In the mission to research COVID-19 in North Louisiana, it takes a village.
Louisiana Tech University, Grambling State University, LSU Health Shreveport and several health clinics across the region are working together to sequence the COVID-19 virus to learn how it's spreading and if any new variants arise.
Genomic sequencing allows scientists to identify and monitor how the coronavirus changes over time into new variants, understand how these changes affect the characteristics of the virus and use this information to better understand how it might impact health.
Through these partnerships, the institutions are offering greater learning opportunities for their students and building community trust and education in public health. The project is funded by a grant from the Rockefeller Foundation.
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Previously, there wasn't much research about how COVID was spreading or evolving in the region. Paul Kim, associate professor of biological sciences at Grambling, said before the project began less than 0.5% of positive cases in Lincoln Parish were sequenced, compared to about 2% sequenced across the country.
“COVID-19 models suggest that we need to sequence 5 percent of all positive cases to detect emerging variants early,” Kim said.
This setback was mainly due to lack of resources, said Jamie Newman, associate dean for research and graduate studies in the College of Applied and Natural Sciences at La. Tech. For a time, LSU Health Shreveport was the only institution in the region with sequencing capabilities. Because of this, other samples from the region would be shipped elsewhere, making them less likely to get sequenced in a timely manner, Newman said. Now that Grambling also has sequencing capabilities, scientists can collect COVID samples and study them in time to actually act upon the information collected.
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"We just weren't in a position where we had easy access to sequencing," Newman said. "But with new technology and resources at each institution coming together, the research is now being made possible."
Folks who come into participating clinics and test positive for COVID are asked if they would like to submit their swab for the sequencing project. Submitted swabs are then taken to a lab at either LSU or Grambling, and results are analyzed by researchers from the three universities and made available for the public online at nla-health.com.
Social workers also play a role in this project. Elise Reed, assistant professor and director for Grambling's School of Social Work, said the school helps by building partnerships in the community, engaging citizens for the project and educating them about crucial public health topics.
Tonya Oaks Smith, executive director of university communications and marketing for La. Tech, said the project's combination of health information dissemination and COVID data collection has helped bring equal access to healthcare and healthcare information for the North Louisiana population.
"We've talked about inequity and imbalance in healthcare and availability for all of our populations, and so I think this partnership really helps to start balancing that out," Smith said.
For example, Reed said they were able to set up food distribution for patients in need at one of the clinics. They've also incorporated educational materials, such as on basic COVID information, when people decide to partake in the project.
"I think it's just awesome that social work is involved," Reed said. "Our profession is based on building relationships. Before we go into any type of helping process, a person has to trust you; there has to be some level of rapport, and I believe that's what we bring to the table."
Dr. Jackie White, medical director for The Health Hut, a partnering clinic, said patients at participating clinics are presented with a one-page consent form to learn about the project and decide if they want to participate. So far, no patients have declined to be part of the research project, said Chelsea Streets, office manager at The Health Hut. This is significant because in the past, patient samples have been largely taken without patient consent, according to Newman.
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"We really want to be transparent about what we're doing and give that information back to the members of the community so that they can see how they're contributing," Newman said.
Findings to date show the delta variant is still prominent in the area, but samples for the project haven't been coming in as often because COVID numbers are down. If that changes, and the number of COVID cases goes back up, the same infrastructure will be in place to collect more swabs. Newman said the project will also look to study other diseases in the future, such as influenza.
"We're definitely looking at the the potential of what we've established here with with COVID for other pathogens, other viruses," Newman said. "We may not learn a tremendous amount by sequencing the flu, but certainly being able to understand the infections that exist in your community and maybe how they change over time can lead to in vaccines, the ways we treat people or the ways we screen people — and the ways we prepare as a community for any type of health outbreak."
Follow Sabrina LeBoeuf on Twitter @_sabrinakaye and on Facebook at https://bit.ly/3B8sgHo.
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Two researchers from Edward Via College of Osteopathic Medicine’s Louisiana campus helped publish a new study last month identifying a key evolution in SARS-CoV-2, the virus responsible for the COVID-19 pandemic.
VCOM Louisiana's Lin Kang and Pawel Michalak worked on the study with researchers from Virginia Tech University to figure out how the virus may have adapted from animals to humans. The study, published in the scientific journal "Cell," discovered that the virus's spike protein — the protrusions from the virus that help it bind to human cells — had replaced the threonine amino acid with alanine, therefore increasing how much the virus was then able to connect with human cells.
"We don't really know exactly which coronavirus was ancestral to SARSCoV-2, so that's why now we're looking at the opposite end of it, to see what happens when the virus switches to new hosts, what new mutations are required in the process," Michalak said.
This change allowed the virus to become 20 times stronger when replicating in human lung cells, according to Kang. The researchers also believe the mutation "contributed to SARS-CoV-2 emergence from animal reservoirs or enabled sustained human-to-human transmission."
“This is a critical scientific study that establishes the likely genetic changes in the SARS CoV-2 virus that allowed it to jump from animals to humans,” said Harold “Skip” Garner, associate vice provost for research development at VCOM Virginia. “This establishes an approach for this and potential future pandemic-causing viruses that could allow us to predict detectable changes that could result in the virus becoming more contagious, and open avenues to potentially detect, intercept and mitigate mutating viruses with these changes."
VCOM Louisiana is housed on the campus of the University of Louisiana Monroe.
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Technology advancements gave researchers an abundance of genomes
The study began roughly one year ago. The researchers screened more than 182,00 genomes for selective sweep signatures, which happens when a mutation starts to reoccur frequently. They found other mutations in the genomes but remained focused on the spike protein adaptation.
"We're not limited to the spike gene or protein itself, we can actually look at it from a whole, general perspective," Kang said. "Like all the vaccines, all the focus is on this spike because it just bonding to the ACE2 (hACE2), to the human side."
Since the beginning of the study, Kang said the number of genomes available has increased tenfold. Michalak said SARSCoV-2 has so many sequenced genomes due to the advancement of technology as well as the abundance of the virus.
"What's so striking is the amount of genomic information available for for the coronavirus, which is quite a unique situation," Michalak said. "I don't think it's comparable to anything else before. The virus itself is being sequenced a lot, so that (there are) more than 2 million genome sequences right now."
Researchers had special clearance to work with the coronavirus
Another highlight of the study was that researchers at Virginia Tech were able to work with the actual coronavirus. Kang and Michalak said that many studies concerning the coronavirus do not involve the virus itself due to safety reasons. However, fellow researcher James Weger-Lucarelli had the clearance and the lab needed to conduct experiments for the study.
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The genomes used in the study came mainly from the first round of COVID-19 cases, and as the researchers worked on the study, more strains of COVID-19 developed, with the most prominent one now being the delta variant.
Now, the researchers are going through the millions of genomes to consider a more complete dataset from various angles, including what month the genomes come from and what locale they originate from.
"Like in India, (the) Indian subcontinent is of special interest because this is where that (delta) variant originated," Michalak said. "Hopefully, we can detect some interesting adaptive changes there just within the set of Indian samples. It would be interesting to see how the virus genome was reshaped by the variant's success."
Follow Sabrina LeBoeuf on Twitter @_sabrinakaye and on Facebook at https://bit.ly/3B8sgHo.