Random changes are an important component of all living things. It drives diversity, and that’s why there are so many different species. Viruses are no exception. Most viruses are specialists in changing genomes to adapt to the environment. We now have evidence that the virus that causes Covid, SARS-CoV-2, is not only changing but also changing in important ways. This is the fourth part of a series of articles on how the virus changes and what it means for humanity. Read the rest: part one,, part two,, part three, and part four.
The researchers identified two new variants of SARS-CoV-2 by genome sequencing in Columbus, Ohio, according to a preprint report pending publication on bioRxiv. This is the first study to confirm our fear that options have been evolving in the U.S. all along – we just weren’t looking for them. But this will not be the last. In fact, another preprint of the study, conducted in Illinois, was published just today.
The following is an analysis of a quickly issued preprint sent to me in advance by a colleague from Wexner Medical Center.
Previously, I discussed how a virus changes through random changes in its genetic code that accumulate with each passage of the host. The greater the viral transmission, the more variants the virus lurks. These variants may develop virus-enhancing properties, such as greater infectivity, as we have seen in the UK and South Africa variants, or immune resistance arising from natural antibodies or vaccines.
The variants sorted in the Ohio study differ from the strains of the United Kingdom and South Africa, B.1.1.7 and 501.V2, respectively, which spread to most of the world. An analysis of their origins revealed that they actually live in the United States, becoming the dominant strain in Columbus.
The study, conducted by scientists at Ohio State University, examines the genomic sequences of two new variants of SARS-CoV-2, taken from 222 samples taken from April 2020 to January 2021. The first, which was observed in late December, has several mutations in S, N proteins and M. During the week of Dec. 21, these mutations were detected in 10 percent of the sequenced samples. By next week, their number had grown to 30 percent. The following week it was a staggering 60 per cent – a sharp enough increase to suggest that the option is highly contagious.
A second potentially troubled variant, COH.20G / 501Y, was also identified – this time having two mutations observed in the UK variant, N501Y and ORF8 R521. It is believed that a mutational mutation in the N501Y protein increases virus transmission, although ORF8 R521 may also play a role. This option is probably very infectious. However, unlike the first option, it was highlighted in only one sample. Although the sample size is so small, the change may be due to a super-spread event, the choice of beneficial mutations implies a wider arc of evolution.
Most research in Ohio underscores an old saying: if you look, you will find. Now that we are building up our ability to investigate the virus and follow us, we also need to evolve from a place of complacency to one of heightened vigilance. The goal is to anticipate and prevent the further spread of new options, not to lag behind forever. While we cannot predict the exact mutations we expect, we can specifically look for patterns that prescribe certain hazards, such as increased infectivity, virulence, or immune escape.
Another lesson we can learn from research in Ohio is that currently the focus on the protein shell with spikes is too narrow. Instead of going through a tunnel just on a spike, we need to expand our sights to include the entire genome. SARS-CoV-2 produces a number of proteins that go by the common name open reading frame gene (orf), followed by a number and sometimes an additional letter to distinguish one. Although we do not know as much about them as about protein, but all we know orf genes, such as ORF8, may play a crucial role in enhancing the suitability of new variants. Similarly, other structural proteins and nonstructural proteins that have so far been excluded from the scope of the study could.
These new options by Ohio and others, which are likely to be isolated in the near future, could shed light on the aggressive rise in cases the U.S. has faced in recent weeks. The exchange of similar mutations with variants in the UK, which has been confirmed to increase bandwidth and is a major reason for the current UK blockade, suggests that a similar increase in transmission is occurring in the US. As the number of infected people increased and as the virus became fully and partially present in mixed immune states, the virus gained ample opportunity to spread, mutate, and enhance viral potency. These opportunities will only increase if they are not opposed by strict health measures and ongoing vaccination.