Category Archives: Transhuman News

Patients across the UK will benefit from better healthcare, treatments and faster diagnosis as the government sets out how it will continue to deliver world-leading genomic healthcare.

Genomics is the study of genetic information and can help diagnose diseases earlier and more accurately, reduce some invasive procedures and enable tailored treatments. Building on the success of the 100,000 Genomes Project, the UK government has committed to sequence one million whole genomes 500,000 genomes in the NHS and 500,000 in UK Biobank which will transform healthcare in the UK and create jobs.

In addition, genomics has also been used to better understand Covid-19 and the variants that have increasingly become one of the biggest concerns of the pandemic.

Each variant is made up of a collection of mutations. The majority of mutations dont change how the virus behaves. However, some mutations can change the properties of the virus, and potentially give rise to a new variant. Many of these mutations of interest occur in the spike protein, which is what gives the virus its ability to target, latch onto and enter the cells that it infects.

Working with key partners across the genomics community, the bold new Genome UK implementation plan 2021 to 2022, published in May, sets out 27 commitments to deliver over the next year, including five high-priority actions: faster diagnosis; whole genome sequencing for patients with rare diseases; engagement closely with different communities to ensure diverse datasets; recruitment of up to five million people representative of the UK population; to develop global standards and policies for sharing genomic and related health data.

Faster diagnosis and treatment of cancer using genomics through a partnership between Genomics England and NHS England will help researchers and healthcare professionals identify technologies that could be used to provide faster and more comprehensive genomic testing for cancer.

Whole genome sequencing for patients with rare diseases and cancer, as part of the NHS Genomic Medicine Service, will build on the success of the 100,000 Genomes Project, and aims to increase the amount of genomic data available to researchers.

The drive for larger and more diverse datasets from different communities aims to ensure that everyone across the UK can benefit from genomic healthcare and genomic databases that are representative of such a diverse population. This is essential for equitable access to new techniques, such as polygenic risk scores (PRS), which compares a persons risk to others with a different genetic makeup, and pharmacogenomics, which examines the role of the genome in the bodys response to drugs.

Developing global standards and policies for sharing genomic and related health data ensures accurate and quick sharing of research data, which will help to benefit the entire genomics community.

The National Institute for Health Research, Medical Research Council and Wellcome Trust will, over the next five years, provide 4.5m of funding to the Global Alliance for Genomics and Health, ensuring standards are easily accessible and usable by global genomic programmes and data-sharing initiatives, placing the UK at the forefront of secure sharing of international genomic and health-related data.

Matt Hancock, the UKs Health Secretary, said: We will transform the UK into a life sciences superpower. Well build on the success story of our life sciences during the pandemic, which has led the world in everything from vaccine development, to finding effective treatments that work, to genomic sequencing.

Today weve published our Genome UK implementation plan for how we can build on this even further, including our commitment to sequence one million whole genomes. Because genomics saves lives, and Im determined the UK stays at the forefront of this vital new technology, Hancock continued. If we draw on ingenuity like this, we can keep up the fight against Covid-19, and also tackle the other things that stop us living healthier lives like cancer, dementia and heart disease.

So, were increasing UK investment in research and development, bringing much more of the supply chain onshore, sparing no effort to attract the brightest innovators and the best manufacturers, he concluded.

Minister for Innovation Lord Bethell said: The UK has a proud history in developing genetic and genomic technologies which improve the lives of patients across the country and globally.

This implementation plan demonstrates the great strides we have already made since the launch of Genome UK, and outlines the actions we are taking to progress key commitments over the next year.

It is vital that we continue to maintain and develop our global leadership in this field, to realise the full potential offered by genomics, Lord Bethell added.

This first phase implementation plan follows on from Genome UK: the Future of Healthcare published in 2020, which set out a vision to create the most advanced genomic healthcare system in the world, to deliver better healthcare at lower cost.

Genomics is just one example of the governments commitment to driving forward health innovation in the UK, which will be central to the future health resilience, the growth of the UKs life sciences sector and improving patient care.

Chris Wigley, Genomics England CEO, said: Since the days of Darwin, Rosalind Franklin, Crick and Watson, and Fred Sanger, the UK has been at the forefront of genomic science. With this publication its exciting to see the next chapter of that story coming to life. Our ecosystem has come together as never before through the difficult times of the pandemic and this implementation plan will allow us to build on this collaboration between all of the world-leading genomics institutions in the UK.

Professor Dame Sue Hill, NHS Englands Chief Scientific Officer, said: The NHS is already a global leader in genomics and has introduced a range of new cutting-edge tests for people with rare diseases and cancer over the last year, despite the pandemic.

Genomics can truly transform the way patient care is delivered, helping to predict and prevent disease, personalise treatments and ultimately save lives.

In February 2021, the UKs Covid-19 Genomics UK Consortium (COG UK) launched the COG-UK Mutation Explorer (COG-UK-ME) an interface that provides access to data on Sars-CoV-2 mutations and variants of interest in the COG-UK genome sequence dataset. COG-UK-ME allows anyone to view information about important changes in the Sars-CoV-2 genome over time.

The tool is updated twice weekly, and largely focuses on spike gene mutations of potential or known importance; providing information on cumulative frequency and data for the last 28 days, to give an approximate assessment of recent changes.

COG-UK-ME draws UK genome data from the MRC-CLIMB database. This data visualisation tool allows anyone to follow information over time on important changes in the Sars-CoV-2 genome.

Selecting the Mutational Explorer tab takes you to three tables. Table 1 lists mutations in the spike gene that have led to an amino acid change (called a substitution, which is concentrated on because it may change the way that the virus interacts with humans).

Mutations are ranked by frequency in the MRC-CLIMB database (the most common mutations first). A search function allows individual mutations to be selected, and a file downloaded containing a list of COG-UK identifiers, dates and lineages. For example, selection of E484K provides links to information for each genome that carries this mutation, the date of the sample, and the lineage the isolate belongs to.

Data can also be visualised for each mutation in a graph by clicking the visualiser tab. This shows the number of times the selected mutation has been detected over time.

COG-UK-ME also displays mutations that could affect the way that the virus interacts with the human immune response based on laboratory studies (Antigenic information tab).

Scientific evidence is graded. High confidence is applied when a mutation is found by multiple independent studies using multiple different approaches, including studies using polyclonal (convalescent or post-vaccine) antisera; medium confidence means this has been found by multiple independent studies; and lower confidence indicates this has been found by a single study only. Mutations with an antigenic role can also be filtered by domains of the spike protein.

The Explorer will be updated with new functions over time, based on scientific observations and ways of describing and thinking about variants. The current Covid-19 pandemic, caused by Sars-CoV-2, represents a major threat to health. The Covid-19 Genomics UK (COG-UK) consortium has been created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government.

Led by Professor Sharon Peacock of Cambridge University, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and 12 academic partners providing sequencing and analysis capacity. Professor Peacock is also on a part-time secondment to PHE as director of science, where she focuses on the development of pathogen sequencing through COG-UK.

COG-UK was established in April 2020 supported by 20m funding from the Covid-19 rapid-research-response fighting fund from the UK government, and administered by the National Institute for Health Research, UK Research and Innovation and the Wellcome Sanger Institute.

The consortium was also backed by the Department of Health and Social Cares Testing Innovation Fund in November last year to facilitate the genome sequencing capacity needed to meet the increasing number of Covid-19 cases in the UK over the winter.

More here:
UK at the forefront of genomics research - Scientific Computing World

The move to study genome sequences of the virus that infected children is part of Karnataka's effort to prepare for the third wave of infections.

June 17, 2021 / 01:52 PM IST

Karnataka has started genome sequencing of the SARS-CoV-2 virus among children who tested positive during the second wave to determine whether the infections are being caused by the newer variants of the virus.

The state has tasked Prof V Ravi, a former professor of virology, to study the gene sequences in samples of children who tested positive for COVID-19, as per an Indian Express report.

Track this LIVE blog for latest updates on coronavirus pandemic

Ravi said that samples are being collected and they need to be processed. "We should have data and information in about 15 days, he said, as quoted by the publication.

The move to study genome sequences of the virus that infected children is part of the state's effort to prepare for the third wave of infections.

"We have discussed the issue of infections among children and some additional work is required to study the genomic sequencing of viruses from samples of children," said Prof MK Sudarshan, the chairman of the state technical advisory committee, as per the report.

The state government had earlier in June formed a Genomic Surveillance Committee to identify the emerging strains early so that scientists can establish the transmissibility of the new strain.

The committee, under the leadership of Dr V Ravi, will assist the Karnataka COVID-19 Task Force in taking decisions towards controlling the COVID-19 pandemic.

The panel has also been tasked with "Genome sequencing to study virus variations/mutations and conduct an in-depth analysis of genome surveillance and vaccination to identify immune escape versions of virus and their spread".

Meanwhile, Karnataka reported 7,345 new cases of COVID-19 and 148 fatalities on June 16, taking the total number of infections to 27,84,355 and the deaths to 33,296, the Health Department said. The total number of active cases in the state is 1,51,566.

Excerpt from:
Coronavirus third wave: Karnataka begins genome sequencing of children to prepare - Moneycontrol

Most are familiar with the field of genomics in relation to ancestry mapping such as 23andMe and Ancestry.com 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 universitys plans for a full return to face-to-face instruction in the fall.

One 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 were able to track the spread of the virus, Azarian says. What we want to do is build a ring of protection around the students and employees at the school so that basically were identifying cases as early as possible and implementing public health measures. Well also be able to assess the effectiveness of those measures using viral sequencing data.

Azarians lab takes samples with individuals identities redacted from positive COVID-19 tests and isolates the virus 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.

I like to describe this as building family trees of pathogens, he says. By looking at the relatedness between strains, we can infer a number of things 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.

By looking at the relatedness between strains, we can infer a number of things 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. 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 UCFs strengths in biomedical sciences, evolution and ecology, and computer science.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.

Its 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.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 privacy and personal information through the process is a priority and that no ones DNA is retained anywhere.

Were only interested in the RNA of the virus, he says. In any of the work that we do, we are not looking for the human DNA that may be present in the sample. Were only focusing on the virus 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.

Azarians work in his lab is assisted by two undergraduate students, a recent graduate and two post-doctoral fellows at UCF.

As an aspiring physician, being involved in such a project is an honor and a once-in-a-lifetime opportunity, says Anita Samadabadi 20, a Burnett Honors Scholar who graduated in December with a bachelors degree in biomedical sciences. This 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.

Azarian says this field will continue to be critical even as more of the worlds population is vaccinated.

We 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 everyones mind is, Did we win the fight? he says.

Right 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, its 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 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.

Continued here:
What Is Genomic Surveillance and Why Is It Being Done at UCF? - UCF

A ball of 4,000-year-old hair frozen in time tangled around a whalebone comb led to the first ever reconstruction of an ancient human genome just over a decade ago.

The hair, which was preserved in arctic permafrost in Greenland, was collected in the 1980s and stored at a museum in Denmark. It wasn't until 2010 that evolutionary biologist Professor Eske Willerslev was able to use pioneering shotgun DNA sequencing to reconstruct the genetic history of the hair.

He found it came from a man from the earliest known people to settle in Greenland known as the Saqqaq culture. It was the first time scientists had recovered an entire ancient human genome.

Now a review of the first decade of ancient genomics of the Americas published in Nature today (June 16 2021) written by Professor Willerslev a Fellow of St John's College, University of Cambridge, and director of The Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, with one of his longstanding collaborators Professor David Meltzer, an archaeologist based at Southern Methodist University, Texas, shows how the world's first analysis of an ancient genome sparked an incredible 'decade of discovery'.

Professor Willerslev said: "The last ten years has been full of surprises in the understanding of the peopling of the Americas - I often feel like a child at Christmas waiting to see what exciting DNA present I am about to unwrap! What has really blown my mind is how resilient and capable the early humans we have sequenced DNA from were - they occupied extremely different environments and often populated them in a short space of time.

"We were taught in school that people would stay put until the population grew to a level where the resources were exhausted. But we found people were spreading around the world just to explore, to discover, to have adventures.

"The last 10 years have shown us a lot about our history and what it means to be human. We won't ever see that depth of human experience on this planet again - people entered new areas with absolutely no idea of what was in front of them. It tells us a lot about human adaptability and how humans behave."

For decades, scientists relied on archaeological findings to reconstruct the past and theories weren't always accurate. It was previously thought, that there were early non-Native American people in the Americas but the ancient DNA analysis so far has shown that all of the ancient remains found are more closely related to contemporary Native Americans than to any other population anywhere else in the world.

Professor Meltzer, who worked on the review with Professor Willerslev while the former was at St John's College as a Beaufort Visiting Scholar added: "Genomic evidence has shown connections that we didn't know existed between different cultures and populations and the absence of connections that we thought did exist. Human population history been far more complex than previously thought.

"A lot of what has been discovered about the peopling of the Americas could not have been predicted. We have seen how rapidly people were moving around the world when they have a continent to themselves, there was nothing to hold them back. There was a selective advantage to seeing what was over the next hill."

In 2013, scientists mapped the genome of a four-year-old boy who died in south-central Siberia 24,000 years ago. The burial of an Upper Palaeolithic Siberian child was discovered in the 1920s by Russian archaeologists near the village of Mal'ta, along the Belaya river. Sequencing of the Mal'ta genome was key as it showed the existence of a previously unsampled population that contributed to the ancestry of Siberian and Native American populations.

Two years later, Professor Willerslev and his team published the first ancient Native American genome, sequenced from the remains of a baby boy ceremonially buried more than 12,000 years ago in Anzick, Montana.

In 2015, their ancient genomic analysis was able to solve the mystery of Kennewick Man, one of the oldest and most complete skeletons ever found in the Americas, and one of the most controversial.

The 9,000-year-old remains had been surrounded by a storm of controversy when legal jurisdiction over the skeleton became the focus of a decade of lawsuits between five Native American tribes, who claimed ownership of the man they called Ancient One, and the United States Army Corps of Engineers.

Professor Willerslev, who has rightly learnt to be mindful of cultural sensitivities when searching for ancient DNA, has spent much of the past decade talking to tribal community members to explain his work in detail and seek their support.

This meant he was able to agree with members of the Colville Tribe, based in Washington State where the remains were found, that they would donate some of their DNA to allow Professor Willerslev and his team to establish if there was a genetic link between them and Kennewick Man.

Jackie Cook, a descendant of the Colville Tribe and the repatriation specialist for the Confederated Tribes of the Colville Reservation, said: "We had spent nearly 20 years trying to have the Ancient One repatriated to us. There has been a long history of distrust between scientists and our Native American tribes but when Eske presented to us about his DNA work on the Anzick child, the hair on my arms stood up.

"We knew we shouldn't have to agree to DNA testing, and there were concerns that we would have to do it every time to prove cultural affiliation, but our Council members discussed it with the elders and it was agreed that any tribal member who wanted to provide DNA for the study could."

The Kennewick Man genome, like the Anzick baby, revealed the man was a direct ancestor of living Native Americans. The Ancient One was duly returned to the tribes and reburied.

Cook added: "We took a risk but it worked out. It was remarkable to work with Eske and we felt honoured, relieved and humbled to be able to resolve such an important case. We had oral stories that have passed down through the generations for thousands of years that we call coyote stories - teaching stories. These stories were from our ancestors about living alongside woolly mammoths and witnessing a series of floods and volcanoes erupting. As a tribe, we have always embraced science but not all history is discovered through science."

Work led by Professor Willerslev was also able to identify the origins of the world's oldest natural mummy called Spirit Cave. Scientists discovered the ancient human skeleton back in 1940 but it wasn't until 2018 that a striking discovery was made that unlocked the secrets of the Ice Age tribe in the Americas.

The revelation came as part of a study that genetically analysed the DNA of a series of famous and controversial ancient remains across North and South America including Spirit Cave, the Lovelock skeletons, the Lagoa Santa remains, an Inca mummy, and the oldest remains in Chilean Patagonia.

Scientists sequenced 15 ancient genomes spanning from Alaska to Patagonia and were able to track the movements of the first humans as they spread across the Americas at 'astonishing' speed during the Ice Age and also how they interacted with each other in the following millennia.

The team of academics not only discovered that the Spirit Cave remains was a Native American but they were able to dismiss a longstanding theory that a group called Paleoamericans existed in North America before Native Americans. Spirit Cave was returned to The Fallon Paiute-Shoshone Tribe, a group of Native Americans based in Nevada, for burial.

Professor Willerslev added: "Over the past decade human history has been fundamentally changed thanks to ancient genomic analysis - and the incredible findings have only just begun."

Reference:Willerslev E, Meltzer DJ. Peopling of the Americas as inferred from ancient genomics. Nature. 2021;594(7863):356-364. doi:10.1038/s41586-021-03499-y

This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.

Original post:
Ancient Genomics Has Taught Us What It Means To Be Human - Technology Networks

NEW YORK A team led by researchers at the University of North Carolina at Chapel Hill has tracked down more than 150 parts of the genome that seem to influence the microstructure of white matter in the human brain, including loci that overlap with sites previously linked to brain diseases and other traits or conditions.

For a study published in Science on Thursday, the researchers performed a genome-wide association study that included more than 43,800 individuals who had diffusion magnetic resonance imaging, or dMRI,of their brain done, focusing in on variants at 151 new or known loci that were significantly linked to white matter microstructure.

Along with loci previously implicated in glioma or other brain conditions, they saw ties between white matter microstructure and dozens of other traits or diseasesand found genes linked to white matter structure that are targeted by existing drugs.

"The targets of many drugs commonly used for disabling cognitive disorders have genetic associations with white matter, which suggests that the neuropharmacology of many disorders can potentially be improved by studying how these medications work in the brain white matter," senior author Hongtu Zhu, a researcher at UNC Chapel Hill, and his colleagues wrote.

The team's various analyses clarified some of the implications of these genetic contributors. For example, the associations highlighted the importance of glial cells, such as oligodendrocytes, in white matter architecture, as common variants influencing the regulation of these brain cells tended to be overrepresented among white matter-related variants detected in the study.

In a related perspectives article in Science, University of Colorado researcher Christopher Filley, who was not involved in the study, emphasized that a "complete portrait of the structural basis of cognition and emotion cannot neglect the white matter because it interacts so intimately with its gray matter counterpart."

For the discovery stage of the GWAS, Zhu and colleagues considered dMRI and genotyping data for more than 34,000 UK Biobank participants, focusing on five diffusion tensor imaging-based microstructure metrics that offer a look at 21 specific white matter tracts in the cerebral cortex.

From these data, the researchers narrowed in on 42 loci linked to white matter tract structure in the past, along with 109 new loci associated with the diffusion tensor imaging metrics. They noted that 30 of those novel loci structures were found through analyses centered on specific white matter tracts.

"Our results illuminate the broad genetic control of white matter microstructural differences and the contribution of tract-specific [fractional anisotropy principal components] in identifying genetic variants associated with white matter tracts," the authors reported, adding that the genetic effects detected "are spread across a large number of genomic regions, consistent with the observed polygenic genetic architecture of many brain-related traits."

After validating suspicious variants in another 17,700 individuals from nine prior studies, the team performed meta-analyses that included discovery and validation cohort participants from European and non-European ancestry groups, along with gene-centered and drug target analyses that pointed to more than a dozen white matter-related genes that are targeted by existing antipsychotic, antidepressant, antidementia, and other neuropsychiatric drugs.

The team cautioned that the current findings largely stemmed from genetic data for individuals with European ancestry, and centered on diffusion tensor imaging parameters, leaving untapped genetic insights for other white matter metrics and populations.

"The emerging recognition of white matter and its contribution to human behavior will advance medicine as well as neuroscience," Filley wrote in his perspectives article. "Considering both environmental and genetic factors clarifies the structure and function of normal and abnormal tracts, and this knowledge promises in turn to improve the diagnosis and treatment of people in whom white matter dysfunction may be disturbing neurobehavioral capacity."

Read more here:
GWAS Reveals New Loci Linked to Brain White Matter Microstructure - GenomeWeb

According to a new market research report launched by Inkwood Research, the Global Digital Genome Market is propelling at a CAGR of 9.43% and is anticipated to generate $20606.9 million by 2028.

According to a new market research report launched by Inkwood Research, the Global Digital Genome Market is propelling at a CAGR of 9.43% and is anticipated to generate $20606.9 million by 2028.

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A digital genome refers to a complex digitalized set of genetic material in a cell or organism. It allows immediate access and supports trait combinations that help in resolving endless custom queries. The technology has sparkled a revelation of innovation-centric research & systems biology to enhance understanding of the most complex genetic structure. Moreover, it is an easier way of gathering information about chronic diseases.

The global digital genome market is primarily driven by increasing partnerships and collaborative research, growing investments in precision medicine, and the presence of significant market players. In addition, several initiatives, which include the government of India for start-ups in biotechnology, are likely to foster the market. However, lack of professionals, risks associated with security issues, and inadequate knowledge about genomic technology are key restraints hampering the market globally.

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Advancing Technology to Create Opportunities in the Global Digital Genome Market - Digital Journal

A University of Central Florida infectious-disease epidemiologist is working with The Rockefeller Foundation and the University of Florida on a new collaboration to strengthen the ongoing response to SARS-CoV-2.

The work could affect approaches to control the virus, such as isolation strategies and vaccine development, and establish infrastructure to respond to future emerging infectious diseases.

The project is funded by philanthropic organization The Rockefeller Foundation as part of several recently announced grants and collaborations to strengthen global capabilities to detect and respond to pandemic threats.

UCF will receive the funds in partnership with UF to become part of a U.S. Regional Accelerators for Genomic Surveillance program that will provide strategic, coordination, and operational support toward improved and diversified regional surveillance efforts across a network of institutions. These institutions include the Broad Institute of MIT and Harvard, Louisiana State University Health Shreveport, and University of Wisconsin-Madison.

UCF and UF together will receive $340,000 for the project.

The work at UCF will be led by Taj Azarian, an assistant professor and infectious-disease epidemiologist in the Burnett School of Biomedical Sciences. Azarian will work closely with Marco Salemi, the projects lead at UF and a member of UFs Emerging Pathogens Institute.

The Florida experts and their labs will work to establish a network of public, private, and industry partners that will strive to increase the representativeness of SARS-CoV-2 monitoring around the state, Azarian says.

They will do this by genome sequencing SARS-CoV-2 isolates from positive SARS-CoV-2 test samples taken from around Florida with individuals identities redacted.

Azarian says particular interest will be placed on monitoring cases of reinfection or vaccinated cases who become sick with COVID-19. These viral isolates will be prioritized for genome sequencing, which will allow the experts to identify new variants and understand how the virus is spreading in the community, he says.

So, lets say someone had COVID-19 early, like last summer, and then they get tested and theyre infected again, Azarian says. Were interested in tracking that and looking at the viral genomes to see how different they are from the virus that was circulating earlier when they were infected.

We also want to monitor cases of vaccine breakthrough, he says. For example, someone received a vaccine and got sick weeks later with COVID.

Another priority is monitoring the populations that are either unvaccinated or undervaccinated, he says.

Knowing this information can help with vaccination and community-level control efforts, Azarian says.

Overall, we are trying to stay one step ahead of the virus, Azarian says.

He says the selection of UCF to work on the project was made possible by the concentrated expertise of the Genomics and Bioinformatics cluster at UCF, the collaboration with the Salemi Laboratory, and also his recent work on rapid, onsite COVID-19 detection and viral sequencing on campus through a Higher Education Emergency Relief Fund II award.

One of the things that we do in my laboratory is apply genome sequencing of pathogens to understand how they spread and transmit in the community, he says.

Getting funding through the university to start up our genomic surveillance on campus and do everything in-house provided a good springboard to show that we have the resources to be able to help increase the regional and national capacity to do genomic surveillance.

Azarian received his doctorate in epidemiology from the University of Florida and completed a postdoctoral fellowship at Harvards T.H. Chan School for Public Health in the Center for Communicable Disease Dynamics. He was recruited to UCF through the Genomics and Bioinformatics Cluster initiative and joined UCFs Burnett School of Biomedical Sciences, part of UCFs College of Medicine, in 2018.

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UCF Expert Will Help Track COVID Spread, Reinfection and Vaccine Breakthroughs - UCF