Despite the focused efforts of scientists, medical professionals and public health experts to defeat SARS-CoV-2, the novel coronavirus that causes COVID-19, the pandemic has continued to weave its way 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 outsmart the latest treatments and stay active.
And so it goes, with early strains like alpha, beta and gamma giving way to later mutations like delta and omicron and its many sublines (e.g. BA.1 and BA.2, BA.3 and currently BA.4 and BA.5) . So how does science keep up with the COVID-19 treatments when the virus itself is a moving target?
The answer is gene sequencing, a process by which scientists determine the order of the four building blocks that make up a DNA strand. Those 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 that contains all the genetic information that drives us.
When an organism reproduces, it passes on a copy of its entire genome to its offspring. However, errors sometimes occur during the replication process, meaning one or more of the four building block nucleotides are switched, deleted, or otherwise altered. This, in turn, can modify genes and affect the functions of the replicated genome. In humans, genetic modifications or mutations help determine characteristics such as eye color. In a virus like SARS-CoV-2, they can change the organism’s ability to spread from host to host, the severity of the infection, or the ability to evade vaccines and other potential treatments for better or worse.
Gene sequencing in general has long been a tool used by microbiologists, and it is an important public health response to the COVID-19 pandemic. Shalyn Almodóvar, Ph.D., a researcher for the Department of Immunology and Molecular Microbiology at Texas Tech University Health Sciences Center (TTUHSC) School of Medicine, said the methods used to perform sequencing can be adapted to nearly any situation, meaning its potential uses are virtually endless.
“In the specific case of the COVID-19 pandemic, gene sequencing is the tool through which we get to know the virus we are fighting,” Almodóvar said. “Every time the virus finds a host to replicate, the new viruses with mutations appear. Viral gene sequencing allows us to identify those mutations, how quickly they reproduce, where those mutations are spread in terms of geographic location and in what time of year this is happening. All of that is key to what we call virus surveillance.”
Most mutations are harmless to the host, but they will eventually increase the chance that the virus will replicate more efficiently in the next host. Almodóvar said tracking virus mutations is critical because that’s exactly how new variants are identified.
“This is how we know the enemy we are fighting,” Almodóvar added. “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, saying that the Texas Tech Institute for Environmental and Human Health (TIEHH), founded in 1999 as a bioterrorism response lab, initiated a genomic sequencing program for classifying of variants of the SARS-COV-2 virus. The program helps public health officials better understand the progress of the virus and the impact of its variants on local populations.
“While gene sequencing is being done by many labs in the state, country and the world, it is important to know the COVID-19 variants circulating in West Texas,” Berk explains. “The TIEHH lab is providing that information to doctors, hospitals and public health officials.”
Information provided by the TIEHH laboratory is helping health professionals prepare for new developments related to the pandemic. Should there be another delta-like variant, or additional infectious or virulent variants, Afzal A. Siddiqui., Ph.D., director of TTUHSC’s Center for Tropical Medicine and Infectious Diseases, would say gene sequencing would identify and help the strain. determine whether or not new public health measures — or a return to previous guidelines — may be necessary.
“Gene Sequencing” [also] will alert us to any variants that could evade the immune system of vaccinated individuals,” Siddiqui said. “It will also help us track new strains from one place to another and provide clues about how strains spread among populations.”
The TIEHH gene sequencing lab provides a very important tool to continue the effective fight against the COVID 19 pandemic in West Texas. Berk said TTUHSC, its regional campuses and centers of excellence are an integral part of that endeavor.
“The faculty and staff of the TTUHSC are facilitating the collection and transportation of samples from member hospitals to TIEHH in a concerted effort to prepare for the next wave of COVID-19,” he added.
Gene sequencing is also important in vaccine development. Whenever a new variant is identified, one of the first questions that is asked is whether our current vaccine strategy will protect the public from the new variant, or should we make adjustments? That adjustment could be either adding another round of booster shots or reformulating the vaccine.
When a new variant appears, Almodóvar said it is critical to examine the correlation between the viral sequencing (or viral identity) of the new variant, the damage it causes in the host, and the extent to which current vaccines continue to develop. damage may or may not be prevented. † And while gene sequencing is a very powerful tool at this stage of the pandemic, she said prevention measures will continue to play their part in ending this pandemic.
“The number of cases is now low, but now more than ever we must not drop the ball,” Almodóvar emphasized. “We must remain conscientious about what we can do to prevent further infections and thus new viral genetic mutations. I think order is key at this point. As we appear to see the light at the end of this pandemic tunnel, COVID-19 sequencing is keeping our eyes open in case new variants emerge and increasing our overall preparedness for a pandemic.”
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