New tool enables study of SARS-CoV-2 mutant spectrum by ultrasequencing

SARS-CoV-2 genome is three times larger than influenza genome. Both consist of NRA molecules that mutate when replicate. It is essential to know its mutant spectrum, in other words, its "fingerprints", to achieve an appropriate treatment that reduces its infectivity -the capacity of pathogens to invade organisms and cause infections-, since its composition of variants could determine how infection would develop in each patient.

Researchers of the University of Malaga (UMA) will be able to examine the depth of these spectra by genetic ultrasequencing techniques thanks to the innovative system they have designed: "QuasiFlow", a tool that enables the analysis of variants present in each patient individually.

"We are interested in reaching a deep understanding of the genetic variability of the virus to find out the best way to attack, its weak spot", explains Professor Ana Grande from the Department of Cellular Biology, Genetics and Physiology of the UMA, who will lead a study next year, funded by the Government of Andalusia, to step up research into new rapid implementation therapies for COVID-19.

New antiviral therapy

Particularly, this researcher of the UMA will coordinate a multidisciplinary team of scientists that will test a new combination antiviral therapy, which combines the so-called lethal mutagenesis strategy and inhibitors of the ExoN proofreading and MTase activities of coronavirus, in order to prevent the virus from evading the innate immune response.

"The idea is to increase the mutation capacity of the virus to turn it against the virus, alter its mutant spectrum so that it loses its infectivity", says Ana Grande, who asserts that she has already achieved this on other RNA viruses, such as the lymphocytic choriomeningitis arenavirus or the hepatitis C virus, by applying nucleoside or base analogues, similar to the basic pieces which genomes are made up of.

The expert clarifies that, this time, they will combine it with peptides -molecules comprised of a few amino acids-, specifically designed against its "Achilles heel", the enzyme that corrects the errors that can wipe it out, to make lethal mutagenesis more effective and obtain better results.

The scientist of the UMA, who has been studying this type of therapies on animal and plant viruses since 1999, assures that SARS-CoV-2 is not an exception, and that it has already been proven that it is sensitive to these mutagenesis therapies.

Phases of research

This way, in the first phase, which is already under way, researchers will apply the UMA software "QuasiFlow" to analyze the mutant spectrum of samples from Virgen de la Victoria University Hospital of Malaga. They will analyze viral samples obtained from patients with different clinical cases, from asymptomatic to severe cases, including reinfected patients, in order to find clear differences in their spectra.

This first phase is conducted by the researchers and bioinformatics scientists of the UMA Gonzalo Claros, Enrique Viguera, Pedro Seoane, Luis Díaz, Josefa Gómez y Diego Lozano, as well as the specialists of Virgen de la Victoria University Hospital of Malaga Jesús Santos and Isabel Viciana.

After ultrasequencing and analyzing the mutant spectra, Ugo Bastolla, researcher of the Centre for Molecular Biology "Severo Ochoa" (CBM) of the Spanish National Research Council (CSIC), will carry out the modeling phase to identify the best analogue to perform the mutagenesis. Ana María Fernández and Gregorio Fernández, experts in protein structures of Miguel Hernández University of Elche, will be in charge of designing the peptides.

"These scientists will design a tailored therapy based on the previous sequencing of the virus", clarifies the researcher of the UMA, who adds that this realization is essential to achieve new treatments to combat COVID-19, that different strategies should be studied because "we cannot risk everything on one throw" with this virus.

The trial on host cells to test the effectiveness of the combination of these two therapies constitutes the final phase of the study. Researchers will have one year to conduct the trial and EUR 94,800 from the COVID-19 Fund of the Government of Andalusia, to be charged to the ERDF fund.