COVID-19: Advances in diagnostic tools, treatment strategies, and vaccine development

Abstract

An unprecedented worldwide spread of the SARS-CoV-2 has imposed severe challenges on healthcare facilities and medical infrastructure. The global research community faces urgent calls for the development of rapid diagnostic tools, effective treatment protocols, and most importantly, vaccines against the pathogen. Pooling together expertise across broad domains to innovate effective solutions is the need of the hour. With these requirements in mind, in this review, we provide detailed critical accounts on the leading efforts at developing diagnostics tools, therapeutic agents, and vaccine candidates. Importantly, we furnish the reader with a multidisciplinary perspective on how conventional methods like serology and RT-PCR, as well as cutting-edge technologies like CRISPR/Cas and artificial intelligence/machine learning, are being employed to inform and guide such investigations. We expect this narrative to serve a broad audience of both active and aspiring researchers in the field of biomedical sciences and engineering and help inspire radical new approaches towards effective detection, treatment, and prevention of this global pandemic.

Full text

Review
COVID-19: Advances in diagnostic tools, treatment strategies,
and vaccine development
MSREEPADMANABH,AMIT KUMAR SAHU and AJIT CHANDE*
Molecular Virology Laboratory, Indian Institute of Science Education and Research, Bhopal, India
*Corresponding author (Email, ajitg@iiserb.ac.in)
MS received 26 June 2020; accepted 15 October 2020
An unprecedented worldwide spread of the SARS-CoV-2 has imposed severe challenges on healthcare
facilities and medical infrastructure. The global research community faces urgent calls for the development of
rapid diagnostic tools, effective treatment protocols, and most importantly, vaccines against the pathogen.
Pooling together expertise across broad domains to innovate effective solutions is the need of the hour. With
these requirements in mind, in this review, we provide detailed critical accounts on the leading efforts at
developing diagnostics tools, therapeutic agents, and vaccine candidates. Importantly, we furnish the reader
with a multidisciplinary perspective on how conventional methods like serology and RT-PCR, as well as
cutting-edge technologies like CRISPR/Cas and artificial intelligence/machine learning, are being employed to
inform and guide such investigations. We expect this narrative to serve a broad audience of both active and
aspiring researchers in the field of biomedical sciences and engineering and help inspire radical new
approaches towards effective detection, treatment, and prevention of this global pandemic.
Keywords. Artificial intelligence; CRISPR/Cas; SARS-CoV-2; treatment strategies; viral diagnostics
1. Introduction
The ongoing COVID-19 pandemic has had devastating
effects on populations, social structures, and economic
growth. These are further exacerbated by the increasing
extent of global connectivity and geographical mobility,
which expedite infection spread at an uncontrollable pace.
The causative agent of this outbreak has been identified as
the recently discovered SARS-CoV-2 coronavirus.
Effective control and containment of this pathogen require
reliable diagnostic assays and potent therapeutic agents.
Recent advances in computational technology and
biomedical engineering have placed a toolkit of immense
potential in our hands, with a formerly unimaginable
capability to enable multidisciplinary innovations and
highly accelerated discoveries. In this review, we provide
a critical evaluation of diagnostic techniques and treat-
ment strategies targeted at the SARS-CoV-2. Alongside
an eclectic selection of such reports, our analysis also
focuses on the applications, advantages, and pitfalls of
emerging technologies like CRISPR/Cas, immune-infor-
matics, artificial intelligence, and machine learning.
2. Diagnostic tools for detecting SARS-CoV-2
Figure 1provides a graphical summary of the various
approaches discussed herein.
2.1 RT-PCR
PCR-based methods are considered the gold standard
for viral detection. SARS-CoV-2 requires RT-PCR-
based approaches, by virtue of being an RNA virus. In
this section, we highlight some interesting develop-
ments as well as possible pitfalls of this technique, in
the context of viral diagnosis.
This article is part of the Topical Collection: COVID-19:
Disease Biology & Intervention.
http://www.ias.ac.in/jbiosci
J Biosci (2020) 45:148 ÓIndian Academy of Sciences
DOI: 10.1007/s12038-020-00114-6 (0123456789().,-volV)(0123456789().,-volV)

One of the earliest workflows set up in response to
the outbreak was by Christian Dorsten and colleagues
(Corman et al. 2020). The team established an accurate,
sensitive, and specific RT-PCR protocol against the
SARS-CoV-2. Later research, including a comparative
study by Nalla et al., have attested to its superior
sensitivity (Nalla et al. 2020). A notable feature of this
pioneering work was that the assays were designed
without access to any actual SARS-CoV-2 genomic
specimens or patient samples, by relying on genome
information sourced from Chinese researchers and
synthetic nucleic acid technology. An interesting
comparison between two commercially available test-
ing kits – (the TaqMan
TM
2019-nCoV Assay Kit v1
(ThermoFisher) and the 2019-nCoV CDC qPCR Probe
Assay (Integrated DNA Technologies)) – was recently
reported, results from which indicate that the former is
capable of reliably detecting SARS-CoV-2 presence in
nasopharyngeal swab samples without any RNA
extraction steps (Beltra´n-Pavez et al. 2020). Most
diagnostic devices relying on RT-PCR-based amplifi-
cation suffer from the drawback of requiring either
sample lysis or purified nucleic acid samples, a step
that involves additional reagents, increased testing
time, human errors and costs, in addition to significant
compromises on the field-applicability of the test.
Subject to further validation, the above result
represents a potential breakthrough for rapid and
accessible diagnosis in low-resource settings, by
enabling the development of accessible point-of-care
devices. Additionally, while nasopharyngeal/oropha-
ryngeal swabs are recommended sample collection
techniques for SARS-CoV-2 testing, these pose a high
risk of exposing healthcare workers to large numbers of
potentially infected individuals, in addition to causing
patient discomfort. An alternative in the form of saliva
specimens as a non-invasive method of sample col-
lection has been proposed to address these concerns
(To et al. 2020).
In order to enhance the sensitivity and fidelity of RT-
PCR assays, a worthwhile strategy is to evaluate the
potential of various viral components as probe targets
and compare the relative performance of each. For
instance, an early RT-PCR-based detection assay used
probes against the ORF1b and N region of the viral
genome (Chu et al. 2020). Subsequently, another study
developed three novel assays aimed at the viral spike
protein (S), nucleocapsid (N), and RNA-dependant
RNA polymerase (RdRp)/Helicase (Hel) genes, out of
which, the RdRp/Hel-based assay demonstrated no
cross-reactivity with common respiratory pathogens as
well as the lowest detection limit in vitro (Chan et al.
2020). Exploring such novel targets may help develop
superior assays, which can improve the sensitivity and
Figure 1. Summary of the various approaches towards diagnosis of SARS CoV-2 infection.
148 Page 2 of 20 M Sreepadmanabh et al.

accuracy of detection. Furthermore, a comparative
analysis by Nalla et al. evaluated seven different assay
kits and reported the E-gene primer/probe set (as
described by Corman et al. (2020)) and the N2 set
(developed by the Division of Viral Diseases, Center
for Disease Control and Prevention) as the most sen-
sitive assays available. The importance of such inde-
pendent assessments of reported/published studies
needs to be underscored in healthcare crisis scenarios
such as the present one, wherein resources are limited
and must be judiciously allocated.
2.2 Chest CT scans
A few studies have also pointed out the liabilities of
RT-PCR-based techniques. While some publications
and in vitro assays may report excellent parameters of
performance, clinical testing and feedback raise several
red flags. A most elementary instance of this was
reported in a case wherein two patients who were
SARS-CoV-2 infected returned negative RT-PCR
results, leading the authors to suggest chest CT scans as
an essential part of clinical diagnosis (Li et al. 2020a).
Similar issues with a high false-negative rate of RT-
PCR testing on patients over the course of disease
progression and treatment have been reported sepa-
rately as well (Li et al. 2020e). Such observations have
promoted recommendations to include clinical param-
eters such as CT scan diagnosis as factors to be con-
sidered in addition to the aforementioned assays while
making decisions on patient discharge, evaluation of
recovery/response to treatment protocols. A retrospec-
tive study reached similar conclusions in favor of CT
scans, ascribing a 97.2% sensitivity to CT, as compared
to 83.3% using RT-PCR (Long et al. 2020a).
At this juncture, we would like to emphasize a few
recent studies which have underscored the potential of
chest CT scans as a viable diagnostic technique. Work
by Cao et al. and Dai et al. seeks to formulate a
standard set of characteristic features indicative of a
SARS-CoV-2 infection. The former, a systematic
review and meta-analysis of infected patients, estab-
lishes the most common clinical symptoms as fever,
cough, chest distress, fatigue, and dyspnea, along with
major imaging features as ground-glass opacities and
bilateral pneumonia (Cao et al. 2020a). The latter
provides a more comprehensive treatment in which
over two hundred patients were studied to report
bilateral multiple lung lobes in both the periphery and
lower portion of the lungs as being present in over
94.98% of the cases (Dai et al. 2020). Additionally,
ground-glass opacities and vascular enhancement were
identified as characteristic signatures, as well as fibro-
sis, air, trapping, and interlobular septal thickening. It is
worthwhile to note that highly concordant observations
have been made across different patient cohorts, and
the general agreement between these is an indicator of
the proposed technique’s versatility and broad-spec-
trum applicability. A more extensive and detailed elu-
cidation of the same may be found in the recent review
by Hani et al. (Hani et al. 2020). Furthermore, time-
point-based CT scan data may be an invaluable tool to
assess disease progression, treatment response, devel-
opment of complications, and understanding the
pathophysiology of the disease, as has been stressed by
Bernheim et al. (2020). Additionally, an artificial
intelligence (AI)-based platform has also been devised
which utilizes a neural network to evaluate X-ray
images and automatically detects SARS-CoV-2-in-
fected positive specimens with an accuracy of 97.82%
(Apostolopoulos and Bessiana 2020). Harnessing
advances in computer science for medical diagnostics
may serve as an essential tool to standardize and speed
up the testing process. Similar applications of machine
learning and AI to aid in the pandemic control efforts
will be further elaborated in Sect. 4.
2.3 Antibody-based techniques
The evident advantage of antibodies over nucleic acids
amplification is higher specificity, accuracy, as well as
rapid testing times since it does not require time-con-
suming amplification steps, nor involves cumbersome
extraction/purification processes. A recent report has
also highlighted that antibody titers may be a more
reliable indicator of SARS-CoV-2 infections, especially
for asymptomatic and suspected carriers who return
negative RT-PCR results (Long et al. 2020b).
The classic Enzyme-linked Immunosorbent Assay
(ELISA) may be readily adapted to serve as a SARS-
CoV-2 detection test. Accordingly, this has been
employed against the recombinant viral nucleocapsid
proteins and the recombinant viral spike proteins,
which were used to detect the IgM and IgG antibody
levels (Liu et al. 2020). This study established that
spike protein-based assay would be more sensitive for
detecting IgM. Along similar lines, the comparative
performance of ELISA-based and Gold-immunochro-
matographic Assay (GICA)-based methods have also
been evaluated (Xiang et al. 2020). The rapid testing
times and high sensitivity observed posit serological
assays as superior alternatives to RT-PCR on account
COVID-19: advances in diagnostics and treatment Page 3 of 20 148

of ease of sample collection (blood, which poses
minimal risk to healthcare staff compared to swab
samples) and low false-negative rates. In this regard, an
efficient point-of-care device for diagnostic testing
which combined the IgG-IgM testing platform with a
testing time of fifteen minutes was recently reported (Li
et al. 2020f). While the repurposing of cross-reactive
antibodies from highly similar species like the SARS-
CoV is a viable idea, an interesting report notes some
pitfalls (Tian et al. 2020). Despite the relative identity
between the SARS-CoV and the SARS-CoV-2, the
authors point out that highly potent receptor binding
site-targeting SARS-CoV neutralizing antibodies (like
the CR3014 and m396) fail to engage the SARS-CoV-2
spike protein. This indicates that effective management
of novel pathogens may necessitate the development of
novel antibodies and those homology-based strategies
to repurpose existing therapeutics should be rigorously
vetted.
However, an over-reliance on antibody-based
approaches is impractical. Designing nucleic acid
probes is a far more straightforward process, and one
much more rapidly deployable. Also, the detection of
antibodies may be difficult in the early stages of
infection, until a significant titer of IgG/IgM has
accumulated in circulation. This may contribute
towards significant false-negative rates during large-
scale screenings, especially when periodic sampling
and extended observation of test subjects may not be
feasible. Hence, despite the salient advantages of
antibody-based techniques as discussed above, several
assay kits and field-testing protocols have remained in
the domain of PCR amplification-based methods.
Accordingly, our object of focus for the next section
will be one such recently evolved technology, loop-
mediated isothermal amplification (LAMP).
2.4 RT-LAMP
LAMP-based protocols enable the efficient amplifica-
tion of nucleic acids at a single point temperature. This
feature makes it a strong contender for direct field
applications, since incorporating the thermal cycling
steps in PCR assays has traditionally been a significant
limitation for point-of-care devices. LAMP’s inherent
advantages are not limited to isothermal operability
alone. This robust technique works efficiently even
with crude sample preparations, compared to tradi-
tional PCR methods, and also offers a very high
amplification efficiency since it is not limited by a
doubling-per-cycle threshold (Becherer et al. 2020).
We wish to highlight two particular tests, both of
which report colorimetric detection capability – a major
boon for point-of-care devices. A team led by Di Liu
and Jing Yuan reported RT-LAMP assays for SARS-
CoV-2 detection, with ORF1ab and S genes as the
primer-probe targets (Yan et al. 2020). The work
claims complete detection within 60 min, using a col-
orimetric detection system that employs fluorescent
calcein, where a color change from orange to green
indicates positive reactions (visually detectable by the
naked eye). Another effort by Renfei Lu et al.
involving primers targeted at the RdRp utilizes cresol
red (a pH-sensitive indicator dye) for the assay readout
(Lu et al. 2020). Since a proceeding amplification can
progressively change the buffer pH from alkaline to
acidic, a color change from burgundy to orange/yellow
signals a positive reaction. These innovations in assay
readout methodology imply a significant advancement
since they make it possible to have even untrained
healthcare workers administer, conduct, and interpret
diagnostic tests.
A noteworthy instance of adapting RT-LAMP for a
truly bedside point-of-care application is the innovative
closed-tube test developed by Song and colleagues (El-
Tholoth et al. 2020). Combining straightforward sam-
ple collection with single or two-step RT-LAMP
amplification protocols, along with a visual detection
system based on LCV (leucocrystalviolet – an inter-
calating agent which colorimetrically detects double-
stranded LAMP amplicons), this device is a readily
deployable and highly portable testing method that
promises to be a cheap and reliable alternative suit-
able for all testing environments.
2.5 Emerging techniques: reactive polymers
and CRISPR/Cas-based systems
This subsection is devoted to a couple of non-con-
ventional detection methods, which may well serve as a
versatile platform in the future. The first is a reactive
polymer-grafter device which utilizes antibodies to
detect dsRNA (Ku et al. 2020). A suitable polymer-
coated surface-reactive poly(pentafluorophenyl acetate)
in this case is used to immobilize J2 antibodies on the
surface. Following the preparation of the platform, it
may be directly applied to detect dsRNA as the J2
antibodies may bind dsRNA molecules specifically.
The principal advantage, in this case, is that the anti-
body binding is sequence-independent; hence the
platform may serve as a universal virus detection unit.
However, it may be noted that such one-size-fits-all
148 Page 4 of 20 M Sreepadmanabh et al.

approaches suffer from an inherent lack of specificity.
In this case, the sequence-independent nature of
detection suggests a high possibility of false positives.
Such a scenario would necessitate secondary tests
using established protocols for reliable confirmations of
diagnosis, thereby positing the J antibodies-based
technique as a potential preliminary screening step,
rather than as a standalone entity.
The second major innovation involves the use of
CRISPR-Cas-based techniques for the detection of
viral nucleic acids. Recently, such CRISPR-based
detection systems, notably SHERLOCK and
DETECTR, were reported as emerging diagnostic
tools. The fundamental principle involves the acti-
vation of a suitable Cas variant (Cas13 for SHER-
LOCK, Cas12a for DETECTR) by binding of the
appropriate target sequence (ssRNA or mRNA for
Cas13 and dsDNA for Cas12a), which enables the
Cas variants to promiscuously cleave and degrade
surrounding ssRNA and ssDNA, respectively. The
ssRNA/ssDNA meant for the latter reaction may be
coupled with a quenchable fluorophore, which pro-
duces a quantifiable signal upon being released by
cleavage. Hence, the detection of the exact target
sequence is indicated by an assay readout in the
form of a fluorescence signal. This system allows for
rapid and accurate detection of viral RNA samples
since amplification of these (along with suit-
able modifications as per the system used) can then
allow for precise targeting and detection by the Cas-
based assay described above. This remarkable ability
has been recently demonstrated by using the
DETECTR system as a diagnostic tool for SARS-
CoV-2 infections in a rapid lateral flow assay
incorporating RT-LAMP using nasal swab samples
(Broughton et al. 2020). Additionally, a series of
reports may be found on the Broad Institute’s web-
site (https://www.broadinstitute.org/news/enabling-
coronavirus-detection-using-crispr-cas13-open-access-
sherlock-research-protocols-and), wherein a team
comprising of Feng Zhang, Omar Abudayyeh, and
Jonathan Gootenberg aim to develop paper-based
platforms for rapid and straightforward SARS-CoV-2
detection (B Institute 2020).
3. Treatment strategies for SARS-CoV-2 infections
In this section, we endeavor to review some of the
established and emerging treatment paradigms which
are being currently employed or recommended on the
basis of published literature and empirical evidence
from clinical case studies. The major ones have been
pictorially represented in figure 2.
3.1 Drugs-based conventional approaches
Amongst drug-based treatment strategies, the broad-
spectrum antiviral chloroquine and its derivative
hydroxychloroquine have received much attention. As
early as February 2020, both remdesivir and chloro-
quine were identified as potential inhibitors of the
SARS-CoV-2 in vitro (Wang et al. 2020b). Remdesivir,
a potential candidate against Ebola, SARS-CoV, and
MERS-CoV, is an adenosine analog that inhibits viral
replication. On the other hand, chloroquine targets
endosomal fusion by elevating the endosomal pH,
alongside interfering with the glycosylation of ACE2.
The rationale for using chloroquine is further buttressed
by a variety of possible antiviral effector functions
(Devaux et al. 2020). Experimental evidence for a
putative mechanism was provided by structural data
and molecular modeling approaches, where a con-
served ganglioside binding domain at the N terminus of
the viral S protein was identified as the target for
chloroquine and hydroxychloroquine. This inhibition
of viral attachment and entry appears to explain
chloroquine and its derivative hydroxychloroquine’s
apparent efficacy against SARS-CoV-2 infections
(Fantini et al. 2020). However, it is important to rec-
ognize that evidence for the clinical benefits of these
much-touted drugs is contentious at best and unreliable
at worst. While hydroxychloroquine and azithromycin
were earlier claimed as potentially effective drugs
against SARS-CoV-2 infections, the reporting study
has since come under criticism for the lack of a control
group and incomplete descriptors of actual clinical
outcomes and patient inclusion criteria (Gautret et al.
2020). A separate randomized trial enrolling 62
patients did, however, report a statistically significant
positive effect of hydroxychloroquine treatment in
alleviating patient symptoms (Chen et al. 2020c).
These claims are offset by three additional reports,
none of which conclude any significant benefit from
this treatment method (Borba et al. 2020; Magagnoli
et al. 2020; Mahevas et al. 2020). An emerging class of
candidate drugs are corticosteroids, which have
recently generated great interest in the context of
COVID-19 treatment approaches. While early skepti-
cism did reign over corticosteroids usage, considering
its propensity to elicit adverse reactions in severely ill
patients, evidence from recent clinical trials and meta-
analyses have hinted at significant benefits from this
COVID-19: advances in diagnostics and treatment Page 5 of 20 148

drug for the management of critically ill patients. This
has led to a growing advocacy of corticosteroids as a
leading candidate in the global effort against COVID-
19 (Halpin et al. 2020;Maet al. 2020b; Sanders et al.
2020; Singh et al. 2020; Yang et al. 2020b;Yeet al.
2020; Zha et al. 2020).
Emerging technologies powered by AI offer sys-
tematic and highly modular solutions for urgent drug
discovery and identification requirements. A study
published in The Lancet (Richardson et al. 2020)
employed Benevolent AI, a platform for AI-guided
drug discovery and clinical development, to offer
suggestions for drugs targeted explicitly at SARS-CoV-
2. Using a systematic knowledge graph, the platform
was able to identify baricitinib, a Janus kinase inhibitor
that binds the AAK1 (AP2-associated protein kinase 1,
a regulator of endocytosis). Section 4will deal with
this domain in greater detail.
3.2 Docking simulations and molecular dynamics-
based approaches
Powerful computational resources can greatly enhance
our ability to rapidly screen for drugs and inhibitory
agents against emerging pathogens. The SARS-CoV-2
protease has been a popular target for such docking
simulations and molecular dynamics-based studies (Liu
and Wang 2020), in part due to the recent availability
of its structure. A broad screening effort of over 1.3
billion compounds from the ZINC15 database used an
upgraded docking protocol (termed DeepDocking) to
identify over a thousand such potential inhibitors of the
SARS-CoV-2 protease (Ton et al. 2020). A more sys-
tematic approach along similar lines screened 687
million compounds via docking, followed by molecular
dynamics simulations to evaluate ligand-binding ener-
gies, stability, toxicity assessment, as well as off-target
binding (Fischer et al. 2020). Alongside such screening
efforts for existing molecules, the identification of
promising lead compounds that could serve as scaf-
folds for further modification is an essential step to
enable the development of novel drugs. This require-
ment was addressed by a recent in-silico study, which
provided a clustered report of twenty short-listed
compounds into three groups, each of which could
serve as leads for the development of SARS-CoV-2
inhibiting drugs (Ortega et al. 2020).
While the ability of advanced computational facili-
ties to virtually screen multitudinous drugs and com-
pounds – numbering anywhere from a few thousand to
even a billion – might be unmatched by traditional
methods, the importance of physical assay-based
screens is indispensable. The recent report of a large-
scale (12,000?compounds) repositioning survey of
FDA-approved and under-trial drugs in the context of
Figure 2. Some established and emerging treatment paradigms being currently employed or recommended on the basis of
published literature and empirical evidence from clinical case studies.
148 Page 6 of 20 M Sreepadmanabh et al.

SARS-CoV-2-targeted antivirals attests to this (Riva
et al. 2020). Following an initial selection based on
inhibition of cytopathic effects, an orthogonal valida-
tion assay was used to delineate the compounds which
specifically inhibited viral replication. This study also
provided classification and categorization of target
annotations and drug target genes for the short-listed
drugs. The identification of these specific domains can
help similar such efforts in the future to be more
focussed on specific drug types and targets that have
been identified to exert the most promising antiviral
effect on SARS-CoV-2. Another notable effort com-
bined virtual screening methods with high-throughput
assays to enable the rapid identification of promising
drug candidates (Jin et al. 2020). Using a FRET-based
assay to assess the enzymatic activity of SARS-CoV-2
protease, over 10,000 compounds were screened for
inhibitory effects on the enzyme. Additionally, the
authors extensively analyzed a compound termed N3,
initially developed using computer-aided drug design
as an inhibitor of multiple coronavirus proteases. Fol-
lowing molecular docking, kinetic analysis of the
protease, and determination of its crystal structure with
the SARS-CoV-2 protease, the inhibitory effects of N3
were ascertained. The comprehensive approach adop-
ted by this study is an exemplar model for similar
investigations. The obvious merits of virtual screening
methods notwithstanding, strong emphasis needs to be
laid on developing high-throughput biochemical and
cellular assays for experimental validation of pharma-
cologically active compounds. The importance of this
cannot be overstated, as such empirical evidence helps
establish a reliable standard for ascertaining the actual
merits of proposed therapeutic approaches, which may,
at least at the current stage of research, only be sup-
plemented by computational studies.
3.3 Plasma therapy
Alongside treatment with drugs, convalescent plasma
(CP) therapy is being advocated as a clinically effective
practice. The procedure involves using blood plasma
obtained from recovered patients as an adaptive
immune therapy for critical cases. The underlying
principle at work is that the donor plasma contains a
high titer of antibodies that are effective against the
pathogen, hence provides an immunity boost to the
recipient. CP has been advocated as an alternative
therapy for SARS-CoV-2 infections (Chen et al. 2020a)
and therapeutic plasma exchange has been recom-
mended as a suitable strategy to deal with the often
associated acute respiratory distress syndrome (ARDS)
(Keith et al. 2020). An initial four-patient sample
established that CP could have therapeutic benefits for
critically ill patients (Zhang et al. 2020a). While all
four patients showed a progression towards negative
RT-PCR results, the authors of the study stress that it
would be difficult to rule out confounding factors as
well as the effects of additional supportive care and
treatments such as antiviral drugs and intravenous
immunoglobulin. A similar study involving a ten-pa-
tient cohort demonstrated that CP dosages could either
increase or maintain the existing levels of neutralizing
antibodies in the recipients (Duan et al. 2020). Addi-
tionally, the clinical symptoms were also observed to
improve progressively, leading up to the absence of
viremia. The study highlights two other salient out-
comes – one, that CP appeared to be tolerated well by
the recipients without adverse reactions, and two, that
transfusion of CP alleviated inflammation. It is
important to note, however, that these studies need to
be further supplemented by rigorous and controlled
clinical trials to discount both the effects of external
factors, as well as establish proper protocols for CP
therapy concerning the dosage, duration, and other
appropriate parameters.
3.4 Managing cytokine storm responses
Among the several complications associated with
SARS-CoV-2 infections, cytokine storm responses,
which are a by-product of immune hyperactivation and
loss of regulatory control over pro-inflammatory
cytokines, pose a major risk for patient survival and
may lead to rapid deterioration of patient health. The
stimulation of CD-4?T-cells to differentiate into Th1
helper cells along with IL-6, interferon-gamma, and
GM-CSF (granulocyte-macrophage colony-stimulating
factor) production, amongst other proinflammatory
cytokines, are considered as the steps leading up to a
cytokine storm-like condition. The persistently high
levels of certain cytokines like IP-10, MCP-3, and IL-
1ra may be characteristic of such an onset, and these
may be developed as screening parameters to ascertain
the same (Yang et al. 2020a).
Extensive efforts to safely manage this condition
have been undertaken. For instance, the use of an IL-
6 receptor antagonist drug such as tocilizumab has
been suggested, since the IL-6 has been identified as
a key driver of cytokine storm response (Zhang et al.
2020b). Writing in The Lancet, Mehta et al. also
recommend similar IL-6 targeted strategies (Mehta
COVID-19: advances in diagnostics and treatment Page 7 of 20 148

et al. 2020). While a previous study had failed to
establish a significant connection between the
administration of corticosteroids and improved treat-
ment outcomes (Zha et al. 2020), Mehta et al. rec-
ommend consideration of such a course of treatment
to tackle hyperinflammation. However, there is no
concrete evidence to support corticosteroid-based
treatment as being of overall therapeutic value, in
addition to the associated risks of lung injury (Rus-
sell et al. 2020). A detailed review also suggests
several strategies by which cytokine storm responses
may be dealt with, including the use of the above-
cited IL-6R agonist tocilizumab. Glycyrrhetinic acid,
another IL-6 and STAT3 signaling inhibitor has been
suggested as a potential candidate. Additionally,
mesenchymal stem cell infusions have been high-
lighted due to the immunomodulatory and anti-in-
flammatory potential of these cells (Cheng et al.
2020). An alternate approach to managing cytokine
storm response has been suggested in the form of
artificial blood purification systems. Essentially, this
involves using an external filtration-cum-treatment
setup to modulate the various factors and chemokines
responsible for orchestrating the proinflammatory
response. This may be achieved by the use of
scavenging inflammatory mediators and plasma
exchange. At the same time, continuous venovenous
hemofiltration units may be employed, as demon-
strated for the successful containment of cytokine
storm responses in critically afflicted H7N9 influenza
patients (Zhang et al. 2020d). The merits of blood
purification therapy for alleviating similar symptoms
in SARS-CoV-2 infected patients have also been
demonstrated by a recent study from Wuhan
involving three patients (Ma et al. 2020a).
3.5 Other emerging treatment strategies
Strategies aimed at halting viral entry are not limited to
drug-based approaches alone, as peptide inhibitors can
play a vital role in achieving similar effects. To this
end, the team led by Shibo Jiang and Lu Lu has built
upon previous work that generated fusion inhibitors
against the SARS-CoV spike protein’s HR1 region to
design HR2P as a fusion inhibitor against SARS-CoV-
2, as well as EK1 (a pan-coronavirus fusion inhibitor).
In a follow-up study, the team generated a series of
EK1-derived lipopeptides to determine the ones
exhibiting the most potent inhibition of fusion (variant
identified as EK1C4). Suitable formulations of such
peptide preparations, as suggested by the authors, may
be a valuable treatment resource for SARS-CoV-2
infections (Xia et al. 2020a; Xia et al. 2020b).
The value of mesenchymal stem cell transplants in
improving patient health for SARS-CoV-2 infections
was demonstrated in a clinical study involving seven
patients (Leng et al. 2020). Several outcomes were
characteristic of the suggestions made by Cheng et al.
as mentioned earlier, including immunomodulatory
effects, an attenuating effect on proinflammatory
cytokines, and elevated IL-10 levels. An interesting
observation made by the authors of the clinical study
was that such mesenchymal stem cells lacked both
ACE2 and TMPRSS2 gene expression, which could
effectively render them immune to SARS-CoV-2
infection. The possible benefits of cell therapy-based
therapeutic approaches may be immense and have been
explored at length in a recent review (Khoury et al.
2020).
The potential of melatonin as an adjuvant in clinical
treatment on account of its immune-enhancing, anti-
inflammatory, and anti-oxidative effects has been
extolled at length in a recent review (Zhang et al.
2020c). Another study focused on the antagonists of
the lipid-dependant attachment process of viral parti-
cles to host cells (Baglivo et al. 2020). Given that
SARS-CoV-2 utilizes structures such as lipid rafts to
mediate its entry process, the authors recommend
exploring the possibilities of employing substances like
cyclodextrin and sterols to interfere with such viral
attachment and entry-enabling mechanisms. Along
similar lines of conjecturing prospective therapeutic
candidates, EZH2-mediated H3K27me3 at ACE2 pro-
moter regions has been demonstrated to inhibit the
expression of ACE2 receptors in mammalian cell lines,
as indicated by data from RNA-Seq and CHIP-Seq
experiments (Li et al. 2020d).
A major cause of patient mortality in severe SARS-
CoV-2 infections is the ARDS as well as coagulopathy.
Fibrinolytic therapy to target the fibrin deposition in the
pulmonary vasculature (a potential contributor towards
ARDS) has been shown to improve survival, along
with administration of tissue plasminogen activators
(which converts plasminogen to plasmin, that can fur-
ther breakdown blood clots). This strategy has been
shown to improve conditions in a three patient study,
and further clinical trials to ascertain its applicability as
a standard clinical practice for critically ill SARS-CoV-
2 infected patients with ARDS have been recom-
mended (Wang et al. 2020a).
The development of effective prophylactic agents is
an essential component of a comprehensive approach
towards tackling a global pandemic of this scale and
148 Page 8 of 20 M Sreepadmanabh et al.

severity. The importance of administering prophylaxis
to frontline healthcare workers, screening personnel,
and researchers, among others, cannot be overstressed,
as the safety and continued productivity (which
necessitates sound health) of these key players is
paramount to maintain any sustained effort at con-
taining the pandemic and providing healthcare and
treatment of adequate quality to affected patients. In
this regard, a concise review of established protocols
and proposed strategies currently under scrutiny has
been recently published in the form of correspondence
(Agrawal et al. 2020).
Considering the rapidly evolving status of COVID-
19 treatment protocols, it is of utmost importance to
critically evaluate the most up-to-date evidence avail-
able while designing guidelines for clinical practice. Of
equal pertinence are social awareness campaigns and
the regular dissemination of accurate information
regarding clinically proven treatment protocols. This
assumes greater importance in light of a growing
inclination towards scientifically unsubstantiated
claims based on anecdotal/circumstantial evidence or
misrepresented facts placed out of context. We further
present a brief, non-exhaustive listing (table 1)of
leading therapeutic agents frequently associated with
COVID-19 treatment, as well as the current opinion of
the scientific community regarding each of these, based
on the evidence from reported/ongoing clinical trials.
4. Emerging technologies for biomedical research:
artificial intelligence and machine learning
The fields of Artificial Intelligence (AI) and Machine
Learning (ML) have undergone tremendous growth in
scope and popularity in the recent past, establishing
them as important paradigms for future innovation.
More importantly, the development of modules suit-
able for biomedical applications has transformed AI
and ML into attractive tools for the current global effort
to tackle the SARS-CoV-2 pandemic.
With regard to infectious diseases, AI-based plat-
forms may be employed to monitor outbreak and
clustering trends, as well as evaluate the impact of
containment programs and carry out risk assessment
with minimal human intervention. The AI-based
service BlueDot deserves a noteworthy mention of
having raised one of the earliest alarms on SARS-
CoV-2’s potential for broad global spread (Bogoch
et al. 2020). Additionally, these hold immense pro-
mise for dynamic situational monitoring of patients
in real-time, enabling critical evaluation and
optimization of trial treatment protocols in a much
more efficient manner. ML-based solutions can be
expected to consistently enhance and refine such
designs over time, provided they are trained on a
readily updated and expertly-curated dataset. This
represents an important caveat, as the efficacy and
accuracy of ML-based pattern prediction and recog-
nition may be maintained only if the training dataset
is free of biases and a diverse range of scenarios are
well-represented (Fitzpatrick et al. 2020). We had
previously referred to the work by Apostolopoulos
and Bessiana, which could screen for SARS-CoV-2
infections using X-ray images. This has been sup-
plemented by a neural network-based platform using
X-ray images, with a maximum prediction accuracy
of 98% (Narin et al. 2020). Furthermore, an auto-
mated AI-based protocol to identify SARS-CoV-2
infections and distinguish these from other lung
diseases or community-acquired pneumonia has been
recently formulated (Li et al. 2020a,b,c,d,e,f). It
must be noted that both these models were trained
on datasets consisting of actual patient X-ray images,
which is in line with a point we have reiterated
above – that training datasets should necessarily be
accurate, well-represented, and as free of biases as
possible. An exciting new development reported by
the Broad Institute’s Sabeti lab concerns an ML-
based platform for automated Cas13-based SHER-
LOCK assay design (Metsky et al. 2020). Such an
advance represents a potential breakthrough, as
highly optimized and expanded open-access plat-
forms of this nature can aid researchers the world
over in rapidly designing standardized tests for novel
and emerging pathogens using just the knowledge
about their genomic sequence. This can help accel-
erate the deployment of rapid responses to outbreaks
and thereby greatly enhance early screening and
containment efforts. Understandably, a confident
reliance on such automated processes may only be
possible once multiple field applications have vali-
dated the same and demonstrated similar, if not
superior, performance in comparison with existing
assay design pipelines.
Section 3.1 of this review highlights the study which
determined baricitinib as a potential drug against
SARS-CoV-2 (Richardson et al. 2020). Writing in The
Lancet, the same team extended this workflow to
develop more comprehensive treatment strategies
aimed at shortlisting drugs that offered both antiviral as
well as anti-inflammatory effects (Stebbing et al.
2020). The highly modular nature of AI-based
knowledge graphs, an example of which has been
COVID-19: advances in diagnostics and treatment Page 9 of 20 148

Table 1. Leading therapeutic agents against COVID-19, evaluated and described across common parameters
Drug Parameters Details
Azithromycin Status/Remarks No improvement on clinical outcomes, but no significant increase in detrimental
side-effects either
Drug type/
Original purpose
Antibiotic
Mode of
Administration
Oral/Intravenous
Mechanism of
Action
Inhibits mRNA translation by binding to 50s subunit of bacterial ribosome
References Furtado et al. (2020), Oldenburg and Doan (2020)
Baricitinib Status/Remarks Improvement in patient status observed, no adverse side-effects reported.
Currently in phase III clinical trials conducted by Eli Lilly and Co
Drug type/
Original purpose
For rheumatoid arthritis treatment
Mode of
Administration
Oral
Mechanism of
Action
Janus kinase inhibitor. Shows anti-inflammatory activity
References Cantini et al. (2020)
CD24Fc Status/Remarks In phase III clinical trials. Preliminary results suggest effective management of
COVID-associated symptoms
Drug type/
Original purpose
nonpolymorphic regions of CD24 attached to the Fc region of human IgG1
Mode of
Administration
Intravenous
Mechanism of
Action
Immunomodulator, tempers inflammatory responses
References OncoImmune (2020)
Colchicine Status/Remarks Has been hypothesized to address inflamatory responses in COVID-19 infection,
but concerns regarding adverse side-effects have been raised. Currently under
clinical trial
Drug type/
Original purpose
Anti-gout agent
Mode of
Administration
Oral
Mechanism of
Action
Inhibits microtubule polymerization, proinflammatory responses, neutrophil
migration, and mitosis
References Cumhur Cure et al. (2020), Dalili (2020)
Dexamethasone Status/Remarks Shown to lower mortality rate in a recent trial, currently being provisionally
approved for patient treatment in certain regions. May be effective in critically ill
patients
Drug type/
Original purpose
Corticosteroid
Mode of
Administration
Oral/Intravenous/Intramuscular
Mechanism of
Action
Immunosuppresant. Shows anti-inflammatory effects
References Horby et al. (2020)
EIDD-2801 Status/Remarks Potent antiviral activity observed in mouse models and primary human cells.
Currently under phase 2 clinical trial
Drug type/
Original purpose
Antiviral drug. Nucleoside derivative N4-hydroxycytidine
Mode of
Administration
Oral
Mechanism of
Action
Interferes with viral replication by introducing mutations
References Ridgeback Biotherapeutics (2020), Sheahan et al. (2020)
148 Page 10 of 20 M Sreepadmanabh et al.

Table 1 (continued)
Drug Parameters Details
Favipiravir Status/Remarks Clinical studies show faster viral clearence and improvement in chest imaging. A
recent clinical trial from India by Glenmark showed faster and more effective
recovery rate
Drug type/
Original purpose
Pyrazinecarboxamide derivative
Mode of
Administration
Oral/Intravenous
Mechanism of
Action
Inhibits the viral RNA-dependent RNA polymerase
References Glenmark (2020), Irvani (2020)
Hydroxychloroquine Status/Remarks Discontinued as a recommended drug for treatment. Clinical studies show no
significant benefit for patients. Adverse cardiovascular effects have been
reported. However, the study by Mehra et al., claiming no significant benefits of
HCQ administration, has since been withdrawn
Drug type/
Original purpose
Chloroquine derivative. Antimalarial drug
Mode of
Administration
Oral
Mechanism of
Action
Increases lysosomal pH. Also dampens inflammatory response
References Chen et al. (2020c), Gautret et al. (2020), Li et al. (2020a,b,c,d,e,f), Mahevas
et al. (2020), WHO (2020b)
Ivermectin Status/Remarks Emerging candidate against COVID-19. Initial concerns were raised over its high
effective dosage concentration by Caly et al., but this is being explored as a safer
and more effective alternative to HCQ
Drug type/
Original purpose
Avermectin derivative
Mode of
Administration
Oral/topical
Mechanism of
Action
Targets ligand-gated ion channels of invertebrate neural cells
References Caly et al. (2020), Gupta et al. (2020), Heidary and Gharebaghi (2020)
Lopinavir–ritonavir Status/Remarks Clinical studies have demonstrated no significant benefits of lipinavir-ritonavir in
COVID-19 affected patients
Drug type/
Original purpose
Antiretroviral drug
Mode of
Administration
Oral
Mechanism of
Action
HIV protease inhibitor
References Cao et al. (2020b), WHO (2020b)
Remdesivir Status/Remarks Significant benefits from administration of this drug are doubtful. Clinical studies
have reported a marginal improvement in critically ill patients
Drug type/
Original purpose
Nucleoside analog
Mode of
Administration
Intravenous
Mechanism of
Action
Inhibits the viral RNA-dependent RNA polymerase
References Grein et al. (2020), Wang et al. (2020a,b)
COVID-19: advances in diagnostics and treatment Page 11 of 20 148

shown in figure 3, posit these as versatile tools for
efforts aimed at rapid drug prediction from extensive
libraries. A similar report was published which used a
drug repositioning framework employing ML and sta-
tistical analysis. The results were validated by testing
its predictions for MERS-COV and SARS-COV, which
were shown to be in line with the experimentally
observed results (Ge et al. 2020). A reverse vaccinol-
ogy study employing Vaxign-ML (a machine learning-
based application) was recently carried out (Ong et al.
2020). The basic workflow involves a bioinformatic
analysis of the genome/proteome, based upon which
suitable targets are scored. Given the number of
existing and reported studies targeting the viral spike
protein (which also received the highest score using
Vaxign-ML), the authors of this study decided to focus
on the nsp3 which was ascribed the second-highest
score by the aforementioned algorithm. It appears that
vaccine candidate identification efforts stand to benefit
from such ML-driven analysis, which may have an
inherent edge in unearthing unconventional and gen-
erally non-obvious targets offering similar or superior
outcomes as compared to those determined using tra-
ditional workflows or established tenets.
Table 1. (continued)
Drug Parameters Details
Tocilizumab Status/Remarks Studies appear to recommend this drug for critically ill patients, especially for the
alleviation of COVID-19-associated pneumonia and cytokine storm management
Drug type/Original
purpose
Humanized monoclonal antibody against IL-6 receptor
Mode of
Administration
Intravenous
Mechanism of
Action
Immunosuppressant
References Biran et al. (2020), Guaraldi et al. (2020), Luo et al. (2020), Zhang et al. (2020b)
Figure 3. An example illustrating the highly modular nature of AI-based knowledge graphs.
148 Page 12 of 20 M Sreepadmanabh et al.

5. Vaccine development for SARS-CoV-2
Considering the highly contagious nature of the SARS-
CoV-2 infection, the only long-term sustainable solu-
tion is the development of robust vaccination protocols.
In this brief section, we wish to draw the reader’s
attention to some innovative, cutting-edge approaches
towards determining potential vaccine candidates.
An approach based on comparing the human and
viral proteomes to search for pentapeptide sequences
unique to the SARS-CoV-2 was proposed by
Guglielmo Lucchese, as these would be expected to
have high immunogenicity as well as specificity
(Lucchese 2020). Immunoinformatics-guided investi-
gations may also play a significant role in the identi-
fication of suitable target epitopes, as shown by two
recent papers (Ahmed et al. 2020; Baruah and Bose
2020). Baruah and Bose screened the SARS-CoV-2’s
surface glycoprotein for CTL and B-cell epitopes,
further supplemented by molecular dynamics simula-
tions to adjudge the interactions of the former with
MHC Class I types majorly represented in the Chinese
population (Baruah and Bose 2020). The work by
Ahmed et al. incorporated insights from the study of
immunogenic SARS-CoV proteins and B/T-cell epi-
topes derived from the same to obtain a set of such
epitopes for the SARS-CoV-2, which have also been
verified to be invariable amongst the published SARS-
CoV-2 genomes, thereby making these attractive tar-
gets (Ahmed et al. 2020). Another notable effort
undertook an in-silico approach aimed at designing a
multi-epitope vaccine candidate by predicting B/T-cell
epitopes based on analysis of the viral nucleocapsid,
ORF3a, and membrane protein (Enayatkhani et al.
2020). It is conceivable that a comprehensive screen of
epitopes identified in the above-cited (and other rela-
ted) literature in suitable animal models may yield lead
candidates for vaccine trials.
Data generated by previous studies on the SARS-
CoV significantly facilitates current vaccine devel-
opment efforts against the SARS-CoV-2. For
instance, an analysis of the antigenic and glycosyla-
tion variation between SARS CoV and SARS-CoV-2
revealed that while several novel glycosylation sites
were observed in the receptor-binding domain of
SARS-CoV-2, the structure of the glycoprotein
showed no significant divergence (Kumar et al.
2020). Additionally, despite the antigenic variability
between both the strains, certain CTL epitopes were
found to be conserved, suggesting that existing
peptide-based vaccine candidates against the SARS-
CoV could be repurposed for testing against
SARS-CoV-2. This observation is supplemented by a
recently published report, wherein Conformational-
Epitope BLAST (which identifies antigenic similarity
of a new pathogen to existing ones) was used to
identify cross-reactive epitopes in the ACE2 receptor
binding region of SARS-CoV-2’s S protein (Qiu
et al. 2020). Along similar lines, polyclonal anti-
bodies against the SARS-CoV receptor-binding
domain have been shown to cross-react with SARS-
CoV-2 receptor-binding domain (RBD), thereby
inhibiting SARS-CoV-2’s entry into cells (Tai et al.
2020). A largely concordant line of reasoning has
also advocated the consideration of the RBD219-N1
(a yeast-expressed potential vaccine candidate against
SARS-CoV) as a heterologous vaccine against the
SARS-CoV-2 (Chen et al. 2020b). These examples
serve to highlight that alongside initiatives to develop
novel vaccine candidates, repurposing efforts could
help provide immediate solutions to address the
urgent needs imposed by the ongoing pandemic
situation.
A cell-based antigen delivery system against the
SARS-CoV-2 has also been proposed recently using
decoy cells displaying viral spike protein (Ji et al.
2020). The report provides evidence from the liter-
ature to support and justify the approach, in partic-
ular, citing the example of GM-CSF expressing
irradiated cells being well tolerated in clinical trials
against cancer. However, no records of assays or in-
vivo animal model studies have been provided at the
moment; hence it is premature to comment on the
suitability of this concept in the context of SARS-
CoV-2 infections.
The recent review by Iwasaki and Yang raises
important caveats regarding vaccine development
efforts, in particular, the phenomenon of antibody-
dependant enhancement (ADE). ADE occurs when
therapeutically administered antibodies can exacer-
bate the existing pathology by enabling infection of
immune cells by the invading virus, promoting
inflammation, downregulation of anti-inflammatory
factors like IL-10, and aberrant activation of the
immune system leading up to tissue injury. The
dangers associated with hyper-inflammation and
immune dysregulation in the context of SARS-CoV-2
infections have been elucidated at length in Sect. 3.4.
The authors outline several possible contributing
factors towards ADE, including antibody specificity,
choice of target epitope, affinity, subtype (IgM or
IgG), dosage, and patient status. Such concerns
underscore the need for well-rounded vaccine
development protocols and extensive preclinical
COVID-19: advances in diagnostics and treatment Page 13 of 20 148

evaluations in order to optimize the choice of
adjuvants, mode of administration, and other relevant
parameters as enlisted above. A more thorough
elaboration may be found in the publication refer-
enced (Iwasaki and Yang 2020).
The World Health Organization (WHO) is currently
maintaining publicly accessible, comprehensive, and
authoritative databases (https://www.who.int/publica
tions/m/item/draft-landscape-of-covid-19-candidate-
vaccines) listing all the vaccines under clinical or
preclinical evaluation (WHO 2020a). At the time of
writing, 33 vaccine candidates are under clinical trial,
which have been summarized in table 2. Additionally,
the WHO’s COVID-19 modeling ad hoc expert
working group (https://www.who.int/publications/m/
item/covid-19-animal-models—summary-of-progress-
made-by-the-who-covid-19-modelling-(march-04-june-
2020)) has also reported (based on the available results
from studies across the world) that Rhesus macaques
and ferrets appear to be the most suitable large animal
models for studying SARS-CoV-2 infections to date
(WHO 2020). Such public information initiatives are of
immense benefit to encourage collaboration, avoid
unnecessary and wasteful duplication of effort, and
disseminate valuable data rapidly across the research
community. We would also like to direct the interested
Table 2. Vaccines being developed against COVID-19 currently in clinical trial stages
COVID-19 vaccine developer/manufacturer Vaccine platform Phase
Inovio Pharmaceuticals/ International Vaccine Institute DNA 1/2
Osaka University/ AnGes/ Takara Bio DNA 1/2
Cadila Healthcare Limited DNA 1/2
Genexine Consortium DNA 1/2
Sinovac Inactivated 3
Wuhan Institute of Biological Products/Sinopharm Inactivated 3
Beijing Institute of Biological Products/Sinopharm Inactivated 3
Institute of Medical Biology, Chinese Academy of Medical Sciences Inactivated 1/2
Research Institute for Biological Safety Problems, Rep of Kazakhstan Inactivated 1/2
Bharat Biotech Inactivated 1/2
University of Oxford/AstraZeneca Non-Replicating Viral
Vector
3
CanSino Biological Inc./Beijing Institute of Biotechnology Non-Replicating Viral
Vector
3
Gamaleya Research Institute Non-Replicating Viral
Vector
3
Janssen Pharmaceutical Companies Non-Replicating Viral
Vector
3
ReiThera/LEUKOCARE/Univercells Non-Replicating Viral
Vector
1
Anhui Zhifei Longcom Biopharmaceutical/Institute of Microbiology, Chinese Academy
of Sciences
Protein Subunit 2
Novavax Protein Subunit 1/2
Kentucky Bioprocessing, Inc Protein Subunit 1/2
Clover Biopharmaceuticals Inc./GSK/Dynavax Protein Subunit 1
Vaxine Pty Ltd/Medytox Protein Subunit 1
University of Queensland/CSL/Seqirus Protein Subunit 1
Medigen Vaccine Biologics Corporation/NIAID/Dynavax Protein Subunit 1
Instituto Finlay de Vacunas, Cuba Protein Subunit 1
FBRI SRC VB VECTOR, Rospotrebnadzor, Koltsovo Protein Subunit 1
West China Hospital, Sichuan University Protein Subunit 1
Institute Pasteur/Themis/Univ. of Pittsburg CVR/Merck Sharp & Dohme Replicating Viral Vector 1
Moderna/NIAID RNA 3
BioNTech/Fosun Pharma/Pfizer RNA 3
Curevac RNA 2
Arcturus/Duke-NUS RNA 1/2
Imperial College London RNA 1
People’s Liberation Army (PLA) Academy of Military Sciences/Walvax Biotech. RNA 1
Medicago Inc. VLP 1
148 Page 14 of 20 M Sreepadmanabh et al.

reader to refer to an excellent summary of the SARS-
CoV-2 vaccine landscape by Nature Reviews Drug
Discovery and authors affiliated with the Coalition for
Epidemic Preparedness Innovations (CEPI) (Le et al.
2020).
6. Conclusion
As the current progress of the SARS-CoV-2 outbreak
has made obvious, clinical management of these
infections has been under multiple pressures ranging
from high false-negative rates of diagnosis, contentious
results on the efficacy of proposed drugs, and the threat
of severely detrimental symptoms like ARDS and
cytokine storm responses. The development of acces-
sible point-of-care diagnostic devices tailor-made for
low-resource settings continues to be a pressing
requirement. This may be achieved by cell lysis-free
workflows, increasingly sensitive and robust bioassays,
improved sample collection and processing methods
which minimize risks to healthcare workers, and ready-
to-use kits not requiring technical expertise, among
other possible innovations. In this regard, RT-LAMP
and CRISPR/Cas-based methods like SHERLOCK and
DETECTR are notable advancements that could be
explored as promising alternatives. With regard to
portable diagnostic devices, few technologies hold as
much promise as paper-based microfluidics. The
applicability of this has already been demonstrated in
the context of the Ebola and Zika outbreaks (Kaarj
et al. 2018; Magro et al. 2017). While a comprehensive
overview of the microfluidics domain is beyond the
scope of this work, considering the immense potential
of this technology we would like to direct the interested
reader to refer to a dedicated review of paper-based
microfluidic platforms for nucleic acid detection (Kaur
and Toley 2018).
Advocating accelerated vaccine development
efforts might prove to be a risky gamble, on account
of the associated safety caveats which have been
underscored in the preceding sections. Instead, an
emphasis on designing and adopting reliable bio-
physical assays for comprehensive, yet rapid pre-
clinical evaluation may be beneficial in reducing the
historically high attrition rate among candidates
under clinical trials. This holds especially true for
studies proposing novel therapeutic agents as well,
for which emerging techniques like the CETSA
(cellular thermal shift assay) may help deter the
occurrence of misleading false positives (Martinez
Molina et al. 2013). Furthermore, as regards the
application of AI/ML-based platforms in biomedical
research and diagnostics, a confluence of cross-do-
main expertise is crucial to ensure the development
of reliable models and workflows which faithfully
capture real-world dynamics. As instances of gov-
ernments and healthcare agencies employing AI-
based containment and prevention strategies increase,
it is important that critical studies be undertaken to
ascertain the true benefits and outcomes of such
technological integration, rather than a reliance on
anecdotal evidence alone.
Throughout our discussion, certain points have been
recurrent – the advantages of leveraging existing
knowledge on closely related species like the SARS
CoV, the potent efficacy of seemingly disparate
techniques when applied in tandem, and the impor-
tance of collaborative efforts coupled with rapid,
timely dissemination of results which may inform
ongoing efforts. Requirements key to enabling these
include the availability of genomic sequences, struc-
tural data, and expertly curated databases. The push
towards developing modular assay workflows (with
elements of automation involved) may well be a
defining paradigm of future responses to such sce-
narios. The advent of in silico epitope screening,
algorithmic vaccine and inhibitor design, and prelim-
inary evaluation of drug libraries by molecular
docking has the potential to greatly facilitate wet-lab-
based and clinical investigations while expediting
results. However, we reiterate our concerns over
adequate quality testing and rigorous experimental
validation before adopting such approaches as an
established norm. Skepticism must also be extended
in light of a growing tendency to extrapolate trends
observed from in vitro setups and unsuitable animal
models to recommend clinical guidelines. We con-
clude our narrative on the hopeful note that the topical
coverage should have appealed to both experts in
virology and biomedical engineers, as well as recent
entrants in these research domains. The purpose of
this effort would be best served if the diverse studies
described herein motivate and help lay the foundation
for ambitious multidisciplinary undertakings aimed at
the advancement of public health.
Acknowledgements
The authors thank Hitaishi Desai for helping with
illustrations and designs for the figure panels, and Dr.
Ankit Kumar Sahu and Minita Desai for proofreading
and editing of the final draft. AC thanks India Alliance,
COVID-19: advances in diagnostics and treatment Page 15 of 20 148

IISER Bhopal and DBT for supporting various research
programs in the lab.
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