Most are familiar with the field of genomics in relation to ancestry mapping 麻豆精品 S� such as 23andMe and Ancestry.com 麻豆精品 S� uncovering relatives and identifying genetic risk factors for disease. However, genomics has also widely been applied to tracking infectious disease through sequencing the genomes of bacteria, parasites and viruses.
Now, it is helping us to better understand how to combat the coronavirus.
Assistant Professor Taj Azarian, an infectious-disease epidemiologist, is heading up genomic surveillance of SARS-CoV-2 at UCF ahead of the university 麻豆精品 S檚 plans for a full return to face-to-face instruction in the fall.
麻豆精品 S淥ne component to help us with a safe return in the fall is vaccination of as many people as possible. Another is incorporating genomic surveillance of SARS-CoV-2 so we 麻豆精品 S檙e able to track the spread of the virus, 麻豆精品 S� Azarian says. 麻豆精品 S淲hat we want to do is build a ring of protection around the students and employees at the school so that basically we 麻豆精品 S檙e identifying cases as early as possible and implementing public health measures. We 麻豆精品 S檒l also be able to assess the effectiveness of those measures using viral sequencing data. 麻豆精品 S�
Azarian 麻豆精品 S檚 lab takes samples 麻豆精品 S� with individuals 麻豆精品 S� identities redacted 麻豆精品 S� from positive COVID-19 tests and isolates the virus 麻豆精品 S� RNA, or genetic code. The samples are obtained from random testing on campus as well as symptomatic patients at the Student Health Center and the Parking Garage A testing site.
The lab prepares the RNA sample and then inputs it into a genome sequencing platform that enables hundreds of samples to be simultaneously analyzed with the aid of the high-performance computing cluster at UCF. This allows the lab to compare viral sequences among individuals with COVID-19 to look for similarities or differences.
For instance, Azarian says, this analysis could determine if a set of cases is linked to one residence hall, or a social event, which would help officials identify additional cases and determine appropriate public health interventions.
麻豆精品 S淚 like to describe this as building family trees of pathogens, 麻豆精品 S� he says. 麻豆精品 S淏y looking at the relatedness between strains, we can infer a number of things 麻豆精品 S� like how fast an epidemic is spreading, how fast it is evolving and whether it is developing resistance to any of our interventions such as vaccines. 麻豆精品 S�
麻豆精品 S淏y looking at the relatedness between strains, we can infer a number of things 麻豆精品 S� like how fast an epidemic is spreading, how fast it is evolving and whether it is developing resistance to any of our interventions such as vaccines. 麻豆精品 S� 麻豆精品 S� Taj Azarian, assistant professor
Azarian says he was drawn to working at UCF because of its genomics and bioinformatics faculty cluster, which was created to inspire cross-cutting research that leverages UCF 麻豆精品 S檚 strengths in biomedical sciences, evolution and ecology, and computer science.聽That faculty cluster has played a role in aiding his genomic surveillance work during the pandemic.
Since the beginning of the pandemic, he has been working with the Florida Department of Health to monitor the emergence and spread to COVID-19 in the community.
Now his focus will shift to doing the same for UCF, where his lab will be able to compare viral sequences from UCF to those collected throughout Florida and abroad.
It 麻豆精品 S檚 part of a broader initiative led by the Centers for Disease Control and Prevention, which works closely with researchers and public health labs in the United States to generate, share and analyze viral sequencing data. Researchers and public health officials can analyze and compare the data in a larger context to better understand the virus, detect a potential outbreaks of related cases, develop interventions, and monitor emerging variants.聽Recently, Azarian and a colleague at the University of Florida were appointed to collaborate on a project funded by The Rockefeller Foundation to become part of a U.S. Regional Accelerators for Genomic Surveillance program.
Monitoring variants has become increasingly crucial due to their potential to spread easier or cause more severe disease. Azarian says that there is a growing concern for variants for which the vaccine is less effective.
Azarian emphasizes that ensuring individuals 麻豆精品 S� privacy and personal information through the process is a priority and that no one 麻豆精品 S檚 DNA is retained anywhere.
麻豆精品 S淲e 麻豆精品 S檙e only interested in the RNA of the virus, 麻豆精品 S� he says. 麻豆精品 S淚n any of the work that we do, we are not looking for the human DNA that may be present in the sample. We 麻豆精品 S檙e only focusing on the virus 麻豆精品 S� sequence, and once we perform the viral RNA extraction, those samples are discarded. Furthermore, when our results are uploaded to the online repository, we do a screening to make sure there is no human DNA data being uploaded. 麻豆精品 S�
Azarian 麻豆精品 S檚 work in his lab is assisted by two undergraduate students, a recent graduate and two post-doctoral fellows at UCF.
麻豆精品 S淎s an aspiring physician, being involved in such a project is an honor and a once-in-a-lifetime opportunity, 麻豆精品 S� says Anita Samadabadi 麻豆精品 S�20, a Burnett Honors Scholar who graduated in December with a bachelor 麻豆精品 S檚 degree in biomedical sciences. 麻豆精品 S淭his opporutnity allows me to apply what I learned in the classroom about biomedical research to real-world scenarios. My hope is that we all will learn valuable lessons from the COVID-19 pandemic so we never have to face another pandemic again in the future. But if that unfortunately happens, I am sure that the lessons and experiences I am acquiring by being part of this project will help me be an asset for my community. 麻豆精品 S�
Azarian says this field will continue to be critical even as more of the world 麻豆精品 S檚 population is vaccinated.
麻豆精品 S淲e as a community are starting to see the light at the end of the tunnel because of the vaccine, and I think the No. 1 question on everyone 麻豆精品 S檚 mind is, 麻豆精品 S楧id we win the fight? 麻豆精品 S� 麻豆精品 S� he says.
麻豆精品 S淩ight now, I feel like we are in a race between getting people immunized and the spread of some of these new variants. Even as immunization rates are climbing, it 麻豆精品 S檚 imperative we continue this surveillance so we can identity whether those variants continue to emerge and what that means for the future of the vaccine 麻豆精品 S� whether it will need to be updated at some point to be more like the seasonal influenza vaccine, or if this one is going to work against the strains now and the ones that may emerge in the future. Genomic surveillance will help us answer these questions. 麻豆精品 S�
