Revealing the Genetic Mechanisms Driving SARS-CoV-2 Variants

The SARS-CoV-2 virus, responsible for COVID-19, exhibits a troubling tendency to produce variants frequently. While viruses commonly mutate, the rapid spread of SARS-CoV-2 during the pandemic, resulting in millions of deaths, presented a significant challenge: its ongoing evolution continually tested the efficacy of human immune response and impeded vaccine development efforts.

Gaining insight into the genetic mechanism underlying SARS-CoV-2's capacity to produce variants can be very helpful in preventing COVID-19 outbreaks. Researchers at Baylor College of Medicine and affiliated institutions used a novel technique called tARC-seq to calculate the mutation rate of SARS-CoV-2 and uncover a genetic mechanism influencing the virus's divergence. The study was published in Nature Microbiology.

Additionally, the researchers used tARC-seq to identify novel mutations in SARS-CoV-2 infected cells, which confirmed findings from global pandemic viral sequencing data. The results may help track the evolution of viruses in the human population.

The SARS-CoV-2 virus uses RNA, instead of DNA, to store its genetic information. Our lab has long been interested in studying RNA biology, and when SARS-CoV-2 emerged we decided to investigate its process of RNA replication, which is typically error prone in RNA viruses.”

Dr. Christophe Herman, Corresponding Author and Professor, Department of Molecular and Human Genetics, Baylor College of Medicine

To better understand how the virus evolves, changes, and adapts as it spreads throughout the human population, the researchers wanted to track RNA replication errors. However, the precision of current methods made it difficult to identify rare new SARS-CoV-2 mutations, especially in samples with low viral counts, like those from patients.

Because samples from patients have very few SARS-CoV-2 RNA copies, it is difficult to distinguish between the errors made by SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), the enzyme that makes copies this virus’ RNA, and the errors from the other enzymes used in the sequence analysis. We have developed a technique that we call Targeted Accurate RNA Consensus sequencing (tARC-seq), which allows us to measure true errors when copying specific RNA present in very low amounts.”

Dr. Christophe Herman, Corresponding Author and Professor, Department of Molecular and Human Genetics, Baylor College of Medicine

A New Perspective on the Drivers of SARS-Cov-2 Variant Diversity

Initially, the assumption was that SARS-CoV-2, equipped with an internal mechanism to rectify errors made by RdRp, would not undergo rapid evolution or mutation.

Herman said, “This idea contrasted with the fact that during the pandemic new COVID variants emerged often around the world. Since the pandemic began, we've seen a number of prominent variants, including Alpha, Beta, Delta and Omicron, as well as variants within these groups.”

Using their newly developed analytical instrument, Herman and colleagues were able to precisely ascertain the types and frequency of SARS-CoV-2 mutations in both clinical samples and lab-cultured cell lines.

Herman said, “We found that the mutation rate was higher than originally expected and this helps explain the frequent appearance of COVID variants.”

Additionally, they found that certain regions of the SARS-CoV-2 RNA, known as hotspots, are more likely than others to undergo mutation.

“For example, we identified a hotspot on the RNA region corresponding to the spike protein, the protein that allows the virus to invade cells. Also, RNA of the spike protein makes up many vaccines,” Herman added.

The tARC-seq method also revealed that the generation of new variants involved template switching.

Herman continued, “We determined that, as RdRp is copying one RNA template or sequence, it jumps to another template on a nearby virus and then continues copying the RNA, so the resulting new RNA copy is a mixture of both RNA templates. This template switching will result in sequence insertions or deletions that bring about viral variability. We also observed complex mutations. SARS-CoV-2 takes advantage of these two powerful biological mechanisms, template switching and complex mutations, that allow it to evolve quickly, generating variants to adapt to and persevere in human populations.”

Herman concluded, “It was interesting and exciting to see that tARC-seq allowed us to capture in laboratory cell cultures the emergence of new mutations that recapitulate the mutations observed with worldwide pandemic sequencing data. Our new technology captures a snapshot of new mutations in clinical samples from individual patients and can be useful for monitoring viral evolution in the human population.”