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Artificial Intelligence and Bioinformatics Promise Smart and Secure Healthcare:

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50 Advances in Computing Communications and Informatics, 2024, Vol. 7, 50-68

CHAPTER 3
Artificial Intelligence and Bioinformatics Promise
Smart and Secure Healthcare: A COVID-19
Perspective
S. Sheik Asraf1,*, Jins K. Abraham1 and Shalini Mohan1
1
Department of Biotechnology, School of Bio, Chemical and Processing Engineering,
Kalasalingam Academy of Research and Education (deemed to be) University, Anand Nagar,
Krishnankoil, Tamil Nadu, India

Abstract: Recent developments in the fields of Artificial Intelligence (AI) and

bioinformatics have played a vital role in securing smart healthcare. Notable
contributions have been made in the field of viral immunology after the COVID-19
outbreak with the help of AI and bioinformatics. Various diseases and disorders such as
viral diseases, metabolic disorders, and genetic disorders require the application of AI
and bioinformatics to provide safe and error-free treatment. The tools of bioinformatics
and modern-day biology used for smart and secure health care include single-cell
genomics, proteomics, and next-generation sequencing technologies. During the
COVID-19 outbreak, AI and bioinformatics helped to create methods and services to
combat the pandemic. In this chapter, we elaborately highlight the principle, procedure,
and applications of AI equipped with bioinformatics knowledge to create opportunities,
and prospects and answer the challenges met by academicians, researchers, students,
and industry professionals from the background of computer science, bioinformatics,
and healthcare.

Keywords: Artificial intelligence, Bioinformatics, Covid, Healthcare.

INTRODUCTION
Recent advances in the bioinformatics and AI domains have been crucial in
ensuring the safety of smart health care. After the COVID-19 outbreak, notable
advancements in the field of viral immunology were accomplished with the use of
AI and bioinformatics. To provide safe and error-free treatment for a variety of
illnesses and disorders, including viral infections, metabolic disorders, and genetic
disorders, bioinformatics and AI must be applied.
*
Corresponding author S. Sheik Asraf: Department of Biotechnology, School of Bio, Chemical and Processing
Engineering, Kalasalingam Academy of Research and Education (deemed to be) University, Anand Nagar,
Krishnankoil, Tamil Nadu, India; E-mail: ssasraf@gmail.com

Arvind K. Sharma, Dalip Kamboj, Savita Wadhawan, Gousia Habib, Samiya Khan and Valentina Emilia Balas
(Eds.)
All rights reserved-© 2024 Bentham Science Publishers
Bioinformatics Promise Smart Advances in Computing Communications and Informatics, Vol. 7 51

Modern biology and bioinformatics tools like single-cell genomics, proteomics,

and next-generation sequencing technologies are applied to provide smart and
secure healthcare. AI and bioinformatics were crucial in developing healthcare
tools and services. As of April 17, 2020, SARS-CoV2 is the pathogen causing the
COVID-19 pandemic. The disease, which has touched practically every nation on
earth, exhibits symptoms that are more typical of flu illnesses. However, this virus
evolves quickly, with 8 * 10−4 changes per site and roughly one mutation every
two weeks. Due to the ability of the viral species in bat cells, the refractory
resistance of the bat, and the innate and adaptive immunity in bats, bats are good
repositories for viral species. Although there are several barriers to viral spill-
overs, they occasionally happen because of ecological opportunities for contact,
cellular and molecular compatibility between the virus and host, and evaded
immune responses. This has led to a significant number of bat-borne zoonotic
viral spillovers. After rodents, which make up 20% of the diversity of mammals,
bats are the mammal species with the greatest diversity. A diversified viral niche
could be produced by the variety of bat species. Bats living in every region of the
world contain viruses with all forms of genetic material according to the
Baltimore classification. Therefore, a comparative examination of the SARS-
CoV2 genome and proteome with those of other possible bat viral candidates that
can infect humans may aid in the discovery of new therapeutic targets as well as
vaccine epitopes. This chapter examines the sequence alignment of SARS-CoV2
and other viral species from the bat virome using EMBOSS online tools and
phylogenetic analysis using MegaX software. We specifically highlight the
principle, process, and applications in this chapter.
ARTIFICIAL INTELLIGENCE AND BIOINFORMATICS
It was formally established in 1956 that AI is the study of building intellectual
machines. Whereas, bioinformatics solution typically entails the following
essential steps:
1. Compiling statistical data on numerous biological topics.
2. Creating an algorithm or computational tool based on the data.
3. Run an algorithm simulation program on the statistical data.
AI can be used in the aforementioned phases to produce improved performance
and obtain the optimized result [1]. The scientific community now has access to a
greater variety of datasets thanks to the use of large databases and the expanding
body of current knowledge on biological processes. This has made it possible to
model and optimize jobs in various processes or to conduct an analysis to make it
simpler to acquire relevant information [2]. The goal of bioinformatics is to create
new techniques for logically analyzing enormous amounts of data. Algorithms
52 Advances in Computing Communications and Informatics, Vol. 7 Asraf et al.

based on AI applications make it possible to do molecular dynamic simulations,

develop vaccinations for diseases, analyze molecular docking data, locate novel
chemicals, detect ADMET features, and forecast in silico structure. These
algorithms are employed to produce knowledge quickly [3]. AI strategy for
protein structure prediction will have a substantial impact on bioinformatics
research and development and offer a new framework for managing innovation in
the biotechnology sector. The top methods now available for predicting the
tertiary structures of proteins are examined in a large-scale study known as
CAPSP [4].
Role of Bioinformatics in Healthcare
Data about healthcare comprises expense details, spending vouchers, reviews on
patient care, medical data from various parts of the body, and cost information.
Before bioinformatics, the telemedicine concept that uses electronic-based
technologies to deliver medical care to those who live far away had usage in the
field of medicine, including consultations, diagnostics, nursing, medications and
treatments, psychiatry and psychology, rehabilitation, and some specialized
services. Rural inhabitants who live distant from healthcare professionals can be
connected through the use of telemedication [5]. With the use of computer
techniques and technology, biological details are analyzed with the help of
bioinformatics. Ailments like metabolic illnesses, kidney ailments, genetic
disorders, and diseases can be discovered early on using bioinformatics
techniques [6]. Bioinformatics has grown from providing essential services like
sequence alignment, structural predictions, and phylogenetic analysis into a stand-
alone, data-driven field. Future biological research will heavily rely on big data
sets, of which we are only witnessing the tip of the iceberg. New potential calls
for creative solutions that demand the capacity to deal with noisy, unstructured
data to give relevant biological insights [7]. Bioinformatics uses computational
software and methods to investigate massive biological data. The primary focus is
on processing biological data for use in basic biological domains. Data analytics
are being used in the healthcare sector to mine understanding and make informed
decisions as a result of the data explosion [8]. Translational bioinformatics (TBI)
grew in popularity in the early 2000s due to the Human Genome Project. TBI’s
primary goal is to provide personalized care with the capacity to combine
biological data. It effectively speeds up drug development and re-purposing while
causing the patient little long-term harm [9]. Genomic information reveals the
inherited disease-causing components, which aids in the identification and
treatment of diseases and disorders. The socioeconomic, medicolegal, and
technical aspects of incorporating genetic data into healthcare raise several
questions. Bioinformatics, a crucial integration component, presents a sizable
number of unanswered problems [10]. Clinical bioinformatics delivers biological
Bioinformatics Promise Smart Advances in Computing Communications and Informatics, Vol. 7 53

and medical data to enable personalized treatment. After analyzing the complete
human genome sequences, researchers can explore online biological databases
and utilize the knowledge in their medical practices. The healthcare industry will
be able to improve practice guidelines by making better use of the enormous
amount of biological data generated by these tools [11]. Here are some
perspectives on how bioinformatics is impacting healthcare. Cancer diagnosis and
prognosis are significantly impacted by computational approaches like Bayesian
networks, incoherent rationality, ANN, genetic algorithms, data mining, ML, etc
[12].
Role of Artificial Intelligence in Healthcare
AI and bioinformatics may hold great promise for use in the healthcare industry,
according to a recent report [13]. The informatics methods used in the virtual
branch range from active physician treatment assistance to deep learning
information management. The best example of the physical branch is a robot that
assists an old patient or a surgeon in the operating room. Additional consideration,
proof of their medical utility, economic worth, and societal worth are required
before they are widely deployed [14]. One early possibility for AI technology is in
the healthcare industry, where it could be used to improve patientcare and reduce
costs [15]. There is a need for sophisticated human-machine interaction. The
ability of medical practitioners to effectively use new medical information in
practice will depend on technology like AI. The new technology, its advantages
and drawbacks must be effectively explained to medical practitioners [16]. AI
aims to imitate cognitive processes in humans and can analyze many kinds of
healthcare data. Processing for unstructured data and structured data involves the
use of NLP and ML. Three significant illness areas that employ AI technologies
are cancer, neurology, and cardiology [17]. As healthcare data becomes more
widely available and analysis techniques advance quickly, it is providing a new
approach to healthcare. The most revolutionary technology of the twenty-first
century, AI has been considered as a promising early prospect to revolutionize the
healthcare industry [18]. There is a lot of anticipation that AI may soon
outperform humans in the healthcare industry. Better disease prevention,
detection, diagnosis, and treatment might be made possible by AI. Malignancy,
nervous system-related diseases, circulatory system-related diseases, and diabetes
are the major diseases for which AI tools are used. As AI has improved human
lives in numerous ways, it is becoming a well-known discipline in computer
science [19]. In the field of cancer research, AI algorithms now execute at an
expert level. Only a small number of AI-based apps have been approved for usage
in actual settings [20]. Massive amounts of recently made data offer a chance to
use AI and ML to advance the field of drug safety science [21]. Big data is
frequently used in many applications using deep machine learning and AI. For
54 Advances in Computing Communications and Informatics, Vol. 7 Asraf et al.

instance, accurate imaging in the field of cardiovascular imaging is now

integrated with big data from eHealth records, pathology, and accurate imaging to
better identify the condition. By understanding the biology of a tumor, cancer care
is being enhanced in clinical work and imaging [22]. Health officials must be
aware of the state of AI technologies and their applications [23].
Various sizes, types, and specializations of healthcare organizations are becoming
more interested in how AI has developed and is supporting patient demands and
care [24]. AI is being used to produce output without human input in a variety of
healthcare situations, including bioinformatics, genomics, and image analysis.
Despite the possibility of this technology improving diagnosis and treatment
procedures, there may be difficulties and mistakes because of numerous safety
worries [25]. Payers, care providers, and life sciences companies currently use
several types of AI. Implementation challenges will delay the broad automation of
healthcare professional occupations for some time [26]. A paradigm shift in
medicine has been brought about by advances in AI where it has outperformed
humans in some areas. By utilizing analytical methods, AI has been widely
adopted in the healthcare industry as a result of rapidly expanding healthcare data
and the development of analytical methods [27]. A fundamental understanding of
the various machine learning processes is necessary, even though medical doctors
and paramedics often do not receive formal instruction in the field throughout
their primary school. Along with people, it is essential to have requirements,
information, systems, training, and an understanding of how to make the
processes as useful as possible [28]. Clinical oncology’s future has changed
thanks to the development of next-generation sequencing technology. Next
Generation Sequencing (NGS) is used in illness detection, sequencing- and
imaging-based diagnosis, precise prognosis, biomarker identification, and
therapeutic target identification for new drug creation. Through the use of NGS
and high-resolution medical imaging, cancer diagnosis and prognostic prediction
are improved. Despite technological breakthroughs, AI still has several difficulties
and restrictions [29]. Cancer diagnosis and treatment clinical applications of AI
and ML are the future of personalized medicine [30]. Understanding the evolving
scenario and patent collaboration network in the AI-medical sector has practical
value and serves as a guide for future strategy planning, development, and
technology marketization [31].
Artificial Intelligence, Healthcare, and Bioinformatics: A Win-Win
Combination
Digital innovation and transformation has significant application in healthcare,
agriculture, food, finance, and education [32]. Applications in translational
healthcare for AI and other recent developments in bioinformation and
Bioinformatics Promise Smart Advances in Computing Communications and Informatics, Vol. 7 55

biostatistics are significant and current. Both non-immune and immunological

factors have an impact on how healthcare is administered, as well as the degree to
which immune cells and soluble substances regulate viral immune surveillance is
one instance [33]. In a recent report, IgA-containing immune complexes are
known to be deposited in the glomeruli of the kidney, triggering an inflammatory
response. Patients’ illnesses frequently worsen over. To understand IgAN, a
comprehensive analysis is required. Such information can be gathered using
cutting-edge technologies like SCS, NGS, proteomics, and advanced imaging
techniques [34]. Precision medicine has the potential to advance traditional
medicine. Personalized disease progression has made it difficult to use healthcare
evidence in clinical management. Improving patient outcomes depends on
utilizing the ability of patient records to integrate various data, identify the
personalized progression of the disease, and apply efficient personalized precision
medicine [35].
Biology of SARS-COV2
The COVID-19 pandemic, which has touched practically all nations worldwide, is
caused by the SARS-CoV2 virus. These illnesses can spread from person to
person, and cases of them infecting both patients and medical personnel have been
documented. Typically, coronaviruses are 125 nm in diameter and have positive
single-stranded RNA as their genetic material. Along with 12 non-structural
proteins, they also have structural proteins such as spike, membrane,
nucleocapsid, and envelop proteins (NSP). The pathogenesis of SARS-CoV2
infection includes the following phases: Viral entrance occurs when the virion has
bound to the host’s ACE 2 receptor (Angiotensin Converting Enzyme). The viral
DNA and nucleoproteins are released. The production of polyproteins results from
the translation of the viral mRNA genome. After being created, functional protein
units are created by proteolyzing the polyproteins. The replicase-transcriptase
complex then helps the RNA molecules multiply. Transcription and replication
follow the production of RNA molecules. The required viral protein particles are
produced by transcribed RNA. The young virions are then put together using the
replicated RNA molecules as their genome. The structural protein is subsequently
folded to cause the virion to develop. The developed virions are expelled from the
cell after maturation.
BATS and SARS-COV-2
After rodents, bats are recognized as the animal species with the greatest
diversity. The majority of animal-origin pathogens that affect humans are spread
by bats, which also serve as a reservoir for viruses including the Ebola, Marburg,
Nipah, Hendra, and coronaviruses that cause SARS, MERS, and SARS-CoV-2.
56 Advances in Computing Communications and Informatics, Vol. 7 Asraf et al.

Numerous studies on the viral ecology in bats conducted up until this point have
shown that the animals are home to thousands of viral species from at least 28
families. The ability of the virus to remain in bat cells bat immunological
responses, and bat resistance factors are only a few of the distinctive
characteristics of bats that make them a special viral host. The potential for
diversity in viral niches is increased by the diversity of bats. Bats are frequently
utilized as model systems to quantify viral diversity since they have more
zoonotic viral infections per species than rodents do. The enhanced developments
in metagenomics research have provided a wealth of knowledge on the bat
virome.
Bioinformatics Study of SARS-COV-2
One of the most vital tools for sequence annotation of SARS-COV-2 is pairwise
sequence alignment. To match sequences end to end and find the best score,
global alignment is used. The global alignment method is the Needleman-Wunsch
algorithm. The Smith-Waterman technique is used for local alignment to find the
conserved areas between the sequences. The conserved sequence pattern of
SARS-COV-2 that can result from evolution or ancestry relationships can be
discovered utilizing multiple sequence alignment. The development of
phylogenetic trees could be used to analyze the evolutionary and taxonomic links
of SARS-COV-2 between organisms. Additionally, the pattern and process of
evolutionary changes may be shown through phylogenetic analysis of RNA
viruses like SARS-COV-2. The distribution of mutations and their co-occurrence
could be further examined to better understand the SARS-COV-2 viral evolution.
ARTIFICIAL INTELLIGENCE AND BIOINFORMATICS PROMISE
SMART AND SECURE HEALTHCARE AMIDST COVID-19 OUTBREAK
The number of COVID-19 infection-related fatalities has been rising rapidly day
after day, prompting numerous countries to take action to stop the sickness from
spreading. There is a global health and healthcare crisis due to COVID-19.
Rapidly identifying and monitoring patients so that decisions about their care,
monitoring, and management may be made promptly is one of the biggest issues
[36]. SARS-CoV-2 was the primary cause of the first significant outbreak in the
modern time. Computational methods have been widely used to handle the
resulting global health catastrophe [37]. The pandemic of COVID-19 has
illustrated the need for international cooperation and consensual decisions to solve
the most serious issues and dangers to humanity. One of the most difficult
elements of accessing and sharing the full and accurate clinical data collected by
Electronic Health Records is doing so despite its crucial relevance [38]. The
diagnosis of COVID-19 primarily depends on MRI and other cutting-edge
Bioinformatics Promise Smart Advances in Computing Communications and Informatics, Vol. 7 57

imaging techniques. Advances in the diagnosis process, treatment of diseases, and

early detection of symptoms have been made possible by machine learning
techniques. As conditions improve, AI will emerge as the most significant
disruptive technology and enabler for society [39]. AI-supported SARS-CoV-2
diagnosis is based on POC sensing technology, IoT and AI tools [40]. Apart from
using the blockchain in data management, it could also be efficiently used for
genomic and healthcare and could be used for faster transactions and storage of
data. This could potentially improve the progress in the research of COVID-19.
Blockchain technology in genomics could accelerate the transfer of authentic data
of the virome of bats present in various locations around the globe. This
information might help in arriving at a consensus between the bat virome and
SARS-CoV2.RT-PCR is a common method used to diagnose coronavirus, but this
approach leads to erroneous outcomes. One of the subjects that has received the
greatest attention recently is artificial intelligence (AI) [41 - 44].
IN SILICO COMPARATIVE ANALYSIS OF GENOME AND PROTEOME
OF SARS-COV2 WITH THE BAT, VIROME PROMISES GATEWAY
FOR HEALTH-CARE
After rodents, bats have the second-highest diversity among mammalia, with
about 22% of them being recognized species.
Selection of Target Organisms
A literature survey was performed for the identification of positive viral strains in
bat virome that has the potential to cause infection in human. The following study
strains were chosen for the study (Table 1).

Table 1. List of positive sense RNA viruses found in bat virome.

Virus Family Enveloped Virus Viral Species

Astroviridae No Bat astrovirus
Calciviridae No Bat norovirus
Coronaviridae Yes Bat coronavirus
Coronaviridae Yes SARS-CoV2
Flaviviridae Yes Dengue virus
Flaviviridae Yes Japanese encephalitis virus
Flaviviridae Yes St Louis encephalitis virus
Flaviviridae Yes West Nile virus
Flaviviridae Yes Yellow fever virus
Flaviviridae Yes Zika virus
58 Advances in Computing Communications and Informatics, Vol. 7 Asraf et al.
(Table 1) cont.....

Virus Family Enveloped Virus Viral Species

Hepeviridae No Hepatitis E virus
Picornaviridae Yes Human enterovirus
Picornaviridae Yes Human parechovirus
Togaviridae No Chickungunya virus
Togaviridae No Western equine encephalitis virus
Togaviridae No Eastern equine encephalitis virus
Togaviridae No Venezuelan equine encephalitis virus
Togaviridae No Babanki virus
Togaviridae No Sindbis virus

Global and Local Pairwise Alignment of the Genomes of SARS-CoV2 and the
Study Species from Bat Virome
The genome and the RNA-dependent RNA polymerase sequences of SARS-CoV2
and the study species were obtained from the NCBI database for genome and
protein respectively. Both the genome and protein sequences were downloaded in
FASTA format. Sequence alignments including both the pairwise and multiple
sequence analysis were performed using Emboss Needle (for global
alignment), Emboss Water (for local alignment), and Clustal Omega (for multiple
sequence alignment) with the default parameters. The results of the global and
pairwise sequence alignments are given as follows (Table 2).

Table 2. Global and local pairwise alignment of the genomes of SARS-CoV2 and the study species from
bat virome.

Global Alignment Local Alignment

S. No Target Organism
Similarity %
1 Hepatitis E Virus 15.1 34.8
2 Venezuelan equine encephalitis virus 24.2 37.8
3 Sindbis virus 24.8 37
4 Western equine encephalitis virus 24.3 39.7
5 Babanki virus 25.6 36.9
6 Human enterovirus 16.2 36.7
7 Human parechovirus 15.4 38.9
8 Zika virus 22.8 38.6
9 Bat norovirus 16.4 34
10 Japanese encephalitis virus 23 38.1
Bioinformatics Promise Smart Advances in Computing Communications and Informatics, Vol. 7 59
(Table 2) cont.....

Global Alignment Local Alignment

S. No Target Organism
Similarity %
11 Dengue virus 22.9 37.9
12 West Nile virus 23.6 36.7
13 Yellow fever virus 23.2 38.3
14 Eastern equine encephalitis virus 25.2 36.8
15 Chikungunya virus 25.3 37.3
16 Saint Louis encephalitis virus 23.7 36.5
17 Bat astrovirus 11.8 37.3
18 Bat coronavirus 42.3 52.8

PAIRWISE ALIGNMENT OF GENOME

BAT CORONAVIRUS 42.3 52.8

BAT ASTROVIRUS 11.8 37.3

SAINT LOUIS 23.7 36.5

CHIKUNGUNYA 25.3 37.3

EASTERN EQUINE 25.2 36.8

YELLOW FEVER 23.2 38.8

WEST NILE VIRUS 23.6 36.7

DENGUE VIRUS 22.9 37.9

STUDY SPECIES

JAPANESE 23 38.1

BAT NOROVIRUS 16.4 34

ZIKA VIRUS 22.8 38.6

HUMAN 15.4 38.9

HUMAN 16.2 36.7

BABANKI VIRUS 25.6 36.9

WESTERN EQUINE 24.3 39.7

SINDBIS VIRUS 24.8 37

VENEZUELAN 24.2 37.8

HEPATITIS E VIRUS 15.1 34.8

% SIMILARITY
Global alignment Local alignment

Fig. (1). Global and local pairwise alignment of SARS-CoV2 and the study species from bat virome.
60 Advances in Computing Communications and Informatics, Vol. 7 Asraf et al.

The sequence alignment was performed with online tools using the Needle-
Wunsch and Smith-Waterman algorithm with an emphasis on AI. These
algorithms could enhance the sequence alignment with increased computational
speed. Online tools like EMBOSS-NEEDLE and EMBOSS-WATER were used
for global and local alignment of the bat virome and SARS-CoV2.
A comparison of the viral species present in the bat virome with the SARS-CoV2
virus, which is responsible for the COVID-19 pandemic, is necessary because bats
are also a potential natural reservoir host of many viral species and there are
numerous indications that there could be many viral spillovers from bats. The
examination of the SARS-CoV2 genome and proteome, as well as that of other
viral species from the bat virome, is the main emphasis of this study. Bat
coronaviruses exhibited a higher degree of similarity to SARS-CoV2 than other
species, according to pairwise sequence alignment of the genomes and proteomes
of SARS-CoV2 and a few research species (Table 2, Fig. 1). From Table 2 and
Fig. 1, it is found that Bat coronavirus and SARS-CoV2 had more sequence
similarity of genome compared to other viral study species.
Phylogenetic Tree Analysis
The evolutionary analysis of the genome and protein sequences was performed
using MegaX software by constructing a phylogenetic tree using the neighbor-
joining method with 500 bootstrapping. The phylogenetic tree constructed for the
genomes of SARS-COV2 and the study species from bat virome with 500
bootstrapping is as follows (Fig. 2). The genomes of SARS-COV2, Hepatitis E
Virus, Bat Astrovirus, and RdRp Sequences of SARS-COV2 and Human
Enterovirus are more evolutionarily related, according to phylogenetic research.
The viral proteome’s NSP 12 is the RNA-dependent RNA polymerase. The
structure has a right-hand RdRp domain, an N-terminal domain that is unique to
nidoviruses, and it frequently forms a complex with other proteins. Since
replication and transcription of this molecule can be blocked, it may be utilized as
a possible therapeutic target to stop the spread of RNA viruses. From Fig. (2), it is
observed that the genome of SARS-CoV2 is more related to the genomes of
Hepatitis E virus and Astrovirus.
From the global and local alignment of the SARS-CoV2 genome, it was found
that the bat coronavirus had increased similarity compared to other viruses in the
bat virome. In the viruses considered, the similarity in local alignment is more
compared to global alignment showing the presence of coding regions in the
genome dispersedly.
Bioinformatics Promise Smart Advances in Computing Communications and Informatics, Vol. 7 61

Global and Local Pairwise Alignment of the RNA-dependent RNA

Polymerase Sequences of SARS-CoV2 and the Study Species from bat
Virome
The results of the global and local pairwise alignments are as follows in Table (3).
From Table. (3) and Fig. (3), it can be found that the RNA-dependent RNA
polymerase of SARS-CoV2 and Bat coronavirus have increased similarity
compared to other viral study species.

Fig. (2). Neighbor-joining phylogenetic tree of the genomes of SARS-CoV2 and the viral study species with
500 bootstrapping.

Table 3. Global and local pairwise alignment of the genomes of SARS-CoV2 and the study species from
bat virome.

Global Alignment Local Alignment

S. No Target Organism
Similarity %
1 Hepatitis E Virus 1.1 55.6
2 Venezuelan equine encephalitis virus 13.9 30.5
3 Sindbis virus 10.4 30.4
4 Western equine encephalitis virus 12.7 31.2
5 Babanki virus 3.6 42.6
6 Human enterovirus 5.7 35.1
62 Advances in Computing Communications and Informatics, Vol. 7 Asraf et al.
(Table 3) cont.....

Global Alignment Local Alignment

S. No Target Organism
Similarity %
7 Human parechovirus 18.8 37.2
8 Zika virus 10.9 30.5
9 Bat norovirus 8.8 44.7
10 Japanese encephalitis virus 19.2 33
11 Dengue virus 11.6 36.2
12 West Nile virus 3 37
13 Yellow fever virus 8.6 29.5
14 Eastern equine encephalitis virus 6.4 29.4
15 Chikungunya virus 2.3 38.2
16 Saint Louis encephalitis virus 23.3 28.5
17 Bat astrovirus 5.6 52
18 Bat coronavirus 6.8 85.3

PAIRWISE ALIGNMENT OF RNA DEPENDENT RNA

POLYMERASE
BAT CORONAVIRUS 6.8 85.3

BAT ASTROVIRUS 5.6 52

SAINT LOUIS
ENCEPHALITIS VIRUS 23.3 28.5
CHIKUNGUNYA
VIRUS
2.3 38.2
EASTERN EQUINE
ENCEPHALITIS VIRUS 6.4 29.4
YELLOW FEVER
VIRUS
8.6 29.5

WEST NILE VIRUS 3 37

DENGUE VIRUS 11.6 36.2

JAPANESE
ENCEPHALITIS VIRUS 19.2 33

BAT NOROVIRUS 8.8 44.7

STUDY SPECIES

ZIKA VIRUS 10.9 30.5

HUMAN
PARECHOVIRUS 18.8 37.2
HUMAN
ENTEROVIRUS 5.7 35.1

BABANKI VIRUS 3.6 42.6

WESTERN EQUINE
ENCEPHALITIS VIRUS
12.7 31.2

SINDBIS VIRUS 10.4 30.4

VENEZUELAN
EQUINE... 13.9 30.5

HEPATITIS E VIRUS .1 55.6

Global alignment Local alignment
% SIMILARITY

Fig. (3). Global/local alignment of the RNA depend., RNA polymerase seq., of SARS-CoV2.

Multiple Sequence Alignment of RNA-dependent RNA Polymerase

Sequences of SARS-CoV2 and the viral Study Species from Bat Virome
Similar to this, multiple sequence alignment of the RNA dependent RNA
polymerase sequences revealed that SARS-COV2-like active site residues were
conserved in at least half of the research species (Figs. 4 and 5). To better analyze
Bioinformatics Promise Smart Advances in Computing Communications and Informatics, Vol. 7 63

the connections between SARS-COV2 and the viral research species from bat
virome, recombination experiments could be carried out. The multiple sequence
alignments of RdRp sequences of SARS-CoV2 and the study species from bat
virome had the conserved amino acids.

SARS-CoV-2 LVY ALRHFDE NCDTL 145

Coronavirus 0
Enterovirus 0 SARS-CoV-2 IVGVLTLDNQOLNGNWYDFGOFIQTTPGSGVPVVDSYLS MPILTLTRALTAESHVDD 263
Parechovirus 0
Astrovirus 8 Coronavirus 0
Enterovirus 0
Norovirus 0 Parechovirus 0
Yellow TVNAPO KPSLDISLETVAID PAEARKVCYSAVLTNVKINDKCPST-GEAHL 367 Astrovirus 0
Dengue 0 Norovirus 0
Japanese 0 Yellow 389
Zika 0 Dengue 0
West 0 Japanese 0
Hepatitis 0 Zika 0
Chikungunya 0 West 0
Eastern TIYTEERILLRSWHLPNVFHLKGKTSFT RCNTIVSCEGYVVKKITISPGIYGKVDNLAS 303 Hepatitis 0
Western Chikungunya 0
TIYTEORSLLRSWHLPNVFHLKGKSNFT RCGTIVSCEGYVIKKITISPGLYGKVENLAS 303 Eastern ATDVSVDDAQK VGL -NQRIVVNGRTORNIN 375
Venezuelan TIYHEKRDLLRSWHL PSVF HLR GKQNYT RCETIVSCDGYVVKRIAISPGLYGKPSGYAA 305 Western ATDVSVDDAQK VGL -NQRIVVNGRTORNIN 375
Babanki 0 Venezuelan ATDVSVDDAQK VGL -NQRIVVNGRTORNIN 377
Sindbis 0 Babanki 0
KEILVTYNCCDDOYFNKKDWYDFVENPDILRVYANLGERVRQ --ALLKTVQICDAMANAG 203 Sindbis 0
SARS-CoV-2
Coronavirus 0 SARS-CoV-2 VLFSTVFPPTSFGPLVRFVDGVPFVWSTGYHFREL GVVHNQDVNLHSSRLSFKELLVY 377
Enterovirus 0 Coronavirus 0
Parechovirus 0 Enterovirus 0
Astrovirus 0 Parechovirus GIVTET-PIQPMYINTKTQIHKSPVYGAVEVK MGPAVLS 39
Norovirus 0 Astrovirus 8
Yellow EEENEGDNACKRTYSD RGWGNG 389 Norovirus 0
Yellow CAKSHSLFEVDQTKIQYVAQ LHV-GAKQENWNTDIKTLKFDALS 450
Dengue 0 0
Japanese 0 Dengue
Japanese 0
Zika 0 0
West 0 Zika
West 0
Hepatitis 0 Hepatitis 0
Chikungunya 0 Chikungunya 0
Eastern TMHREGFLSCKVTDTL RGERVSFPVCTYVPATICDQMTGIL 344 Eastern THKITSIYKKPGTQTIKK PAVENSFVIP QLNS-YGLDIGLRRRIKMLLEEKKK 475
Western TMHREGFLSCKVTDTL RGERVSFPVCTYVPATICDQMTGIL 344 Western TQKITSIYKKPGTQTIKK PAVENSFVIP RLTS-HGLDMGFRRRLKLLLEPTVK 475
Venezuelan TMHREGFLSCKVTDTL NGERVSFPVCTYVPATICDQMTGIL 346 Venezuelan RHKITSIYKRPOTQTIIK ONSDFHSFVLP RIGS-NTLEIGLRTRIRKMLEEHKE 477
Babanki 0 Babanki 0
Sindbis 0 Sindbis 0

Fig. (4). Multiple sequence alignment of RNA dependent RNA polymerase seq., of SARS-CoV2.

SARS-COV-2 A ADPAMHA SGT LLD 393 SARS-COV-2 RYNLPTMCDIRQLLFIWEV VDKY FDCYD 487
Coronavirus 0 Coronavirus 0
Enterovirus 0 Enterovirus 0
Parechovirus K SDPRLE 46 Parechovirus FREIFGINGI VDM K 96
Astrovirus 8 Astrovirus 30
Norovirus 0 Norovirus 0
Yellow GSQEAEFTGYGRATLECQVQTAVDF SNT IAEMEKESWIVOKQWAQDLTLP 501 Yellow PEDPVKLASIVKAS LEGKCGLNSVDSL EHEMWRSRADEINAILEENE 861
Dengue 0 Dengue 0
Japanese 0 Japanese 0
Zika 0
Zika 0 West 0
West 0 Hepatitis 0
Hepatitis 0 Chikungunya 0
Chikungunya 0 Eastern MCLKV HEICTEVYHKSISRRCTKTVTAIVSTLFYDKRMRTVNPCSD 870
Eastern P--APIITEADVAHLKGMQEEAEAVAEAEAVRA LP LPEVERETV EADIDLI 527 Western MCLKVHDICTEVYHKSISRRCTQTVTAIVSTLFYDKRMKTVNPCAD 870
Western P--APAITHADVEHLRGLOQEAEEVAAEEIRE LPS LPEIEKETV EAEVDLI 527 Venezuelan MCLKV HEICTQVFHKSISRRCTKSVTSVVSTLFYDKKMRTTNPKET 872
Venezuelan P--SPLITAEDVQEAKCAADEAKEVREAEELRA LP AADVEEPTL EADVDLM 529 Babanki 0
Babanki 0 Sindbis 0
Sindbis 0
SARS-COV-2 YPKCORAMPNMLRIMA SLVLARKHTTC 648
SARS-COV-2 NWAFQT 413 Coronavirus CORALPNMIRMIS AMILGSKHVTC 24
Coronavirus 0 Enterovirus YSGYDASLSPVWFRAL E LV L R E I 77
Enterovirus 0 Parechovirus YSQYDGSLSSMLLWEA VEVLAYCH 264
Parechovirus 58 Astrovirus 30
Astrovirus 25
Norovirus Norovirus 0
0
Yellow APCRIPVNVADOLTA AVNKGILV TVNPIASTNDDEVLIEVNPPFGDSYI 663
Yellow YKECEWPLTHTIGTSVEESDMFMPRSIGGPVSSHNHIP GYKVQTNGPWMQVPLEVKREAC 1058
Dengue 0 Dengue 0
Japanese 0 Japanese 0
Zika 0 Zika 0
West 0 West 0
Hepatitis 0
Chikungunya
Hepatitis 0
0
Eastern TAIPIPDFQALSESATIVYNERE FUNRYLHHIAINGGAINTDEEY YKV 656
Chikungunya 0
Western TAVPVQOFQALSESATIVFNEREFVNRYLHHIAINGGALNTDEEY YKT 656 Eastern YP GEFSATLEEWQAEHDAIMERILETPASSDV YQNKVRVCWAKALEPVLATAN 1023
Venezuelan HAIPVQOFQALSESATIVYNEREFVNRYLHHIATHGGALNTDEEY YKT 658 Western YS GDFTASLDDWQREHDAIMARVLDKPQTADV FQNKVNVCWAKALEPVLATAN 1023
Babanki 0 Venezuelan YP GNFTATIEEWQAEHDAIMRHILERPDPTDV FQNKANVCWAKALVPVLKTAG 1025
Sindbis 0 Babanki 0
Sindbis 0

Fig. (5). Multiple sequence alignment of RNA-dependent RNA polymerase seq.,of SARS-CoV2.

From Fig. (4 and 5), the conserved regions in the protein sequence could be found
and were represented by highlighting them in red color.
64 Advances in Computing Communications and Informatics, Vol. 7 Asraf et al.

Phylogenetic Analysis
The phylogenetic tree constructed for the RNA-dependent RNA polymerase
sequences of SARS-CoV2 and the study species from bat virome with 500
bootstrapping is shown in Fig. (6).

Fig. (6). Neighbor-joining phylogenetic tree of the RNA-dependent RNA polymerase sequences of SARS-
CoV2 and the viral study species with 500 bootstrapping.

From the global and local alignment of the RNA-dependent RNA polymerase of
the SARS-CoV2, it was found that the similarity in local alignment is more
compared to global alignment showing the presence of coding region in the
genome dispersedly. Among the study viruses, bat coronavirus and hepatitis E
virus had increased similarity upon aligning locally showing the dominance of the
RNA-dependent RNA polymerase region in the genes of other viruses.
From Fig. (6), it is observed that the RdRp sequences of SARS-CoV2 and
Enterovirus are more related compared to other study strains. The genome of
SARS-CoV2 shows increased similarity with Bat coronavirus compared to other
study species. The genome of SARS-CoV2 seems to be closely related to the
Hepatitis E virus and Bat astrovirus. The RdRp of SARS-CoV2 was more similar
to Bat coronavirus compared to other study species. The phylogenetic analysis of
the RdRp of SARS-COV2 revealed that SARS-CoV2 was closely related to
Enterovirus. From the multiple sequence alignment of the RdRp, it was found that
Asp760, Asp761, and Phe812 in the active site were conserved in almost half of
the study species. Hence the conserved regions of the RdRp could be analyzed for
characteristics of a potential drug target.
Bioinformatics Promise Smart Advances in Computing Communications and Informatics, Vol. 7 65

CONCLUSION AND FUTURE SCOPE

Life sciences researchers are under more pressure than ever to innovate quickly.
Large, multidimensional, and integrated datasets have the potential to speed up
scientific advances. Even though there is more data than ever available, very little
of it has been processed or studied. India’s healthcare system faces many risks as
a result of this pandemic, underscoring the necessity for encouraging hospitals to
transition from paper-based medical records to electronic medical-related data. It
is important to examine the requirements of both patients and those who provide
healthcare and Medicare services. In the future, it is anticipated that reliable data
management platforms and AI methods will make it possible to analyze vast
amounts of surveillance and infectious disease data efficiently and support
governmental organizations, healthcare providers, and medical professionals in
their response to disease. The recombination rates of both the genome and protein
sequences of SARS-CoV2 and the study species from bat virome could be further
analyzed to determine a better evolutionary relationship in them as well as to
identify better drug targets and vaccine epitopes.
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