- 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

An analysis of 86 complete or near-complete SARS-CoV-2 genomes acquired from GISAID was done to examine mutations in the SARS-CoV-2 genome. The samples of SARS-CoV-2 were taken from patients in China, the USA, Australia, Japan, France, Singapore, England, Taiwan, South Korea, Belgium, Germany, and Vietnam.

Smith College

Investigations are still ongoing in determining the current evolution and mutating nature of SARS-CoV-2, which will aid scientists in understanding more about this virus and in developing effective treatments and vaccines against the disease. 

Evolution and Mutations of SARS-CoV-2

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

Mutation "hotspots" of SARS-CoV-2

The type and number of mutations can differ based on region. SARS-CoV-2 in Europe and North America were found to have higher rates and variety of mutations compared to regions closer to the origin of the virus like Asia. Differences in mutations per region increased overtime outside of Asia. 

Mutations of SARS-CoV-2 can differ by Region

Evolution of SARS-CoV-2 by Origin

Through careful examination of viral structural/non-structural proteins as well as infection mechanism, the 2003 SARS-CoV and the current 2019nCoV are thought to be very similar in phylogenic. Based on complete sequencing, the current 2019-nCoV is evolutionary related to SARS-CoV long range-conserved amino acid sequences with a few variations in the accessory proteins and base substitutions in non-structural proteins (Wu et al., 2020). Even before 2003, many different coronaviruses have similar conserved proteins and replication pathway all leading to annually 15-30% of respiratory infections in humans. Individuals of older age, with pre-existing illnesses, or with compromised immunity are the most susceptible to infections and often associated with the highest mortality. 
Currently, the 2019-nCoV has been reported to have the highest pathenogenicity and fatality out of all coronaviruses. This can be explained based on differences in tolerance to genetic variability. For instance, both the 2003 SARS-CoV and current 2019-nCoV are very tolerant to genetic variations. Both strains of coronaviruses have shown their potential to pass through species barrier from bats, pangolins, mice, and bovine all the way to mammals including humans (Guan et al., 2003). In other words, higher tolerance to genetic variability could imply greater chances of horizontal gene transfer across species. Looking back to 2003, the same characteristics can be seen in SARS-CoV, where it was hypothesized to be found first in Chinese horseshoe bats in Guangdong Province.

Phylogeny and Tropism

- COVID-19 Virology in Comparison to SARS-CoV and MERS
- Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis

Comparison of SARS-CoV-2 genomes to other related genomes

- Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study

Deletions in the SARS-CoV-2 Genome

Researchers at the University of Bologna conducted the largest genomic study of SARS-CoV-2 to date, analyzing 48,635 different genomes and their mutations. There are currently six known strains around the world with differential geographic and genomic distribution, though there is little genetic variability between them, which is beneficial because a viable vaccine would likely be effective in fighting all of them.


The Six Strains of COVID-19

As of mid-December 2020, a new strain of SARS-CoV-2, the virus that causes COVID-19, was discovered in the United Kingdom. According to recent studies, this new strain can be up to 70% more transmissible.

UK Variant of SARS-CoV-2

A new strain of the SARS-CoV-2 virus was discovered in the Eastern Cape of South Africa as of the end of 2020. This new strain is called 501Y.V2.

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