CoV-2-infected ferrets shed

[12/22, 3:38 AM] ......: wrought havoc in China and caused a pandemic situation in the worldwide
population, leading to disease outbreaks that have not been controlled to date, although extensive
efforts are being put in place to counter this virus (25). This virus has been proposed to be
designated/named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International
Committee on Taxonomy of Viruses (ICTV), which determined the virus belongs to the Severe acute
respiratory syndrome-related coronavirus category and found this virus is related to SARS-CoVS (26).
SARS-CoV-2 is a member of the order Nidovirales, family Coronaviridae, subfamily Orthocoronavirinae,
which is subdivided into four genera, viz., Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and
genera Alphacoronavirus and Betacoronavirus originate from bats, while Gammacoronavirus and
Deltacoronavirus have evolved from bird and swine gene pools (24, 28, 29, 275).

Deltacoronavirus (3, 27). The

Coronaviruses possess an unsegmented, single- stranded, positive-sense RNA genome of around 30 kb,
enclosed by a 5'-cap and 3'-poly(A) tail (30). The genome of SARS-CoV-2 is 29,891 bp long, with a G+C
content of 38% (31). These viruses are encircled with envelope containing viral an

[12/22, 3:38 AM] ......: 8 PREVENTION

The WHO and other agencies such as the CDC have published protective measures to mitigate the
spread of COVID-19. This involves frequent hand washing with handwash containing 60% of alcohol and
soap for at least 20 seconds.

Another important measure is avoiding close contact with sick people and keeping a social distance of 1
metre always to everyone who is coughing and sneezing. Not touching the nose, eyes and mouth was
also suggested. While coughing or sneezing, covering the mouth and nose with a cloth/tissue or the bent
elbow is advised. Staying at home is recommended for those who are sick, and wearing a facial mask is
advised when going out among people. Furthermore, it is recommended to clean and sterilise frequently
touched surfaces such as phones and doorknobs on a daily basis.5 Staying at home as much as possible
is advisable for those who are at higher risk for severe illness, to minimise the risk of exposure to COVID-
19 during outbreaks.53 51,52

[12/22, 3:38 AM] ......: turtles, ducks, fish, Siamese crocodiles, and other animal meats without any fear
of COVID-19. The Chinese government is encouraging people to feel they can return to normalcy.
However, this could be a risk, as it has been mentioned in advisories that people should avoid contact
with live-dead animals as much as possible, as SARS-CoV-2 has shown zoonotic spillover. Additionally,
we cannot rule out the possibility of new mutations in the same virus being closely related to contact
with both animals and humans at the market (284). In January 2020, China imposed a temporary ban on
the sale of live- dead animals in wet markets. However, now hundreds of such wet markets have been
reopened without optimizing standard food safety and

sanitation practices (286).

With China being the most populated country in the world and due to its domestic and international
food exportation policies, the whole world is now facing the menace of COVID-19, including China itself.
Wet markets of live-dead animals do not maintain strict food hygienic practices. Fresh blood splashes
are present everywhere, on the floor and tabletops, and such food customs could encourage many
pathogens to adapt, mutate, and jump the species barrier. As a result, the whole world is suffering from
novel SARS-CoV-2, with more than

[12/22, 3:39 AM] ......: significance of frequent and good hand hygiene and

sanitation practices needs to be given due emphasis (249-252). Future explorative research needs to be
conducted with regard to the fecal-oral transmission of SARS-CoV-2, along with focusing on
environmental investigations to find out if this virus could stay viable in situations and atmospheres
facilitating such potent routes of transmission. The correlation of fecal concentrations of viral RNA with
disease severity needs to be determined, along with assessing the gastrointestinal symptoms and the
possibility of fecal SARS-CoV-2 RNA detection during the COVID-19 incubation period convalescence
phases of the disease (249-252). or

The lower respiratory tract sampling techniques, like bronchoalveolar lavage fluid aspirate, are
considered the ideal clinical materials, rather than the throat swab, due to their higher positive rate on
the nucleic acid test (148). The diagnosis of COVID- 19 can be made by using upper-respiratory-tract
specimens collected using nasopharyngeal and oropharyngeal swabs. However, these techniques are
associated with unnecessary risks to health care workers due to close contact with patients (152).
Similarly, a single patient with a high viral load was reported to contaminate an entire endoscopy room
by shedding the virus, which may remain viable for at
[12/22, 3:39 AM] ......: visible signs of infection, making it challenging to identify animals actively
excreting MERS-CoV that has the potential to infect humans. However, they may shed MERS-CoV
through milk, urine, feces, and nasal and eye discharge and can also be found in the raw organs (108). In
a study conducted to evaluate the susceptibility of animal species to MERS-CoV infection, llamas and
pigs were found to be susceptible, indicating the possibility of MERS- CoV circulation in animal species
other than dromedary camels (109).

Following the outbreak of SARS in China, SARS-CoV-like viruses were isolated from Himalayan palm
civets (Paguma larvata) and raccoon dogs (Nyctereutes procyonoides) found in a live-animal market in
Guangdong, China. The animal isolates obtained from the live-animal market retained a 29-nucleotide
sequence that was not present in most of the human isolates (78). These findings were critical in
identifying the possibility of interspecies transmission in SARS-CoV. The higher diversity and prevalence
of bat coronaviruses in this region compared to those in previous reports indicate a host/pathogen
coevolution. SARS-like coronaviruses also have been found circulating in the Chinese horseshoe bat
(Rhinolophus sinicus) populations. The in vitro and in vivo studies carried

[12/22, 3:39 AM] ......: COVID-19 patients showing severe signs are treated symptomatically along with
oxygen therapy. In such cases where the patients progress toward respiratory failure and become
refractory to oxygen therapy, mechanical ventilation is necessitated. The COVID-19-induced septic shock
can be managed by providing adequate hemodynamic support (299). Several classes of drugs are
currently being evaluated for their potential therapeutic action against SARS-CoV-2. Therapeutic agents
that have anti-SARS-CoV-2 activity can be broadly classified into three categories: drugs that block virus
entry into the host cell, drugs that block viral replication as well as its survival within the host cell, and
drugs that attenuate the exaggerated host immune response (300). An inflammatory cytokine storm is
commonly seen in critically ill COVID-19 patients. Hence, they may benefit from the use of timely anti-
inflammation treatment. Anti-inflammatory therapy using drugs like glucocorticoids, cytokine inhibitors,
JAK inhibitors, and chloroquine/hydroxychloroquine should be done only after analyzing the risk/benefit
ratio in COVID-19 patients (301). There have not been any studies concerning the application of
nonsteroidal anti-inflammatory drugs (NSAID) to COVID-19-infected patients. However, reasonable
pieces of evidence are available that link NSAID

[12/22, 3:39 AM] ......: 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

[12/22, 3:40 AM] ......: with SARS and MERS (117).

SARS-CoV-2 invades the lung parenchyma, resulting in severe interstitial inflammation of the lungs. This
is evident on computed tomography (CT) images as ground-glass opacity in the lungs. This lesion initially
involves a single lobe but later expands to multiple lung lobes (118). The histological assessment of lung
biopsy samples obtained from COVID-19-infected patients revealed diffuse alveolar damage, cellular
fibromyxoid exudates, hyaline membrane formation, and desquamation of pneumocytes, indicative of
acute respiratory distress syndrome (119). It was also found that the SARS-CoV-2-infected patients often
have lymphocytopenia with or without leukocyte abnormalities. The degree of lymphocytopenia gives
an idea about disease prognosis, as it is found to be positively correlated with disease severity (118).
Pregnant women are considered to have a higher risk of getting infected by COVID-19. The
coronaviruses can cause adverse outcomes for the fetus, such as intrauterine growth restriction,
spontaneous abortion, preterm delivery, and perinatal death.

Nevertheless, the possibility of intrauterine

maternal-fetal transmission (vertical transmission) of

CoVs is low and was not seen during either the

SARS- or MERS-CoV outbreak (120). However,

[12/22, 3:40 AM] ......: helicase activity.

Among the evaluated compounds, 4-(cyclopent-

1-en-3-ylamino)-5-[2-(4-

iodophenyl)hydrazinyl]-4H-1,2,4-triazole-3-thiol and 4-(cyclopent-1-en-3-ylamino)-5-[2-(4-

chlorophenyl)hydrazinyl]-4H-1,2,4-triazole-3-thiol were found to be the most potent. These compounds
were used for in silico studies, and molecular docking was accomplished into the active binding site of
MERS-CoV helicase nsp13 (21). Further studies are required for evaluating the therapeutic potential of
these newly identified compounds in the management of COVID-19 infection.

Passive Immunization/Antibody Therapy/MAb

Monoclonal antibodies (MAbs) may be helpful in the intervention of disease in CoV-exposed individuals.
Patients recovering from SARS showed robust neutralizing antibodies against this CoV infection (164). A
set of MAbs aimed at the MERS- CoV S protein-specific domains, comprising six specific epitope groups
interacting with receptor- binding, membrane fusion, and sialic acid-binding sites, make up crucial entry
tasks of S protein (198, 199). Passive immunization employing weaker and strongly neutralizing
antibodies provided considerable protection in mice against a MERS-

[12/22, 3:40 AM] ......: Swine acute diarrhea syndrome coronavirus

(SADS-CoV) was first identified in suckling piglets

Alphacoronavirus (106). The outbreak

having severe enteritis and belongs to the genus was associated with considerable scale mortality of
piglets (24,693 deaths) across four farms in China (134). The virus isolated from the piglets was almost
identical to and had 95% genomic similarity with horseshoe bat (Rhinolophus species) coronavirus
HKU2, suggesting a bat origin of the pig virus (106, 134, 135). It is also imperative to note that the SADS-
CoV outbreak started in Guangdong province, near the location of the SARS pandemic origin (134).
Before this outbreak, pigs were not known to be infected with bat-origin coronaviruses. This indicates
that the bat-origin coronavirus jumped to pig by breaking the species barrier. The next step of this jump
might not end well, since pigs are considered the mixing vessel for influenza A viruses due to their ability
to be infected by both human and avian influenza A viruses (136).

Similarly, they may act as the mixing vessel for coronaviruses, since they are in frequent contact with
both humans and multiple wildlife species. Additionally, pigs are also found to be susceptible to
infection with human SARS-CoV and MERS-COV, making this scenario a nightmare (109, 137). It is

[12/22, 3:40 AM] ......: and SARS, along with adopting and strengthening a
few precautionary measures owing to the unknown nature of this novel virus (36, 189). Presently, the
main course of treatment for severely affected SARS-CoV-2 patients admitted to hospitals includes
mechanical ventilation, intensive care unit (ICU) admittance, and symptomatic and supportive therapies.
Additionally, RNA synthesis inhibitors (lamivudine and tenofovir disoproxil fumarate), remdesivir,
neuraminidase inhibitors, peptide (EK1), anti-inflammatory drugs, abidol, and Chinese traditional
medicine (Lianhuaqingwen and ShuFengJieDu capsules) could aid in COVID-19 treatment. However,
further clinical trials are being carried out concerning their safety and efficacy (7). It might require
months to a year(s) to design and develop effective drugs, therapeutics, and vaccines against COVID-19,
with adequate evaluation and approval from regulatory bodies and moving to the bulk production of
many millions of doses at commercial levels to meet the timely demand of mass populations across the
globe (9). Continuous efforts are also warranted to identify and assess viable drugs and
immunotherapeutic regimens that revealed proven potency in combating other viral agents similar to
SARS-CoV-2.

COVID-19 patients showing severe signs are

[12/22, 3:41 AM] ......: Coronavirus is the most prominent example of a virus that has crossed the
species barrier twice from wild animals to humans during SARS and MERS outbreaks (79, 102). The
possibility of crossing the species barrier for the third time has also been suspected in the case of SARS-
CoV-2 (COVID-19). Bats are recognized as a possible natural reservoir host of both SARS-CoV and MERS-
CoV infection. In contrast, the possible intermediary host is the palm civet for SARS-CoV and the
dromedary camel for MERS-CoV infection (102). Bats are considered the ancestral hosts for both SARS
and MERS (103). Bats are also considered the reservoir host of human coronaviruses like HCoV-229E and
HCoV-NL63 (104). In the case of COVID-19, there are two possibilities for primary transmission: it can be
transmitted either through intermediate hosts, similar to that of SARS and MERS, or directly from bats
(103). The emergence paradigm put forward in the SARS outbreak suggests that SARS-CoV originated
from bats (reservoir host) and later jumped to civets (intermediate host) and incorporated changes
within the receptor-binding domain (RBD) to improve binding to civet ACE2. This civet-adapted virus,
during their subsequent exposure to humans at live markets, promoted further adaptations that
resulted in the epidemic strain (104). Transmission can also

[12/22, 3:41 AM] ......: (96.7%), and S genes (90.4%). The RBD of S protein in CoV isolated from pangolin
was almost identical

(one amino acid difference) to that of SARS-CoV-2. A comparison of the genomes suggests
recombination between pangolin-CoV-like viruses with the bat-CoV-RaTG13-like virus. All this suggests
the potential of pangolins to act as the intermediate host of SARS-CoV-2 (145).

Human-wildlife interactions, which

are increasing in the context of climate change (142), are further considered high risk and responsible
for the emergence of SARS-CoV. COVID-19 is also suspected of having a similar mode of origin. Hence, to
prevent the occurrence of another zoonotic spillover (1), exhaustive coordinated efforts are needed to
identify the high-risk pathogens harbored by wild animal populations, conducting surveillance among
the people who are susceptible to zoonotic spillover events (12), and to improve the biosecurity
measures associated with the wildlife trade (146). The serological surveillance studies conducted in
people living in proximity to bat caves had earlier identified the serological confirmation of SARS- related
CoVs in humans. People living at the wildlife-human interface, mainly in rural China, are regularly
exposed to SARS-related CoVs (147). These findings will not have any significance until a

[12/22, 3:41 AM] ......: route warrants the introduction of negative fecal viral nucleic acid test results as
one of the additional discharge criteria in laboratory-confirmed cases of COVID-19 (326).

The COVID-19 pandemic does not have any novel factors, other than the genetically unique pathogen
and a further possible reservoir. The cause and the likely future outcome are just repetitions of our
previous interactions with fatal coronaviruses. The only difference is the time of occurrence and the
genetic distinctness of the pathogen involved. Mutations on the RBD of CoVs facilitated their capability
of infecting newer hosts, thereby expanding their reach to all corners of the world (85). This is a
potential threat to the health of both animals and humans. Advanced studies using Bayesian
phylogeographic reconstruction identified the most probable origin of SARS-CoV-2 as the bat SARS-like
coronavirus, circulating in the Rhinolophus bat family (86).

Phylogenetic analysis of 10 whole-genome sequences of SARS-CoV-2 showed that they are related to
two CoVs of bat origin, namely, bat-SL- CoVZC45 and bat-SL-COVZXC21, which were reported during
2018 in China (17). It was reported that SARS-CoV-2 had been confirmed to use ACE2 as an entry
receptor while exhibiting an RBD similar

[12/22, 3:41 AM] ......: rates, disease outbreaks, community spread,

clustered transmission events, hot spots, and superspreader potential of SARS-CoV-2/COVID warrant full
exploitation of real-time disease mapping by employing geographical information systems (GIS), such as
the GIS software Kosmo 3.1, web-based real-time tools and dashboards, apps, and advances in
information technology (356-359). Researchers have also developed a few prediction tools/models, such
as the prediction model risk of bias assessment tool (PROBAST) and critical appraisal and data extraction
for systematic reviews of prediction modeling studies (CHARMS), which could aid in assessing the
possibility of getting infection and estimating the prognosis in patients; however, such models may
suffer from bias issues and, hence, cannot be considered completely trustworthy, which necessitates the
development of new and reliable predictors (360).

VACCINES, THERAPEUTICS, AND DRUGS

Recently emerged viruses, such as Zika, Ebola, and Nipah viruses, and their grave threats to humans
have begun a race in exploring the designing and developing of advanced vaccines, prophylactics,
therapeutics, and drug regimens to counter emerging

[12/22, 3:41 AM] ......: infected by human beings. However, evidence of cat-

to-human transmission is lacking and requires further studies (332). Rather than waiting for firmer
evidence on animal-to-human transmission, necessary preventive measures are advised, as well as
following social distancing practices among companion animals of different households (331). One of the
leading veterinary diagnostic companies, IDEXX, has conducted large-scale testing for COVID-19 in
specimens collected from dogs and cats. However, none of the tests turned out to be positive (334).

In a study conducted to investigate the potential of different animal species to act as the intermediate
host of SARS-CoV-2, it was found that both ferrets and cats can be infected via experimental inoculation
of the virus. In addition, infected cats efficiently transmitted the disease to naive cats (329). SARS- CoV-2
infection and subsequent transmission in ferrets were found to recapitulate the clinical aspects of
COVID-19 in humans. The infected ferrets also shed virus via multiple routes, such as saliva, nasal
washes, feces, and urine, postinfection, making them an ideal animal model for studying disease
transmission (337). Experimental inoculation was also done in other animal species and found that the
dogs have low susceptibility, while the chickens,

[12/22, 3:42 AM] ......: and Middle East respiratory syndrome coronavirus (MERS-CoV), but has lower
fatality. The global impact of this new epidemic is yet uncertain.

Keywords: 2019-nCOV, SARS-CoV-2, COVID-19, Pneumonia, Review

Introduction

The 2019 novel coronavirus (2019- nCoV) or the severe acute respiratory syndrome corona virus 2
(SARS-COV-2) as it is now called, is rapidly spreading from its origin in Wuhan City of Hubei Province of
China to the rest of the world [1]. Till 05/03/2020 around 96,000 cases of coronavirus disease 2019
(COVID-19) and 3300 deaths have been reported [2]. India has reported 29 cases till date. Fortunately so
far, children have been infrequently affected with no deaths. But the future course of this virus is
unknown. This article gives a bird's eye view about

[12/22, 3:42 AM] ......: 10 RECOMBINANT SUBUNIT VACCINE

Clover Biopharmaceuticals is producing a recombinant subunit vaccine based on the trimeric S-protein
of COVID-19.55 The oral recombinant vaccine is being expanded by Vaxart in tablet formulation, using
its proprietary oral vaccine platform.

11 CLINICAL MANAGEMENT AND TREATMENT

In severe COVID-19 cases, treatment should be given to support vital organ functions. People who think
they may have been exposed to COVID-19 should contact their healthcare provider immediately.
Healthcare personnel should care for patients in an Airborne Infection Isolation Room (AIIR). Precautions
must be taken by the healthcare professional, such as contact precautions and airborne precautions
with eye protection.56

Individuals with a mild clinical presentation may not require primary hospitalisation. Close monitoring is
needed for the persons infected with COVID-19. Elderly patients and those with prevailing chronic
medical conditions such as

[12/22, 3:43 AM] ......: The results of the studies related to SARS-CoV-2 viral loads reflect active
replication of this virus in the upper respiratory tract and prolonged viral shedding after symptoms
disappear, including via stool. Thus, the current case definition needs to be updated along with a
reassessment of the strategies to be adopted for restraining the SARS-CoV-2 outbreak spread (248). In
some cases, the viral load studies of SARS-CoV-2 have also been useful to recommend precautionary
measures when handling specific samples, e.g., feces. In a recent survey from 17 confirmed cases of
SARS-CoV-2 infection with available data (representing days 0 to 13 after onset), stool samples from
nine cases (53%; days 0 to 11 after onset) were positive on RT-PCR analysis. Although the viral loads
were lower than those of respiratory samples (range, 550 copies per ml to 1.21X105 copies per ml), this
has essential biosafety implications (151).

The samples from 18 SARS-CoV-2-positive patients in Singapore who had traveled from Wuhan to
Singapore showed the presence of viral RNA in stool and whole blood but not in urine by real-time RT-
PCR (288). Further, novel SARS-CoV-2 infections have been detected in a variety of clinical specimens,
like bronchoalveolar lavage fluid,

[12/22, 3:43 AM] ......: assays offer high accuracy in the diagnosis of SARS- CoV-2, but the current rate of
spread limits its use due to the lack of diagnostic assay kits. This will further result in the extensive
transmission of COVID-19, since only a portion of suspected cases can be diagnosed. In such situations,
conventional serological assays, like enzyme-linked immunosorbent assay (ELISA), that are specific to
COVID-19 IgM and IgG antibodies can be used as a high-throughput alternative (149). At present, there
is no diagnostic kit available for detecting the SARS- CoV-2 antibody (150). The specific antibody profiles
of COVID-19 patients were analyzed, and it was found that the IgM level lasted more than 1 month,
indicating a prolonged stage of virus replication in SARS-CoV-2-infected patients. The IgG levels were
found to increase only in the later stages of the disease. These findings indicate that the specific
antibody profiles of SARS-CoV-2 and SARS-CoV were similar (325). These findings can be utilized for the
development of specific diagnostic tests against COVID-19 and can be used for rapid screening. Even
though diagnostic test kits are already available that can detect the genetic sequences of SARS-CoV- 2
(95), their availability is a concern, as the number of COVID-19 cases is skyrocketing (155, 157). A major
problem associated with this diagnostic kit is

[12/22, 3:44 AM] ......: 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

[12/22, 3:44 AM] ......: These findings will not have any significance until a significant outbreak occurs
due to a virus-like SARS-CoV-2.

There is a steady increase in the reports of COVID-19 in companion and wild animals around the world.
Further studies are required to evaluate the potential of animals (especially companion animals) to
serve as an efficient reservoir host that can further alter the dynamics of human-to-human transmission
(330). To date, two pet dogs (Hong Kong) and four pet cats (one each from Belgium and Hong Kong, two
from the United States) have tested positive for SARS-CoV-2 (335). The World Organization for Animal
Health (OIE) has confirmed the diagnosis of COVID-19 in both dogs and cats due to human-to-animal
transmission (331). The similarity observed in the gene sequence of SARS- CoV-2 from an infected pet
owner and his dog further confirms the occurrence of human-to-animal transmission (333). Even though
asymptomatic, feline species should be considered a potential transmission route from animals to
humans (326). However, currently, there are no reports of SARS- CoV-2 transmission from felines to
human beings. Based on the current evidence, we can conclude that cats are susceptible to SARS-CoV-2
and can get infected by human beings. However, evidence of cat-

[12/22, 3:46 AM] ......: subfammy and is entirely different from the
viruses responsible for MERS-CoV and SARS-CoV (3). The newly emerged SARS-CoV-2 is a coronavirus
(2). The genome sequences of SARS- group 2B CoV-2 obtained from patients share 79.5% sequence
similarity to the sequence of SARS-CoV (63).

As of 13 May 2020, a total of 4,170,424 confirmed cases of COVID-19 (with 287,399 deaths) have been
reported in more than 210 affected countries worldwide (WHO Situation Report 114

[12/22, 3:46 AM] ......: 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 the on 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).

[12/22, 3:46 AM] ......: samples obtained from lower respiratory tracts. Hence, based on the viral load,
we can quickly evaluate the progression of infection (291). In addition to all of the above findings,
sequencing and phylogenetics are critical in the correct identification and confirmation of the causative
viral agent and useful to establish relationships with previous isolates and sequences, as well as to know,
especially during an epidemic, the nucleotide and amino acid mutations and the molecular divergence.
The rapid development and implementation of diagnostic tests against emerging novel diseases like
COVID-19 pose significant challenges due to the lack of resources and logistical limitations associated
with an outbreak (155).

SARS-CoV-2 infection can also be confirmed by isolation and culturing. The human airway epithelial cell
culture was found to be useful in isolating SARS-CoV-2 (3). The efficient control of an outbreak depends
on the rapid diagnosis of the disease. Recently, in response to the COVID-19 outbreak, 1-step
quantitative real-time reverse transcription-PCR assays were developed that detect the ORF1b and N
regions of the SARS-CoV-2 genome (156). That assay was found to achieve the rapid detection of SARS-
CoV-2. Nucleic acid-based assays offer high accuracy in the diagnosis of SARS-

[12/22, 3:47 AM] ......: 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

[12/22, 3:47 AM] ......: 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).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

[12/22, 3:47 AM] ......: 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 alternative on
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,

[12/22, 3:47 AM] ......: 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

[12/22, 3:48 AM] ......: markets, promoted further adaptations that resulted

in the epidemic strain (104). Transmission can also occur directly from the reservoir host to humans
without RBD adaptations. The bat coronavirus that is currently in circulation maintains specific "poised"
spike proteins that facilitate human infection without the requirement of any mutations or adaptations
(105). Altogether, different species of bats carry a massive number of coronaviruses around the world
(106).

The high plasticity in receptor usage, along with the feasibility of adaptive mutation and recombination,
may result in frequent interspecies transmission of coronavirus from bats to animals and humans (106).
The pathogenesis of most bat coronaviruses is unknown, as most of these viruses are not isolated and
studied (4). Hedgehog coronavirus HKU31, a Betacoronavirus, has been identified from amur hedgehogs
in China. Studies show that hedgehogs the reservoir of are Betacoronavirus, and there is recombination
(107). evidence of
The current scientific evidence available on MERS infection suggests that the significant reservoir host,
as well as the animal source of MERS infection in humans, is the dromedary camels (97). The infected
dromedary camels may not show any visible signs of infection. making it challenging to

[12/22, 3:48 AM] ......: in vitro and in vivo 155-158. Compared with convalescent plasma, which has
limited availability and cannot be amplified, monoclonal antibodies can be developed in larger quantities
to meet clinical requirements. Hence, they provide the possibility for the treatment and pre- vention of
COVID-19. The neutralizing epitopes of these monoclonal antibodies also offer important infor- mation
for vaccine design. However, the high cost and limited capacity of manufacturing, as well as the prob-
lem of bioavailability, may restrict the wide application of monoclonal antibody therapy.

Vaccines

Vaccination is the most effective method for a long-term strategy for prevention and control of COVID-
19 in the future. Many different vaccine platforms against SARS-CoV-2 are in development, the
strategies of which include recombinant vectors, DNA, mRNA in lipid nano- particles, inactivated viruses,
live attenuated viruses and protein subunits 159-161. As of 2 October 2020, ~174 vac- cine candidates
for COVID-19 had been reported and 51 were in human clinical trials (COVID-19 vaccine and
therapeutics tracker). Many of these vac- cine candidates are in phase II testing, and some have already
advanced to phase III trials. A randomized double-blinded phase II trial of an adenovirus type vectored
vaccine expressing the SARS-CoV-2 S protein, developed by CanSino Biologicals and the Academy of
Military Medical Sciences of China, was conducted in 603 adult volunteers in Wuhan. The vaccine has
proved to be safe and induced considerable humoral and cel- lular immune response in most recipients
after a single immunization 162. Another vectored vaccine, ChAdOx1,

[12/22, 3:48 AM] ......: a polybasic cleavage site (RRAR), which enables effec- tive cleavage by furin and
other proteases27. 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 China28 (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 receptor29.
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 demonstrated26.

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 outbreak30. Such ORF8 deletion may be
indicative of human adaptation after cross-species transmission from an animal host. different SARS

[12/22, 3:49 AM] ......: trimeric S1 locates itself on top of the trimeric S2 stalk (45). Recently, structural
analyses of the S proteins of COVID-19 have revealed 27 amino acid substitutions within a 1,273-amino-
acid stretch (16). Six substitutions are located in the RBD (amino acids 357 to 528), while four
substitutions are in the RBM at the CTD of the S1 domain (16). Of note, no amino acid change is seen in
the RBM, which binds directly to the angiotensin-converting enzyme-2 (ACE2) receptor in SARS-CoV (16,
46). At present, the main emphasis is knowing how many differences would be required to change the
host tropism. Sequence comparison revealed 17 nonsynonymous changes between the early sequence
of SARS-CoV-2 and the later isolates of SARS-CoV. The changes were found scattered over the genome
of the virus, with nine substitutions in ORFlab, ORF8 (4 substitutions), the spike gene (3 substitutions),
and ORF7a (single substitution) (4). Notably, the same nonsynonymous changes were found in a familial
cluster, indicating that the viral evolution happened during person-to-person transmission (4, 47). Such
adaptive evolution events are frequent and constitute a constantly ongoing process once the virus
spreads among new hosts (47). Even though no functional changes occur in the virus associated with
this adaptive evolution, close monitoring of the viral

[12/22, 3:50 AM] ......: Coronaviruses are a diverse group of viruses infecting many different animals, and
they can cause mild to severe respiratory infections in humans. In 2002 and 2012, respectively, two
highly pathogenic coronaviruses with zoonotic origin, severe acute respiratory syndrome coronavirus
(SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), emerged in humans and
caused fatal respiratory illness, making emerging coronaviruses a new public health concern in the
twenty-first century. At the end of 2019, a novel coronavirus designated as SARS-CoV-2 emerged in the
city of Wuhan, China, and caused an outbreak of unusual viral pneumonia. Being highly transmissible,
this novel coronavirus disease, also known as coronavirus disease 2019 (COVID-19), has spread fast all
over the world2,3. It has overwhelmingly surpassed SARS and MERS in terms of both the number of
infected people and the spatial range of epidemic areas. The ongoing outbreak of COVID-19 has posed
an extraordinary threat to global public health. In this Review, we summarize the cur- rent
understanding of the nature of SARS-CoV-2 and COVID-19. On the basis of recently published findings,
this comprehensive Review covers the basic biology of SARS-CoV-2, including the genetic characteristics,
the potential zoonotic origin and its receptor binding. Furthermore, we will discuss the clinical and
epide- miological features, diagnosis of and countermeasures against COVID-19.

Emergence and spread In late December 2019, several health facilities in

Wuhan, in Hubei province in China, reported clusters of

patients with pneumonia of unknown cause. Similarly

to patients with SARS and MERS, these patients showed

symptoms of viral pneumonia, including fever, cough

[12/22, 3:51 AM] ......: range of hosts, producing symptoms and diseases ranging from the common cold
to severe and ultimately fatal illnesses, such as SARS, MERS, and, presently, COVID-19. SARS-CoV-2 is
considered one of the seven members of the CoV family that infect humans (3), and it belongs to the
same lineage of CoVs that causes SARS; however, this novel virus is genetically distinct. Until 2020, six
CoVs were known to infect humans, including human CoV 229E (HCOV-229E), HCoV-NL63, HCoV-OC43,
HCOV- HKU1, SARS-CoV, and MERS-CoV. Although SARS-CoV and MERS-CoV have resulted in outbreaks
with high mortality, others remain associated with mild upper-respiratory-tract illnesses (4).

Newly evolved CoVs pose a high threat to global public health. The current emergence of COVID-19 is
the third CoV outbreak in humans over the past 2 decades (5). It is no coincidence that Fan et al.
predicted potential SARS- or MERS-like COV outbreaks in China following pathogen transmission from
bats (6). COVID-19 emerged in China and spread rapidly throughout the country and, subsequently, to
other countries. Due to the severity of this outbreak and the potential of spreading on an international
scale, the WHO declared a global health emergency on 31 January 2020: subsequently

[12/22, 3:51 AM] ......: The interferon response is one of the major innate immunity defences against
virus invasion. Interferons induce the expression of diverse interferon-stimulated genes, which can
interfere with every step of virus replication. Previous studies identified type I interfer- ons as a
promising therapeutic candidate for SARS 149. In vitro data showed SARS-CoV-2 is even more sen- sitive
to type I interferons than SARS-CoV, suggesting the potential effectiveness of type I interferons in the
early treatment of COVID-19 (REF.150). In China, vapor inhalation of interferon-a is included in the
COVID-19 treatment guideline¹¹. Clinical trials are ongoing across the world to evaluate the efficacy of
different therapies involving interferons, either alone or in combination with other agents152.

Immunoglobulin therapy. Convalescent plasma treat- ment is another potential adjunctive therapy for
COVID-19. Preliminary findings have suggested improved clinical status after the treatment 153,154. The
FDA has provided guidance for the use of COVID-19 convalescent plasma under an emergency
investigational new drug application. However, this treatment may have adverse effects by causing
antibody-mediated enhance- ment of infection, transfusion-associated acute lung injury and allergic
transfusion reactions.

Monoclonal antibody therapy is an effective immuno- therapy for the treatment of some viral infections
in select patients. Recent studies reported specific mon- oclonal antibodies neutralizing SARS-CoV-2
infection

[12/22, 3:51 AM] ......: challenge with MERS-COV (109). The intranasal
administration of the recombinant adenovirus-based

vaccine in BALB/c mice was found to induce long- lasting neutralizing immunity against MERS spike
pseudotyped virus, characterized by the induction of systemic IgG, secretory IgA, and lung-resident
memory T-cell responses (177). Immunoinformatics methods have been employed for the genome-wide
screening of potential vaccine targets among the different immunogens of MERS-CoV (178). The N
protein and the potential B-cell epitopes of MERS- CoV E protein have been suggested as
immunoprotective targets inducing both T-cell and neutralizing antibody responses (178, 179).

The collaborative effort of the researchers of Rocky Mountain Laboratories and Oxford University is
designing a chimpanzee adenovirus-vectored vaccine to counter COVID-19 (180). The Coalition for
Epidemic Preparedness Innovations (CEPI) has initiated three programs to design SARS-CoV-2 vaccines
(181). CEPI has a collaborative project with Inovio for designing a MERS-CoV DNA vaccine that could
potentiate effective immunity. CEPI and the University of Queensland are designing a molecular clamp
vaccine platform for MERS-CoV and other pathogens, which could assist in the easier identification of
antigens by the immune system (181). CEPI has also funded Moderna to develop a

[12/22, 3:52 AM] ......: appeared asymptomatic. 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 uncertain46.

Receptor use and pathogenesis

SARS-CoV-2 uses the same receptor as SARS-CoV, angiotensin-converting enzyme 2 (ACE2) 11,47.
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 antibodies50,51
(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-

[12/22, 3:52 AM] ......: • 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

[12/22, 3:53 AM] ......: proteins without the presence of S protein would not confer any noticeable
protection, with the absence of detectable serum SARS-CoV-neutralizing antibodies (170). Antigenic
determinant sites present over S and N structural proteins of SARS-CoV-2 can be explored as suitable
vaccine candidates (294). In the Asian population, S, E, M, and N proteins of SARS- CoV-2 are being
targeted for developing subunit vaccines against COVID-19 (295).

The identification of the immunodominant region among the subunits and domains of S protein is
critical for developing an effective vaccine against the coronavirus. The C-terminal domain of the S1
subunit is considered the immunodominant region of the porcine deltacoronavirus S protein (171).
Similarly, further investigations are needed to determine the immunodominant regions of SARS- CoV-2
for facilitating vaccine development.

However, our previous attempts to develop a universal vaccine that is effective for both SARS- CoV and
MERS-CoV based on T-cell epitope similarity pointed out the possibility of cross- reactivity among
coronaviruses (172). That can be made possible by selected potential vaccine targets that are common
to both viruses. SARS-CoV-2 has been reported to be closely related to SARS-COV (173, 174). Hence,
knowledge and understanding of

[12/22, 3:53 AM] ......: another study, the average reproductive number of

COVID-19 was found to be 3.28, which is significantly higher than the initial WHO estimate of 1.4 to 2.5
(77). It is too early to obtain the exact Ro value, since there is a possibility of bias due to insufficient
data. The higher Ro value is indicative of the more significant potential of SARS-CoV-2 transmission in a
susceptible population. This is not the first time where the culinary practices of China have been blamed
for the origin of novel coronavirus infection in humans. Previously, the animals present in the live-animal
market were identified to be the intermediate hosts of the SARS outbreak in China (78). Several wildlife
species were found to harbor potentially evolving coronavirus strains that can overcome the species
barrier (79). One of the main principles of Chinese food culture is that live- slaughtered animals are
considered more nutritious (5).

After 4 months of struggle that lasted from December 2019 to March 2020, the COVID-19 situation now
seems under control in China. The wet animal markets have reopened, and people have started buying
bats, dogs, cats, birds, scorpions, badgers, rabbits, pangolins (scaly anteaters), minks, soup from palm
civet, ostriches, hamsters, snapping turtles, ducks, fish, Siamese crocodiles, and other

[12/22, 3:53 AM] ......: had >95% homology with the bat

coronavirus and > 70% similarity with the SARS-COV. Environmental samples from the Huanan sea food
market also tested positive, signifying that the virus originated from there [7]. The number of cases
started increasing exponentially, some of which did not have exposure to the live animal market,
suggestive of the fact that human-to-human transmission was occurring [8]. The first fatal case was
reported on 11th Jan 2020. The massive migration of Chinese during the Chinese New Year fuelled the
epidemic. Cases in other provinces of China, other countries (Thailand, Japan and South Korea in quick
succession) were reported in people who were returning from Wuhan. Transmission to healthcare
workers caring for patients was described on 20th Jan, 2020. By 23rd January, the 11 million population
of Wuhan was placed under lock down

[12/22, 3:53 AM] ......: fever, cough, and sputum (83). Hence, the clinicians

must be on the look-out for the possible occurrence

of atypical clinical manifestations to avoid the possibility of missed diagnosis. The early transmission
ability of SARS-CoV-2 was found to be similar to or slightly higher than that of SARS-CoV, reflecting that
it could be controlled despite moderate to high transmissibility (84).

Increasing reports of SARS-CoV-2 in sewage and wastewater warrants the need for further investigation
due to the possibility of fecal-oral transmission. SARS-CoV-2 present in environmental compartments
such as soil and water will finally end up in the wastewater and sewage sludge of treatment plants (328).
Therefore, we have to reevaluate the current wastewater and sewage sludge treatment procedures and
introduce advanced techniques that are specific and effective against SARS-CoV-2. Since there is active
shedding of SARS-CoV-2 in the stool, the prevalence of infections in a large population can be studied
using wastewater-based epidemiology. Recently, reverse transcription- quantitative PCR (RT-qPCR) was
used to enumerate the copies of SARS-CoV-2 RNA concentrated from wastewater collected from a
wastewater treatment plant (327). The calculated viral RNA copy numbers determine the number of
infected individuals. The

[12/22, 3:53 AM] ......: 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

[12/22, 3:54 AM] ......: absence of this protein is related to the altered virulence of coronaviruses due to
changes in morphology and tropism (54). The E protein consists of three domains, namely, a short
hydrophilic amino terminal, large hydrophobic transmembrane a domain, and an efficient C-terminal
domain (51). The SARS-CoV-2 E protein reveals a similar amino acid constitution without any
substitution (16).

N Protein

The N protein of coronavirus is multipurpose. Among several functions, it plays a role in complex
formation with the viral genome, facilitates M protein interaction needed during virion assembly, and
enhances the transcription efficiency of the virus (55, 56). It contains three highly conserved and distinct
domains, namely, an NTD, an RNA-binding domain or a linker region (LKR), and a CTD (57). The NTD
binds with the 3' end of the viral genome, perhaps via electrostatic interactions, and is highly diverged
both in length and sequence (58). The charged LKR is serine and arginine rich and is also known as the
SR (serine and arginine) domain (59). The LKR is capable of direct interaction with in vitro RNA
interaction and is responsible for cell signaling (60, 61). It also modulates the antiviral response of the
host by working as an antagonist for interferon

[12/22, 3:54 AM] ......: (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

[12/22, 3:54 AM] ......: system (30).

Bovine coronaviruses (BoCoVs) are known to infect several domestic and wild ruminants (126). BoCoV
inflicts neonatal calf diarrhea in adult cattle, leading to bloody diarrhea (winter dysentery) and
respiratory disease complex (shipping fever) in cattle of all age groups (126). BoCoV-like viruses have
been noted in humans, suggesting its zoonotic potential as well (127). Feline enteric and feline infectious
peritonitis (FIP) viruses are the two major feline CoVs (128), where feline CoVs can affect the
gastrointestinal tract, abdominal cavity (peritonitis), respiratory tract, and central nervous system (128).
Canines are also affected by CoVs that fall under different genera, namely, canine enteric coronavirus in
Alphacoronavirus and canine respiratory coronavirus in Betacoronavirus, affecting the enteric and
respiratory tract, respectively (129, 130). IBV, under Gammacoronavirus, causes diseases of respiratory,
urinary, and reproductive systems, with substantial economic losses in chickens (131, 132). In small
laboratory animals, mouse hepatitis virus, rat sialodacryoadenitis coronavirus, and guinea pig and rabbit
coronaviruses are the major CoVs associated with disease manifestations like enteritis, hepatitis, and
respiratory infections (10, 133).

Swine acute diarrhea syndrome coronavirus

[12/22, 3:55 AM] ......: 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

[12/22, 3:55 AM] ......: 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 condition. 250% hoTTO POGOTORed and

[12/22, 3:55 AM] ......: comprised a small population and, hence, the

possibility of misinterpretation could arise. However, in another case study, the authors raised concerns
over the efficacy of hydroxychloroquine- azithromycin in the treatment of COVID-19 patients, since no
observable effect was seen when they were used. In some cases, the treatment was discontinued due to
the prolongation of the QT interval (307). Hence, further randomized clinical trials are required before
concluding this matter.

Recently, another FDA-approved drug, ivermectin, was reported to inhibit the in vitro replication of
SARS-CoV-2. The findings from this study indicate that a single treatment of this drug was able to induce
an ~5,000-fold reduction in the viral RNA at 48 h in cell culture. (308). One of the main disadvantages
that limit the clinical utility of ivermectin is its potential to cause cytotoxicity. However, altering the
vehicles used in the formulations, the pharmacokinetic properties can be modified, thereby having
significant control over the systemic concentration of ivermectin (338). Based on the pharmacokinetic
simulation, it was also found that ivermectin may have limited therapeutic utility in managing COVID-19,
since the inhibitory concentration that has to be achieved for effective anti-SARS-CoV-2 activity is far
higher than the

[12/22, 3:56 AM] ......: 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

[12/22, 3:56 AM] ......: 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

[12/22, 3:56 AM] ......: 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 cuheat

[12/22, 3:58 AM] ......: Origin and Spread of COVID-19 [1, 2, 6]

In December 2019, adults in Wuhan, capital city of Hubei province and a major transportation hub of
China started presenting to local hospitals with severe pneumonia of unknown cause. Many of the initial
cases had a common exposure to the Huanan wholesale seafood market that also traded live animals.
The surveillance system (put into place after the SARS outbreak) was activated and respiratory samples
of patients were sent to reference labs for etiologic investigations. On December 31st 2019, China
notified the outbreak to the World Health Organization and on 1st January the Huanan sea food market
was closed. On 7th January the virus was identified as a coronavirus that had >95% homology with the
bat

[12/22, 3:59 AM] ......: with COVID-19 showed typical features on initial CT, including bilateral multilobar
ground-glass opacities with a peripheral or posterior distribution118,119. Thus, it has been suggested
that CT scanning combined with repeated swab tests should be used for individu- als with high clinical
suspicion of COVID-19 but who test negative in initial nucleic acid screening¹18. Finally, SARS-COV-2
serological tests detecting antibodies to N or S protein could complement molecular diagnosis,
particularly in late phases after disease onset or for retro- spective studies 116,120,121. However, the
extent and dura- tion of immune responses are still unclear, and available serological tests differ in their
sensitivity and specific- ity, all of which need to be taken into account when one is deciding on
serological tests and interpreting their results or potentially in the future test for T cell responses.

Therapeutics
To date, there are no generally proven effective thera- pies for COVID-19 or antivirals against SARS-CoV-
2, although some treatments have shown some benefits in certain subpopulations of patients or for
certain end points (see later). Researchers and manufacturers are conducting large-scale clinical trials to
evaluate var- ious therapies for COVID-19. As of 2 October 2020, there were about 405 therapeutic
drugs in development for COVID-19, and nearly 318 in human clinical trials (COVID-19 vaccine and
therapeutics tracker). In the following sections, we summarize potential therapeutics against SARS-CoV-
2 on the basis of published clinical data and experience.

[12/22, 3:59 AM] ......: 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

[12/22, 3:59 AM] ......: such instance was in 2002-2003 when a new coronavirus of the ẞ genera and with
origin in bats crossed over to humans via the intermediary host of palm civet cats in the Guangdong
province of China. This virus, designated as severe acute respiratory syndrome coronavirus affected
8422 people mostly in China and Hong Kong and caused 916 deaths (mortality rate 11%) before being
contained [4]. Almost a decade later in 2012, the Middle East respiratory syndrome coronavirus (MERS-
CoV), also of bat origin, emerged in Saudi Arabia with dromedary camels as the intermediate host and
affected 2494 people and caused 858 deaths (fatality rate 34%) [5].

Origin and Spread of COVID-19 [1, 2, 6]

In December 2019, adults in Wuhan, capital city of Hubei province and a

[12/22, 4:00 AM] ......: 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

[12/22, 4:00 AM] ......: 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

[12/22, 4:01 AM] ......: article gives a bird's eye view about this new virus. Since knowledge about this
virus is rapidly evolving, readers are urged to update themselves regularly.

History

Coronaviruses are enveloped positive sense RNA viruses ranging from 60 nm to 140 nm in diameter with
spike like projections on its surface giving it a crown like appearance under the electron microscope;
hence the name coronavirus [3]. Four corona viruses namely HKU1, NL63, 229E and OC43 have been in
circulation in humans, and generally cause mild respiratory disease.

There have been two events in the past two decades wherein crossover of animal betacorona viruses to
humans has resulted in severe disease. The first such instance was in 2002-2003 when a of the D

[12/22, 4:01 AM] ......: pandemic flu where patients were asked to resume work/school once afebrile for
24 h or by day 7 of illness. Negative molecular tests were not a prerequisite for discharge.

At the community level, people should be asked to avoid crowded areas and postpone non-essential
travel to places with ongoing transmission. They should be asked to practice cough hygiene by coughing
in sleeve/ tissue rather than hands and practice hand hygiene frequently every 15-20 min. Patients with
respiratory symptoms should be asked to use surgical masks. The use of mask by healthy people in
public places has not shown to protect against respiratory viral infections and is currently not
recommended by WHO. However, in China, the public has been asked to wear masks in public and
especially in crowded places and large scale gatherings are prohibited (entertainment parks etc). China
is also
[12/22, 4:01 AM] ......: mask and practice cough hygiene. Caregivers should be asked to wear a surgical
mask when in the same room as patient and use hand hygiene every 15-20 min.

The greatest risk in COVID-19 is transmission to healthcare workers. In the SARS outbreak of 2002, 21%
of those affected were healthcare workers [31]. Till date, almost 1500 healthcare workers in China have
been infected with 6 deaths. The doctor who first warned about the virus has died too. It is important to
protect healthcare workers to ensure continuity of care and to prevent transmission of infection to
other patients. While COVID-19 transmits as a droplet pathogen and is placed in Category B of infectious
agents (highly pathogenic H5N1 and SARS), by the China National Health Commission, infection control
measures recommended are those for

[12/22, 4:01 AM] ......: Splits Tree phylogeny analysis.

In the unrooted phylogenetic tree of different betacoronaviruses based on the S protein, virus
sequences from different subgenera grouped into separate clusters. SARS-CoV-2 sequences from Wuhan
and other countries exhibited a close relationship and appeared in a single cluster (Fig. 1). The CoVs
from the subgenus Sarbecovirus appeared jointly in Splits Tree and divided into three subclusters,
namely, SARS-CoV-2, bat-SARS-like- CoV (bat-SL-CoV), and SARS-CoV (Fig. 1). In the case of other
subgenera, like Merbecovirus, all of the sequences grouped in a single cluster, whereas in Embecovirus,
different species, comprised of canine respiratory CoVs, bovine CoVs, equine CoVs, and human CoV
strain (OC43), grouped in a common cluster. Isolates in the subgenera Nobecovorus and Hibecovirus
were found to be placed separately away from other reported SARS-CoVS but shared a bat origin.

CURRENT WORLDWIDE SCENARIO OF SARS-CoV-2

This novel virus, SARS-CoV-2, comes under the subgenus Sarbecovirus of the Orthocoronavirinae
subfamily and is entirely different from the viruses

[12/22, 4:02 AM] ......: Practice Points from an Indian Perspective

At the time of writing this article, the risk of coronavirus in India is extremely low. But that may change
in the next few weeks. Hence the following is recommended:

• Healthcare providers should take travel history of all patients with respiratory symptoms, and any
international travel in the past 2 wks as well as contact with sick people who have travelled
internationally.
They should set up a system of triage of patients with respiratory illness in the outpatient department
and give them a simple surgical mask to wear. They should use surgical masks themselves while
examining such

[12/22, 4:02 AM] ......: specimens, like bronchoalveolar lavage fluid, sputum, nasal swabs,
fibrobronchoscope brush biopsy specimens, pharyngeal swabs, feces, and blood (246).

The presence of SARS-CoV-2 in fecal samples has posed grave public health concerns. In addition to the
direct transmission mainly occurring via droplets of sneezing and coughing, other routes, such as fecal
excretion and environmental and fomite contamination, are contributing to SARS-CoV-2 transmission
and spread (249-252). Fecal excretion has also been documented for SARS-CoV and MERS-CoV, along
with the potential to stay viable in situations aiding fecal-oral transmission. Thus, SARS-CoV-2 has every
possibility to be transmitted through this mode. Fecal-oral transmission of SARS- CoV-2, particularly in
regions having low standards of hygiene and poor sanitation, may have grave consequences with regard
to the high spread of this virus. Ethanol and disinfectants containing chlorine or bleach are effective
against coronaviruses (249-252). Appropriate precautions need to be followed strictly while handling the
stools of patients infected with SARS-CoV-2. Biowaste materials and sewage from hospitals must be
adequately disinfected, treated, and disposed of properly. The significance of frequent and good hand
hygiene and

[12/22, 4:03 AM] ......: respiratory infection (SARI) and respiratory distress, shock or hypoxaemia.
Patients with SARI can be given conservative fluid therapy only when there is no evidence of shock.
Empiric antimicrobial therapy must be started to manage SARI. For patients with sepsis, antimicrobials
must be administered within 1 hour of initial assessments. The WHO and CDC recommend that
glucocorticoids not be used in patients with COVID-19 pneumonia except where there are other
indications (exacerbation of chronic obstructive pulmonary disease).59

Patients' clinical deterioration is closely observed with SARI; however, rapidly progressive respiratory
failure and sepsis require immediate supportive care interventions comprising quick use of
neuromuscular blockade and sedatives, hemodynamic management, nutritional support, maintenance
of blood glucose levels, prompt assessment and treatment of nosocomial pneumonia, and prophylaxis
against deep venous thrombosis (DVT) and gastrointestinal (GI) bleeding.60 Generally, such patients give
way to their primary illness to secondary complications like sepsis or 48 multiorgan system failure.4

[12/22, 4:04 AM] ......: the SARS-CoV. Environmental samples from the Huanan sea food market also
tested positive, signifying that the virus originated from there [7]. The number of cases started
increasing exponentially, some of which did not

have exposure to the live animal

market, suggestive of the fact that

human-to-human transmission was

occurring [8]. The first fatal case was

reported on 11th Jan 2020. The massive

migration of Chinese during the

Chinese New Year fuelled the epidemic.

Cases in other provinces of China,

other countries (Thailand, Japan and

South Korea in quick succession) were reported in people who were returning from Wuhan.
Transmission to healthcare workers caring for patients was described on 20th Jan, 2020. By 23rd
January, the 11 million population of Wuhan was placed under lock down with restrictions of entry and
exit from the region. Soon this lock down was

[12/22, 4:04 AM] ......: 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

[12/22, 4:04 AM] ......: (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

[12/22, 4:05 AM] ......: developed for rapid and colorimetric detection of this virus (354). RT-LAMP serves
as a simple, rapid, and sensitive diagnostic method that does not require sophisticated equipment or
skilled personnel (349). An interactive web-based dashboard for tracking SARS-CoV-2 in a real-time
mode has been designed (238). A smartphone-integrated home-based point- of-care testing (POCT) tool,
a paper-based POCT combined with LAMP, is a useful point-of-care diagnostic (353). An Abbott ID Now
COVID-19 molecular POCT-based test, using isothermal nucleic acid amplification technology, has been
designed as a point-of-care test for very rapid detection of SARS-CoV-2 in just 5 min (344). A CRISPR-
based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) diagnostic for rapid detection of
SARS-CoV-2 without the requirement of specialized instrumentation has been reported to be very useful
in the clinical diagnosis of COVID-19 (360). A CRISPR-Cas 12-based lateral flow assay also has been
developed for rapid detection of SARS-CoV-2 (346). Artificial intelligence, by means of a three-
dimensional deep-learning model, has been developed for sensitive and specific diagnosis of COVID-19
via CT images (332).

Tracking and mapping of the rising incidence rates, disease outbreaks, community spread,

[12/22, 4:05 AM] ......: might be lower. Further genetic analysis is required

between SARS-CoV-2 and different strains of SARS-CoV and SARS-like (SL) CoVs to evaluate the
possibility of repurposed vaccines against COVID-19. This strategy will be helpful in the scenario of an
outbreak, since much time can be saved, because preliminary evaluation, including in vitro studies,
already would be completed for such vaccine candidates.

Multiepitope subunit vaccines can be considered a promising preventive strategy against the ongoing
COVID-19 pandemic. In silico and advanced immunoinformatic tools can be used to develop
multiepitope subunit vaccines. The vaccines that are engineered by this technique can be further
evaluated using docking studies and, if found effective, then can be further evaluated in animal models
(365). Identifying epitopes that have the potential to become a vaccine candidate is critical to
developing an effective vaccine against COVID-19. The immunoinformatics approach has been used for
recognizing essential epitopes of cytotoxic T lymphocytes and B cells from the surface glycoprotein of
SARS-CoV-2. Recently, a few epitopes have been recognized from the SARS-CoV- 2 surface glycoprotein.
The selected epitopes explored targeting molecular dynamic simulations,

[12/22, 4:05 AM] ......: respectively¹40. However, this study did not include a control arm, and most of
the trials of favilavir were based on a small sample size. For more reliable assess- ment of the
effectiveness of favilavir for treating COVID-19, large-scale randomized controlled trials should be
conducted.

Lopinavir and ritonavir were reported to have in vitro inhibitory activity against SARS-CoV and MERS-
CoV141,142. Alone, the combination of lopinavir

[12/22, 4:05 AM] ......: virological, radiological,

pathological

and 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

[12/22, 4:06 AM] ......: snakes, and various other wild animals (20, 30, 79, 93, 124, 125, 287). Coronavirus
infection is linked to different kinds of clinical manifestations, varying from enteritis in cows and pigs,
upper respiratory disease in chickens, and fatal respiratory infections in humans (30).

Among the CoV genera, Alphacoronavirus and Betacoronavirus infect mammals, while
Gammacoronavirus and Deltacoronavirus mainly infect birds, fishes, and, sometimes, mammals (27, 29,
106). Several novel coronaviruses that come under the genus Deltacoronavirus have been discovered in
the past from birds, like Wigeon coronavirus HKU20, Bulbul coronavirus HKU11, Munia coronavirus
HKU13, white-eye coronavirus HKU16, night-heron coronavirus HKU19, and common moorhen
coronavirus HKU21, as well as from pigs (porcine coronavirus HKU15) (6, 29). Transmissible
gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), and porcine hemagglutinating
encephalomyelitis virus (PHEV) are some of the coronaviruses of swine. Among them, TGEV and PEDV
are responsible for causing severe gastroenteritis in young piglets with noteworthy morbidity and
mortality. Infection with PHEV also causes enteric infection but can cause encephalitis due to its ability
to infect the nervous

[12/22, 4:06 AM] ......: 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

[12/22, 4:06 AM] ......: Abstract

There is a new public health crises threatening the world with the emergence and spread of 2019 novel
coronavirus (2019-nCoV) or the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The
virus originated in bats and was transmitted to humans through yet unknown intermediary animals in
Wuhan, Hubei China in December 2019. There have been around 96,000 reported cases of coronavirus
disease 2019 (COVID-2019) and 3300 reported deaths to date (05/03/2020). The disease is transmitted
by inhalation or contact with infected droplets and the incubation period ranges from 2 to 14 d. The
symptoms are usually fever, cough, sore throat, breathlessness, fatigue, malaise among others. The
disease is mild in most people; in some the elderly and those with

comorbidities) it may progress to

[12/22, 4:06 AM] ......: populations. The in vitro and in vivo studies carried

out on the isolated virus confirmed that there is a potential risk for the reemergence of SARS-CoV
infection from the viruses that are currently circulating in the bat population (105).
CLINICAL PATHOLOGY OF SARS-CoV-2 (COVID-19)

The disease caused by SARS-CoV-2 is also named severe specific contagious pneumonia (SSCP), Wuhan
pneumonia, and, recently, COVID- 19 (110). Compared to SARS-CoV, SARS-CoV-2 has less severe
pathogenesis but has superior transmission capability, as evidenced by the rapidly increasing number of
COVID-19 cases (111). The incubation period of SARS-CoV-2 in familial clusters was found to be 3 to 6
days (112). The mean incubation period of COVID-19 was found to be 6.4 days, ranging from 2.1 to 11.1
days (113). Among an early affected group of 425 patients, 59 years was the median age, of which more
males were affected (114). Similar to SARS and MERS, the severity of this nCoV is high in age groups
above 50 years (2, 115). Symptoms of COVID-19 include fever, cough, myalgia or fatigue, and, less
commonly, headache, hemoptysis, and diarrhea (116, 282). Compared to

the SARS-CoV-2-infected patients in Wuhan during

[12/22, 4:07 AM] ......: Initially, the epicenter of the pandemic was China, which reported a significant
number of deaths associated with COVID-19, with 84,458 laboratory-confirmed cases and 4,644 deaths
as of 13 May 2020 (Fig. 4). As of 13 May 2020, SARS-CoV-2 confirmed cases have been reported in more
than 210 countries apart from China (Fig. 3 and 4) (WHO Situation Report 114) (25, 64). COVID-19 has
been reported on all continents except Antarctica. For many weeks, Italy was the focus of concerns
regarding the large number of cases, with 221,216 cases and 30,911 deaths, but now, the United States
is the country with the largest number of cases, 1,322,054, and 79,634 deaths. Now, the United
Kingdom has even more cases (226,4671) and deaths (32,692) than Italy. A John Hopkins University web
platform has provided daily updates on the basic epidemiology of the COVID-19 outbreak

[12/22, 4:07 AM] ......: 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

[12/22, 4:07 AM] ......: adaptive evolution, close monitoring of the viral mutations that occur during
subsequent human-to- human transmission is warranted.

M Protein

The M protein is the most abundant viral protein present in the virion particle, giving a definite shape to
the viral envelope (48). It binds to the nucleocapsid and acts as a central organizer of coronavirus
assembly (49). Coronavirus M proteins are highly diverse in amino acid contents but maintain overall
structural similarity within different genera (50). The M protein has three transmembrane domains,
flanked by a short amino terminus outside the virion and a long carboxy terminus inside the virion (50).
Overall, the viral scaffold is maintained by M-M interaction. Of note, the M protein of SARS-CoV-2 does
not have amino acid an substitution compared to that of SARS-CoV (16).

E Protein

The coronavirus E protein is the most enigmatic and smallest of the major structural proteins (51). It
plays a multifunctional role in the pathogenesis, assembly, and release of the virus (52). It is a small
integral membrane polypeptide that acts as a viroporin (ion channel) (53). The inactivation or

[12/22, 4:07 AM] ......: N Protein

The N protein of coronavirus is multipurpose. Among several functions, it plays a role in complex
formation with the viral genome, facilitates M protein interaction needed during virion assembly, and
enhances the transcription efficiency of the virus (55, 56). It contains three highly conserved and distinct
domains, namely, an NTD, an RNA-binding domain or a linker region (LKR), and a CTD (57). The NTD
binds with the 3' end of the viral genome, perhaps via electrostatic interactions, and is highly diverged
both in length and sequence (58). The charged LKR is serine and arginine rich and is also known as the
SR (serine and arginine) domain (59). The LKR is capable of direct interaction with in vitro RNA
interaction and is responsible for cell signaling (60, 61). It also modulates the antiviral response of the
host by working as an antagonist for interferon (IFN) and RNA interference (62). Compared to that of
SARS-CoV, the N protein of SARS-CoV-2 possess five amino acid mutations, where two are in the
intrinsically dispersed region (IDR; positions 25 and 26), one each in the NTD (position 103), LKR
(position 217), and CTD (position 334) (16).

nsps and Accessory Proteins

[12/22, 4:10 AM] ......: nsps and Accessory Proteins

Besides the important structural proteins, the SARS-CoV-2 genome contains 15 nsps, nspl to nsp10 and
nsp12 to nsp16, and 8 accessory proteins (3a, 3b, p6, 7a, 7b, 8b, 9b, and ORF14) (16). All these proteins
play a specific role in viral replication (27). Unlike the accessory proteins of SARS-CoV, SARS-CoV-2 does
not contain 8a protein and has a longer 8b and shorter 3b protein (16). The nsp7, nsp13, envelope,
matrix, and p6 and 8b accessory proteins have not been detected with any amino acid substitutions
compared to the sequences of other coronaviruses (16).

The virus structure of SARS-CoV-2 is depicted in