Researchers have created a new technology called tARC-seq, which has uncovered a genetic mechanism that influences SARS-CoV-2 divergence and has allowed the team to calculate the mutation rate of SARS-CoV-2. With tARC-seq, the researchers were able to detect new mutations in SARS-CoV-2 within infected cells in the laboratory, which mirrored the observations made by worldwide pandemic viral sequencing data. These findings could be valuable for tracking the evolution of the virus in the human population.
The SARS-CoV-2 virus, which causes COVID, has the unsettling ability to frequently generate variants of itself. While other viruses also mutate, SARS-CoV-2 seems to do so at a higher rate.The virus quickly spread through the global population during the pandemic, causing widespread death. Its rapid evolution presented a major problem as it continuously challenged the immune system and slowed down the development of updated vaccines.
A better understanding of the genetic process driving the virus’s ability to create new variants can play a crucial role in controlling COVID-19. A recent study published in Nature Microbiology by researchers at Baylor College of Medicine and other institutions introduced a new technology called tARC-seq. This technology unveiled a genetic mechanism affecting the virus’s ability to generate variants.g The team used tARC-seq to study the divergence of SARS-CoV-2 and calculate its mutation rate. They also identified new mutations in SARS-CoV-2 in infected cells in the lab, which matched observations from global viral sequencing data. These findings are important for tracking the evolution of the virus in the human population.
“SARS-CoV-2 stores its genetic information in RNA, not DNA. Our lab has always been interested in RNA biology, so when SARS-CoV-2 emerged, we wanted to study its RNA replication process, which is known to be error-prone in RNA viruses,” said corres.Dr. Christophe Herman, a professor of molecular and human genetics and molecular virology and microbiology at Baylor, stated that the goal of the study was to track the errors in RNA replication in order to better understand how the virus evolves and adapts as it spreads through the human population. Current methods were not precise enough to detect rare mutations in the SARS-CoV-2 virus, especially in samples with a low number of viruses, like those from patients. Dr. Herman explained that it is challenging to distinguish between the errors made by the SARS-CoV-2 virus due to the low number of RNA copies present in patient samples.RNA polymerase (RdRp), the enzyme responsible for replicating this virus’ RNA, and the errors produced by other enzymes used in the sequence analysis,” explained Herman, a member of the Dan L Duncan Comprehensive Cancer Center. “We have created a method called Targeted Accurate RNA Consensus sequencing (tARC-seq), which enables us to accurately measure errors when replicating specific RNA that is present in very low quantities.”
A fresh perspective on the factors contributing to SARS-CoV-2 variant diversity
Initially, it was believed that because SARS-CoV-2 has an internal mechanism for fixing mistakes made by RdRp, the virus should not undergo evolution. However, a new technique called tARC-seq has challenged this notion.
The mutation rate of SARS-CoV-2 is high and new COVID variants emerge frequently around the world,” Herman explained. Several prominent variants, such as Alpha, Beta, Delta, and Omicron, have emerged since the pandemic began. With their enhanced analytical tool, Herman and his team accurately identified the mutation frequency and types of mutations in both lab cell cultures and clinical samples. They discovered that the mutation rate was higher than initially anticipated, which helps to explain why the virus mutates so rapidly.
According to Herman, COVID variants are appearing frequently. The researchers also found certain spots in the SARS-CoV-2 RNA that are more likely to mutate. One of these hotspots is in the RNA region that corresponds to the spike protein, which is responsible for the virus’s ability to invade cells. This spike protein RNA is also a key component of many vaccines, Herman explained.
The tARC-seq method also showed that the creation of new variants involves template switching. This means that while RdRp is copying one RNA sequence, it switches to another nearby sequence and continues copying from there.
e RNA is copied from two different RNA templates, resulting in a new RNA copy that contains a combination of both templates,” Herman explained. This process of template switching leads to the insertion or deletion of sequences, leading to viral variability. The researchers also observed complex mutations. The SARS-CoV-2 virus utilizes these two biological mechanisms, template switching and complex mutations, to evolve rapidly and produce variants that can adapt to and thrive in human populations.”
“It was fascinating and thrilling to observe that tARC-seq allowed us to observe the emergence of new mutations in laboratory cell cultures that mirror the mutations seen in the global pandemic.Herman explained that their new technology can capture new mutations in clinical samples from individual patients, which is helpful for monitoring viral evolution in the human population. The contributors to this work include Catherine C. Bradley, Chen Wang, Alasdair J.E. Gordon, Alice X. Wen, Pamela N. Luna, Matthew B. Cooke, Brendan F. Kohrn, Scott R. Kennedy, Vasanthi Avadhanula, Pedro A. Piedra, Olivier Lichtarge, Chad A. Shaw, and Shannon E. Ronca. These authors are associated with Baylor College of Medicine, University of Washington, and Texas Children’s Hospital.l.
The research received support from National Institutes of Health grants R01GM088653, 3R01AG061105-03S1, 1R21CA259780, and 1R21HG011229, as well as National Science Foundation grant DBI-2032904.
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