A Comprehensive Report on SARS-CoV-2 Variants and Their Implications

This report provides a comprehensive analysis of the SARS-CoV-2 virus, also known as the coronavirus, focusing on its variants and their implications. It begins with an acknowledgement of the research's support and an abstract summarizing the study's scope, which encompasses the virus's history, pathogenicity, and the impact of mutations. The report includes a detailed literature review exploring phylogenetic analysis of structural proteins (Spike, Membrane, Envelope, and Nucleocapsid), multiple sequence analysis, and the effects of mutations on vaccine efficacy, pathogenicity, epidemiology, and diagnosis. It also examines the structural differences between variant proteins. The research methodology and results are presented, followed by findings, discussion, and conclusions. The report aims to determine the impact of SARS-CoV-2 variants' mutations on pathogenicity, diagnosis, and vaccines, addressing specific research questions related to protein analysis, mutation effects, and vaccine efficacy, ultimately contributing to a better understanding of the virus and its variants.

CORONAVIRUS

ACKNOWLEDGEMENT
In this, I want to show my gratitude and also express my thanks to professor as well as to
my teacher and other lecturer who provide me this golden opportunity and also, they help me
with every angle by giving their time for assisting me in this research. I am really thankful to my
teacher and my friend who supported me with every dimension in this specific topic.

ABSTRACT
As per this, the particular research topic is about the recent ongoing issue which change
the paradigm of the worldwide. This issue is biological in nature and named is coronavirus. This
is also known as the COVID-19. In this, the corona virus uses to change the dimension of world.
Now a day, this virus is more population collecting criteria and this virus infect up to maximum
people and formulate the condition of threat. This virus is called as deadly virus. As per this, this
virus has their history and background that cause number of situations in past. Their pathogen-
city is a vital factor which is create number of issues related with health. This virus is originated
in 2019 and they called as COVID-19. There are number of factor and their pathophysiology
alter the physiology of human body and create the situations of illness. This virus is
communicable in nature and they have high rate of spread rate. In this, there variability and their
variant are discussed with their pathogen-city, diagnose and their vaccination process.

Table of Contents
ACKNOWLEDGEMENT...............................................................................................................2
ABSTRACT.....................................................................................................................................3
INTRODUCTION...........................................................................................................................1
RESEARCH AIM............................................................................................................................2
RESEARCH OBJECTIVE..............................................................................................................3
RESEARCH QUESTION................................................................................................................3
RATIONALE OF THE RESEARCH..............................................................................................3
SIGNIFICANCE OF THE RESEARCH.........................................................................................4
SUMMARY OF THE CHAPTER...................................................................................................4
LITERATURE REVIEW................................................................................................................5
Phylogenetic analysis of the four various types of structural protein (Spike, Membrane,
Envelope, and Nucleocapsid).................................................................................................5
The multiple sequence analysis of the proteins......................................................................6
The effect and impact of the variance mutation on vaccine efficacy.....................................8
Impact of the mutation on pathogen-city, epidemiology and diagnosis.................................9
Factors affecting the efficacy of vaccine..............................................................................11
Structural difference between variant protein (S, E, M & N)..............................................13
Structure of E protein...........................................................................................................14
Structure of M protein..........................................................................................................15
Structure of N protein...........................................................................................................15
RESEARCH METHODOLOGY...................................................................................................16
RESULTS......................................................................................................................................19
FINDING, DISCUSSION AND CONCLUSION.........................................................................23
REFERENCES..............................................................................................................................26

INTRODUCTION
In this, the SARS is defined as the severe acute respiratory syndrome which is caused by
the factor which is associated with the coronavirus. This is being well identified that this disease
is usually caused by number of factors. In this, the SARS is an airborne disease which is
communicable in nature and they are transferred from one individual to other by the water
droplet or small droplet of saliva in the similar way to the cold and influenza. This all are the first
severe and this can readily transmissible in the aspect of new disease to emerge in the current
time (Balasubramanian and et. al., 2020). They have clear capacity to spread to the number of
people along with the international air travel and this can gather maximum number of infections
by their virus. As per this, the number of patients is identified as the SARS which is previously
for the health adults age 25 year to 70 years. The case of fatality among person with the proper
illness which is define the case definition for the condition and suspected case of SARS is in
around 3 percent. The SARS is usually having number of variants which is identified in
numerous years. This all started with a specific country and after that they came at the point of
pandemic. This is also stated that the SARS is a viral respiratory disease which is originated
from the zoonotic origin caused by the severe acute respiratory syndrome coronavirus. This is
also mentioned like SARS-CoV or SARS-CoV-1. The first identified strain which is provide the
SARS for the coronavirus species such as severe acute respiratory syndrome which is related
with the coronavirus. This syndrome is usually caused the 2002-2004 which is based on the
severe acute respiratory syndrome. As per previous identified research this is well analyse that
there is various Chinese scientist traced the virus which help me to go through the intermediary
of the Asian palm civets which is usually determined the horseshoe bat in the town of Yunnan
(Clancy and et. al., 2020).
There are number of variants which is used to follow the various number of sequences.
As per this, they are used to create various enormous function in body. Such as the whole virus
which is used to replicate including the factor of SARS-CoV-2. In context with this, they take
time of evolve. When a virus replicates or make copies of itself. Then it will create number of
factors such as they use to choose the copies of itself. It sometime changes the factor of covid in
the ratio of normal bit. These kinds of factor are used to cause the mutation. There are number of
new and more mutant. The mutation is referred as the variant of the original virus. As per this
they follow sequence of the variant in the different countries. This kind of the changes are
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undergoing and create a rapid mutation and formulate various form of covid. In this, most of the
viral mutation have a little to no impact on the virus ability to cause various number of infections
which is used to formulate disease. This all aspect is depending on the various changes. This all
study is held under taking the aspect of UK, Brazil and South Africa (Fioranelli and et. al.,
2020).
In another aspect, in December 2019 there is another kind of strain which is well
identified as the severe acute respiratory syndrome which is coronavirus 2 called as SARS-CoV-
2. As per this, the new strain causes to the coronavirus disease which is established with the
2019. There is various disease which is brought about the pandemic of the COVID-19. As per
this, there are various number of factors which is associated with this. The primary route of
transmission for the SARS-CoV is the contact of the membrane of mucus membrane with the
factor with respiratory droplets or fomites (Han and et. al., 2020). In this context, the diarrhoea is
common with the people with the SARS with mode of faecal route. They do not be common
mode of appear in order to create the transmission. There are various basic chapter of the
reproduction number of SARS-CoV, Ro which is lies in the range of from 2 to 4 which is used to
depend on the various number of analysis (He and et. al., 2020). This all-control measure which
is introduced in order to reduce the in the April 2003 and this lies in the range of R to 0.4. The
virus that caused the COVID-19 is the variant of the SARS family. As doing comparison from
other this is identified as the recent virus us more transmissible than the wild type of SARS-
CoV-2and this was detected and came in the origin at November 2020. This is started to the
begin with quickly by spreading by mid-December and this all are corrected with the significant
enhancement in the SARS. This is all increase is the process of through which has to be partly
because of one and more. This all are mutational in nature. As per this, the virus used to grow
through the spike protein. This type of variant is not notable for having the more alteration in the
gene and the DNA of the virus and they change their DNA and turn themselves into the deadlier
virus (Khan and et. al., 2020). As per this, they are used to take various protein in this to form
various course of action. In this, the surface protein, membrane protein, and envelope protein and
nucleocapsid protein are used to understand the topic of coronavirus. This all variants which
show the upcoming nature that may be from the various such as UK and Brazil and so on.
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RESEARCH AIM
To determine the impact of SARS CoV-2 variants’ mutation on pathogenicity, diagnosis
and vaccine.
RESEARCH OBJECTIVE
 To perform the phylogenetic analysis of the four various types of structural protein
(Spike, Membrane, Envelope, and Nucleocapsid).
 To perform the multiple sequence analysis of the proteins.
 To determine the effect and impact of variance mutation on vaccine efficacy.
 To compare the impact of mutation on pathogenicity, epidemiology, and diagnosis.
 Analyse how some mutations affect the efficacy of the vaccine.
 Analyse the structural difference between the variants’ proteins (S, E, M & N).
RESEARCH QUESTION
 What are the phylogenetic analysis of the four various types of structural protein (Spike,
Membrane, Envelope, and Nucleocapsid)?
 What are the multiple sequence analysis of the proteins?
 What are the effect and impact of variance mutation on vaccine efficacy?
 What are the impact of mutation on pathogenicity, epidemiology, and diagnosis?
 How some mutations affect the efficacy of the vaccine?
 What are the structural difference between the variants’ proteins (S, E, M & N)?
RATIONALE OF THE RESEARCH
In this, the main theme is to choosing this topic is to examine and evaluate the various
cause and outcome. There are number of factors which is associated with the topic. As per this,
the topic state about the various scenario of coronavirus and this help to know their implications.
This topic is help to study about the phylogenetic analysis of the four various types of structural
protein (Spike, Membrane, Envelope, and Nucleocapsid) and in this it helps analyse the multiple
protein. As per this, the overall study helps to evaluate the measurement which is related with the
personal and professional growth and development. There are number of view point which is
helpful in this. Some of the expert share their view due the recent factor which create various
hindrance in the system of living and the pattern of life. They have number of variants which
show progress growth in their unit. Moreover, some the analysis which is relatable in this are
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their various mutant which is growing now day and may affect a huge population. Usually, their
other species is also show the crown like structure and inhibit the other approach which is
tremendous and have ability to control. However, the study of the various mutant of coronavirus
uplift the knowledge and skill. This help in the development of sound professional career and in
the aspect of future long perspective along with this code of effectiveness which help in other
ways to cope in find productive loop. This can create the sense of process and their limitation
and help to create the matter of various issue. In this, the proper aspect which is help to
determine the issue and eradicate this by using the proper analysis of problem.
SIGNIFICANCE OF THE RESEARCH
In this, there are number of factors which is associated with this and cause various issue
which associated with this topic. This research indicates various of outline and outlook for the
causes and their majority of theme. The effect and impact of the variance mutation on the
vaccine and their efficacy are well discussing. This is some of the objective in which the research
is conducted. Usually, this research helps to identify various impact and effect which is studied
and analyse the way by measuring the mutation on their pathogenicity, epidemiology and
diagnosis. This all study used to provide effective knowledge and skill about the topic and this
approach is helpful for the researching about the theme and aim. The main importance of this
research is to provide the knowledge which is related with the topic. As per this, there are
various of determinants of the relevant point in order the possible ways to reduce the proper rate
of impact and their phylogenetic structure which is help to know the structure protein which is
called as spike protein membrane, envelop and nucleocapsid. Some the factor which is essential
in this are study about the variant of protein which show the numeric data their impact in other
population.
SUMMARY OF THE CHAPTER
This topic state about the various aspect of coronavirus such as it states about the number
of phylogenetic structures of the different type of structural protein which is spike membrane,
envelop and also a sensitive protein which is defined as the nucleocapsid. In this, the summarised
way which is show the condition such as it is used to create the sequence which is useful in the
analysis of protein. In this, they are used to know the other segment of factor which is stated and
overviews. In this, the evaluation is based on the effect and impact of the variance which help to
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build to the mutation on the effectively. There are number of mutational techniques which help
to follow the pathogenicity which is help in the epidemiology, and help in the diagnosis. While
communicating with this, they used to create proper vaccine which is important for their various
variant. As per this, the affectivity of the vaccine which may be decreased due to this. In this
section of work, the structural and combinational differences are allowed in ways which help to
put the diversification in number of variant proteins. So, the overall coronavirus is studied as per
base of their protein and other aspect of vaccination while formulating and what are the other
factor which is associated with this. This research is conducted over a year or many numbers of
time zone. This also provide proper control behaviour to manage the flow of protein.
LITERATURE REVIEW
Phylogenetic analysis of the four various types of structural protein (Spike, Membrane,
Envelope, and Nucleocapsid)
The phylogeneticity is defined as the development and diversification of a species which
has proper group of organisms and they are used to provide the feature of an organism. In this
scenario this all aspect is based on the protein which have significant structure and they have
proper trait and method. The nomenclature of the protein is based on their species and their
nature. As per this, the causative agent which is well determined as a novel RNA virus of the
family which is stated as the coronviridae and this is subsequently designated as the SARS-CoV-
2. This all are high level of protein. This is helpful in the factor of outbreak which is severe acute
respiratory syndrome which is extend between the human which is associated with the 2002 and
2004. In this, the previous studies are used to analyse the SARS-CoV-2 genome which is helpful
in the human between 2002 and 2004. This all aspect is used to made the epidemic and estimated
at the time of early month. This is in order to make a hypothesis which is used to show the
SARS-CoV-2 which may undergone on a period of cryptic transmission is asymptomatic or
mildly symptomatic which is caused as the unit and identified the cluster report. SARS-CoV-2
has spread which is throughout the world in this there are ongoing pandemic. As per this, the
SARS-CoV-2 which is associated with the Beta coronavirus belonging from the coronaviridae
family. In this, the coronavirus is enveloped in the positive sense which is associated with RNA
virus with the large factor and create the non-segmented genome. This all include the five major
open reading frame such as ORF1a, ORF1ab and these all four structural proteins which is
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associated with the plus a number of accessory gene. The first two overlapping ORFs which is
located at the end of 5' prime. In this, there are various viral RNA are involved which is used to
occupy about the third of the genome and encode the protein which are autoproteolytically
processed which is comes under the section of 16 non-structural proteins. There are number of
interactions among the several SARS-CoV-2 which is used to define the non-RNA replication
and transcription. In this, the number of interactions is used and show the approach which is
related with the RNA replication and transcription. The human interaction which is accessible
among the SARS-CoV-2 which show the non-structural and combination of human protein. The
third end point which is fragile in nature and show 3 prime factors from the genome which is
viral in nature that encode the major component show the structural protein such as spike,
envelope, membrane and nucleocapsid. That all are required for the structure base scenario in the
viral particle. The coronavirus which is associated with S protein which is trimeric glycoprotein
which that is belong to the class one fusion of test. This allow to viral entry by attaching the S1
subunit which is associated with the host cell receptor that is angiotensin converting enzyme two.
By this segment the S1 receptor binding domain. This all process requires the factor of S protein
which show the function of priming by host proteases such bas TMPRSS2 in the form of rupture
site such as S1/S2 which show the data of poly basic such as motif at the S1 and S2 boundary.
The E protein which is less abundant protein which show the essential assembly and as per this
there are various interaction with the M protein. This all protein is associated with the critical
aspect of the viral life cycle and this lacking the e protein. Some of the make promising vaccine
for the candidate. As per this, they are used to show the effect which is ordinary in nature and
this all variant are used show the numerous of factor that is associated with the spike protein and
this is originated from the UK.
The multiple sequence analysis of the proteins
There are number of multiple sequence alignment called as MSA which is defined as the
method which is refer for the solution of alignment which is related to the sequences. As per this,
they are used to taking the account which is evolutionary events such as mutation, insertion,
deletion and rearrangement which is comes under the certain condition. These methods are used
in such a way which is usually applied to show the faith of DNA, RNA or a protein sequence.
The multiple theory is used in such a way which is analyse the model or a method which show
the biological method. There are number of most scientific paper and survey show the time and
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indeed. Despite of a large number of in silico analyse depend on the MSA method. These
include domain analysis which show the factor of domain analysis, phylogenetic reconstruction
which is depend on the motif finding and a whole range of other applications, extensively used to
provide the range of applications and this is well described.
Multiple sequence analysis which is used to show the important modelling tool which is
associated with the development that is required for the addressing a complex situation which
help to provide the collaboration of computational and biological issue. In this, the computation
of an accurate multiple sequence analysis shows the long-term factor which is known by NP
complete problem, situation that explain why this alteration method have been developed these
past three decades. The multiple sequence analysis shows the method and their application which
is show the several review.
In addition to this, the MSA show the various number of results on the basis of 10 amino
acids as per the acid sequence which is associated with the 10 amino acid. The M protein which
is comes under the form the various coronavirus (4 SARS-associated and 6 other known). The
model is basically used in the profile of HMM (hidden Markov model). This model shows the
various training was implemented through the SAHMM which is called as the self-adapting
hidden Markov model. This software is developing by number of authors for their safety and to
analyse the sequentially pattern of protein.
Some of the researching unit evaluate the protein sequence analysis of coronavirus such
as they used to provide the following sequence for coronavirus which is included such as:
Amino acid composition analysis: In this, the use of single sequence, multi-sequence analysis
and other techniques which help to provide to analyse the component of amino acid composition
analysis.
Protein motif prediction: In this, the motif amino acid which comes the sequence pattern that
help to stabilise the signature of the protein family and this show the vital important biological
significance. This can be predicted which show the presence of motif protein that analyse the
protein function.
Signal peptide prediction: This all well analyse the signal peptide which is used to follow the
section of the N terminus of most of the formulation of synthesize protein and this help to
contribute the protein which show the presence of transport and hidden Markov model which
help to provide the channel of variety for the cell sequence.
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