Mutational meltdown: Can we push SARS CoV-2 off an evolutionary cliff?

May 18, 2020

From New York to Luxembourg, Namibia, Iceland and Bhutan, the novel coronavirus SARS CoV-2 has turned the modern world into a crisis zone. An unprecedented global effort is underway to understand the elusive pathogen and find effective therapies.

An intriguing approach to treating COVID-19, the disease caused by the novel coronavirus, has recently been suggested by Arizona State University faculty members Jeff Jensen from the Center for Evolution and Medicine and Michael Lynch from the Biodesign Center for Mechanisms of Evolution. Mutational meltdown This graphic shows a series of viral replication cycles for a hypothetical viral population within a patient — with four representative virus genomes shown at each time point. At the time of infection, no mutations are present. Over time, mutations accumulate, and if natural selection fails to eliminate these harmful mutations, each generation may become less fit than the preceding. In this way, the most fit genome carries more and more deleterious mutations over time. This phenomenon, known as Muller’s ratchet, sets the viral population on a one-way path to extinction. Graphic courtesy of Shireen Dooling Download Full Image

The strategy they describe for vanquishing SARS CoV-2 is rooted in evolutionary theory. The basic idea is simple: If a particular drug could sufficiently boost the virus’ rate of mutation, it may be possible to saddle the pathogen with so many harmful genetic errors that the viral population within a patient collapses.

The phenomenon, known as mutational meltdown, was first described by Lynch three decades ago in the context of preventing extinction in small or endangered populations.

In the new research, the goal instead is to encourage extinction in large viral populations, through a ruinous accumulation of viral mutations. (The concept is similar to a later-described phenomenon known as lethal mutagenesis.)

“This is a great example of well-established principles in evolutionary theory being repurposed for solving significant practical problems,” Lynch said.

In addition to providing a hopeful candidate for the treatment of SARS CoV-2, mutational meltdown could offer a new blueprint for treating a broad range of infectious diseases. The method is particularly attractive as it holds the potential to deliver a knockout blow to infectious agents, causing such widespread damage to their genomes that they are unable to develop antiviral or antibiotic drug resistance.

Lynch and Jensen recently outlined the strategy in the journal Heredity.

In earlier proof-of-concept research, Jensen, his postdoctoral associate Claudia Bank, now a faculty member at the University of Berne, Switzerland, and their colleagues at the University of Massachusetts Medical School demonstrated that the drug favipiravir, if given at sufficiently high dosage, could effectively induce mutational meltdown in laboratory populations of the influenza A virus.

New killer on the block

As of May 14, 2020, confirmed cases of COVID-19 number over 4.5 million globally. Over 300,000 have died and the numbers almost certainly represent a significant undercount.

The success of SARS CoV-2 in invading human cells and rapidly disseminating through the global population is due to the virus likely having undergone specific mutations, allowing it to make a leapSuch species-straddling pathogens are called zoonotic. from some reservoir species to humans.

Genetic mutations are nature’s ultimate double-edged sword. They provide the raw material for evolution to act upon and account for the astonishing diversity observed across species, including humans. Through natural selection, mutations conferring an adaptive advantage in nature’s great game can become fixed in a population and transmitted to offspring through generations.

Most genetic mutations, however, are deleterious and these account for a dizzying range of diseases, from mild to lethal. Over successive generations, natural selection can act on these errors, increasing the probability of ultimate fixation for mutations that are advantageous, and decreasing the probability for those that are deleterious, owing to the reduced biological fitnessFitness is a measure of an organism’s ability to grow to adulthood and successfully contribute progeny to the next generation. of organisms carrying these harmful mutations.

While harmful mutations can wreak havoc in individuals who acquire them, over time, populations tend to shed the majority of detrimental mutations. In organisms that reproduce sexually, this purging process is helped along by the recombination of genetic elements provided to offspring from two genetically distinct parents.

Ratchet of doom

Although evolution acts to remove deleterious mutations from the population through purifying selection, there are limits to this cleansing process. Should the overall population number fall below a certain threshold, purifying selection can’t keep pace with the accumulation of bad mutations.

professor's portrait

Michael Lynch directs the Biodesign Center for Mechanisms of Evolution and is a professor in ASU's School of Life Sciences.

“This is because the efficiency of selection is reduced in small populations, owing to the increased noise in the transmission process across generations,” Lynch said.

In this case, biological fitness in the remaining population will be continually degraded, placing the organism on a one-way path to extinction.

For example, a population initially bearing no harmful mutations will eventually degrade to a population with all members bearing at least 1 bad mutation, later, 2, then 3 and so on. Such populations grow successively sicklier over time, further reducing population size, in a snowball effect.

This irreversible mechanism, long recognized by evolutionary biologists, is known as Muller’s ratchet, for the ratchet-like, one-way accumulation of harmful mutations in a population. This process is traditionally viewed as being the result of genetic drift, a random evolutionary process, but under high mutation rate regimes these "clicks of the ratchet" may be driven by mutation itself.

Hacking the viral genome

Typically, single-stranded RNA viruses have a 100- to 1000-fold higher mutation rate per replication than humans do per human generation. Coronaviruses like SARS CoV-2, however, are unique among RNA viruses as they possess a proofreading domain used to reduce mutational accumulation.

The strategy outlined seeks to target this proofreading apparatus through drug therapy, damaging its functionality. If the virus could be induced to pick up deleterious mutations at an accelerated pace, Muller’s ratchet may begin clicking, eventually reducing population fitness to the point of no return: mutational meltdown.

professor's portrait

Jeff Jensen is a population geneticist and professor in the Biodesign Center for Mechanisms of Evolution, the Center for Evolution and Medicine, and ASU's School of Life Sciences.

"Practically, a key question here is how much the mutation rate must be turned up to achieve this effect," Jensen said, "as one certainly doesn't want to run the risk of an insufficient rate increase that may generate adaptive mutations without generating a sufficient deleterious mutational load to ensure extinction."

If a viral invader like SARS CoV-2 were treated with a mutation-boosting drug at sufficient dosage, the result would be to shower the entire viral genome with mutations, which could make it very hard for the virus to evolve resistance.

The drug favipiravir is one such mutation-enhancing candidate, which has already shown promise in this regard in a number of RNA viruses, including Ebola, yellow fever, chikungunya, enterovirus and notovirus.

In the previous work on influenza A virus, Jensen and colleagues accurately predicted the subtle dynamics of mutational meltdown due to favipiravir, which involved a linear rate of mutational accrual leading to a fatal transition point, beyond which harmful mutations rapidly accumulated prior to the collapse of the viral population.

Recently, another drug, remdesivir, has shown promise against a clinical isolate of SARS-CoV-2. Like favipiravir, the treatment appears to confuse the virus’ genetic proofreading system. As Lynch notes, “anything we could do to muck up the proofreader would increase the mutation rate around 20-fold.”

Such therapies could be used in conjunction with other drugs targeting different aspects of viral assembly or replication, further increasing the likelihood of achieving effective meltdown. Much more work is needed however — both experimental and theoretical — to determine if the strategy can be safely and effectively applied to treat COVID-19, or indeed be used as a general antiviral strategy in future unknown pandemics.

Richard Harth

Science writer, Biodesign Institute at ASU


ASU opera singer rebuilds her voice and discovers new artistic path

May 18, 2020

Editor's note: This story is part of a series of profiles of notable spring 2020 graduates.

ASU graduate student Stephanie Sadownik, DMA in voice performance, started suffering from undiagnosed vocal health issues soon after she auditioned for the voice program at the School of Music in ASU’s Herberger Institute for Design and the Arts. So, she created new opportunities and carved out new artistic pathways for herself — all while refusing to give up on her dream of performing. Stephanie Sadownik Stephanie Sadownik Download Full Image

“Even though my first instruments were clarinet and percussion, I always sang, especially musical theater,” she said. “I was involved in all the school plays and musicals and loved performing.”

After nearly a decade of performing as a professional singer and teaching in community music schools in Las Vegas, Sadownik came to ASU to earn her doctoral degree in music and study with mezzo-soprano Stephanie Weiss, assistant professor of voice in the ASU School of Music.

Sadownik entered the voice program at ASU with significant unidentified vocal health issues that began after her audition. During her first year and despite her vocal difficulties, she performed her DMA recital with unique chamber orchestra programming of Mahler’s “Kindertotenlieder” and Respighi’s “Il tramonto,” was a soloist with the Chamber Singers Bach concert at Tempe Center for the Arts and performed in the Music Theatre and Opera’s New Works readings of “The Halloween Tree” and “Marie Begins.”

In her second year, Sadownik was diagnosed with a disorder that caused the muscles in her neck to function incorrectly, which led to her vocal health issues. Since there was no damage to her vocal chords, she studied speech pathology exercises and with the assistance of Weiss began to rebuild her voice.

Because singing and performing were still a struggle, Sadownik focused on her other main interests: directing and entrepreneurship.  

She directed the ASU Music Theatre and Opera’s student lab productions of “Trouble in Tahiti,” an original adaptation of Purcell’s “The Fairy Queen” and double-bill “Nora at the Alter-Rail” and “Hand of Bridge.”

“Stephanie is a charismatic and versatile performer, stage director and producer, and one of the most creative, innovative and energetic people I have ever met,” said Weiss. “She possesses a world-class, colorful mezzo-soprano voice, which she uses in combination with her love for acting and storytelling to become a complete artist.”

Sadownik was the assistant director to David Lefkowitch for “Les Mamelles de Tirésias” for Music Theatre and Opera. She was selected to attend the competitive Yale Summer Directing Intensive for summer 2019. And, in fall 2019, she staged Dominick Argento’s “From the Diaries of Virginia Woolf” with Duo au Courant.

“Working with Stephanie as both a singer and director was exciting as she was able to use what she has learned from me as a singer and, in turn, teach me about the character I was singing from a director’s point of view,” said Weiss. “This was an extremely special moment for me as a mentor.”

Vocally progressing in her third year, she performed the role of Zita in Music Theatre and Opera’s “Gianni Schicchi.” She designed her final voice recital, based on the works of Chausson and Elgar, as an innovative, socially-active artistic experience for the audience. In addition to singing, she was the assistant director for Arizona Opera’s “La bohème” and the director for the ASU Music Theatre and Opera New Works reading of guest artist Laura Kaminsky’s “Hometown to the World.”

Sadownik was selected as a national semifinalist for the Fulbright Award to Germany. Though she did not win, she conducted research on Emilie Mayer, an unknown but prolific German female composer, at the Berlin Library and retrieved Mayer’s manuscripts as part of her doctoral document project.

She was a graduate teaching assistant for the voice program, Weiss’ assistant in undergraduate studio classes and co-instructor for the Undergraduate Opera Scenes class. In addition to teaching at ASU, Sadownik also teaches private voice lessons at Linton-Milano Music School in Mesa. She is the artistic director and co-founder of the Arizona Women's Collaborative, an all-female-identifying new works initiative composed of singers, composers and poets, which has commissioned and premiered 10 new works to date with music and lyrics by female-identifying artists.

Before coming to ASU, Sadownik was an apprentice artist with Sarasota Opera, PORTopera and a three-time Opera Fellow at Aspen Opera Center. She received her BM in vocal performance and a minor in Italian from the Indiana University Jacobs School of Music (2006) and her MM in opera performance from the University of Maryland (2009). 

Question: What was your “aha” moment, when you realized you wanted to study the field you majored in?

Answer: My "aha" moment and introduction into classical singing occurred when I saw my first live opera, “La bohéme,” by Puccini, and was utterly spellbound and deeply moved by the singing. I had no idea one could train to sing like that, and I was very fortunate to encounter a teacher in high school who encouraged me to do so.

Q. What’s something you learned while at ASU — in the classroom or otherwise — that surprised you or changed your perspective?

A. Opening night of my first opera I ever directed certainly changed my creative abilities and perspective. I had never directed anything before, and this was an original adaptation of Henry Purcell’s opera “The Fairy Queen” and William Shakespeare’s “A Midsummer Night’s Dream” that I wrote with my musical director, Kamna Gupta. We had undergraduates and graduate students involved, a live band, choreography and it was outside. It was the most difficult project I had even taken on and I was terrified, but I threw everything I had into this production. Through the difficulty, I found immense resilience in myself, faith in my own creative sensibilities, expansion in my capabilities in team building and vast enjoyment being a director. I was so pleased and proud with how the production turned out and how well the singers performed. It built my self-confidence immeasurably, knowing what I am capable of, that my voice and ideas are valid, and sparked a passion in directing I didn’t know I had. I realized, along with being a voice teacher, I really love working with young singers in helping them discover stagecraft for themselves.

Q. Why did you choose ASU? 

A. I chose ASU because of the other graduate programs offered; it seemed the most diverse as far as what classes you are able to take, performance opportunities as well as having a wonderful faculty who I greatly admired.

Q. Which professor taught you the most important lesson while at ASU?

A. My amazing voice teacher Stephanie Weiss taught me the most valuable lesson: Never give up. Singing opera is difficult at the best of times, and there are moments of vocal transition and changes that everyone goes through. It can leave one feeling a bit hopeless and frustrated. Stephanie Weiss instilled in me that even when you are having a bad singing day, month or year, just keep going one foot in front of the other and you will eventually get the other side of the mountain. This has been monumental for me in so many ways.

Q. What’s the best piece of advice you’d give to those still in school?

A. Go outside of your box. ASU is one of those schools that gives its students a bit of free reign when it comes to their schedules and what they can take. I would encourage all students to get out of their comfort zones, be a part of a club that interests them that may have nothing to do with their major. Meet new people and learn how to collaborate with others. You never know whom you will strike up a conversation with or who will be your next partner in some project. The more you expand your skill set, ASU will be there to help seed your ideas and projects and see them through to fruition.

Q. What was your favorite spot on campus, whether for studying, meeting friends or just thinking about life?

A. For a school that is technically in the middle of the desert, I was surprised and pleased with the amount of greenery and fountains on the Tempe campus. Waiting between classes, I would sit at the fountain in the School of Music courtyard or a take a nice walk through campus and visit the Biodesign Garden.

Q. What are your plans after graduation?

A. My hopes are to continue building my creative life as a teacher of voice, a stage director and a producer of new works. In all the uncertainty of these times, it is difficult to know how my goals will pan out. Nevertheless, the good thing about being a musician is that one gets used to uncertainty, and at least I have more time to practice.

Q. If someone gave you $40 million to solve one problem on our planet, what would you tackle? 

A. As an opera singer in the United States and for many musicians, the option of a steady job with one company is not a reality. Even as a teacher, you are working as an independent contractor, not usually a company employee. This makes obtaining and keeping affordable and quality health care especially difficult. I know so many artists, including myself, who are concerned about falling ill and having no recourse. If I had to choose just one problem, I would use the $40 million to work toward a functional, affordable and reliable health care system here in the United States.

Lynne MacDonald

communications specialist, School of Music