Mutagenic antivirals: the evolutionary risk of low doses

Mutagenic antivirals: the evolutionary risk of low doses

Chase W. Nelson1, Sarah P. Otto2

  1. Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA;
  2. Department of Zoology, University of British Columbia, Vancouver BC Canada V6T 1Z4;

Vaccines and antiviral drugs both have critical parts to play in the fight against COVID-19. Oral antivirals are of particular interest given their potential for equitable distribution, the occurrence of vaccine-breakthrough infections, and increasingly transmissible variants of concern.

Merck recently announced the mutagenic (mutation-inducing) antiviral molnupiravir, which improves COVID-19 outcomes when administered twice a day for five days (Merck & Co., Inc. 2021a; Merck & Co., Inc. 2021b). The drug is already authorized for emergency use in the U.K., and the U.S. Food and Drug Administration will meet to discuss emergency use authorization on Tuesday, November 30.

Antivirals can work via several mechanisms. Protease inhibitors, like masitinib (Drayman et al. 2021) and paxlovid (PF-07321332; ritonavir; Pfizer, Inc. 2021), prevent the production of mature viral proteins. Mutagens, like molnupiravir, instead increase the viral mutation rate beyond a tolerable limit. Specifically, molnupiravir is a nucleoside analog that incorporates into replicating RNA, preferentially inducing C→U mutations (Gordon et al. 2021). At the recommended doses, it is proposed to cause lethal mutagenesis (Loeb et al. 1999): newly replicated viral genomes accumulate so many errors as to become nonviable, an endpoint known as error catastrophe (Eigen and Schuster 1977) or mutational meltdown (Lynch and Gabriel 1990).

One drawback of self-administered oral medications is the risk of low drug concentrations due to missed doses, incomplete courses, or low initial drug penetrance at the site of action (e.g., mucosal membranes in the nasal passages or lungs). Critically, in the case of mutagenic antivirals like molnupiravir, low drug concentrations might increase the mutation rate without reaching the level required for error catastrophe, instead inducing only sublethal mutagenesis (Sadler et al. 2010). This could accelerate within-host evolution of the virus, potentiating new variants of concern that enhance transmissibility or immune escape (Pillai et al. 2008). Indeed, another antiviral, ribavirin, has mutagenic properties and induces adaptive mutations in other RNA viruses (Beaucourt and Vignuzzi 2014; Mejer et al. 2020). Moreover, previous SARS-CoV-2 variants of concern likely acquired adaptive combinations of mutations during single chronic infections (Kemp et al. 2021; Otto et al. 2021).

Given the potential for sublethal mutagenesis of SARS-CoV-2, steps should be taken to understand the evolutionary consequences of both drug concentration and improper administration for pathogen evolution. Among the issues to consider are:

  1. Peak viral shedding is likely to coincide with low initial drug concentration. Molnupiravir will often be used by patients with recent symptom onset, when viral shedding is near its peak. Because the drug is initially absent and builds over time, peak viral shedding is therefore likely to occur when there are still low drug concentrations at the sites of action (i.e., during the first days of administration). This could potentiate the release of mutant—but viable—virus.
  2. Molnupiravir has a short plasma half-life. Molnupiravir’s short plasma half-life (Painter et al. 2021) makes low concentrations easier to achieve, e.g., as a result of missed or inconsistently timed doses.
  3. Coronaviruses have a propensity for recombination. Recombination can help purge viral genomes of deleterious mutations, or generate adaptive combinations of beneficial or compensatory mutations. Thus, it is critical to include recombination and interactions between mutations (i.e., epistasis) in models and simulations.
  4. Sequence content limits mutation rate elevation. SARS-CoV-2 has a pre-existing bias for C→U mutations (Rice et al. 2020), a genomic G:C content of 38%, and a plus-strand C content of 18% (genotype Wuhan-Hu-1). These characteristics limit the extent to which molnupiravir can raise the mutation rate from its current value.
  5. Mutation and transmission limit evolution. Epidemiological spread of adaptive mutations is limited by both their generation via mutation within hosts, as well as the size of transmission bottlenecks between hosts, i.e., the number of viral genomes that establish a new infection.
  6. Individual virus genomes vary in their mutational burden. Even when the mean number of mutations per viral genome is high, the overall distribution of mutation counts can still include a class of minimally mutated viable genomes, due to either the mechanism of mutation or the existence of ‘compartments’ with low drug concentrations within the host.
  7. The mutational robustness of SARS-CoV-2 is not known. The highest mutation rate tolerated by a virus, just possibly 1-5 per genome, depends on the size of the functional genome and the expendability of ‘accessory’ genes.

Clinicians and patients must all be alerted to the critical importance of taking mutagenic antivirals as directed, and should strictly quarantine while doing so, lest transmission occur. Meanwhile, studies assessing the risk of onward transmission of mutated virus should be made a top priority for epidemiologists and evolutionary biologists.

It is easy to underestimate the potential of SARS-CoV-2 to mutate and adapt — a reality made clear by the repeated emergence of variants of concern. We therefore suggest that, until data are obtained on molnupiravir’s potential to generate viable mutated virus, measures are needed to ensure that SARS-CoV-2 is not inadvertently handed mutational resources for the accelerated generation of new variants.


The authors thank Richard J. A. Buggs for raising the main concern addressed herein to C.W.N.; Jesse D. Bloom for raising the issue of mutation- versus bottleneck-limited evolution; and Richard J. A. Buggs, Xinzhu (April) Wei, Zachary Ardern, Fabio Romerio, and Tony Goldberg for discussion and feedback on earlier versions of this manuscript. All views and any errors are our own.

Conflicts of Interest

None declared.

Submission History

  1. SUBMITTED to Nature as Correspondence on October 7, 2021; REJECTED on October 21, 2021
  2. SUBMITTED to Science as Letter on November 3, 2021; REJECTED on November 6, 2021
  3. SUBMITTED to The Lancet as Correspondence on November 9, 2021; WITHDRAWN FROM CONSIDERATION on November 29, 2021
  4. POSTED to Virological on November 29, 2021


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