Received: 14 September 2020 | Revised: 14 October 2020 | Accepted: 19 October 2020

DOI: 10.1002/jmv.26615

REVIEW

SARS‐CoV‐2‐specific virulence factors in COVID‐19

Ashutosh Kumar1,2 | Pranav Prasoon1,3 | Chiman Kumari1,4 |

1,5 1,6 1,2
Vikas Pareek | Muneeb A. Faiq | Ravi K. Narayan |
1,7
Maheswari Kulandhasamy | Kamla Kant1,8

1
Etiologically Elusive Disorders Research
Network (EEDRN), New Delhi, India Abstract
2
Department of Anatomy, All India Institute The paucity of knowledge about severe acute respiratory syndrome coronavirus 2
of Medical Sciences (AIIMS), Patna, India
(SARS‐CoV‐2)‐specific virulence factors has greatly hampered the therapeutic
3
Pittsburgh Center for Pain Research, School
of Medicine, University of Pittsburgh, management of patients with coronavirus disease 2019 (COVID‐19). Recently, a
Pittsburgh, Pennsylvania, USA cluster of studies appeared, which presented empirical evidence for SARS‐CoV‐2‐
4
Department of Anatomy, Postgraduate specific virulence factors that can explain key elements of COVID‐19 pathology.
Institute of Medical Education and Research
(PGIMER), Chandigarh, India These studies unravel multiple structural and nonstructural specifics of SARS‐CoV‐
5
National Brain Research Center, Manesar, 2, such as a unique FURIN cleavage site, papain‐like protease (SCoV2‐PLpro),
Haryana, India
ORF3b and nonstructural proteins, and dynamic conformational changes in the
6
New York University (NYU) Langone Health
structure of spike protein during host cell fusion, which give it an edge in infectivity
Center, NYU Robert I Grossman School of
Medicine, New York, New York, USA and virulence over previous coronaviruses causing pandemics. Investigators pro-
7
Department of Biochemistry, Maulana Azad vided robust evidence that SARS‐CoV‐2‐specific virulence factors may have an
Medical College (MAMC), New Delhi, India
impact on viral infectivity and transmissibility and disease severity as well as the
8
Department of Microbiology, All India
Institute of Medical Sciences (AIIMS), development of immunity against the infection, including response to the vaccines.
Bathinda, India In this article, we are presenting a summarized account of the newly reported
studies.
Correspondence
Ashutosh Kumar, Department of Anatomy, All
India Institute of Medical Sciences (AIIMS), KEYWORDS
Patna 801505, India. COVID‐19, host immune response, interferon, SARS‐CoV‐2, virulence factors
Email: drashutoshkumar@aiimspatna.org

1 | INTRODUCTION transmembrane serine protease 2 (TMPRSS2) or Cathepsin B or L

Currently, the world is engulfed by a pandemic of coronavirus dis-
ease 2019 (COVID‐19) from a novel strain severe acute respiratory
syndrome coronavirus‐2 (SARS‐CoV‐2). The paucity of knowledge
about SARS‐CoV‐2‐specific virulence factors has greatly impacted
the therapeutic management of the disease. SARS‐CoV‐2 belongs to
the genus of betacoronaviruses, which also contained SARS‐CoV‐1
and MERS‐CoV (causative agents for severe acute respiratory syn-
drome [SARS] in 2002 and the Middle East respiratory syndrome
[MERS] in 2012, respectively) as the members. SARS‐CoV‐2 entry
into human cells is mediated by a cell surface receptor angiotensin‐
converting enzyme‐2 (ACE2), which binds to the receptor‐binding
domain (RBD) of SARS‐CoV‐2 spike (S) protein. Following ACE2
binding, cleavage of the viral spike protein (S) by the proteases like
(CTS‐B or L), or FURIN is considered as the essential step to effec-
tuate host cell membrane fusion and virus infection.1–3 Molecular
mechanisms leading to viral infection of human tissues in COVID‐19
is now largely known; however, knowledge of virus or host‐specific
properties driving tissue disease pathogenesis is still in progress.
Recently, a cluster of studies appeared (including some preliminary
reports), which demonstrated SARS‐CoV‐2‐specific virulence factors,
that can explain key elements of COVID‐19 pathology. These studies
unravel structural and nonstructural specifics of SARS‐CoV‐2, such
as a unique FURIN cleavage site (FCS), papain‐like protease (SCoV2‐
PLpro), ORF3b, and certain nonstructural proteins (NSPs), and dy-
namic conformational changes in the structure of spike protein
during host cell fusion. Many of such features were not known for
the previous coronaviruses, including SARS‐CoV‐1 and MERS‐CoV.

J Med Virol. 2021;93:1343–1350. wileyonlinelibrary.com/journal/jmv © 2020 Wiley Periodicals LLC | 1343

1344 | KUMAR ET AL.

The SARS‐CoV‐2‐specific virulence factors are mainly directed to
escape detection by host immune cells or to manipulate host immune
responses, including delaying of interferon (IFN)‐mediated protec-
tion and efficient production of neutralizing (preventing infection)
antibodies, or driving host cell machinery favoring viral replication. In
this article, we are presenting a summarized account of those newly
reported studies.
2 | SARS ‐C O V‐ 2 ‐SPECIFIC VIRULENCE
F A CT O R S
2.1 | A unique FCS in SARS‐CoV‐2
SARS‐CoV‐2 has structural similarity to the coronaviruses causing
previous pandemics, more specifically SARS‐CoV‐1, to which it has
close genomic (79.5%) and protein homology (95%–100%).4,5
Moreover, it also shared with SARS‐CoV‐1, its key host cell entry
receptor—ACE2. However, insertion of an FCS containing multi‐basic
amino acids (PRRAR) at the S1/S2 intersection of viral spike protein
(S) has made it distinct from SARS‐CoV‐1 or other SARS‐related
viruses.3 Although FCS is present in a number of other CoV family
members, including MERS‐CoV, HKU1‐CoV, and OC43‐CoV, it is said
to be an evolutionary gain in SARS‐CoV‐2 and is speculated to be a
6
key factor behind its high infectivity and transmissibility.
FCS has been a known feature in influenza viruses and is con-
sidered to contribute to their higher virulence. Whether it is making
any contribution to the virulence in SARS‐CoV‐2 is not still well
understood.7
Although, the S1/S2 site of SARS‐CoV‐2 S is efficiently cleaved
by a wide range of other proteases, including TMPRSS2 and
cathepsin‐B or L (CTS‐B or L)8; the insertion of FCS might have
provided some advantage to SARS‐CoV‐2, which needs to be ade-
quately explored. A recent study by Johnson et al.6 showed that a
SARS‐CoV‐2 mutant lacking FCS in the spike protein had reduced
replication in Calu3 cells, a human respiratory cell line, and had at-
tenuated disease in a hamster pathogenesis model, providing pre-
liminary indications that FCS may have contributed to SARS‐CoV‐2
virulence.
2.2 | SARS‐CoV‐2 manipulates host immune
response
A majority of the newly reported studies showed that SARS‐CoV‐2‐
specific virulence factors are mainly directed against host immune
responses. Of note, a hyperactive innate immune response char-
acterized by “cytokine storm” is a usual finding in severe COVID‐19
patients.9 New data suggested, a virus‐mediated tricking can result in
a dichotomous host immune response—a delayed but hyperactive

F I G U R E 1 SARS‐CoV‐2 manipulates host immune response. Patients with severe COVID‐19 show a dampened IFN (type I and III) response
but paradoxically highly raised cytokines as early as 10 days postappearance of symptoms. The dampening of early IFN response is found to be
mediated by the viral proteins ORF3b and SARS‐CoV‐2‐PLpro. SARS‐CoV‐2‐PLpro preferentially cleaves the ubiquitin‐like protein ISG15 from
IRF3, attenuating type I IFN response. Additionally, SARS‐CoV‐2 infection of lymphoid tissue causes loss of germinal centers and depletion of a
specific subset of T cells—Tfh cells, and a specific population of B cells—Bcl6+—which are involved in antibody formation. IFN, interferon; IRF3,
IFN responsive factor 3; ISG 15, interferon‐stimulated gene 15; ORF3b, open‐reading frame 3b; SARS‐CoV‐2‐PLpro, SARS‐CoV‐2‐encoded
enzyme papain‐like protease; Tfhcell, T follicular helper cell
KUMAR ET AL.
innate immune response creating a cytokine storm, which conse-
quently can lead to dampening of T"‐cell mediated antiviral functions
(Figure 1). Lucas et al.10 serially analyzed immune responses in 113
COVID‐19 patients with moderate (non‐ICU) and severe (ICU) dis-
ease. Their data indicated sharp differences in the expression of in-
flammatory markers along disease progression between these two
groups of patients. These investigators identified the development of
a maladapted immune response profile associated with severe
COVID‐19 outcome. Immune profiling of the patients revealed an
overall increase in innate cell lineages with a concomitant depletion
of T cells. The nasopharyngeal viral load of the infected patients
correlated with plasma levels of IFNs and cytokines. The viral load
declined at a slower pace in patients who were admitted to the ICU.
Investigators also noted an association between early, elevated cy-
tokines and worse disease outcomes.10 Following an early increase in
cytokines, COVID‐19 patients with moderate disease displayed a
progressive reduction in type 1 and 3 (antiviral and antifungal, re-
10
spectively) innate immune responses. In contrast, patients with
severe disease maintained these elevated responses throughout the
course of the disease. The severe disease was also accompanied by
an increase in multiple type 2 (anti‐helminths) innate immune re-
sponse markers, including interleukin‐5 (IL‐5), IL‐13, immunoglobulin
10 10
E, and eosinophils. The findings of Lucas et al. signify the im-
portance of early immunological interventions that target in-
flammatory markers, which are predictive of severe symptoms rather
than targeting the late‐appearing cytokines.
T‐cell‐mediated immune response is an important parameter,
which can be used to predict survival outcomes, and at some stages
of disease progression T‐cell suppression is not unusual in re-
spiratory viral infections, including SARS and MERS.11 Beyond the
set assumptions, the recent studies showed that T‐cell suppression is
a feature associated with every stage of COVID‐19, including
asymptomatic cases, which points toward direct involvement of a
SARS‐CoV‐2 as its etiology.12,13 Blood profiling of the COVID‐19
patients further showed that increased levels of cytokines, includ-
ing tumor necrosis factor‐α (TNF‐α), IL‐6, IL‐8, and IL‐10 levels were
negatively correlated to T‐cell counts in severe COVID‐19, which
meant that, other than a direct SARS‐CoV‐2‐mediated virulence, high
levels of these cytokines might be an additional factor involved in the
causation of T‐cell suppression.12,13 Cytokine storm is a well‐known
clinical feature in many viral respiratory infections, including the beta
coronaviruses SARS‐CoV‐1 and MERS‐CoV.14 Surprisingly, in pa-
tients with COVID‐19, cytokines storm showed some peculiar fea-
tures, for example, IL‐10—which has known anti‐inflammatory,
albeit, immunosuppressive functions (hence, it can induce T‐cell
exhaustion)—was observed distinctively raised in severe cases of
COVID‐19, which is anomalous (in SARS it was seen raised in con-
15
valescent patients only). Markers of T‐cell exhaustion, like TIM‐3
and cell death‐like PD‐1, were also reported to be elevated in severe
12
COVID‐19.
An early IFN‐I‐mediated innate immune response is considered
essential to enhance viral clearance in respiratory infection.16 De-
laying or the dampening of the host's IFN‐I‐mediated innate immune
| 1345
response are the tactics used by the respiratory viruses, including
SARS‐CoV‐1 and MERS‐CoV, which can increase their infectivity and
stay in the host tissue.17,18 Surprisingly, SARS‐CoV‐2 was shown to
use a very distinctive strategy to trick with the host innate immune
response (not even seen in SARS‐CoV‐1 and MERS‐CoV, influenza
virus type A [IVA]).19 Recent cell culture studies with SARS‐CoV‐2
showed a dampened IFN‐I and ‐III response but paradoxically highly
raised cytokines.19,20 The dampening of early IFN response was
found to be mediated by a viral protein ORF3b.20 A similar ob-
servation was recently presented by Hadjadj et al.,21 who performed
an integrated immune analysis on a cohort of 50 COVID‐19 patients
with various disease severities. They found highly impaired IFN‐I
response (characterized by no IFN‐β and low IFN‐α production and
activity), associated with a persistent blood viral load and an ex-
acerbated inflammatory response in patients with severe disease
symptoms.21
Poor adaptive immune response and short‐lasting antibody for-
mation against SARS‐CoV‐2 proteins in convalescent patients with
COVID‐19 have been often reported;22–24 however, the pathological
basis for that has been only indicated now, in a recent study, by
Kaneko et al.25 These authors showed lesions in lymphoid tissue,
including lymph nodes, Peyer's patches, and spleen in autopsy spe-
cimens of COVID‐19 patients. They noted distinct atrophy or ab-
sence of germinal centers in the lymphoid tissues, which induce
the production of antibodies from differentiated B cells (or plasma
cells) in patients with severe COVID‐19 disease, as early as
10 days from the start of symptoms. They particularly zeroed down
that COVID‐19 patients had a lower number of a specific subset of
T cells—T follicular helper (Tfh), cells and a specific population of
B cells—Bcl6+—which mediate antibody formation—at the germinal
centers25 (Figure 1). SARS‐CoV‐2‐mediated atrophy and lesion of the
human lymphoid tissues like the spleen and lymph nodes were also
reported recently by Chen et al.26 Presence of germinal centers in
the lymphoid tissues are crucial to facilitate the selection of high‐
affinity B cell with a long lifespan.27 In contrast to coronaviruses,
antibody‐mediated immune responses sustain far longer (for dec-
ades) for some infectious diseases, which not only ensures protection
of the individuals from the re‐infection but also can contribute to
herd immunity when a substantial portion of a population is infected.
Thus, short lasting of viral specifies antibodies in COVID‐19 indicates
that herd immunity in COVID‐19 may be a difficult task to achieve.25
Coronaviruses require a viral‐encoded enzyme papain‐like pro-
tease (PLpro) (also known as NSP3) for processing viral polyproteins
to generate a functional replicase complex and enable viral spread.
PLpro is also implicated in cleaving proteinaceous posttranslational
modifications on host proteins, which is an evasion mechanism
against host antiviral immune responses.28 A recent study by Shin
et al.29 provided a biochemical, structural, and functional char-
acterization of the SARS‐CoV‐2‐PLpro (SCoV2‐PLpro) and outlined
the differences to SARS‐CoV‐1 PLpro (SCoV1‐PLpro) in controlling
host IFN and NF‐κB pathways. While SCoV2‐PLpro and SCoV1‐
PLpro shared an 83% sequence identity, they exhibited different
host substrate preferences. In particular, SCoV2‐PLpro preferentially
1346 | KUMAR
cleaved the ubiquitin‐like protein ISG15, whereas SCoV1‐PLpro
predominantly targeted ubiquitin chains. The crystal structure of
SCoV2‐PLpro in complex with IFN‐stimulated gene 15 (ISG15) re-
vealed distinctive interactions with the amino‐terminal ubiquitin‐like
domain of ISG15.29 Furthermore, upon infection, SCoV2‐PLpro
contributed to the cleavage of ISG15 from IFN responsive factor 3
(IRF3) and attenuated type I IFN responses. Importantly, inhibition of
SCoV2‐PLpro with GRL‐0617 impaired the virus‐induced cyto-
pathogenic effect, fostered the antiviral interferon pathway, and
reduced viral replication in infected cells.29 Thus, their results high-
lighted a dual therapeutic strategy in which targeting of SCoV2‐
PLpro can suppress SARS‐CoV‐2 infection and promote antiviral
immunity29 (Figure 1). This evidence suggested that SCoV2‐PLpro
can be a promising target for therapeutic intervention against
COVID‐19. Many known inhibitors of this molecule30,31 provide an
opportunity for the rapid development of SCoV2‐PLpro‐based anti‐
COVID‐19 therapeutics.
2.3 | SARS‐CoV‐2 spike proteins facilitate host
cell invasion and escape from detection
New reports also presented evidence in support of the direct role of
SARS‐CoV‐2 proteins in mediating host cell invasion. Viral spike
protein catalyzes fusion between viral and host cell membranes to
initiate infection. Cai et al.32 using cryo‐EM showed that SARS‐CoV‐2
spike protein exists in two distinct forms, representing its prefusion
(2.9 Å resolution) and postfusion (3.0 Å resolution) conformations,
respectively. They further showed that the postfusion structure of
the S2 subunit of spike protein was strategically decorated by N‐
linked glycans, suggesting this form may have protective roles
against host immune responses (it may induce non‐neutralizing an-
tibody responses to evade the host immune system) and shield from
32
harsh external conditions. The revelation that SARS‐CoV‐2 spike
protein may exist in two conformational states in the host cells has a
huge impact on postinfection immunity and development of vaccines,
which mainly target spike protein. Conformational change of spike
protein to postfusion form may cause failure to form neutralizing
antibodies in many individuals against natural infections as well as in
response to vaccines. Whereas, any such report from the running
trials of COVID‐19 vaccines are still not known, failure to form
neutralizing antibodies (directed to spike proteins) against natural
SARS‐CoV‐2 infection in some patients has been occasionally
reported.33–35
Apart from spike protein, some recent studies have unraveled
many SARS‐CoV‐2 NSPs, which contributed to the viral pathogenesis
in the host cells. Thoms et al.36 showed that nsp1 from SARS‐CoV‐2
bound to the 40S ribosomal subunit, resulting in the shutdown of
mRNA translation both in vitro and in cells. Further, structural
analysis by cryo‐electron microscopy (cryo‐EM) of in vitro recon-
stituted nsp1‐40S and various native nsp1‐40S and ‐80S complexes
revealed that the nsp1 C terminus bound to and obstructed the mRNA
entry tunnel, thereby effectively blocking retinoic acid‐inducible gene
ET AL.
I (RIG‐I) and interferon‐stimulated genes (ISGs), which are the key
mediators of innate immune responses against viral infection.36 In a
similar study, Viswanathan et al.37 showed nsp16, in conjunction with
nsp10, methylated the 5′‐end of virally encoded mRNAs to mimic
cellular mRNAs, thus protecting the virus from host innate immune
restriction. SARS‐CoV‐2‐specific NSPs, which shutdown or mimic host
mRNA machinery, present promising antiviral drug targets for
COVID‐19 and may be exploited therapeutically.
2.4 | SARS‐CoV‐2 mimics an epithelial ion channel
to hijack host cell machinery
SARS‐CoV‐2‐driven molecular mechanisms in the host cells are lar-
gely unknown. Recently, a SARS‐CoV‐2‐specific molecular mechan-
ism was proposed by a study, which may have important bearings on
immunopathogenesis and development of ARDS in COVID‐19.38
Anand et al. in a bioinformatics‐based analysis, showed that S1/S2
cleavage site of spike protein (S) of SARS‐CoV‐2 has striking protein
sequence similarity to the FURIN‐cleavable peptide segment on the
human epithelial sodium channel α‐subunit (ENaC‐α). The structural
mimicry of the SARS‐CoV‐2 spike protein segment to ENaC‐α im-
plied that virus in the infected cells could compete for the available
FURIN, in turn, can hamper proteolytic activation of ENaC‐α38
(Figure 2). Literature suggests that ENaC‐α has important roles in
immune cell activation and cytokine‐/chemokine‐mediated ARDS in
inflammatory disorders.39,40 A SARS‐CoV‐2‐mediated dysregulation
of ENaC‐α may have important implications for the development of
ARDS in severe COVID‐19 patients.
Mimicry of ENaC‐α in lung epithelial cells by SARS‐CoV‐2 may
also link to a yet unresolved issue in COVID‐19 patients—the role of
smoking in virus caused lung injury. Recent literature does suggest a
higher risk of severe complications and increased mortality among
smokers hospitalized with COVID‐19, howbeit, pathogenic mechan-
isms responsible for this remain largely unknown.41 Existing litera-
ture informs that cigarette smoke condensate,42 more specifically its
major ingredient crotonaldehyde (CRO), can cause dose‐dependent
inhibition of ENaC‐α subunit expression in pneumocytes, leading to
edematous acute lung injury43; thus, an added SARS‐CoV‐2 infection
to that may only worsen the condition. Whether ENaC‐α inhibition
may be a potential mechanism causing severe respiratory symptoms,
particularly in smokers, any direct evidence for this in COVID‐19
patients is currently lacking and deserves due attention of the
investigators.
2.5 | SARS‐CoV‐2 drives host cell's molecular
pathways
A couple of recent in vitro studies put light on SARS‐CoV‐2‐driven
molecular pathways in host cells.44,45 These studies provided robust
evidence for extensive phosphorylation of SARS‐CoV‐2 viral proteins
by the host proteome, which drove activation of host cell kinases and
KUMAR ET AL.
| 1347

F I G U R E 2 SARS‐CoV‐2 mimics an epithelial ion channel to hijack host cell machinery. The amino acid sequence of the S1/S2 cleavage site of
spike protein (S) of SARS‐CoV‐2 has a very close similarity to the FURIN‐cleavable peptide segment on the human epithelial sodium channel
α‐subunit (ENaC‐α). The structural mimicry of the SARS‐CoV‐2 spike protein segment to ENaC‐α can allow the virus in the infected lung cells to
compete for the available FURIN, which, in turn, can hamper proteolytic activation of ENaC‐α and thus can affect fluid clearance from the
alveolar cells. ENaC‐α dysfunction may get further aggravated with virus‐induced cell injury, immune cell activation, and release of
inflammatory cytokines/chemokines, in consequence, may lead to ARDS. ACE2, angiotensinogen‐converting enzyme 2; ENaC‐α, epithelial
sodium channel α‐subunit; TMPRSS2, transmembrane protease, serine 2

growth factor receptor (GFR) signaling culminating in the hijack of
host protein machinery. In first study, Bouhaddou et al. conducted a
quantitative mass spectrometry‐based phosphoproteomics survey of
SARS‐CoV‐2 infection in Vero E6 cells (a virus‐susceptible cell line
originating from the kidney of a female African green monkey—
Chlorocebus sabaeus). Investigators revealed that SARS‐CoV‐2 in-
fection promoted casein kinase II (CK2) and p38 mitogen‐activated
protein kinase (MAPK) activation, production of diverse cytokines,
44
and shutdown of CDK1/2/5, leading to cell cycle arrest (Figure 3).
Additionally, they showed a unique feature of SARS‐CoV‐2, which
was least known for the respiratory viruses—viral infection markedly
induced unique CK2‐containing filopodia protrusions possessing
budding viral particles, which seemed to facilitate the cell‐to‐cell
44
transfer of the infective virus. This pattern of molecular pathway
activation by SARS‐CoV‐2 can explain, acute inflammation and epi-
thelial cell damage, and vascular endothelial dysfunction, which are
hallmarks of pulmonary tissue injury (and in other organs) in severe
COVID‐19.44 In the second study, Klann et al.45 demonstrated that
SARS‐CoV‐2 infection of a human colonic epithelium cell line—Caco‐
2 cells—activated growth factor receptor (GFR) signaling and its
downstream pathways. They also showed that inhibition of GFR
downstream signaling prevented SARS‐CoV‐2 replication in the cells.
Both the studies have shown using drug–protein network ana-
lysis and in vitro testing that pharmacological agents targeted to the
cell kinases and GFRs can inhibit replication of SARS‐CoV‐2.44,45 Of
note, many of these tested pharmacological agents are approved
drugs for various ailments, thus can be easily repurposed for COVID‐
19. Bouhaddou et al.44 identified several drugs having antiviral ac-
tivity against SARS‐CoV‐2, which are either FDA approved, in clinical
testing, or under preclinical development for various diseases, such
as, silmitasertib (CK2; phase 2), gilteritinib (AXL; FDA approved),
ARRY‐797 (p38; phase2/3), MAPK13‐IN‐1 (p38; preclinical),
SB203580 (p38; preclinical), ralimetinib (p38; phase 2), apilimod
(PIKFYVE; phase 1), and dinaciclib (CDK; phase 3). Klann et al.45
1348 | KUMAR ET AL.

F I G U R E 3 SARS‐CoV‐2 drives host cell's molecular pathways. The phosphorylation of SARS‐CoV‐2 viral proteins by the host proteome
drives activation of growth factor receptor (GFR) signaling and host cell kinases, which in consequence, cause the shutdown of CDK1/2/
5, leading to cell cycle arrest. Pharmacological targeting of host cell kinases like PI‐3K and MAPK may reduce the replication of the virus in the
infected cells. AKT, serine/threonine kinase; CDK1/2/5, cyclin‐dependent kinases 1/2/5; MAPK, mitogen‐activated protein kinase; m‐TORC1/2,
mammalian target of rapamycin complex‐1/2; GSK3, glycogen synthase kinase 3; PDK‐1, phosphoinositide‐dependent kinase‐1; PI3K,
phosphoinositide 3‐kinase

further observed that prominent anticancer drugs—namely pictilisib,
omipalisib, RO5126766, lonafarnib, and sorafenib—prevented SARS‐
CoV‐2 replication at clinically achievable concentrations and hence
made ideal candidates for direct testing in clinical trials.
Apart from providing crucial evidence on host–pathogen inter-
actions, both of the studies also extend important insights on post-
survival clinical implications in COVID‐19 patients. MAPK and CDKs
regulate cell divisions, and GFRs regulate a wide range of cellular
processes, including proliferation, adhesion, or differentiation, and
46
have been widely implicated in cancer pathogenesis. Although an-
ticancer drugs are raising hope for therapeutic use in COVID‐19, no
research until yet has annotated any oncogenic property to SARS‐
CoV‐2. In contrast, robust evidence was presented by Bouhaddou
44
et al. for the CDK‐mediated mitotic arrest in SARS‐CoV‐2‐infected
cells that hinted at possible inhibition of cell growth by the virus in
tissues with high mitotic rate like reproductive and endocrine organs,
mucosal and vascular epithelium, and neurogenic brain regions.
SARS‐CoV‐2 can potentially infect a wide range of human tis-
sues based on the expression of its entry receptor ACE2 and entry‐
associated proteases.1 Matched to tissue distribution of virus re-
ceptors, wide range of clinical symptoms, representing almost all
organs, including the brain, have been reported in COVID‐19 pa-
tients.47 Widespread tissue injuries, along with the emerging evi-
dence for the SARS‐CoV‐2‐induced inhibition of the cell growth
functions, give rise to speculation that, owing to residual damages
and systemic dysfunctions, COVID‐19 survivors may have to face
long‐term health consequences.
Although, at present, the available literature shows limited evi-
dence in support of postsurvival health issues in COVID‐19,48 new
studies by some authors have proposed the possibilities of repeated
lung and intestinal infections, vascular endothelial dysfunction, male
infertility (owing to high expression of ACE2 and TMPRSS2 in male
KUMAR ET AL.
| 1349

reproductive organs, especially, testis), and new onsets of diabetes in 4. Naqvi AAT, Fatima K, Mohammad T, et al. Insights into SARS‐CoV‐2
COVID‐19 survivors.49,50 genome, structure, evolution, pathogenesis and therapies: structural
genomics approach. Biochim Biophys Acta Mol Basis Dis. 2020;
1866(10):165878. https://doi.org/10.1016/j.bbadis.2020.165878
5. Xu J, Zhao S, Teng T, et al. Systematic comparison of two animal‐to‐
3 | SUMMARY human transmitted human coronaviruses: SARS‐CoV‐2 and SARS‐
CoV. Viruses 2020;12(2):244. https://doi.org/10.3390/v12020244
6. Johnson BA, Xie X, Kalveram B, et al. Furin cleavage site is key to
In a nutshell, the new studies presented multiple shreds of new
SARS‐CoV‐2 pathogenesis. bioRxiv Prepr Serv Biol. Published online
evidence on crucial pathogenesis issues in COVID‐19, such as, how August 26 2020. https://doi.org/10.1101/2020.08.26.268854
SARS‐CoV‐2 gets higher tissue infectivity and transmissibility than 7. Xia S, Lan Q, Su S, et al. The role of furin cleavage site in SARS‐CoV‐
previous SARS viruses and modulates the host defense system in 2 spike protein‐mediated membrane fusion in the presence or ab-
sence of trypsin. Signal Transduct Target Ther. 2020;5(1):1‐3. https://
favor of a delayed but hyperactive innate immune response, disables
doi.org/10.1038/s41392-020-0184-0
formation of long‐lasting antibodies against viral proteins, disturbs
8. Jaimes JA, Millet JK, Whittaker GR. Proteolytic cleavage of the
physiological homeostasis in the lung epithelial cells, and drives host SARS‐CoV‐2 spike protein and the role of the novel S1/S2 site.
cell's molecular pathways culminating in reduced cell growth and iScience. 2020;23(6):101212. https://doi.org/10.1016/j.isci.2020.
injury. These new findings are significant and add to our under- 101212
9. Coperchini F, Chiovato L, Croce L, Magri F, Rotondi M. The cytokine
standing of underlying pathomechanisms in COVID‐19, especially
storm in COVID‐19: An overview of the involvement of the
the immunological dysregulation. To develop successful therapeutic chemokine/chemokine‐receptor system. Cytokine Growth Factor Rev.
approaches against COVID‐19, we needed to target these SARS‐ 2020;53:25‐32. https://doi.org/10.1016/j.cytogfr.2020.05.003
CoV‐2‐specific virulence factors. Hopefully, future studies may bring 10. Lucas C, Wong P, Klein J, et al. Longitudinal analyses reveal im-
munological misfiring in severe COVID‐19. Nature 2020;584(7821):
more evidence in this regard.
463‐469. https://doi.org/10.1038/s41586-020-2588-y
11. Channappanavar R, Zhao J, Perlman S. T cell‐mediated immune
C O NF L IC T O F IN T E R ES T S response to respiratory coronaviruses. Immunol Res. 2014;59(1‐3):
The authors declare that there are no conflict of interests. 118‐128. https://doi.org/10.1007/s12026-014-8534-z
12. Diao B, Wang C, Tan Y, et al. Reduction and functional exhaustion of
T cells in patients with coronavirus disease 2019 (COVID‐19). Front
AUTHOR CONTRIBUTIONS Immunol. 2020;11:827. https://doi.org/10.3389/fimmu.2020.00827
Ashutosh Kumar wrote the first draft. Pranav Prasoon, Chiman Ku- 13. Zhang X, Tan Y, Ling Y, et al. Viral and host factors related to the
mari, Vikas Pareek, Muneeb A. Faiq, Ravi K. Narayan, Maheswari clinical outcome of COVID‐19. Nature Published online May 20
2020:1‐7. https://doi.org/10.1038/s41586-020-2355-0
Kulandhasamy, and Kamla Kant revised the draft. Pranav Prasoon
14. Sun X, Wang T, Cai D, et al. Cytokine storm intervention in the early
prepared the figures. stages of COVID‐19 pneumonia. Cytokine Growth Factor Rev
Published online April 25 2020;53:38‐42. https://doi.org/10.1016/
ORCID j.cytogfr.2020.04.002
15. Zhang Y, Li J, Zhan Y, et al. Analysis of serum cytokines in patients
Ashutosh Kumar http://orcid.org/0000-0003-1589-9568
with severe acute respiratory syndrome. Infect Immun. 2004;72(8):
Pranav Prasoon https://orcid.org/0000-0002-5035-3619
4410‐4415. https://doi.org/10.1128/IAI.72.8.4410-4415.2004
Chiman Kumari https://orcid.org/0000-0002-9116-8380 16. Newton AH, Cardani A, Braciale TJ. The host immune response in
Vikas Pareek https://orcid.org/0000-0001-8985-4982 respiratory virus infection: balancing virus clearance and im-
Muneeb A. Faiq https://orcid.org/0000-0002-1430-3139 munopathology. Semin Immunopathol. 2016;38(4):471‐482. https://
doi.org/10.1007/s00281-016-0558-0
Ravi K. Narayan https://orcid.org/0000-0003-2510-6744
17. Channappanavar R, Fehr AR, Zheng J, et al. IFN‐I response timing
Maheswari Kulandhasamy https://orcid.org/0000-0002- relative to virus replication determines MERS coronavirus infection
6769-2596 outcomes. J Clin Invest. 2019;129(9):3625‐3639. https://doi.org/10.
Kamla Kant https://orcid.org/0000-0002-8966-6268 1172/JCI126363
18. Frieman M, Baric R. Mechanisms of severe acute respiratory syndrome
pathogenesis and innate immunomodulation. Microbiol Mol Biol Rev.
R EF E RE N C E S 2008;72(4):672‐685. https://doi.org/10.1128/mmbr.00015-08
1. Hoffmann M, Kleine‐Weber H, Schroeder S, et al. SARS‐CoV‐2 cell 19. Blanco‐Melo D, Nilsson‐Payant BE, Liu WC, et al. Imbalanced host
entry depends on ACE2 and TMPRSS2 and is blocked by a clinically response to SARS‐CoV‐2 drives development of COVID‐19. Cell
proven protease inhibitor. Cell 2020;181(2):271‐280. https://doi. 2020;181(5):1036‐1045. https://doi.org/10.1016/j.cell.2020.04.026
org/10.1016/j.cell.2020.02.052 20. Konno Y, Kimura I, Uriu K, et al. SARS‐CoV‐2 ORF3b is a potent
2. Sungnak W, Huang N, Bécavin C, et al. SARS‐CoV‐2 entry factors interferon antagonist whose activity is further increased by a
are highly expressed in nasal epithelial cells together with innate naturally occurring elongation variant. Cell Rep. 2020;32(12):
immune genes. Nat Med Published online April 23 2020:1‐7. https:// 108185. https://doi.org/10.1016/j.celrep.2020.108185
doi.org/10.1038/s41591-020-0868-6 21. Hadjadj J, Yatim N, Barnabei L, et al. Impaired type I interferon
3. Coutard B, Valle C, de Lamballerie X, Canard B, Seidah NG, activity and inflammatory responses in severe COVID‐19 patients.
Decroly E. The spike glycoprotein of the new coronavirus 2019‐ Science 2020;369(6504):718‐724. https://doi.org/10.1126/science.
nCoV contains a furin‐like cleavage site absent in CoV of the same abc6027
clade. Antiviral Res. 2020;176:104742. https://doi.org/10.1016/j. 22. Long Q‐X, Tang X‐J, Shi Q‐L, et al. Clinical and immunological as-
antiviral.2020.104742 sessment of asymptomatic SARS‐CoV‐2 infections. Nat Med
1350 | KUMAR
Published online June 18 2020:1‐5. https://doi.org/10.1038/
s41591-020-0965-6
23. Ibarrondo FJ, Fulcher JA, Goodman‐Meza D, et al. Rapid decay of anti‐
SARS‐CoV‐2 antibodies in persons with mild COVID‐19. N Engl J Med.
2020;383(11):1085‐1087. https://doi.org/10.1056/NEJMc2025179
24. Liu A, Wang W, Zhao X, et al. Disappearance of antibodies to SARS‐
CoV‐2 in a ‐COVID‐19 patient after recovery. Clin Microbiol Infect
Published online July 2020. https://doi.org/10.1016/j.cmi.2020.
07.009
25. Kaneko N, Kuo H‐H, Boucau J, et al. Loss of Bcl‐6‐expressing T
follicular helper cells and germinal centers in COVID‐19. Cell 2020;
183(1):143‐157.https://doi.org/10.1016/j.cell.2020.08.025
26. Chen yongwen, Feng Z, Diao B, et al. The novel severe acute re-
spiratory syndrome coronavirus 2 (SARS‐CoV‐2) directly decimates
human spleens and lymph nodes [published online ahead of print
March 31, 2020]. medRxiv. https://doi.org/10.1101/2020.03.27.
20045427
27. Victora GD, Nussenzweig MC. Germinal centers. Annu Rev Immunol.
2012;30(1):429‐457. https://doi.org/10.1146/annurev-immunol-
020711-075032
28. Wu C, Liu Y, Yang Y, et al. Analysis of therapeutic targets for SARS‐
CoV‐2 and discovery of potential drugs by computational methods.
Acta Pharm Sin B. 2020;10:766‐788. https://doi.org/10.1016/j.apsb.
2020.02.008
29. Shin D, Mukherjee R, Grewe D, et al. Papain‐like protease regulates
SARS‐CoV‐2 viral spread and innate immunity. Nature 2020:1‐10.
https://doi.org/10.1038/s41586-020-2601-5
30. Shanker AK, Bhanu D, Alluri A, Gupta S. Whole‐genome sequence
analysis and homology modelling of the main protease and non‐
structural protein 3 of SARS‐CoV‐2 reveal an aza‐peptide and a lead
inhibitor with possible antiviral properties. New J Chem. 2020;
44(22):9202‐9212. https://doi.org/10.1039/d0nj00974a
31. Rut W, Lv Z, Zmudzinski M, et al. Activity profiling and structures of
inhibitor‐bound SARS‐CoV‐2‐PLpro protease provides a framework
for anti‐COVID‐19 drug design. bioRxiv Prepr Serv Biol. Published
online 2020. https://doi.org/10.1101/2020.04.29.068890
32. Cai Y, Zhang J, Xiao T, et al. Distinct conformational states of SARS‐
CoV‐2 spike protein. Science 2020;369(6511):1586‐1592. https://
doi.org/10.1126/science.abd4251
33. Goetz L, Yang J, Greene W, Zhu Y. A COVID‐19 patient with re-
peatedly undetectable SARS‐CoV‐2 antibodies. J Appl Lab Med.
Published online August 3 2020. https://doi.org/10.1093/jalm/jfaa137
34. Wu F, Liu M, Wang A, et al. Evaluating the association of clinical
characteristics with neutralizing antibody levels in patients who
have recovered from mild COVID‐19 in Shanghai, China. JAMA
Intern Med. 2020;180(10):1356‐1362. https://doi.org/10.1001/
jamainternmed.2020.4616
35. van der Heide V. Neutralizing antibody response in mild COVID‐19.
Nat Rev Immunol. 2020;20(6):352. https://doi.org/10.1038/s41577-
020-0325-2
36. Thoms M, Buschauer R, Ameismeier M, et al. Structural basis for
translational shutdown and immune evasion by the Nsp1 protein of
SARS‐CoV‐2. Science 2020;369(6508):1249‐1255.
ET AL.
37. Viswanathan T, Arya S, Chan S‐H, et al. Structural basis of RNA cap
modification by SARS‐CoV‐2. Nat Commun. 2020;11(1):3718.
https://doi.org/10.1038/s41467-020-17496-8
38. Anand P, Puranik A, Aravamudan M, Venkatakrishnan AJ,
Soundararajan V. SARS‐CoV‐2 strategically mimics proteolytic ac-
tivation of human ENaC. eLife 2020;9. https://doi.org/10.7554/eLife.
58603
39. Mutchler SM, Kleyman TR. New insights regarding epithelial Na+
channel regulation and its role in the kidney, immune system and
vasculature. Curr Opin Nephrol Hypertens. 2019;28(2):113‐119.
https://doi.org/10.1097/MNH.0000000000000479
40. Wyne BM, Zou L, Linck V, Hoover RS, Ma HP, Eaton DC. Regulation
of lung epithelial sodium channels by cytokines and chemokines.
Front Immunol. 2017;8(Jul). https://doi.org/10.3389/fimmu.2017.
00766
41. Alqahtani JS, Oyelade T, Aldhahir AM, et al. Prevalence, severity and
mortality associated with COPD and smoking in patients with COVID‐
19: a rapid systematic review and meta‐analysis. PLOS One. 2020;15(5):
e0233147. https://doi.org/10.1371/journal.pone.0233147
42. Xu H, Ferro TJ, Chu S. Cigarette smoke condensate inhibits ENaC α‐
subunit expression in lung epithelial cells. Eur Respir J. 2007;30(4):
633‐642. https://doi.org/10.1183/09031936.00014107
43. Li Y, Chang J, Cui Y, et al. Novel mechanisms for crotonaldehyde‐
induced lung edema. Oncotarget 2017;8(48):83509‐83522. https://
doi.org/10.18632/oncotarget.17840
44. Bouhaddou M, Memon D, Meyer B, et al. The global phosphorylation
landscape of SARS‐CoV‐2 infection. Cell 2020;182(3):685‐712.
https://doi.org/10.1016/j.cell.2020.06.034
45. Klann K, Bojkova D, Tascher G, Ciesek S, Münch C, Cinatl J. Growth
factor receptor signaling inhibition prevents SARS‐CoV‐2 replica-
tion. Mol Cell. 2020;80:164‐174. https://doi.org/10.1016/j.molcel.
2020.08.006
46. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000;
100(1):57‐70. https://doi.org/10.1016/S0092-8674(00)81683-9
47. Guan W, Ni Z, Hu Y, et al. Clinical characteristics of coronavirus
disease 2019 in China. N Engl J Med 2020;382(18):1708‐1720.
https://doi.org/10.1056/NEJMoa2002032
48. Yelin D, Wirtheim E, Vetter P, et al. Long‐term consequences of
COVID‐19: research needs. Lancet Infect Dis. 2020;20(10):
1115‐1117. https://doi.org/10.1016/S1473-3099(20)30701-5
49. Rubino F, Amiel SA, Zimmet P, et al. New‐onset diabetes in COVID‐
19. N Engl J Med. 2020;383(8):789‐790. https://doi.org/10.1056/
NEJMc2018688
50. Abobaker A, Raba AA. Does COVID‐19 affect male fertility? World
J Urol. 2020:1‐2. https://doi.org/10.1007/s00345-020-03208-w
How to cite this article: Kumar A, Prasoon P, Kumari C, et al.
SARS‐CoV‐2‐specific virulence factors in COVID‐19. J Med Virol.
2021;93:1343–1350. https://doi.org/10.1002/jmv.26615