Researchers at Dokuz Eylül University, Turkey, have identified mutations in the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that may have contributed to its dominance in Europe and elsewhere.
The study sheds light on how mutations in the main RNA polymerase of the virus affects its mutation rate and spread. SARS-CoV-2 relies on this RNA-dependent RNA polymerase (RdRp) to replicate its viral genome once inside host cells.
The results suggest that one mutation in particular – 14408C>T – is involved in increasing the mutation rate and possibly the transmissibility of the virus.
A pre-print version of the paper can be accessed on the server bioRxiv*, while the paper undergoes peer review.
Novel Coronavirus SARS-CoV-2 Transmission electron micrograph of SARS-CoV-2 virus particles, isolated from a patient. Image captured and color-enhanced at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID
Tracking the evolution of the virus
Since the coronavirus disease 2019 (COVID-19) outbreak, caused by SARS-CoV-2, began in Wuhan, China, in December 2019, researchers have been accumulating thousands of viral genome sequences to help track the evolution of the virus as it has spread across the globe.
SARS-CoV-2 has a single-stranded RNA genome that codes for 12 peptides, including Orf1a and Orf1ab, which undergo cleavage to produce mature peptides, including the membrane glycoprotein and envelope glycoprotein.
Among worldwide isolates of SARS-CoV-2, researchers have identified several mutations in the RdRp coding region of the Orf1ab gene. One of them is the 14408C>T transition, which has been identified in more than 7000 isolates from various continents. One early study of SARS-CoV-2 genomes isolated from North America and Europe suggested that 14408C>T is associated with a higher number of mutations, although the mechanism is not yet fully understood.
What did the current study involve?
To investigate how such RdRp mutations might affect the mutation rate of SARS-CoV-2, Doğa Eskier and team explored their association with mutations identified in the membrane or envelope (MoE) glycoproteins in relationship to location.
On examining the distribution of mutations in RdRp and MoE by location, South America had the highest proportion (93.2%) of RdRp mutants, while Asia had the lowest (32.7%). South America also had the highest proportion (11.0%) of M gene mutations and the second-highest proportion (2.5%) of E gene mutations.
To explore the effects of the most common RdRp mutations on the mutation rate of SARS-CoV-2, the team focused on the ten most frequently observed mutations and compared MoE between them.
The strongest predictors of MoE presence of absence
Univariate logistic regression analysis of the ten individual mutations revealed 14408, 14805, 15324, and 13730 as significant in predicting the presence or absence of MoE, with 14408 identified as the strongest predictor.
“Our results suggest that SARS-CoV-2 genomes with the 14408C>T mutation are 1.5 times more likely to have MoE,” writes the team.
The final univariate logistic regression analysis also revealed a significant relationship between MoE and the same four mutations (14408, 14805, 15324, 13730) and location. Viral genomes in Europe and Oceania were 1.35 times and 1.45 times more likely, respectively, to have MoE than viral genomes in Asia.
“These results indicate that both RdRp mutations and location independently predict MoE status,” say Eskier and colleagues.
While the 14408C>T mutation predicted an increased risk of MoE, the other three RdRp mutations predicted a decreased risk, especially 15324C>T mutation, which predicted that the risk would be reduced by about ten times.
Interpreting the findings
The team says their observation that the two RdRp mutants significantly influence the likelihood of mutations in MoE, which evolve comparatively slowly under selective pressure, “supports the hypothesis that mutations of RdRp contribute significantly to the SARS-CoV-2 genome evolution.”
It would be expected, they say, that a low-fidelity (more error-prone) mutant RdRp “would increase viral genetic diversity and allow the virus spread under different selective pressures, such as spreading to different populations.”
However, a higher-fidelity mutant RdRp would be beneficial once optimal conditions were met and where replication errors would be disadvantageous.
Early studies have suggested that 14408C>T mutation could increase replication errors, but how the 15324C>T mutation might lower mutation rates is less well understood.
“It is possible that 15324C>T modulates the interaction of viral genome with host factors and indirectly affects the 14408C>T mutation through such factors… but this question may be better answered as more viral genome sequences accumulate, and functional studies are performed,” say Eskier and team.
Co-mutations that evolved with 14408C>T
Interestingly the authors describe two other mutations that co-evolved with 14408C>T, namely 23403A>G and 3037C>T.
In Europe, North America and South America, 14408C>T and its two co-mutations became the dominant form, while in Asia, it remained the minor form.
Following identification of the first mutated virus in Europe, 14408C>T then emerged as the dominant form in South America, North America, and Africa five, seven, and eight days later where it comprised 81.3%, 59.4% and 80.3% of viral genomes, respectively.
“Our study sheds light on the effects RdRp mutations, particularly 14408C>T mutation, on the mutability and possibly transmissibility of SARS-CoV-2,” writes the team.
“It is possible that 14408C>T mutation may have contributed to the dominance of its co-mutations in Europe and elsewhere. Further functional studies are required to test our findings,” they conclude.
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.