The mutation and diversity
Since the outbreak of SARS-CoV-2 in China, numerous genome sequence data of the virus have been generated. A study with 7666 public genomic data sets identified 198 recurrent mutations in the SARS-CoV-2 genome [3]. Majority of the mutation is located in Orf1ab encoding Nsp6, Nsp11, Nsp13, and spike protein. The mutation rate of SARS-CoV-2 is approximately 10–6 nucleotides per site per cell, which is similar to SARS-CoV or other RNA viruses [13].
The spike (S) protein, which is projected outward on the surface of the virion is the very important pathogenic determinant. The S protein has two subunits, S1 and S2. The S1 binds on angiotensin-converting enzyme 2 (ACE2), the host cell receptor, and the S2 mediates membrane fusion. The receptor-binding domain (RBD) of S1 binds ACE2. The Cryo-electron microscopic structure of the spike protein of SARS-CoV-2 has been determined at 3.5°A [15]. The study showed SARS-CoV-2 S protein has higher affinity to ACE2 compared to that of SARS-CoV. The mutation at 614 position in the S protein of SARS-CoV-2 from aspartic acid to glycine (D614G) was identified to reduce S1 shedding and increases infectivity [17]. The sequence analysis showed that the G614 genotype has steadily increased from March to May 2020, indicating a transmission advantage of the virus with G614 mutation [17].
The diversity analysis of SARS-CoV-2 with 160 complete genome sequence showed three central variants referred as A, B, and C. The variant-A is the ancestral type. The A and C types are found in Europeans and Americans. The B type is predominant in East Asia [5].