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Coronaviruses and SARS-CoV-2

Authors:
  • İstanbul University-Cerrahpaşa Faculty of Veterinary Medicine

Abstract and Figures

Coronaviruses (CoVs) cause a broad spectrum of diseases in domestic and wild animals, poultry, and rodents, ranging from mild to severe enteric, respiratory, and systemic disease, and also cause the common cold or pneumonia in humans. Seven coronavirus species are known to cause human infection, four of which, HCoV 229E, HCoV NL63, HCoV HKU1 and HCoV OC43, typically cause cold symptoms in immunocompetent individuals. The others namely SARS-CoV (severe acute respiratory syndrome coronavirus), MERS-CoV (Middle East respiratory syndrome coronavirus) were zoonotic in origin and cause severe respiratory illness and fatalities. On 31 December 2019, the existence of patients with pneumonia of an unknown etiology were reported to WHO by the national authorities in China. This virus was officially identified by the Coronavirus Study Group as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the present outbreak of a coronavirus-associated acute respiratory disease was labeled coronavirus disease 19 (COVID-19). COVID-19 was seen for the first cases in Turkey on March 10, 2020 and was number 47,029 cases and 1,006 deaths after 1 month. Infections with SARS-CoV-2 are now widespread, and as of 10 April 2020, 1,727,602 cases have been confirmed in more than 210 countries, with 105,728 deaths.
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http://journals.tubitak.gov.tr/medical/
Turkish Journal of Medical Sciences
Turk J Med Sci
(2020) 50:
© TÜBİTAK
doi:10.3906/sag-2004-127
Coronaviruses and SARS-COV-2
Mustafa HASÖKSÜZ1, Selcuk KILIÇ2,*, Fahriye SARAÇ3
1Department of Virology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, İstanbul, Turkey
2Microbiology Reference Lab and Biological Products Department, General Directorate of Public Health Department,
Republic of Turkey Ministry of Health, Ankara, Turkey
3Pendik Veterinary Control Institute, İstanbul, Turkey
* Correspondence: mhasoksuz@gmail.com
1. Introduction
Before December 2019, 6 strains of coronavirus (CoVs)
were known to infect humans and cause respiratory
diseases. HCoV‐229E, HCoV‐OC43, HCoV‐NL63, and
HKU1 are coronaviruses (CoVs) that normally cause only
mild upper respiratory disease with rare severe infections
occurring in infants, young children, and elderly people
[1]. More dangerous ones are SARS‐CoV and MERS‐CoV,
which can infect lower respiratory tract and trigger a severe
respiratory condition in humans [2]. It is widely known
that some CoVs aect birds, bats, mice, girae, whales,
and many other wild animals, but they can also infect
livestock, causing great economic loss [3,4]. Domestic
animals can also play a role as intermediate hosts that
enable virus transmission from the natural, wild animal
hosts to humans [5,6]. In addition, domestic animals
themselves can also contract bat-borne or closely related
coronavirus diseases [4]. Genomic sequences that are very
similar to porcine epidemic diarrhoea virus (PEDV) have
been detected in bats. In 2016, a large‐scale outbreak of a
disease in pigs in southern China that killed 24,000 piglets
were caused by an HKU2‐related Bat-CoV, swine acute
diarrhoea syndrome CoV [7,8]. is incident was the rst
documented case where a Bat-CoV caused a severe disease
in livestock [8].
2. Structure of coronaviruses
e family Coronaviridae is a monophyletic cluster in the
order Nidovirales members of which are enveloped with a
positive sense, single-stranded RNA genome and measures,
on average, 30 kilobases [9]. Orthocoronavirinae subfamily
contains 4 genera (Alphacoronavirus, Betacoronavirus,
Gammacoronavirus, and Deltacoronavirus), and SARS-
CoV and SARS-CoV-2 belong to genus betacoronavirus
[10,11,12]. e coronavirus (CoV) has a single-stranded,
nonsegmented RNA genome of positive polarity, and
its virion contains 4 major structural proteins: the
nucleocapsid (N) protein, the transmembrane (M) protein,
the envelope (E) protein, and the spike (S) protein (Figure
1). However, with some coronaviruses, the full ensemble
of structural proteins is not necessary for the forming of
a complete, infectious virion; additional proteins may
be encoded with overlapping compensatory functions
[10,11,12].
Abstract: Coronaviruses (CoVs) cause a broad spectrum of diseases in domestic and wild animals, poultry, and rodents, ranging from
mild to severe enteric, respiratory, and systemic disease, and also cause the common cold or pneumonia in humans. Seven coronavirus
species are known to cause human infection, 4 of which, HCoV 229E, HCoV NL63, HCoV HKU1 and HCoV OC43, typically cause
cold symptoms in immunocompetent individuals. e others namely SARS-CoV (severe acute respiratory syndrome coronavirus),
MERS-CoV (Middle East respiratory syndrome coronavirus) were zoonotic in origin and cause severe respiratory illness and fatalities.
On 31 December 2019, the existence of patients with pneumonia of an unknown aetiology was reported to WHO by the national
authorities in China. is virus was ocially identied by the coronavirus study group as severe acute respiratory syndrome coronavirus
2 (SARS-CoV-2), and the present outbreak of a coronavirus-associated acute respiratory disease was labelled coronavirus disease 19
(COVID-19). COVID-19’s rst cases were seen in Turkey on March 10, 2020 and was number 47,029 cases and 1006 deaths aer 1
month. Infections with SARS-CoV-2 are now widespread, and as of 10 April 2020, 1,727,602 cases have been conrmed in more than
210 countries, with 105,728 deaths.
Key words: Human coronaviruses, animal coronaviruses, history of coronaviruses, COVID-19, SARS-CoV-2
Received: 12.04.2020 Accepted/Published Online: 14.04.2020 Final Version: 00.00.2020
Review Article
is work is licensed under a Creative Commons Attribution 4.0 International License.
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HASÖKSÜZ et al. / Turk J Med Sci
e N protein is the only protein that forms the
nucleocapsid and primarily functions to bind to the
coronavirus RNA genome. While the N protein is involved
in viral genome related processes, it plays a role in the
replication of viral RNA and the host’s cellular response
to viral infection. e endoplasmic reticulum localization
of N protein carries a function for this in assembly and
budding. Furthermore, in some coronaviruses, the N
protein expression has been shown to signicantly increase
the production of virus-like particles [13].
Changes in the S glycoprotein are largely responsible
for the host variety of coronaviruses and the variety in
tissue tropism. e S glycoprotein is a type 1 membrane
glycoprotein with dierent functional domains near the
amino (S1) and carboxy (S2) termini. While the S2 subunit
is a transmembrane protein mediating the fusion of viral
and cellular membranes, the S1 subunit is peripheral and
is associated with receptor binding functions [13,14].
Generally speaking, the S glycoprotein facilitates viral
binding to susceptible cells, causes cell fusion, and induces
neutralizing antibodies. Of the 2 functional subunits
containing several antigenic sites, S1 and S2, the S1
monoclonal antibody appears to occur most eciently
because it has a higher level of neutralizing activity
[14,15,16].
In virus assembly, the M protein of coronavirus
plays a central role as it turns cellular membranes into
factories where virus and host factors join to make new
virus particles. e M proteins from SARS-CoV, SARS-
CoV-2, MERS-CoV, MHV, FCoV, IBV, TGEV, and BCoV
are targeted to the vicinity of the Golgi apparatus. Reverse
genetic studies and virus-like protein (VLP) assembly
studies suggest that the M protein encourages assembly
by interacting with the viral ribonucleoprotein (RNP)
and S glycoproteins at the budding site and by creating a
network of M-M interactions capable of excluding some
host membrane proteins from the viral envelope [17].
e smallest but also the most mysterious of the major
structural proteins is the E protein. While the E protein
is plentifully expressed inside the infected cell during the
replication cycle, only a small portion is incorporated into
the virion envelope [11]. Most of the protein is localized at
the ER, Golgi, and ER-Golgi intermediate compartment,
the site of intracellular tracking, where it takes part in
CoV assembly and budding. According to published
studies, 3 roles have been proposed for the CoV E protein:
a) the interaction between the cytoplasmic tails of the M
and E proteins which suggests that E participates in viral
assembly; b) its hydrophobic transmembrane domain is
essential for the release of virions; and c) it is implicated in
the virus’s pathogenesis [11,18].
Interactions between the S protein and its receptor
initiate the initial attachment of the virion to the host cell.
e receptor binding domains (RBD) sites within the S1
region of a coronavirus S protein vary depending on the
virus; some have the RBD at the N-terminus of S1 (MHV),
and others (SARS- CoV and SARS- CoV-2) have the RBD
at the C-terminus of S1 [16]. To gain entry into human
cells, many α coronaviruses (HCoV-229E, TGEV, PEDV,
FIPV, CCoV) employ aminopeptidase N (APN) as their
receptor, HCoV-NL63, SARS-CoV, and SARS-CoV-2
utilize angiotensin converting enzyme 2 (ACE2) as their
Figure 1. e Structure of SARS-CoV-2 virus and ACE2 protein [47].
(Contributed by Rohan Bir Singh; made with Biorender.com)
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HASÖKSÜZ et al. / Turk J Med Sci
receptor, MHV enters through CEACAM1, and MERS-
CoV binds to dipeptidyl-peptidase 4 (DPP4) [18]. Aer
the receptor binding, the virus must next gain access to
the host cell cytosol. is is usually accomplished by
acid-dependent proteolytic cleavage of the S protein by
a cathepsin, TMPRRS2, or another protease, followed by
fusion of the viral and cellular membranes (16).
3. Summary of animal coronaviruses
A wide range of animal diseases are caused by
coronaviruses, and signicant research on these viruses in
the second half of the 20th century was triggered by their
ability to cause severe disease in livestock and companion
animals such as pigs, cows, chickens, dogs, and cats
[19,20,21]. Transmissible gastroenteritis virus (TGEV) and
PEDV, for example, cause severe gastroenteritis in young
piglets that lead to signicant morbidity and mortality
and results in economic losses [22]. e feline infectious
peritonitis virus (FIPV) results in the development of a
lethal disease called feline infectious peritonitis (FIP) [23].
FIP has wet and dry forms and is similar to the human
disease sarcoidosis. FIPV is macrophage tropic and may
cause aberrant cytokine and/or chemokine expression and
lymphocyte depletion, which results in a lethal disease
[23]. e cattle industry has experienced signicant losses
from bovine coronaviruses (BCoV) that caused signicant
losses in the cattle industry, and its infection spread a
variety of ruminants including elk, girae, deer, and
camels [3,15,24]. Infectious bronchitis virus (IBV) aects
the urogenital tract of chickens, causing renal disease. Egg
production is signicantly reduced by the infection of the
reproductive tract with IBV, causing substantial industrial
losses every year [20]. e most intensely studied animal
coronavirus is murine hepatitis virus (MHV) which causes
a variety of conditions in mice, including respiratory,
enteric, hepatic, and neurologic infections. us, MHV
is an excellent model for studying the basics of viral
replication in tissue culture cells as well as for studying the
pathogenesis and immune response to coronaviruses [22].
4. e history of coronaviruses
IBV was the rst coronavirus to be reported, a virus from
chickens with respiratory disease reported by Beaudette
& Hudson in 1937 [20]. e murine and hepatitis
viruses (MHV), another group of animal’s viruses, were
rst identied by Cheever at al. in 1949 [1]. In 1946,
transmissible gastroenteritis in swine was rst recognized.
However, it was not until aer the human coronaviruses
(HCoVs) were discovered in the 1960s and the coronavirus
genus was dened that these 3 animal diseases were found
to be related [1]. An organ culture of human embryonic
trachea taken from a schoolboy with a cold was described
by Tyrrell & Bynoe as the rst human coronavirus (B814)
in 1965 [25]. When examined by an electron microscope,
the virus was found to resemble avian IBV. Hamre &
Procknow recovered 5 virus strains in tissue culture taken
from medical students with colds around the same time
[26]. Almeida & Tyrrell examined the prototype strain
HCoV 229E, and its morphology was found to be identical
to that of B814 and IBV [27]. Using the organ culture
technique, 6 further strains were subsequently recovered
including the prototype strains HCoV OC43 as well as 3
strains considered antigenically unrelated to either OC43
or 229E [1].
In the Guangdong province of China during the
winter of 2002 to 2003, an unusual and oen deadly form
of pneumonia appeared, a disease subsequently labelled
severe acute respiratory syndrome (SARS) [28]. is
disease spread to Hong Kong in late February, and, within
days, international air travel spread the virus over a wide
area, seeding outbreaks in Vietnam, Singapore, Canada,
and elsewhere. In July 2003, at the end of this outbreak,
8422 cases had been recorded, 916 (10.8 %) of them
fatal, in 29 country across 6 continents [28]. e point of
initial emergence of SARS-CoV an animal reservoir were
the live animal markets in Guangdong, where diverse
animal species are held, traded and sold to restaurants
in response to the demand for exotic food [28]. Small
mammals, such as civet cats, sold in these markets were
found to harbour viruses closely related to SARS-CoV, and
the initial interspecies transmission to humans probably
came from these markets [29,30]. MERS-CoV was rst
isolated in 2012 from the lung of a 60-year-old patient
who developed acute pneumonia and renal failure in Saudi
Arabia. Live MERS-CoV identical to the virus found in
humans was isolated from the nasal swabs of dromedary
camels, further indicating that camels serve as the bona
de reservoir host of MERS-CoV. As of February 14, 2020,
over 2500 laboratory conrmed cases were reported with a
high case fatality of 34.4%, making MERS-CoV one of the
most devastating viruses known to humans [28].
5. e history of COVID-19
A 41-year-old man was admitted to the Central Hospitalof
Wuhan on 26 December 2019, 6 days aer the onset of
disease. He had no history of hepatitis, tuberculosis,
or diabetes and reported fever, chest tightness, an
unproductive cough, pain, and weakness for 1 week on
presentation. e Wuhan Centre for Disease Control and
Prevention conducted an epidemiological investigation
and found that the patient worked at a local indoor
seafood market where, in addition to sh and shellsh, a
variety of live wild animals (including hedgehogs, badgers,
snakes, and birds) were available for sale as well as animal
carcasses. However, no bats were available for sale, and the
patient recalled no exposure to live poultry although he
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might have come into contact with wild animals [31].
On 31 December 2019, the WHO China Country
Oce was informed that cases of pneumonia with an
unknown aetiology had been detected in Wuhan City,
in the Hubei province of China [32]. From 31 December
2019 through 3 January 2020, a total of 44 patients with a
pneumonia of unknown aetiology were reported to WHO
by the national authorities in China. No causal agent was
identied during this reporting period. en, on 11 and
12 January 2020, WHO received further details from the
National Health Commission in China that the outbreak
had been associated with one of the seafood markets in
Wuhan City. On 7 January 2020, the Chinese, isolated and
identied a new type of coronavirus so that other countries
could develop specic diagnostic kits. On 12 January 2020,
China shared the genetic sequence of the novel coronavirus
[34]. On 13 January 2020, the Ministry of Public Health of
ailand reported the rst imported case of lab-conrmed
novel coronavirus (2019-nCoV) from Wuhan, Hubei
Province, China. On 15 January 2020, the Ministry of
Health, Labour and Welfare of Japan (MHLW) reported
an imported case of laboratory-conrmed 2019-novel
coronavirus (2019-nCoV) from the same source location
[35]. On 20 January 2020, the National IHR Focal Point
(NFP) for the Republic of Korea reported the rst case of
novel coronavirus, also from Wuhan, China [36]. COVID-
19’s rst cases were seen in Turkey on March 10, 2020
and it was 47,029 cases and 1006 deaths aer 1 month.
Infections with SARS-CoV-2 are now widespread, and as
of 10 April 2020, 1,727,602 cases have been conrmed in
more than 210 countries, with 105,728 deaths [37].
6. SARS-COV-2
In an early study, phylogenetic tree showed that 2019‐
nCoV (previous naming of SARS-CoV-2) signicantly
clustered with bat SARS-like coronavirus sequence isolated
in 2015, whereas structural analysis revealed mutation in
Spike glycoprotein and nucleocapsid protein. us, it is
clear that the new 2019‐nCoV is distinct from the SARS
virus which, aer a mutation that gave it the ability to
infect humans, was probably transmitted from bats [38].
Based on the phylogenetic tree, taxonomy, and established
practice, this virus was ocially identied as severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) by
the Coronavirus Study Group, and the current outbreak
of a coronavirus-associated acute respiratory disease was
called Coronavirus Disease-19 (COVID-19) [39].
Human epidemics with variable clinical severity
featuring respiratory and extra-respiratory manifestations
have been caused by a number of CoVs: SARS-CoV,
SARS-CoV-2, and MERS-CoV (betaCoVs of the B and C
lineage, respectively) [40]. With SARS-CoV and MERS-
CoV, mortality rates have been seen up to 10% and 35%,
respectively which places SARS-CoV-2 in the betaCoVs
category [41]. is variety has a round or elliptic, and oen
pleomorphic form and a diameter of approximately 60–
140 nm. Like other CoVs, it is sensitive to ultraviolet rays
and heat [42]. Another eective means of inactivation is
by lipid solvents including ether (75%), ethanol, chlorine-
containing disinfectant, peroxyacetic acid, and chloroform
except for chlorhexidine [43,44].
SARS-CoV-2 and SARS-CoV-1 have similar stability.
Both viruses could be detected in aerosols up to 3 h post-
aerosolization, up to 4 h on copper, up to 24 h on cardboard
and up to 2 to 3 days on plastic and stainless steel. In
aerosols, SARS-CoV-2, and SARS-CoV-1 exhibited
similar half-lives with median estimates of around 2.7 h
[43]. With the median half-life estimate for SARS-CoV-2
being around 13 h on stainless steel and around 16 h on
polypropylene, both viruses exhibit relatively long viability
on these surfaces compared to copper or cardboard [44].
Chan et al. [45] have shown that, in genetic terms, the
genome of the new HCoV, isolated from a cluster-patient
who presented with atypical pneumonia aer visiting
Wuhan, had a 89% nucleotide identity with bat SARS-like-
CoVZXC21 and 82% with that of human SARS-CoV [45].
For this reason, the new virus was called SARS-CoV-2,
its single-stranded RNA genome containing 29,903
nucleotides encoding for 9860 amino acids (Figure 2) [9].
While its origins are not completely understood, these
genomic analyses suggest that SARS-CoV-2 probably
evolved from a strain found in bats. However, the possible
intermediate between bats and humans, the potential
amplifying mammalian is not known. It is not even certain
that this intermediary exists since the virulence toward
humans could have been directly triggered by the mutation
in the original strain [46].
While it is believed that bats and palm civets were
the natural and intermediate reservoirs for SARS-CoV,
respectively, it has been isolated from animals and adapted
to lab cell culture [46,47]. It is also believed that SARS-
CoV was transmitted from palm civets to humans in an
animal market in southern China, and while the animal
source of the outbreak is currently unknown, SARS-CoV-2
also reportedly infected humans in an animal market
in Wuhan. Critically, the capacity for SARS-CoV-2 to
transmit from human to human has been conrmed [48].
An envelope-anchored spike protein mediates coronavirus
entry into host cells by rst binding to a host receptor and
then fusing viral and host membranes [49].
When the SARS-CoV-2 virus was compared with
S gene of SARS-CoV, bat-CoV (As6526), bat-CoV
(RaTG13), mink-CoV, and pangolin-CoV, it was found
71.41%, 68.17%, 92,86%, 30,89%, and 90% similarity,
respectively [50]. When the homology of SARS-CoV-2
and these coronaviruses is less than 75%, it would be
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presumed that SARS-CoV-2 is not the same virus like
the coronaviruses arising from these wild animals [50]. It
is also clear from these results that the 2 viruses, SARS-
CoV-2 and bat coronavirus RaTG13, are closely related
[50]. It was also reported that the SARS-CoV-2 virus did
not come directly from pangolins (24), so the relationship
between SARS-CoV-2 and pangolin coronavirus and
whether the pangolin is the intermediate host of SARS-
CoV-2 requires further investigation [51,52].
Spike protein contains 2 subunits, S1 and S2 [53].
S1 contains a receptor binding domain (RBD), which is
responsible for recognizing and binding with the cell
surface receptor. S2 subunit is the “stem” of the structure,
which contains other basic elements needed for the
membrane fusion [53]. e spike protein is the common
target for neutralizing antibodies and vaccines. It has been
reported that COVID-19 can infect the human respiratory
epithelial cells through interaction with the human
ACE2 receptor (Figure 3). Indeed, the recombinantSpike
proteincan bind with recombinantACE2protein [54,55].
e ACE2 protein is reportedly present in type 1 and
type 2 pneumocytes, enterocytes of all parts of the small
intestine, the brush border of the proximal arteries, and
veins of all tissues studied, and arterial smooth muscle
cells [54]. is localization of ACE2 explains the tissue
tropism of SARS-CoV for the lung, small intestine, and
kidney. However, notable discrepancies include virus
replication in colonic epithelium, which has no ACE2, and
no virus infection in endothelial cells, which have ACE2,
other receptors, or co-receptors such as LSIG that explain
such discrepancies [54].
e pathophysiology and virulence mechanisms of
CoVs– and thus of SARS-CoV-2–have links to the function of
the nonstructural protein (nsps) and structural proteins. For
Figure 2. Genomic structure of SARS-CoV-2 Wuhan Hu-1 strain. Accession: NC_045512 [9]
Figure 3. Binding, viral entry, and replication cycle of SARS-CoV-2 [47]. (Contributed by
Rohan Bir Singh, made with Biorender.com).
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HASÖKSÜZ et al. / Turk J Med Sci
instance, a nsp can block the host innate immune response
of the host, according to the research. It is known that the
envelope, among the functions of structural proteins, plays a
crucial role in virus pathogenicity because it promotes viral
assembly and release, but many features (e.g., those of nsp 2
and 11) have not been described yet [56].
Infectious disease experts and multiple international
and domestic human and animal health organizations
(CDC, OIE, and WHO) agree that there is no evidence at
this point indicating that pets can spread COVID-19 to
other animals, including people. Although there has not
been reports of pets becoming sick with COVID-19, out of
an abundance of caution,it is recommended that those of
ill with COVID-19 should limit contact with animals until
more information is known about the virus. On the other
hand, Shi et al. [2020] report that cats and ferrets can be
experimentally infected with SARS-CoV-2, but not dogs,
pig, chickens, and ducks. In this study, which is the only
one in this subject, they claim that cats can spread SARS-
CoV-2 by respiratory and other cats can be infected [57].
Ultimately, novel coronaviruses are likely to emerge
periodically in humans because of frequent cross-species
infections and occasional spillover events (Figure 4), given
the high prevalence and wide distribution of coronaviruses,
the large genetic diversity, and frequent recombination of
their genomes, and an increasing level of human-animal
interaction.
Acknowledgements
Mustafa Hasöksüz and Selçuk Kılıç are the members of
COVID-19 Advisory Committee of Ministry of Health of
Turke y.
Figure 4. Animal origins of human coronaviruses [5].
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abb7015
... The first coronavirus found in 1937 was Infectious Bronchitis Virus (IBV) and was of poultry origin discovered by Beaudette & Hudson. The first Human coronavirus was discovered and revealed in the 1960s (Hasöksüz et al., 2020). ...
... E protein is the most peculiar structural protein. During the infection, although the cell produces large amounts of E protein, only a small amount of it is integrated into the envelope of virion (Hasöksüz et al., 2020). Most of the E protein is located at the site of virus assembly, budding, intracellular trafficking, endoplasmic reticulum, and Endoplasmic reticulum Golgi intermediate components organelles. ...
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Humanity has historically been affected by remarkable epidemics and pandemics, including the plague, cholera, influenza, SARS-CoV, and MERS-CoV. A novel coronavirus pandemic known as SARS-CoV-2 is rapidly sweeping the globe. Over the period, the genome of the novel coronavirus has been mutated as it passes 4268 through its primary host. The world is reporting multiple point mutations. So the objective of this study was to observe modifications in the partial region of SARS-CoV-2 for the surveillance. This cross sectional study was carried out to detect the modifications in the SARS-CoV-2. For this purpose initial screening of COVID-19 was done to collect the strain of SARS-CoV-2 using RT-PCR. Then, primers were created in order to amplify the area using the S gene of the SARS-CoV-2. The amplified product was sent for the sequencing and bioinformatic tools were used to observed the mutations and data was compared with the Wild strain of the Virus. During the analysis, one of the most important point mutation was D614G caused by the amino acid substitution of aspartic acid with the glycine. Addition to this point mutation, other important mutations have also been observed. In this research, E484k, N501Y and D614G mutations were seen in the partial receptor binding domain (RBD) and SD1 region of the S gene sequence. As a result of point mutations, the amino acids were altered leading to enhanced transmission, binding affinity to the human ACE2 receptor, and reduced susceptibility against the antibody neutralization. Globally, these alternations pose a threat to public health.
... surface of the virion determines the attachment and the entry of the virus to the host cells [1][2][3]. The binding affinity of the SARS-CoV-2 S protein to its cellular receptor hACE2 is higher as compared to that of S protein of the SARS-CoV-1 [4], making SARS-CoV-2 extremely transmittable [5][6][7][8]. To prevent virus transmission, it is suggested by the World Health Organization (WHO) to wear masks for avoiding the nosocomial transmission of the virus. ...
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Due to the high prevalence of infectious diseases and their concurrent outbreaks, there is a high interest in developing novel materials with antimicrobial properties. Antibacterial and antiviral properties of a range of metal-based nanoparticles (NPs) are a promising means to fight airborne diseases caused by viruses and bacteria. The aim of this study was to test antimicrobial metals and metal-based nanoparticles efficacy against three viruses, namely influenza A virus (H1N1; A/WSN/1933) and coronaviruses TGEV and SARS-CoV-2; and two bacteria, Escherichia coli and Staphylococcus aureus. The efficacy of ZnO, CuO, and Ag NPs and their respective metal salts, i.e., ZnSO4, CuSO4, and AgNO3, was evaluated in suspensions, and the compounds with the highest antiviral efficacy were chosen for incorporation into fibers of cellulose acetate (CA), using electrospinning to produce filter materials for face masks. Among the tested compounds, CuSO4 demonstrated the highest efficacy against influenza A virus and SARS-CoV-2 (1 h IC50 1.395 mg/L and 0.45 mg/L, respectively), followed by Zn salt and Ag salt. Therefore, Cu compounds were selected for incorporation into CA fibers to produce antiviral and antibacterial filter materials for face masks. CA fibers comprising CuSO4 decreased SARS-CoV-2 titer by 0.38 logarithms and influenza A virus titer by 1.08 logarithms after 5 min of contact; after 1 h of contact, SARS-CoV-2 virus was completely inactivated. Developed CuO- and CuSO4-based filter materials also efficiently inactivated the bacteria Escherichia coli and Staphylococcus aureus. The metal NPs and respective metal salts were potent antibacterial and antiviral compounds that were successfully incorporated into the filter materials of face masks. New antibacterial and antiviral materials developed and characterized in this study are crucial in the context of the ongoing SARS-CoV-2 pandemic and beyond.
... COVID-19 is a new global epidemic characterised by high infectivity and variability, posing a significant threat to human life and the global economy (Chakraborty and Maity 2020). The pathogen of COVID-19 is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Hasöksüz, Kiliç et al. 2020), a single-stranded RNA virus of the genus Beta coronavirus and shares 79% nucleotide sequence identity with SARS-CoV, the causative agent of the 2002 SARS epidemic. Other viruses in the same genus include human coronavirus HCoV-HKu1, HCoV-OC43, and Middle East respiratory syndrome coronavirus (MERS-CoV). ...
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Since 2019, the coronavirus disease-19 (COVID-19) has been spreading rapidly worldwide, posing an unignorable threat to the global economy and human health. It is a disease caused by severe acute respiratory syndrome coronavirus 2, a single-stranded RNA virus of the genus Betacoronavirus. This virus is highly infectious and relies on its angiotensin-converting enzyme 2-receptor to enter cells. With the increase in the number of confirmed COVID-19 diagnoses, the difficulty of diagnosis due to the lack of global healthcare resources becomes increasingly apparent. Deep learning-based computer-aided diagnosis models with high generalisability can effectively alleviate this pressure. Hyperparameter tuning is essential in training such models and significantly impacts their final performance and training speed. However, traditional hyperparameter tuning methods are usually time-consuming and unstable. To solve this issue, we introduce Particle Swarm Optimisation to build a PSO-guided Self-Tuning Convolution Neural Network (PSTCNN), allowing the model to tune hyperparameters automatically. Therefore, the proposed approach can reduce human involvement. Also, the optimisation algorithm can select the combination of hyperparameters in a targeted manner, thus stably achieving a solution closer to the global optimum. Experimentally, the PSTCNN can obtain quite excellent results, with a sensitivity of 93.65% ± 1.86%, a specificity of 94.32% ± 2.07%, a precision of 94.30% ± 2.04%, an accuracy of 93.99% ± 1.78%, an F1-score of 93.97% ± 1.78%, Matthews Correlation Coefficient of 87.99% ± 3.56%, and Fowlkes-Mallows Index of 93.97% ± 1.78%. Our experiments demonstrate that compared to traditional methods, hyperparameter tuning of the model using an optimisation algorithm is faster and more effective.
... Severe Acute Respiratory Syndrome-causing coronaviruses SARS-CoV-1 and SARS-CoV-2 were originated from an animal reservoir and cross the species barrier, confirming the potential threat of animal coronaviruses to the human population (Hasoksuz 2020, Zang et al., 2020Zapulli et al., 2020). This has led to a surge of interest in coronavirus research in all species. ...
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Domestic and wild dogs of all ages and breeds are susceptible to Canine Coronavirus (CCoV) infections and be seen in Türkiye and amongst world. CCoV has recently been declared a zoonotic disease agent and the eighth pathogenic human coronavirus. This study was conducted on 143 naturally infected dogs with gastroenteritis which were not vaccinated against CCoV in Türkiye in 2015-2020. The data of dogs were analyzed seroepidemiologically, clinicopathologically and statistically. CCOV antibodies in serum and CCOV antigens in stool were detected by ELISA and lateral immunochromatography. The rising CCoV IgG antibody titers were detected at all dogs and were as follows; 64 ng/L in 81 (81%) dogs. CCOV and Canine Parvovirus (CPV) antigen were detected together in the stool of the 41 (28.7%) dogs. As a result, it was concluded that the CCOV agent is in circulation among dogs living in Türkiye. CCOV and CPV can cause co-infections and increased mortality. Although infection can be seen in dogs of all ages, it can be seen more frequently in dogs younger than 1 year of age, and especially in dogs younger than 6 months, and can cause enteritis, low hemoglobin, erythropenia, lymphopenia, leukopenia, thrombocytopenia, and hypoproteinemia.
... Province wise data reported 577,201 cases in Sindh, 219,616 in KPK, 506,865 in Punjab, 135,312 in Islamabad, 35,494 in Baluchistan, and 43,324/11,748 in AJK/GB. It is the span of about three years and the pandemic is still raging [4]. The greatest number of cases have been reported in the USA amounting to 84,692,706 cases along with the highest number of deaths, that is, 1,028,014. ...
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Coronaviruses (CoVs) can infect a wide range of wild and domestic hosts including animals, avian, mammals, rodents, and human beings. COVID infection has already been reported in whales, bats, mice, birds, and giraffes,s and infection to domestic and life stock cause heavy losses to the economy. These viruses cause mild to severe respiratory, enteric, and systemic infections. Worldwide 525,268,297 (May 19, 2022) individuals have been infected since the first case of COVID-19 was reported in Wuhan China with 6,295,402 deaths (May 19, 2022). In Pakistan, 1,529,560 cases of COVID-19 have been reported with 30,379 deaths (May 19, 2022). Province wise data reported 577,201 cases in Sindh, 219,616 in KPK, 506,865 in Punjab, 135,312 in Islamabad, 35,494 in Baluchistan, and 43,324/11,748 in AJK/GB. This study evaluated the hematological parameters in diabetic patients affected by COVID-19. This cross-sectional retrospective study was conducted at the Department of Pathology, Aziz Bhatti Shaheed Hospital, Gujrat, Pakistan. Data were collected from a total of 111 patients of COVID-19 with DM comorbidities and analyzed for the comparison of Leukocytes parameters, platelets count, Red Blood Cell (RBC) counts, and their indices Packed Cell Volume (PCV), Mean Corpuscular Volume (MCV), Mean Corpuscular Hemoglobin (MCH) and Mean Corpuscular Hemoglobin Concentration (MCHC)] with their reference values. The mean RBC count was 4.45 with SD (±0.84). The data also showed the mean of Hemoglobin (Hb) level as 12.45 g/dl (SD ±3.01), PCV as 36.06 (SD ±9.16), MCV as 81.86 (SD ±7.32), MCH as 29.05 (SD ±6.27), and MCHC as 32.61 (SD ±3.65). A comparison was also made between male and female COVID-19-enrolled patients for associated hematological changes in DM. The frequency distribution of leukocytes and thrombocytes showed lymphocytosis and thrombocytopenia. It was concluded that hematological parameters are important in monitoring disease severity, progression, and management in COVID-19 patients with diabetes comorbidity.
... Among these, the four HCoVs (HCoV-NL63, HCoV-229E, HCoV-HKU1 and HCoV-OC43) normally cause asymptomatic, self-limited and mild respiratory tract symptoms (Zumla et al., 2016). Occasionally, four HCoVs can also result in moderate to even severe respiratory infections, especially for susceptible infants, young children, elderly people, immunocompromised individuals and people with underlying diseases or comorbidities (Hasoksuz et al., 2020;Rajapakse and Dixit, 2021;Veiga et al., 2021). Globally, HCoV-NL63, HCoV-229E, HCoV-HKU1, and HCoV-OC43 infections account for up to 30% of human respiratory tract illnesses (Lim et al., 2016;Fung and Liu, 2019). ...
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Human coronaviruses (HCoVs) HCoV-NL63, HCoV-229E, HCoV-HKU1 and HCoV-OC43 have been circulated in the human population worldwide, and they are associated with a broad range of respiratory diseases with varying severity. However, there are neither effective therapeutic drugs nor licensed vaccines available for the treatment and prevention of infections by the four HCoVs. In this study, we collected nasopharyngeal aspirates of children hospitalized for respiratory tract infection in China during 2014–2018 and conducted next-generation sequencing. Sequences of four HCoVs were then selected for an in-depth analysis. Genome sequences of 2 HCoV-NL63, 8 HCoV-229E, 2 HCoV-HKU1, and 6 HCoV-OC43 were obtained. Based on the full-length S gene, a strong temporal signal was found in HCoV-229E and the molecular evolutionary rate was 6 × 10−4 substitutions/site/year. Based on the maximum-likelihood (ML) phylogenetic tree of complete S gene, we designated H78 as a new sub-genotype C2 of HCoV-HKU1, and the obtained P43 sequence was grouped into the reported novel genotype K of HCoV-OC43 circulating in Guangzhou, China. Based on the complete genome, potential recombination events were found to occur as two phenomena, namely intraspecies and interspecies. Moreover, we observed two amino acid substitutions in the S1 subunit of obtained HCoV-NL63 (G534V) and HCoV-HKU1 (H512R), while residues 534 and 512 are important for the binding of angiotensin-converting enzyme 2 and neutralizing antibodies, respectively. Our findings might provide a clue for the molecular evolution of the four HCoVs and help in the early diagnosis, treatment and prevention of broad-spectrum HCoV infection.
... Due to its severe pathogenicity and ability to spread in March 2020 the World Health Organization (WHO) declared it a global epidemic (1). Symptoms of COVID-19 infection are often nonspecific and heterogeneous, and depend on sex, age, immune status, viral load, associated diseases or possible history of other coronavirus infections (2)(3)(4)(5). Despite the variation of responses from patient to patient, dry cough, fever, dyspnoea, loss of smell and taste are the most common symptoms and, in severe cases the infection may lead to death. ...
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Background: Due to their wide application in the SARS-CoV-2 pandemic, we verified and compared three qualitative serological methods in order to select the most optimal that will best serve its purpose under laboratory conditions. Methods: We assessed the diagnostic characteristics of two automated serological methods (Roche Elecsys® Anti-SARS-CoV-2 and Abbott SARS-CoV-2 IgG) and a POCT test (Colloidal Gold Method SARS-CoV-2 IgM/IgG Antibody Assay Kit). In the process of verification, analytical precision was also assessed for the automated assays. Results: Diagnostic characteristics were determined by measuring antibodies against SARS-CoV-2 in 91 RT-PCR-negative and 60 RT-PCR-positive samples. The POCT test gave the highest number of false positive cases (8.61%). Roche Elecsys® Anti-SARS-CoV-2 gave only 2.65% false positivity and showed the highest diagnostic sensitivity of 98.33% (95% CI: 91.06-99.96), while Abbott SARS-CoV-2 IgG method showed 100.00% (95% CI: 96.03-100.00) diagnostic specificity and an almost perfect agreement with Roche Elecsys® Anti-SARS-CoV-2. When assessing the precision of the automated methods, we observed some variability in the positive control samples, but the values did not affect clinical interpretation. Conclusion: Both automated methods demonstrate superior diagnostic characteristics compared to the Colloidal Gold Method, and this POCT test is not considered as an appropriate choice for routine testing. The two automated methods showed low variability without altering the results and their interpretation.
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The world has not yet completely overcome the fear of the havoc brought by SARS-CoV-2. The virus has undergone several mutations since its initial appearance in China in December 2019. Several variations (i.e., B.1.616.1 (Kappa variant), B.1.617.2 (Delta variant), B.1.617.3, and BA.2.75 (Omicron variant)) have emerged throughout the pandemic, altering the virus’s capacity to spread, risk profile, and even symptoms. Humanity faces a serious threat as long as the virus keeps adapting and changing its fundamental function to evade the immune system. The Delta variant has two escape alterations, E484Q and L452R, as well as other mutations; the most notable of these is P681R, which is expected to boost infectivity, whereas the Omicron has about 60 mutations with certain deletions and insertions. The Delta variant is 40–60% more contagious in comparison to the Alpha variant. Additionally, the AY.1 lineage, also known as the “Delta plus” variant, surfaced as a result of a mutation in the Delta variant, which was one of the causes of the life-threatening second wave of coronavirus disease 2019 (COVID-19). Nevertheless, the recent Omicron variants represent a reminder that the COVID-19 epidemic is far from ending. The wave has sparked a fervor of investigation on why the variant initially appeared to propagate so much more rapidly than the other three variants of concerns (VOCs), whether it is more threatening in those other ways, and how its type of mutations, which induce minor changes in its proteins, can wreck trouble. This review sheds light on the pathogenicity, mutations, treatments, and impact on the vaccine efficacy of the Delta and Omicron variants of SARS-CoV-2.
Chapter
Infectious pathogens are a threat to global healthcare and the socioeconomic progress of the world. Since December 2019, the world has battled with the 2019-novel coronavirus disease (COVID-19), a zoonotic viral infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has resulted in high rates of infection and deaths across continents. Coronaviruses, due to their genetic nomenclature of being RNA viruses, easily undergo genetic mutation during their replication cycle. This has resulted in several SARS-CoV-2 variants of concern. The current state and what the future of COVID-19 holds for mankind is an unresolved question hanging on. Recently, there has been great improvement in the fight against the COVID-19 pandemic. Vaccines have been developed to reduce the risk of infection. Also, insights from the study of previous coronaviruses and previous pandemics have been helpful in the quick development of different effective vaccines and the deployment of various effective interventions. In this chapter, discussions on the genesis of COVID-19, its transmission, impact, preventive measures, and therapeutic advancements are presented.
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SARS-CoV-2 (novel coronavirus, nCoV-2019) outbreak started in December 2019 in China has created a public health concern all around the world. Since infected patients transported out of China, the outbreak status was quickly changed into pandemic. Comparison of available genome sequences of the virus strains enlightened most questions as the cell receptors (ACE2) responsible for the virus tropism which determines possible organs and tissues to be affected by the virus as well as possible involvement of the age groups and host diversity. SARS-CoV-2, new member of Coronaviridae shares some clinical and epidemiological aspects similar to previous high pathogenic human coronavirus, SARS-CoV, existed in 2002. The most outstanding property of SARS-CoV-2 is high transmission rate (reproduction number, R0 ~ 3.58) between suspected and susceptible people. While bats are pointed as the original host and pangolins as an intermediate host, possibility of other species contribution is still unknown. According to recent data, reptiles i.e. snakes seem to be out of the group for possible intermediate hosts. Also there is no data supporting involvement of domestic animals even pets or food producing in the infection spectrum. This review summarizes the key findings of ongoing pandemia since the day disease existed. Molecular divergences now show that disease agent evolved into two types (S and L). Mutations and natural selections besides recombination will still continue to be the common feature of coronaviruses. Though implementation of common global measures and treatments other than rapid sharing the information will contribute prevention efforts and reducing the number of losses.
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Alternative hosts and model animals The severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) pandemic may have originated in bats, but how it made its way into humans is unknown. Because of its zoonotic origins, SARS-CoV-2 is unlikely to exclusively infect humans, so it would be valuable to have an animal model for drug and vaccine development. Shi et al. tested ferrets, as well as livestock and companion animals of humans, for their susceptibility to SARS-CoV-2 (see the Perspective by Lakdawala and Menachery). The authors found that SARS-CoV-2 infects the upper respiratory tracts of ferrets but is poorly transmissible between individuals. In cats, the virus replicated in the nose and throat and caused inflammatory pathology deeper in the respiratory tract, and airborne transmission did occur between pairs of cats. Dogs appeared not to support viral replication well and had low susceptibility to the virus, and pigs, chickens, and ducks were not susceptible to SARS-CoV-2. Science , this issue p. 1016 ; see also p. 942
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Mutation and adaptation have driven the co-evolution of coronaviruses (CoVs) and their hosts, including human beings, for thousands of years. Before 2003, two human CoVs (HCoVs) were known to cause mild illness, such as common cold. The outbreaks of severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS) have flipped the coin to reveal how devastating and life-threatening an HCoV infection could be. The emergence of SARS-CoV-2 in central China at the end of 2019 has thrusted CoVs into the spotlight again and surprised us with its high transmissibility but reduced pathogenicity compared to its sister SARS-CoV. HCoV infection is a zoonosis and understanding the zoonotic origins of HCoVs would serve us well. Most HCoVs originated from bats where they are non-pathogenic. The intermediate reservoir hosts of some HCoVs are also known. Identifying the animal hosts has direct implications in the prevention of human diseases. Investigating CoV-host interactions in animals might also derive important insight on CoV pathogenesis in humans. In this review, we present an overview of the existing knowledge about the seven HCoVs, with a focus on the history of their discovery as well as their zoonotic origins and interspecies transmission. Importantly, we compare and contrast the different HCoVs from a perspective of virus evolution and genome recombination. The current CoV disease 2019 (COVID-19) epidemic is discussed in this context. In addition, the requirements for successful host switches and the implications of virus evolution on disease severity are also highlighted.
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The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
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To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS‐CoV‐2 virus, we reanalyzed virome data sets from pangolins and representative SARS‐related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood‐mapping, and comparative analyses of the genomes. Based on Bayesian time‐scaled phylogenetic analysis using the tip‐dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS‐CoV‐2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10⁻³ substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS‐CoV‐2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS‐CoV‐2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS‐CoV‐2 virus, which is responsible for the recent outbreak of COVID‐19, did not come directly from pangolins. Highlights • We identified a unique peptide (PRRA) insertion in the human SARS‐CoV‐2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility.
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