**4. Coronavirinae: severe acute respiratory syndrome-2 (SARS-2) and corona virus disease-19 (COVID-19)**

As mentioned before, Coronavirinae subfamily is categorized into four geniuses, known as alpha-coronavirus, beta-coronavirus, gamma-coronavirus and deltacoronavirus. The beta-coronavirus, in particular, has four lineages (A, B, C, and D) [62]. The lineage B of beta-coronavirus has a subgenus known as Sarbrcovirus under which SARS-CoV-2 goes [63]. Moreover, (novel coronavirus) or (Severe Acute Respiratory Syndrome Coronavirus-2) (SARS-CoV-2) is known as the causative microorganism associated with coronavirus disease-2019 (COVID-19). COVID-19-suffered patients are manifested with respiratory illnesses examples of which are pneumonia and breathing failure [61].

### **5. Country-wise genomic sequencing of SARS-CoV-2**

Sequencing the genomic materials helps to discover the identity of the causative microorganism. Continues sequencing of the genomic materials is essential to discover changes that may happen during transcription and transmission process of the microorganism genomic materials. Utilizing this information helps in studying the nature of the causative agent whether it is altered or not and if these changes help determine severity of the infection and making right decisions to reduce the impact of the outbreak on several aspects of life consequently.

First of all, a case of pneumonia of unidentified cause has been registered in China, Hubei Province, Wuhan City (December 2019). Additional evaluation for these incidences was conducted to detect the pneumonia causal microorganism [64, 65]. The isolated virus identified and named as (SARS-CoV-2) after genomic characterization by next-generation sequencing (NGS) of the complete sequence has been carried out [66]. The genomic analysis of the virus showed that it is an enveloped RNA virus (sized of 29,903 bp). The phylogenetic sequence analysis

#### *Whole Genome Sequencing: A Powerful Tool for Understanding the Diversity of Genotypes… DOI: http://dx.doi.org/10.5772/intechopen.96260*

displayed that the virus categorized under the subgenus Sarbecovirus of the genus beta-coronavirus and to the Coronaviridae family. Moreover, it was found that around 87.5 percent of genomic material was similar two bat-derived SARS-like CoV strains (bat-SL-CoVZC45 and bat-SL-CoVZXC21) commonly affected humans, including the virus that contributed to the outbreak of SARS-CoV-1 (2003) [62].

The Government of India has reviewed and introduced multi-sectoral initiatives to address this emerging public health problem following the first SARS-CoV-2 study from China. They started with monitoring country boarders at 21 international airports, strengthening state-level surveillance systems and preparedness in designated hospitals for the management of clinical cases. The reported and confirmed cases in India (January, 2020) were then sequenced (next-generation sequencing). The phylogenic analysis, compared with other published SARS-CoV-2 sequence in the database, were carried out to monitor and understand their relationships. The sequences of two out the first three confirmed cases in India were found to be high (about 99.98 percent) identity with Wuhan seafood market pneumonia virus (accession number: NC 045512). The phylogenetic analysis displayed that there were two distinct introductions to India. Therefore, continuous surveillance of the sequences and review shall be crucial to consider the genetic evolution and substitution rates of SARS-CoV-2 from the affected countries [60].

In Bangladesh, the first three cases were detected (March, 2020). However, the Bangladeshi complete genome sequence of novel coronavirus (SARS-CoV-2) isolate was accomplished by Illumina iSeq100 sequencer (April, 2020). Findings from these results showed that 9 mutations in the genome of this sample, compared to the Wuhan strain, reference genome (GenBank accession no. MN908947.3) [67].

In Ecuador, the first reported cases of COVID-19, which was on March, 2020 for a traveler came from Netherlands, and the three other confirmed cases were gnomically sequenced using the MinION platform (Oxford Nanopore Technologies) and ARTIC network protocols respectively. Results from these studies showed that the cases in Ecuador transmitted from three different European countries. The sequences of the confirmed cases in Ecuador were found to have high similarity (99.68 percent) with Wuhan strain reference case (GenBank accession number MN908947). The information discussed in this section is summarized in **Table 1** [68].

Numerous countries all over the world have also sequenced the viral genomic material of confirmed COVID-19 cases and have compared their results with reference cases sequence in China such as Nepal, Australia, USA and Turkey etc.


#### **Table 1.**

*Genomic analysis of COVID-19 confirmed cases from several countries.*
