**7. Coronavirus and its new variants**

Epidemiologists may even decide to label it as 'Variant of Concern' (VOC), like the examples identified in Brazil, South Africa, and the UK. For months, scientists have been striving to work out what's changed in these variants, and what those changes mean. Because a variant spreading does not necessarily mean that it has an advantageous mutation. For example, a small number of people could, by chance, move a variant from one region to another, like tourists traveling back from popular vacation spots. This could cause that variant to start spreading in a new location even though there may be no significant change to the biology of the virus. This is called the 'Founder Effect'. On November 5th, 2020, the United Kingdom went into lockdown [4, 18]. But, despite having the same lockdown measures, infections in Kent, an area outside of London, were still rising. In early December, the overall drop in cases led the country to relax restrictions anyway and then this happened [5]. It was not until around this time that researchers realized that somewhere in Kent, the virus itself had changed. It was a new variant. It was more contagious and it was spreading. By the time scientists gave it a name called B.1.1.7, it had spread to most of southeast England [18]. Two months later it was in 30 other countries. Five months later, it was the most common form of the virus found in the United States [6]. Lately, more and more variants are emerging in various places around the world. XE is a new variant of omicron and it is first detected in the UK. After successful detection of the XE variant, W.H.O has issued a warning against XE. It has been suggested that the variant could be more transmissible than any Covid-19 strain so far. XE is a combination of recombinants of both sub-variants (BA.1 and BA.2) of Omicron. Understanding why a variant has emerged requires a combination of studies. Epidemiology can help detect and trace new variants and flag new or worrying patterns of infection. Meanwhile, lab

studies can start to pinpoint how the mutations are changing the properties of the virus [5, 18, 25]. Some variants are faster spreading like the D614G mutation, known to virologists as Doug. It spread widely in the early days of the pandemic and can be seen in almost all variants [2, 17]. It affects the spike protein that coronavirus particles use to penetrate cells. N501Y also known as Nelly, is another spike protein mutation that appears to be associated with increased transmissibility. This mutation has been detected in the B.1.1.7, B.1.351, and P.1 strains - all variants of concern [5, 26]. The worry of so-called 'immune escape' has also been indicated with another spike protein mutation, E484K or Eek. Eek has been spotted in B.1.351 and P.1, the variants detected in South Africa and Brazil. Lab studies early in 2021 showed that the variant could evade some virus-blocking antibodies, while trials in South Africa suggested that the variant reduced the efficacy of several vaccines [28, 29]. Despite these worries, the coronavirus is mutating very slowly compared to something like influenza and it seems like the vaccines developed so far will remain at least partly effective. It is very important to monitor and trace the emergence of variants and that is not always simple to do [3, 18]. Organizations like the COVID -19 genomics UK consortium or COG-UK, have stepped up their efforts to combine fast sequencing with efficient data sharing. COG-UK has already sequenced over 400,000 SARS-CoV-2 genomes [3–5]. Next step for researchers is the need to look forward to how these mutated strains of SARS CoV-2 could affect global vaccination efforts. Existing vaccines can be redesigned and combinations of vaccines are also being tested but it could be difficult to perform reliable clinical trials amid the ongoing vaccination programmes. Public health policies such as track and trace, social distancing, and vaccine rollouts are powerful tools to interrupt, transmit and keep tabs on new variants [17, 28, 30]. After all, every time the virus is prevented from spreading, it's also prevented from mutating, nipping new variants in the bud before they even have a chance to develop.

#### **Figure 1.**

*Diagrammatic representation of mutations in different regions of SARS CoV-2 giving rise to different variants. Amino acid substitutions are depicted in both structural and non-structural proteins of SARS CoV-2, which modify their affinity to ACE2 receptors, thus making them VOC.*

### *Perspective Chapter: Tracking Trails of SARS CoV-2 – Variants to Therapy DOI: http://dx.doi.org/10.5772/intechopen.106472*

The hotspots and the mechanism of replacement of amino acids that bring about mutations at specific points in the SP's and NSP's have been shown in **Figure 1**. S1 and NSPs are thus considered hotspots for mutations that may have high clinical relevance in terms of virulence, transmissibility, and host immune evasion. NSPs are mostly biocatalyst or catalytic proteins or enzymes that induce viral replication and methylation and may play a critical role in host responses to infection. These genes are encoded in two important groups, namely ORF1a (NSP1-11), and ORF1b (NSP12-16). NSP1 is a principal protein to antagonizes type I interferon induction in the host and benefits the replication of the virus itself. The variants of concern (VOCs) have impacted the global health significantly, especially in the later year of 2020. The major ones are Alpha variant (B.1.1.7), Beta (B.1.351), Gamma (P.1), Kappa and Delta (B.1.617.1 and B.1.617.2) (**Table 1**). **Figure 1** also tries to depict the important mutations in these VOCs, for example, the Alpha variant has an N501 mutation, N asparagine has been replaced with Y tyrosine, as well as K417 where the lysine K is replaced with asparagine N (**Figure 1**). Another emerging variant derived from B.1.1.7 also carries E484 mutation where the glutamic acid E is replaced with lysine K. Both Beta and Gamma variants have more substitutions other than N501. The Beta variant has E484, while the Gamma variant has the E484 and the K417 mutations. The latest variants Delta, and Kappa share two mutations E484 (glutamic acid E substituted by glutamine Q ) and L452 (leucine L altered by arginine R). Other than the two mutations above, Delta also harbors a unique mutation, T478 (threonine T replaced by lysine K) (**Figure 1**) [31].


#### **Table 1.**

*Different variants of coronavirus with scientific names.*

### **8. Variants and their effects on pathogenesis**

Coronavirus is a large family of viruses, which are found in humans and animals [32, 33]. These viruses have had two large-scale outbreaks in the past two decades the SARS virus in 2002 and the MERS (Middle East Respiratory Syndrome) virus in 2012 [34–36]. It's generally been considered that these coronaviruses could cause future disease outbreaks because they are known to be able to evolve with animals and then jump to humans as an intermediate host in SARS. Palm civets and raccoon dogs were identified as the intermediate [37, 38]. According to the current mortality index total cases worldwide are found at 52.3 Cr and deaths confirmed at 62.7 L [34, 39]. The top five nations in terms of deaths in order are the US, India, Mexico, Brazil, and Russia. The UK has a much smaller number of deaths in comparison to these five countries. The highest number of cases are found in the US approximately 8.29 Cr and deaths confirmed 10 L. Coronavirus spreads mainly by respiratory droplets, cough, and sneezing. The aerosol-carrying virus allows it to travel into nasal or all cavities and it can live on surfaces for hours and even up to a few days on some surfaces [32, 35]. Infected touch can transfer the virus to mucous membranes in the eyes, mouth, nose, and upper airway [34, 35]. With that, symptoms arise like the common cold, stuffy nose, headache, sore throat, and fever [40, 41]. It is within the mucosal epithelium of the upper GI tract where primary viral replication is thought to occur similar to SARS CoV-2 is able to get further into the human respiratory system and lung's epithelial cells [38, 42]. ACE-2 receptor interaction with SARS CoV-2 binds S protein to the ACE-2 receptor, this mechanism of binding is followed t in the same way in airway epithelial cells [37, 43, 44]. The host cells have proteases that break down proteins and these cleave spike protein, this process activates a protein to trigger the process of membrane fusion before injecting the viral genome into the host cell [45, 46]. This mechanism is similar to direct cellular entry that facilitates cell entry in the influenza virus. The virus may also enter the cell via endocytosis, where it is engulfed and surrounded by an area of the cell membrane [39, 47]. Further down it forms a vesicle inside the host cell where specific RNA and proteins are synthesized within the cytoplasm [46, 48]. Viral proteins are assembled with the blueprint of information contained within viral RNA using hosts cellular machinery specifically ER and Golgi apparatus with specific processes to form envelope glycoproteins [40, 48]. New variants are assembled by fusing to plasma membranes and released as vesicles via exocytic secretory processes. The stress is placed on cells by a viral infection and the interaction of the immune system with viral antigens presented by infected host cells leads to cell death [47, 49, 50]. During this process of cell death, multiple inflammatory mediators are released and create an inflammatory response leading to a buildup of mucus. Thickening and hyperplasia of cells within airways this inflammation causes irritation of cells lining airways, which leads to cough [42, 51, 52]. In the lower respiratory tract, the virus acts within the lungs to get into the trachea or windpipe this branch is further bifurcated into the left and right main bronchi these bronchi branch into lobar bronchi. Bronchi have three sub-branches here one on the right and two on left, these branches are further segmented into segmental bronchi [49, 51, 53]. The segmental bronchi further branches into respiratory bronchiole and after that respiratory bronchiole culminate in tiny alveoli. COVID-19 infection may lead to inflamed alveolar walls, that get thickened and fill the alveolus with fluid, which can impair their ability to exchange gases [29, 40]. This can lead to the symptom of shortness of breath in some people infected with COVID-19 [38, 39].

*Perspective Chapter: Tracking Trails of SARS CoV-2 – Variants to Therapy DOI: http://dx.doi.org/10.5772/intechopen.106472*

#### **Figure 2.**

*A summarized cycle of SARS CoV-2 depicting (a) different parts of SARS CoV-2 virus (S = spike, M = membrane, E = envelope, viral mRNA, N = nuclear material) being represented on antigen presenting cells (APC) and T helper cells, (B) further initiating the immune responses in the human body that may be cell-mediated or antibody-mediated/innate or adaptive immunity (C) shows the potential immune evasion mechanisms. This shows a common evasion shared by all three respiratory viruses (SARS-CoV, MERS-CoV, and SARS-CoV-2). (1 and 2) shows hindrance created by coronaviruses during RNA sensing, starting the innate immune response and interferon (IFN-1) production. (3) shows the STAT1/2 activation leading to downstream activation of IFN/IFNAR (4) as sown by blocking marks. This blocking or oppression results in the decrease of interferon production thus impacting the adaptive immune response. Thus, helping the persistence of the virus in the host cells thus aggravates immune responses which may lead to immune exhaustion and immune suppression. (D) Shows the type and severity of disease manifestations inside the human host (E) indicates vaccine as the only available therapy which is helping in controlling this fatal viral infection.*

Viruses can lead to an exaggerated immune response with a huge release of proinflammatory mediators causing, which is known as a cytokine storm or cytokine release syndrome. Cytokines are small proteins involved in cell signaling and crucial in mediating immune responses [39, 52]. The cascade of inflammatory mediators causes an uncontrolled systemic inflammatory response, which leads to acute respiratory distress syndrome or ARDS is the rapid and widespread inflammation of the lungs [47, 48]. ARDS causes epithelial and endothelial cells of the lungs to secrete inflammatory mediators, which fill the alveoli and allow these inflammatory signaling cells to recruit other cells of the immune system into the alveoli [50]. It further amplifies the problem and systemic inflammatory state causing increased capillary permeability, resulting in more fluid entering in alveoli causing pulmonary e dema [39, 50, 54]. Compounding the problem overall this pathological process severely impairs the ability of the lungs to exchange oxygen and carbon dioxide. This whole cycle of SARS CoV-2 invasion in general, pathogenesis, disease outcome, and current therapy has been illustrated in **Figure 2**.

### **9. Available therapy**

COVID-19 is one virus that causes serious breathing difficulties other than common flu-like symptoms. Patients who have trouble breathing may be given supplemental oxygen, if the oxygen alone is insufficient to help the patient breathe then the patients are put on mechanical ventilation such as BiPAP, and in some situations, they may need to intubate and oxygenate the patient through conventional ventilators [37, 53]. Individual treatment depends heavily on their health condition and the resources available at a time. Remdesivir is an antiviral drug, which disrupts the virus's ability to replicate and spread within the body [55]. Remdesivir specifically is recommended for patients, who have been hospitalized and require oxygen but are not on mechanical ventilation. Globally remdesivir is in short supply and many health institutions have very limited quantities of it. Dexamethasone is a corticosteroid drug that makes adjustments to how the immune system regulates itself [55, 56]. Dexamethasone or other glucocorticoids similar to it can be used in patients, who need oxygen and can be used on patients who are on mechanical ventilation or non-mechanical ventilation [57]. However, patients who are not on supplemental oxygen are not recommended to take dexamethasone as the side effects of the drug may worsen their condition [41, 54, 58]. There have been some proposed treatment solutions like the use of blood plasma of patients, who have recovered from COVID-19 also called convalescent plasma [58, 59]. But this therapy could not find much success in seriously sick patients with COVID-19. In the spring of 2020, there was a lot of news coverage regarding the use of chloroquine and hydroxychloroquine to treat severe covid-19 patients [23, 60]. In August of 2020, the National Institute of Health issued a statement that recommended against using these drugs as initial trials in Covid-19 had either shown no benefit at all or had led to worst outcomes for patients due to drugs with dangerous side effects [59, 61, 62]. In 2021 India has begun to roll out an antibody cocktail drug therapy for COVID-19 patients and a similar therapy was used to treat former US president, Sir Donald Trump. This was a cocktail of two drugs, casirivimab and imdevimab [63]. The cocktail therapy claims to reduce hospitalization and death in Covid-19 patients by 70%. Each patient's dose is 1200 mg (600 mg of casirivimab and 600 mg of imdevimab) and the price of each patient's dose will be around 60,000 rupees [63–66]. Majority of these drugs are a recipe of monoclonal or artificial antibodies that are generated by cloning a unique white blood cell [67]. These amalgamated antibodies are designed in such a way that they can well bind to the spike protein of SARS CoV-2 and fight against the infection. But the effectiveness of these antibodies is limited to Covid-19 patients with mild to moderate symptoms [64, 65, 68]. Its effectiveness shows best when given during the first seven days of the infection when the virus is multiplying. Thus the viral entry at this time point is ceased. This therapy is not advised for severe Covid-19 patients, who require oxygen therapy [54, 56, 68].

## **10. Vaccine against SARS CoV-2 and its efficacy**

Researchers are racing towards the goal of delivering a safe and effective vaccine that could curb COVID-19 [69]. Production and scale-up for some of the vaccines have already started. New technologies are genetic vaccines and viral vector vaccines [70]. A lot of investment in them has especially focused on their potential to combat emerging infectious diseases and COVID-19 is putting that potential to test [15, 71]. Scientists developed a successful influenza vaccine was in 1953 where they injected viruses into fertilized eggs, which were then incubated to allow viral replication within the eggs [72]. These replicated viruses are then explored for developing two classical vaccine formulations, where the virus is either weakened (Live attenuated

## *Perspective Chapter: Tracking Trails of SARS CoV-2 – Variants to Therapy DOI: http://dx.doi.org/10.5772/intechopen.106472*

virus) or killed (Whole inactivated virus) live attenuated and whole inactivated virus vaccines. These are [34, 70, 72]. These approaches are still in use today, although different cell cultures have replaced the use of eggs. At the current time, vaccinology has introduced multiple other approaches to develop vaccines [71]. This has been summarized in **Figure 3**. Major types of vaccines being deployed against COVID-19 are genetic vaccines, protein subunits, virus-like particles, viral vector vaccines, live attenuated viruses, and whole inactivated virus vaccines [70, 73]. Because of previous research on SARS and MERS, researchers only focus initial attention on the S protein of the SARS CoV-2 virus that is necessary for viral entry into human cells [35, 74]. So, a vaccine that exposes the immune system to just a spike should induce a protective response and that is the strategy behind the majority of COVID-19 vaccines. A comparison between conventional vaccines (that contain the whole virus) and genetic vaccines is interesting. Researchers can take genetic material either as m-RNA or DNA, that codes spike protein and explore this for vaccine development [75]. Two types of genetic vaccines are being investigated for COVID-19, i.e. m-RNA and DNA vaccines. mRNA needs to reach the cytoplasm of host cells, while DNA needs to enter the nucleus. Then this genetic material gets taken up by cell machinery, and cells express spike protein [74, 75]. These spike proteins are recognized by the immune system, hopefully stimulating a protective response. Naked mRNA cannot easily cross cell membranes passively, and it's very susceptible to degradation [32, 43]. In vaccines, mRNA coding for the spike is encased in small carrier molecules called lipid nanoparticles [44, 75]. The goal is to induce immunity against the target antigen, the added genetic cargo. But these vaccines may also induce immunity to the vector itself and viruses used as vectors are attenuated or weakened, so they cannot cause disease. A lot of different viruses have been developed as vectors, and they can be broadly categorized into two types, replication-defective and replication-competent [74, 76]. A very popular choice among potential COVID-19 vaccines is adenoviruses as these viruses are common pathogens that typically cause mild cold or flu-like symptoms [77].

**Figure 3.**

*The diagrammatical representation shows the different types of vaccines against COVID-19.*

Lots of vaccines with adenovirus vector carries DNA coding for the spike to host cells., but it does not display on its surface. Once the virus infects a host cell, it delivers DNA to the nucleus, cells machinery expresses spikes using this DNA which is to genetic vaccines [77, 78]. Adenovirus vectors are replication defective, after the virus infects a cell no more viruses are produced [78]. Replication competent virus vectors used recombinant vesicular stomatitis virus. The wild-type VSV is usually asymptomatic in humans or it causes a mild flu-like illness. Scientists attempted to replace part of the RNA sequence with spike coding RNA of the virus genome [32, 40, 77]. Once the virus (rVSV) infects the host cell, cell machinery starts expressing a spike. This phenomenon mimics a real viral attack more closely [44, 78]. Adenovirus vectors, which are much further ahead in COVID-19 trials, have never been used in an FDAapproved vaccine and there are likewise no FDA-approved DNA or RNA vaccines.
