Gene sequencing, an important tool in the battle against COVID-19

Despite concentrated efforts by scientists, medical professionals and public health experts to defeat SARS-CoV-2, the novel coronavirus that causes COVID-19, the pandemic has continued to creep into our daily lives for more than two years. As promising vaccines and pills are developed, the virus mutates to create a new variant in an effort to outwit the latest treatments and stay active.

And so on, with early strains such as alpha, beta and gamma giving way to later mutations such as delta and omicron and its many sub-lines (e.g. BA.1 and BA.2, BA.3 and currently BA.4 and BA.5). So how does science keep pace with COVID-19 treatments when the virus itself is a moving target?

The answer is gene sequencing, a process by which scientists determine the sequential order of the four building blocks that make up a strand of DNA. These building blocks, known as nucleotides, include adenine, thymine, cytosine, and guanine. Millions and billions of these nucleotides are linked together in each of us, giving us our unique genome which houses all the genetic information that makes us tick.

When an organism reproduces, it passes on a copy of its entire genome to its descendants. However, errors sometimes occur during the replication process, which means that one or more of the four constituent nucleotides are swapped, deleted or otherwise changed. This in turn can alter genes and affect replicated genome functions. In humans, genetic changes or mutations help determine characteristics such as eye color. In a virus like SARS-CoV-2, they can alter, for better or worse, the organism’s ability to spread from host to host, the severity of its infection, or its ability to escape vaccines and other potential treatments.

Gene sequencing in general has long been a tool used by microbiologists, and it is a key public health response to the COVID-19 pandemic. Sharilyn Almodóvar, Ph.D., a researcher in the Department of Immunology and Molecular Microbiology at the Texas Tech University Health Sciences Center (TTUHSC) School of Medicine, said the methods used to perform the sequencing can be adapted to meet to almost any situation, meaning its potential uses are virtually endless.

“In the specific case of the COVID-19 pandemic, gene sequencing is the tool that allows us to know the virus we are fighting,” Almodóvar said. “Every time the virus finds a host to replicate, new viruses appear with mutations. Sequencing viral genes allows us to identify these mutations, how quickly they spread, where these mutations spread in terms of geographic location, and what time of year that is. has passed. All of this is essential to what we call virus monitoring. »

Most mutations are harmless to the host, but they will eventually improve the chances of the virus replicating more efficiently in the next host. Almodóvar said tracking viral mutations is critical because that is precisely how new variants are identified.

“This is how we know the enemy we are fighting,” added Almodóvar. “Coronaviruses have been around for a long time, but this pandemic has been different in many ways.”

TTUHSC School of Medicine Dean Steven L. Berk, MD, agreed and said the Texas Tech Institute for Environmental and Human Health (TIEHH), established in 1999 as a bioterrorism response laboratory, has launched a genomic sequencing program to classify variants of the SARS-COV -2 virus. The program helps public health officials better understand the progression of the virus and the impact of its variants on the local population.

“While gene sequencing is done by many labs across the state, country, and world, it’s important to know what variants of COVID-19 are circulating in West Texas,” Berk explained. “The TIEHH lab provides this information to physicians, hospitals and public health officials.”

The information provided by the TIEHH laboratory will help prepare healthcare workers for any new pandemic-related developments. If there were to be another delta-like variant, or additional contagious or virulent variants, Afzal A. Siddiqui., Ph.D., director of the Center for Tropical Medicine and Infectious Diseases at TTUHSC, said sequencing genes would identify the strain and help determine whether or not new public health measures — or a return to previous guidelines — might be needed.

“Gene sequencing [also] will alert us to any variants that may evade the immune system of vaccinated individuals,” Siddiqui said. “It will also help us track any new strains from place to place and provide clues as to how strains spread among populations.”

The TIEHH Laboratory for Gene Sequencing provides a very important tool to continue the effective fight against the COVID 19 pandemic in West Texas. Berk said the TTUHSC, its regional campuses and centers of excellence are an integral part of this endeavor.

“TTUHSC faculty and staff are facilitating specimen collection and transportation from TIEHH-affiliated hospitals in a concerted effort to prepare for the next outbreak of COVID-19,” he added.

Gene sequencing is also important in vaccine development. Whenever a new variant is identified, one of the first questions asked is whether or not our current vaccine strategy will protect the public against the new variant, or do we need to make adjustments? This adjustment could consist of either adding another round of boosters or reformulating the vaccine.

When a new variant emerges, Almodóvar said it is essential to study the correlation between the viral sequencing (or viral identity) of the new variant, the damage it causes in the host and the measurement in which current vaccines may or may not prevent further harm. . And while gene sequencing is a very powerful tool at this point in the pandemic, she said prevention measures will continue to play their part as we bring this pandemic to an end.

“The cases are low now, but now more than ever we must not let go of the ball,” Almodóvar stressed. “We need to remain conscientious about what we can do to prevent new infections, and therefore new viral genetic mutations. I think that’s how sequencing is key at this point. Now that we seem to see the light at the end of this pandemic tunnel, COVID-19 sequencing keeps our eyes peeled in case new concerning variants arise and increase our overall pandemic preparedness.

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