Researchers say COVID-19 virus may mutate slowly, making vaccine development easier

In 2020, researchers observed small changes in the genome of SARS-CoV-2 as it was spreading across the world. Scientists said if a virus has such few changes over time, developing one global COVID-19 vaccine would be easier.

At the time, the COVID-19 virus, SARS-CoV-2, was spreading fast and killing many people, and scientists were working hard to develop an effective vaccine. They followed changes in the virus genome and looked at how fast the changes occured in different parts of the world. The information was intended to help them to manage the COVID-19 disease better, and to develop a vaccine that will be effective against all circulating virus strains. 

In this study, the researchers analysed changes in the SARS-CoV-2 genome in different parts of the world. They also looked at possibly developing a global vaccine against all SARS-CoV-2 strains.

The researchers collected complete SARS-CoV-2 genome sequences information from 79 countries in 6 continents from a database, and analysed these. They analysed the type and prevalence of changes in each genome. The researchers also compared SARS-CoV-2 genomes across countries, and made family trees to show relationships between the strains.

Their results showed only small changes in the SARS-CoV-2 genomes in all countries studied. Very few samples (5.27%) had changes in more than 1% of the entire genome. For all the 6 continents, the researchers reported few occurrences of changes happening in the same place in the virus genome. Scientists say if many changes occur at the same place of a genome, new virus strains can arise.

The researchers reported that 67.96% of all genome changes they observed in their analysis can affect protein sequences in the virus, but not its structure or function. Only one third of the changes can affect protein structure or function of the COVID-19 virus.

The researchers found only 2 changes in the viral genome to be common in the 6 continents; others were different across continents. Their results also showed that virus strains in Africa were closely related to those in other continents, and all strains in other continents originated from Asia. 

Strains in North America, South America, and Africa come from Europe, while some strains were only in Europe.

The researchers said that the DNA sequence changes in something called the ‘S protein’,  do not seem to affect its structure, and therefore are not likely to have a big impact on vaccine effectiveness. Scientists are interested in the ‘S protein’ when they develop vaccines because it is the protein used by the virus to enter human cells.

The study showed that unlike the flu virus or HIV, the SARS-CoV-2 genome did not change very fast, which would have made it easy for scientists to develop one global COVID-19 vaccine.

The researchers recommended ongoing monitoring of SARS-CoV-2 genomic changes.

Abstract

The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analysed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from 24 December 2019, to 13 May 2020, according to the GISAID database. Our analysis revealed the presence of 3206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (>10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein, and one in each of three proteins: Spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the receptor-binding domain (RBD) of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with intra-genomic divergence of SARS-CoV-2 could indicate that unlike the influenza virus or HIV viruses, SARS-CoV-2 has a low mutation rate which makes the development of an effective global vaccine very likely.

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