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- 2 deletions (3 nucleotides and 24 nucleotides) were on the ORF1ab polyprotein and 1 deletion (10 nucleotides) was in the 3’ end of the genome 
- Nucleotide sequence alignment revealed 93 mutations in the whole SARS-CoV-2 genome

In the whole genome sequence:
- 42 missense mutations – all in major non-structural and structural proteins (excluding the envelope protein)
- 29 in the ORF1ab polyprotein 
- 8 in the spike surface glycoprotein 
- 1 in the matrix protein 
- 4 in the nucleocapsid protein 

Out of the 8 missense mutations in the spike surface glycoprotein, 3 mutations were in the receptor-binding domain, which might induce conformational changes and change antigenicity. This plays an important role in binding to host cells, host tropism, and antibody identification.

Genetic diversity and evolution of SARS-CoV-2 Analysis Results

Phan T. (2020). Genetic diversity and evolution of SARS-CoV-2. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 81, 104260. https://doi.org/10.1016/j.meegid.2020.104260

Genetic diversity and evolution of SARS-CoV-2

Genomic organization of SARS-CoV-2 and pairwise nucleotide sequence alignment showing deletions in the ORF1ab polyprotein and in the 3′ end of the genome

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