Journal of Life Science and Biomedicine
J Life Sci Biomed, 10 (2): 17-20, 2020
Alignment of SARS-CoV-2 in comparison with
Mohamed Samy ABOUSENNA
PhD of Virology, Central Laboratory for Evaluation of Veterinary Biologics (CLEVB), Agricultural Research Center (ARC), Cairo, Egypt
Introduction. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is currently
declared as pandemic according to the WHO. It was initially detected in China and then
rapidly transmitted to most world territories. The SARS-CoV-2 has an ambiguous origin,
with unique properties, pathogenesis and transmission rate, thus making its prevention
and control a difficult task. Aim. In the present study, we investigated the origin hypotheses
through conducting multiple alignments and phylogenetic analysis for surface glycoprotein
and complete genome of SARS-CoV-2 in comparison with other coronaviruses of different
species. All the data used in this study were obtained from NCBI online database and
analyzed using Blast tool. The alignment and phylogenetic analysis of SARS-CoV-2 surface
coronavirus, Bat SARS-like coronavirus, SARS-CoV, BCoV, IBV, ECoV, MHV-JHM, MERS-
CoV, CCoV, HCoV-229E and FCOV indicated close identical matching to spike protein for
Bat coronavirus RaTG13 and Pangolin coronavirus isolate MP789. The similarity was 97.41%
and 96.67%, respectively. Also, multiple alignments of complete genome for SARS-CoV-2 and
Bat coronavirus RaTG13 showed a significant similarity of 96.11%. Recommendation.
Therefore, these relevant results strongly recommend the origin hypothesis of SARS-CoV-2
from Bat coronavirus RaTG13. The nature of evolution is considered to be natural selection.
Rec. 05 March 2020
Rev. 20 March 2020
Pub. 25 March 2020
Severe Acute Respiratory
Coronavirus Disease 2019,
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was recently detected and isolated in Wuhan
Province, China. The virus causes severe acute respiratory illness which is called COVID-19 (Coronavirus
Disease, 2019) . SARS-CoV-2 is the seventh coronavirus which infects humans; SARS-CoV, MERS-CoV, SARS-
CoV-2, HKU1, NL63, OC43, and 229E, while the recorded data till now demonstrate the severe cases of SARS-
CoV-2 not more than 10% and the mortality rate not more than 5 % [2, 3].
SARS-CoV-2 belongs to the family Coronaviridae in the order Nidovirales. It could be classified into four
genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus, whereas alpha- and
betacoronaviruses infect mammals (human coronavirus NL63 (HCoV-NL63), porcine transmissible
gastroenteritis coronavirus (TGEV), PEDV, porcine respiratory coronavirus (PRCV), SARS-CoV, MERS-CoV, bat
coronavirus HKU4, mouse hepatitis coronavirus (MHV), bovine coronavirus (BCoV), and human coronavirus
OC43). Gammacoronaviruses infect avian species e.g.; avian infectious bronchitis coronavirus (IBV) and
deltacoronaviruses infect both mammalian and avian species (porcine deltacoronavirus (PdCV).
Coronaviruses are large, enveloped, positive-stranded RNA viruses. The genome is surrounded by the
nucleocapsid protein (N) and further surrounded by an envelope. The viral envelope is associated with three
structural proteins: the envelope protein (E) and the membrane protein (M) are involved in virus assembly,
whereas the spike protein (S) binds the host cell receptors to mediate virus entry. Furthermore, the spike
protein is a critical determinant of viral host range, tissue tropism and a major inducer of host immune
responses, which is significant for developing vaccines in many species . It was recently confirmed that
SARS-CoV-2 uses the Spike protein (S) to bind human cell receptors to process the cell entry  like other
The present study aimed to investigate the origin hypothesis of SARS-CoV-2 through conducting spike
protein alignment and phylogenetic analysis for different coronaviruses in comparison with SARS-CoV-2.
Citation: Abousenna MS. Alignment of SARS-CoV-2 in comparison with other coronaviruses.
J Life Sci Biomed, 2020; 10(2): 17-20; DOI: