BOLOGNA, Italy — Like all viruses, SARS-CoV-2 mutates, undergoing small changes in its genome over time. This characteristic remains a source of concern because of the possibility that mutation could make the coronavirus more dangerous or respond differently to treatments or vaccines. A recent study from the University of Bologna puts this fear to rest, at least for the time being.
SARS-CoV-2 is, of course, the virus that causes COVID-19. Researchers report that ongoing mutation has produced a total of at least six different virus clades, or groups of virus strains with similar sequences. Despite this, the fundamental sequence of the virus has not changed significantly since its emergence in December 2019. This is good news for drug and coronavirus vaccine development.
The study, published in Frontiers in Microbiology, represents the largest comparative study on SARS-CoV-2 genomic sequences to date. In all, the team analyzed 48,635 complete sequences of the virus collected from labs across the globe. Using advanced sequence analysis software, the researchers compared these sequences to that of a SARS-CoV-2 strain that was isolated in Wuhan, China toward the beginning of the pandemic.
The report confirms that SARS-CoV-2 has a low mutation rate, with an average of only about seven mutations per sample. That’s in comparison to the reference strain from Wuhan. To put this in perspective, seasonal influenza has a mutation rate more than double that.
“The SARS-CoV-2 coronavirus is presumably already optimized to affect human beings, and this explains its low evolutionary change,” says Federico Giorgi, co-author and coordinator of the study, in a statement. “This means that the treatments we are developing, including a vaccine, might be effective against all the virus strains.”
Looking at the six clades of SARS-CoV-2
The researchers used the comparative sequence data to classify the viruses into six different clades. The six clades are designated: L, S, V, G, GH, and GR.
The original L clade includes the reference strain, and is mostly representative of sequences from Asia, where the virus originated. Scientists say that viruses in this clade are gradually disappearing and account for only 7% of the sequenced genomes.
According to the study, the S clade was the next to appear, with the first sequences reported at the beginning of January 2020. Viruses from the S clade are declining, but they can still be found in some areas of the U.S. and Spain.
The study finds that viruses from the V clade and the original G clade appeared around the same time in mid-January 2020. The GH and GR clades, which mutated from the G clade, were not detected until more than a month later, toward the end of February 2020.
Viruses from the G clade are receiving particular attention in the news because they contain a mutation that has been linked to increased infectivity of SARS-CoV-2. That change, labelled D614G, is predicted to occur in the spike protein, which is the viral surface protein that helps SARS-CoV-2 infect cells.
“There is currently little evidence on the clinical and molecular differences between the circulating clades of SARS-CoV-2,” the authors say in the study. “For example, one study has shown that the D614G mutation in the Spike protein may be associated to higher case fatality rates. However, as this coronavirus continues to evolve, surely new features will emerge or mutate alongside the genomic sequences, with clinical and pharmacological repercussions.”
Viruses from the G and G-derived clades are currently the most common and fastest growing viral subpopulation, accounting for 74% of all sequences globally. Generally, the G and GR clade viruses are most frequent across Europe, whereas the GH clade is more prevalent in the Americas.
In addition to the six distinct clades identified by this study, the authors also report the emergence of new mutations and clades beyond the current classification.
“Rare genomic mutations are less than 1% of all sequenced genomes,” explains Giorgi. “However, it is fundamental that we study and analyse them so that we can identify their function and monitor their spread. All countries should contribute to the cause by giving access to data about the virus genome sequences.”