Factors that allow an RNA virus to mutate and facilitate its spread

RNA viruses, which have ribonucleic acid or RNA as their genetic material instead of DNA or deoxyribonucleic acid, have some of the highest mutation rates in nature. This allows them to evade the immune system and spread infection, making it harder to create drugs to prevent this.

Now, a team from the Institute of Integrative Systems Biology (I2SysBio), a joint centre of the Spanish National Research Council (CSIC) and the University of Valencia (UV), has carried out the first analysis of how mutations affect the complete proteome (the entire group of proteins produced by an organism) of an RNA virus, finding significant variability in tolerance to mutations between different viral proteins. This will facilitate the development of drugs that reduce the likelihood of the virus developing resistance.

The high mutation rate of RNA viruses is due to the fact that their replication is controlled by a protein called RNA polymerase, which is prone to making mistakes when generating new copies of the virus genome. These mutations are distributed heterogeneously, suggesting that the different viral proteins differ in the way they tolerate mutations.

To understand this phenomenon, the authors of the study carried out an exhaustive analysis of how mutations in the different proteins encoded by the viral genome affect the viability of a human RNA virus, coxsackievirus B3, which causes severe heart inflammation in humans.

Using a technique called “deep mutational scanning,” which produces virus populations that encode almost all possible mutations and detects the frequency of these changes using the latest genetic sequencing techniques, the authors of the study have been able to determine the effect of more than 40,000 mutations and 1,300 deletions (loss of genetic material) on the viability of the virus. “It is necessary to generate viral populations that contain a large amount of diversity and be able to sequence them with high fidelity. Few laboratories can do this,” says Ron Geller, a CSIC researcher at I2SysBio and co-author of the study.

Artist’s impression of an RNA virus. (Illustration: Amazings / NCYT)

The research team, led by Beatriz Álvarez-Rodríguez, from I2SysBio, found significant variability in tolerance to mutations between different viral proteins. This variability is related to specific structural and functional characteristics of each protein. In addition, the researchers observed that these effects are maintained in different types of cells, with the exception of some residues involved in the entry of the virus into the cell. This highlights the importance of entry factors in the process of viral expansion, as the researchers maintain.

“We analyze the so-called ‘pockets’ [pockets, en inglés]pockets in viral proteins with favorable properties for being attacked by small drug molecules. We found twelve such pockets distributed across different viral proteins,” reveals Geller. “We then discovered that some of these pockets are very intolerant to mutations, so it is likely that any mutation leading to drug resistance is also lethal to the virus, which would prevent the spread of such mutants. Others showed a very high tolerance to mutations, so they may not be good pharmacological targets,” argues the CSIC researcher.

This is the first analysis to date of how mutations affect the complete proteome of a human RNA virus, allowing a direct comparison between different protein classes in terms of their tolerance to mutations, the researchers point out. The results of the study provide a set of data that helps to better understand the biology and evolution of this type of virus, which belongs to a family of viruses with medical relevance for humans (poliovirus, rhinovirus, enterovirus A71…).

“One of the main challenges in the development of antiviral molecules is the emergence of mutations that allow the virus to escape from these drugs,” explains Geller. “The data provided in this study on the tolerance of viral proteins to mutations could be used to identify regions with low tolerance to mutations, facilitating the development of drugs that reduce the likelihood of the virus developing resistance,” he concludes.

The study is titled “Mapping mutational fitness effects across the coxsackievirus B3 proteome reveals distinct profiles of mutation tolerability”. It has been published in the academic journal PLoS Biology. (Source: CSIC)