Tara C. Smith writes:

Viruses evolve. It’s what they do. That’s especially true for a pandemic virus like SARS-CoV-2, the one behind COVID-19. When a population lacks immunity and transmission is extensive, we expect viral mutations to appear frequently simply due to the number of viruses replicating in a short period of time. And the growing presence of immune individuals means that the viruses that can still transmit in these partially immune populations will be favored over the original version. Sure enough, that’s what we’ve been seeing, as news reports warn of the appearance of novel variants (viruses with several mutations, making them distinct from their ancestors) and strains (variants that are confirmed to behave differently from the original).

To be clear, mutations are random errors that occur when a virus reproduces. In the case of SARS-CoV-2, which has an RNA genome based on adenine, cytosine, guanine and uracil, sometimes mistakes happen. Maybe an adenine gets swapped with a uracil (a substitution mutation that could also occur with any of the base pairs), or perhaps one or more bases get inserted or deleted. If a mutation actually changes the protein encoded by that part of the RNA sequence, it’s referred to as a non-synonymous mutation. Mutations that do not result in a protein change are referred to as synonymous, or silent, mutations.

Luckily, the mutation rate of coronaviruses generally is relatively slow, due to a proofreading ability in the virus that allows for some correction of replication mistakes. Typically SARS-CoV-2 will accumulate only two mutations per month among its genome’s 30,000 base pairs; that’s half the rate of an influenza virus, and a quarter of the rate of HIV. But with more than 100 million people infected to date, non-synonymous mutations are inevitable. The bigger issue is determining which mutations actually provide the virus enough of an advantage to increase its spread through the population.

Fortunately, at this point we have the knowledge to answer some of the most pressing questions. [Continue reading…]