**1. Introduction**

According to the World Health Organization (WHO), incidences of pneumonia with an unknown cause were reported in many locations in late 2019 and early 2020 [1]. This pneumonia's pathogen was recognized as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [2] and was given the label coronavirus infectious disease (COVID-19).

SARS-CoV-2 infections affected more than 83 million known COVID-19 patients by the end of 2020, but significant progress had been achieved with the approval and implementation of vaccines and antibody treatments. These treatments target the infectious spike protein, although the advent of vigorous variations puts their effectiveness in danger (**Figure 1**) [3].

These fears have prompted an increase in viral DNA testing and sequencing in infected patients in terms of understanding the risk of transmission, virulence, and potential of variants to avoid modern vaccinations. The number of viral variants in New York City has risen alarmingly. As of March 30, 2021, the B.1.1.7 variant, first discovered in Great Britain (UK) for 26.2% of all the cases of coronavirus disease, and the B.1.526 variant, initially discovered in New York City, contributed to even more than 72% of cases, which were newly admitted (in 42.9%) [3]. The ability of variations to circumvent vaccine-induced immunity and cause asymptomatic infection (and thus viral transmission) or disease is of particular concern. Both repercussions are significant and must be evaluated separately.

Reliable laboratory testing is one of the top priorities for facilitating public actions. A reliable test is now the most efficient method for detecting patients in a large community, especially asymptomatic illnesses, identifying transmission pathways and hosts, evaluating the success of therapeutic options, and determining infection's eradication. As one of the most important instruments for monitoring, isolating, as well as diagnosing COVID-19 pandemics, each country should priorities investing in cutting-edge techniques and offering economic incentives for the implementation and verification of accurate COVID-19 diagnostics. To

**Figure 1.** *Structure of the SARS-CoV-19 variants.*

present, most existing examinations typically meet the expectations of mass testing examination, personal diagnosis, or variation detection; however, capability varies significantly between countries, regions, and races, mainly to socioeconomic inequalities. Because the pathogen of COVID-19 is recognized, as well as the genome, transmission channels, and host antigen for viral attachment, there are two types of tests presently offered: For the identification of viral antigens or host antibodies, there are two types of diagnostics: (1) nucleic-acid-based tests and (2) serology-based tests. Serological techniques identify antibodies found within blood serum and infectious antigens within tissues, discharge fluids, or eliminations by persons who have current or previous infections, whereas nucleic acid tests immediately investigate for viruses RNA via the throat and nose swabs taken from patients [4].

Many common areas in the SARS-CoV-2 genomes were selected as effective objectives for sample preparation in several PCR techniques, and they are used in the majority of COVID-19 molecular diagnoses around the world. According to the WHO [5], at least two targets should be used in clinical practice to avoid SARS-CoV-2 genetic mutation and cross-multiplication with the other COVID-19 viruses. For the construction of primers and probes, three portions that have been preserved (the E, N, and ORF1ab genes) are commonly chosen as standard objectives. Furthermore, sequencing the viral DNA aids in the detection of novel coronavirus variants that emerge over time. Newly developed portable or quantitative sequence alignment techniques, as opposed to classical sequence alignment methods, which are typically highly expensive, may offer accurate elevated diagnostics throughout pandemics.

### **1.1 Epidemiology of SARS-CoV-2 variants**

Coronaviruses have a nuclease enzyme that reduces the likelihood of replication failure in vitro by 15–20 times, resulting in a 10-fold reduced risk of virus mutation in vivo than influenza [6]. When variations with mutated genes infected the same victim [7], however, they gather alterations and produce greater variety through the recombination mechanism. SARS-CoV-2 [8] is considered to have formed as a result of recombination between different SARS-related coronaviruses, and recombination is still occurring among propagating SARS-CoV-2 variants [9], showing the challenges in detecting it based on the similarities among most sequences. As evidenced by the prevalence of C to U changes in specific dinucleotide situations, SARS-CoV-2 diversity is further supported by host-mediated transcriptional control by APOBEC and ADAR enzymes [10, 11].

Although that was initially thought that decreasing immunity would have been the reason for people's frequent reinfection with symptomatic widely accepted COVID-19 viruses [12], recent research suggests that genetic variation could also play a significant role in the absence of lengthy resistance after COVID-19 virus outbreaks [13]. HCoV-229E and HCoV-OC43 sequence data demonstrate a ladder-like phylogenetic evaluation topology over a 30-year period, which has been maintained with the incidence of novel variants going to spread through the global population at a slower rate than seasonal influenza, with pathogens separated from one point and time frequently evading neutralization by blood plasma from individuals infected numerous decades prior [14].

SARS-CoV-2 is thought to evolve at a rate between about 4\*10−4 and 2\*10−3 variations per codon per annum [15–17]. Even though the probability of synonymous variations influencing SARS-CoV-2 morphologic features must be discounted, zero

reviews of this concept happening inside the SARS-CoV-2 spikes genotype have been found. As a result, we refer to an NH2 mutation from the Wuhan-Hu-1 known sequences (GenBank accession: NC 045512.2) as a mutation in this Review.

Because new lineages are sometimes separated from some nucleotides, the classification of emerging SARS-CoV-2 genotypes based on organic evolution has proven difficult [18]. Because the majority of mutations have been identified in a variety of countries, and the number of viruses undergoing sequencing varies substantially between countries, geographical classification has proven difficult. The NextStrain and Phylogenetic Assignment of Named Global Outbreak (PANGO) genealogy [19] systems have been developed for control and prevention. The Phylogenetic Assignment of Named Global Outbreak genealogy approach is more popular and provides greater specificity. Sub-lineages are indicated by an alphabetical beginning as well as termination containing two to three digits interspersed with periods (such as B.1.1.7). However, because the method only supports three levels of hierarchy, the variant's parental relationship cannot be established by adding a new genealogy ending. The linkage of a virus may not always correlate to the changes in its components. For example, a virus may acquire new genetic alterations related to its physiological function without ever being associated with a recent linkage.

The very first evidence of SARS-CoV-2 genetic development evolutionary changes appeared in early 2020 when a unique viral variant with the spike variant D614G arose and spread rapidly to a prevalence of over 100% by June 2020 [20, 21]. By the end of 2020 and early 2021, plenty of variants with long-term mutations (most notably D614G) had been discovered, mostly but not exclusively in the spikes protein. B.1.1.7, a fast-growing species in England connected with an extremely large number of genetic changes, was reported on the virological.org conversation forum27 in December 2020. The first therapeutic specimen of this kind was obtained in late September 2020 in England, according to retrospective analysis.

Two further fast expanding links with significant amounts of genetic variations were found in South Africa within a month [16] and Brazil [22]. The frequency of the B.1.351 variant jumped from 11percentage points in October to 87% in December [23] in South Africa. The P.1 variety was detected in Manaus, Brazil, a town with a 75% infection rate in October 2020, but a spike in new cases began in November 2020 [24, 25]. Following that, the prevalence of a novel variant (B.1.617.2) increased from 2 percentage points around February 2021 to 87% in May 2021 in Maharashtra, India, which, like the rest of the country, experienced a significant increase in the number of cases [26]. Since then, the B.1.617.2 variety has expanded over a number of countries [27] and has shown to be much greater spreadable than that of the B.1.1.7 variant. It has a higher risk of causing disease than prior viral variation (**Figure 2**) [28].

Variants of concern (VOCs) are those that have spread widely and shown evidence of being more transmissible, causing more severe disease, and/or reducing neutralization by immunoglobulin produced during prior infection or vaccination, according to the World Health Organization (WHO), the US Centers for Disease Control and Prevention (CDC), and the COVID-19 Genome sequencing UK Consortium (COG-UK) [29]. Those that have not quite expanded as broadly include alterations comparable to those found in VOCs are of particular relevance (VOIs). On May 31, 2021, the WHO began using the Greek alphabet to classify VOCs and VOIs, with the current VOC classifications being Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (D.1) (B.1.617.2).

*Advances in Diagnosis and Treatment for SARS-CoV-2 Variants DOI: http://dx.doi.org/10.5772/intechopen.107846*

**Figure 2.** *Epidemiology of COVID-19 variants cases.*
