In fact, the UB study suggests traditional anatomical methods for determining the evolutionary relationships between species may not be as accurate as once thought, an article in SciTechDaily reported.
Nevertheless, the UB’s research into convergent evolution is unlocking new insights into how genes evolve over time and this new knowledge may help researchers develop genetic tests that more accurately identify different diseases and health conditions.
Additionally, studies that bring a better understanding of how beneficial genetic mutations work their way into a species’ genome might also aid researchers in developing personalized clinical laboratory testing and therapies based on manipulating a patient’s genetic sequences in ways that would be beneficial.
Gene Sequencing More Accurate at Determining Evolutionary Relationships
The UB study suggests that existing evolutionary (phylogenetic) trees may need to be reconsidered. To put a finer point on the findings, a UB news release on the study states, “determining evolutionary trees of organisms by comparing anatomy rather than gene sequences is misleading.”
The UB scientists used genetic sequencing to quickly—and more cost effectively—determine evolutionary relationships as compared to traditional morphology (anatomy and structure), according to the news release.
They found genetic data that revealed surprising relationships about where the sequenced species originated, and which differed with prior conclusions that were drawn based on the species’ appearance. The findings suggest there may be need to “overturn centuries of scientific work in classifying relation of species by physical traits,” the UB scientists said.
“For over a hundred years, we’ve been classifying organisms according to how they look and are put together anatomically, but molecular data often tells us a rather different story,” said Matthew Wills, PhD (above), Professor of Evolutionary Paleobiology, Milner Center for Education at the University of Bath, in the news release. “Our study proves statistically that if you build an evolutionary tree of animals based on their molecular data, it often fits much better with their geographical distribution.” This new use of genetic sequencing could lead to improved precision medicine treatments and clinical laboratory testing. (Photo copyright: University of Bath.)
Molecular Data Leads to New Insights into Convergent Evolution
The UB study’s use of genetic sequencing led the researchers to a greater understanding of convergent evolution, defined by “a characteristic evolving separately in two genetically unrelated groups of organisms,” according to UB.
For example, wings are a widely developed characteristic. But they are not necessarily a sign of relatedness when it comes to birds, bats, and insects.
“Now with molecular data, we can see that convergent evolution happens all the time—things we thought were closely related often turn out to be far apart on the tree of life,” Wills said, adding, “Individuals within a family don’t always look similar; it’s the same with evolutionary trees, too.”
Family Trees: Morphology Versus Molecular
In their paper, the UB researchers acknowledged the importance of phylogenies (evolutionary history of species) in areas of biology, including medicine. They aimed to study a better way to produce accurate phylogenetic trees.
“Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular,” they wrote, adding, “The superiority of molecular trees has rarely been assessed empirically.”
So, they set out to compare the two approaches to building evolutionary trees:
Traditional morphology analysis, and
Phylogenetic trees developed using molecular data.
Using 48 pairs of morphological and molecular trees, they mapped data geographically.
“We show that, on average, molecular trees provide a better fit to biogeographic data than their morphological counterparts, and that biogeographic congruence increases over research time,” the researchers wrote.
Biogeography a Better Gauge of Relatedness than Anatomy
The study also found animals on molecular trees lived geographically closer as compared to groups on morphological trees.
For example, molecular studies put aardvarks, elephants, golden moles, swimming manatees, and elephant shews in an Afrotheria group, named for Africa, which is where they came from. Therefore, the biogeography matches, however the appearances of these mammals clearly do not, the UB scientists point out.
“What’s most exciting is that we find strong statistical proof of molecular trees fitting better not just in groups like Afrotheria, but across the tree of life in birds, reptiles, insects, and plants,” said Jack Oyston PhD, UB Department of Biology and Biochemistry Research Associate and first author of the study, in the news release.
The researchers believe their findings support the accuracy of genetic-themed trees.
“It being such a widespread pattern makes it much more potentially useful as a general test of different evolutionary trees. But it also shows just how pervasive convergent evolution has been when it comes to misleading us,” Oyston added.
Advantages of Molecular Data
In their Nature Communications Biology paper, the UB scientists wrote that molecular data offer up these advantages over morphology:
Widely available in vast quantity.
Opportunity exists to “search, repurpose, and reanalyze sequenced data alongside novel sequences.”
Less subjectivity in researchers’ analysis.
Well-developed data at the ready and “still in their infancy.”
The University of Bath’s study of convergent evolution, phylogenetic trees, and comparison of molecular data versus morphology, has implications for medical laboratories. Should their research lead to new insights into how genes evolve over time, diagnostics professionals may have new information to identity diseases and work with others to precisely treat patients.
It’s the latest example of how genetic technologies have advanced to the point where DNA can be extracted and sequenced from human remains that are thousands of years old, often generating new insights that can benefit clinical laboratory testing
How might an individual in Pompeii who died in the famous Mount Vesuvius volcanic eruption of 79 AD help medical science today? The answer is that sequencing this individual’s DNA may yield insights into health conditions and infectious diseases of that era that could help scientists better understand disease today in ways that improve diagnosis and clinical laboratory testing.
Additionally, researchers studying genetic sequencing are discovering the technology has many more capabilities that previously thought. One such example involves scientists from the University of Copenhagen, the University of Salento, and victims of the eruption. This research team has determined that even severely damaged biological samples may contain viable DNA.
When Mount Vesuvius erupted, volcanic ash and pumice buried many residents of the town of Pompeii in southern Italy. The ash was estimated to have been about 500 degrees Fahrenheit, which should have been hot enough to cause significant damage to DNA. However, it appears the pyroclastic materials released during the eruption may instead have preserved some of the victims’ DNA.
“One of the main drivers of DNA degradation is oxygen (the other being water),” Gabriele Scorrano, PhD, Assistant Professor, University of Copenhagen and lead author of the study told CNN. “Temperature works more as a catalyst, speeding up the process. Therefore, if low oxygen is present, there is a limit of how much DNA degradation can take place.”
The scientists succeeded in performing completed genetic sequencing on one of the victims of the violent eruption. This has genetic researchers rethinking how DNA could be recovered from damaged biological materials.
“In the future, many more genomes from Pompeii can be studied,” anthropologist Serena Viva, PhD (above), a postdoctoral researcher at the University of Salento in Italy and one of the authors of the study told the Guardian. “The victims of Pompeii experienced a natural catastrophe, a thermal shock, and it was not known that you could preserve their genetic material. This study provides this confirmation, and that new technology on genetic analysis allows us to sequence genomes also on damaged material.” What new clinical laboratory testing may come out of this study is not known. But it shows that there is still much to learn about genetic sequencing. (Photo copyright: University of Salento.)
Findings Suggest High Levels of Genetic Diversity
“There was the expectation that the high temperatures would make our effort in DNA sequencing in Pompeii fruitless,” Scorrano stated. “Cremated bodies, for example, show no sign of DNA preservation according to multiple studies.”
The scientists examined the skeletal remains of two victims found in a building known as Casa del Fabbro or House of the Craftsman to determine if any DNA was present. One skeleton was that of a man in his 30’s who was about five feet four inches in height and the other skeleton was of a woman who appeared to be at least 50 years of age and around five feet tall.
Although the researchers did obtain genetic material from both skeletons, they were only able to sequence the entire genome from the remains of the male skeleton.
The researchers compared his DNA with that of 1,030 other ancient and 471 modern western Eurasian people. The results suggest that the DNA from the male Pompeii skeleton shares the most similarities with people who currently live or lived in central Italy in the past.
Further analysis of the man’s DNA identified groups of genes that are commonly found in people from the island of Sardinia, but not in other people who lived in Italy during the Roman Imperial age. This suggested to the researchers that there may have been high levels of genetic diversity across Italy in 79 AD when Mount Vesuvius erupted.
Additional testing also identified sequences that are commonly found in a group of bacteria known to cause tuberculosis of the spine (Pott disease), a common ailment at that time. This implies the man had the illness when he perished.
The photo above shows the two skeletons (one man and one woman) found in Pompeii’s Casa del Fabbro. Though the University scientists tried to extract full sequences from both skeletons, they only succeeded with the male. (Photo copyright: Notizie degli Scavi di Antichità, 1934, p. 286, fig. 10.)
First Pompeiian Genetic Sequence
Scientists had attempted to sequence DNA from Pompeiian victims before, but previous endeavors to analyze more than small DNA strands failed.
“To our knowledge, our results represent the first successfully sequenced Pompeiian human genome,” they wrote in Nature Scientific Reports. “Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.”
It is unclear how equivalent studies could fare in the future, but the researchers involved in this study hope to use their sequencing techniques on other remains. It is possible that DNA from this Roman man who died in Pompeii in 79 AD may be used to determine if he has any descendants living today.
After months of research and the charting of Cheddar Man’s DNA, the scientists visited a school in Cheddar to extract DNA samples from schoolchildren and look for DNA matches. About 20 samples were taken in total including one from a teacher named Adrian Targett.
“They wanted to take DNA samples from some of the students whose families had lived longest in the area,” Targett told the Los Angeles Times. “I gave a [cheek swab] sample too, just to encourage the children and to make up the numbers.”
Although none of the children were a genetic match to the Cheddar Man, Targett was identified as a direct descendant of the skeleton.
“It’s a bit frightening to think that there are all those links across all those generations,” Targett said. “But the nice thing is that there are links that are so strong. We are all descended from an ancestor like Cheddar Man. Who knows how many people we are related to and don’t know about?”
The Pompeii DNA research is the latest example of how the ongoing reduction in the cost, faster throughput, and increased accuracy of genetic sequencing is allowing scientists to gain new knowledge from ancient artifacts. In turn, some of these new insights may lead to improving how certain health conditions are diagnosed, possibly using novel clinical laboratory tests developed as a result of this research.
Should their research result in new ways to identify and diagnose disease, doctors and clinical laboratories would do confirmatory testing and then initiate a precision medicine plan.
Dan Roden, MD, Senior Vice President for Personalized Medicine at VUMC and Senior Author of the Circulation study, said in a VUMC news release that the findings support the growing use of genetic information in clinical care.
“The questions we asked were: How many people who had no previous indication for cardiac genetic testing had pathogenic or likely pathogenic variants, and how many of those people actually had a phenotype in the electronic health records?” he explained.
Arrhythmia More Common than Previously Thought
The VUMC researchers drew data for their reports from the eMERGE Phase III study, which investigated the feasibility of population genomic screening by sequencing 109 genes across the spectrum of Mendelian diseases—genetic diseases that are caused by a mutation in a single gene—in more than 20,000 individuals. The scientists returned variant results to the participants and used EHR and follow-up clinical data to ascertain patient phenotypes, according to a Northwestern University Feinberg School of Medicine news release.
The research team looked specifically at the 120 consortium participants that had disease-associated pathogenic or likely pathogenic (P/LP) variants in the arrhythmia-associated genes. An analysis of the EHR data showed that 0.6% of the studied population had a variant that increases risk for potentially life-threatening arrhythmia, and that there was overrepresentation of arrhythmia phenotypes among patients, the VUMC news release noted.
The research team returned results to 54 participants and, with clinical follow-up, made 19 diagnoses (primarily long-QT syndrome) of inherited arrhythmia syndromes. Twelve of those 19 diagnoses were made only after variant results were returned, the study’s authors wrote.
Carlos G. Vanoye, PhD, Research Associate Professor of Pharmacology at Northwestern University (NU), said the study suggests arrhythmia genes may be more common than previously thought.
“A person can carry a disease-causing gene variant but exhibit no obvious signs or symptoms of the disease,” he said in the NU news release. “Because the genes we studied are associated with sudden death, which may have no warning signs, discovery of a potentially life-threatening arrhythmia gene variant can prompt additional clinical work-up to determine risks and guide preventive therapies.”
“The take-home message is that 3% of people will carry a pathogenic or likely pathogenic variant in a disease-causing gene and many others will carry variants of uncertain significance,” said Dan Roden, MD (above), Senior Vice President for Personalized Medicine at VUMC and Senior Author of the Circulation study in the VUMC news release. “We can use genetic testing, electronic health record phenotypes, and in vitro technologies to evaluate and find people who have unrecognized genetic disease and save lives by making earlier diagnoses.” Clinical laboratories will play a key role in making those early diagnoses and in managing personalized medical treatment plans. (Photo copyright: Vanderbilt University.)
Variants of Uncertain Significance
According to the NU news release, the scientists determined the functional consequences of the variants of uncertain significance they found and used that data to refine the assessment of pathogenicity. In the end, they reclassified 11 of the variants: three that were likely benign and eight that were likely pathogenic.
In the JAMA Oncology study, the VUMC scientists and other researchers conducted a phenome-wide association study to find EHR phenotypes associated with variants in 23 hereditary cancer genes. According to the VUMC news release, they identified 19 new associations:
The VUMC study findings could improve disease diagnosis and management for cancer patients and help identify high-risk individuals, the researchers noted in their published report.
In an editorial published in Circulation, titled, “First Steps of Population Genomic Medicine in the Arrhythmia World: Pros and Cons,” the professors noted that using genomic information in the case of potentially lethal inherited arrhythmia syndromes could be “lifesaving,” but questioned the benefits of reporting such secondary findings when patients are undergoing genome sequencing for other indications such as cancer.
“The likelihood that these ‘genetic diagnoses’ are translated into clinical diagnoses have not been completely evaluated,” they wrote. “In addition to the challenge of accurately identifying disease-causing genetic variants, defining the penetrance of such variants is critical to this process, i.e., what proportion of individuals in the general population with apparently pathogenic variants will develop the associated phenotype? If penetrance is low for particular gene/phenotype combinations, the costs associated with clinical screening and the psychological effects on individuals informed that they have potentially life-threatening variants may outweigh the benefits of the few new clinical diagnoses.”
These latest studies provide further evidence of the value of big data in healthcare and offer another lesson to clinical laboratories and pathologist about the future role data streaming from clinical laboratories and pathology assays may have in the growth of personalized medicine.
Ultima Genomics says it is emerging from “stealth mode” with millions in fresh capital and technology capable of sequencing whole human genomes for a fraction of the cost
Investors seem to be optimistic that an emerging genetics company has the proprietary solution to sequence a whole human genome for just $100. If true, this is a development that would be of interest to clinical laboratory managers and pathologists.
The company, Ultima Genomics of Newark, Calif., recently announced that it had raised $600 million from the investment community. In a press release last month, the company announced it has “emerged from stealth mode with a new high-throughput, low-cost sequencing platform that delivers the $100 genome.”
The press release goes on to state that Ultima will unleash a new era in genomics-driven discoveries by developing a “fundamentally new sequencing architecture designed to scale beyond conventional approaches, including completely different approaches to flow cell engineering, sequencing chemistry, and machine learning.”
Are we at the cusp of a revolution in genomics? Ultima Genomics’ founder and CEO, Gilad Almogy, PhD, believes so.
“Our architecture is intended for radical scaling, and the $100 genome is merely the first example of what it can deliver,” he said in the press release. “We are committed to continuously drive down the cost of genomic information until it is routinely used in every part of the healthcare system.”
From an Estimated Cost of $3 Billion to $450 in Just 30 Years!
Whole genome sequencing (WGS) has decreased dramatically in cost since research into the technology required got started in the early 1990s with the publicly-funded Human Genome Project. At that time, the cost to sequence the entire human genome was estimated at around $3 billion. Then, in 1998, John Craig Venter created Celera Genomics (now a subsidiary of Quest Diagnostics) and was the first to sequence the whole human genome (his own) and at a significantly lower cost of around $300 million.
The cost continued to drop as technology improved. In 2001, the cost to sequence the whole human genome hovered around $100 million. Twenty years later that cost had dropped to about $450/sequence, according to data compiled by the National Human Genome Research Institute (NHGRI), a division of the National Institutes of Health (NIH).
When DNA sequencer Illumina announced in 2014 the arrival of the $1,000 genome, the news was expected to put whole genome sequencing on the road to becoming routine, Forbes reported. But that prediction didn’t pan out.
Ultima Genomics’ $100 price point, however, could be game changing. It would make the cost of decoding a human genome affordable for nearly everyone and accelerate the growth of personalized medicine in clinical laboratory diagnostics.
Applied Physics versus Biological Sciences
According to GEN, Almogy brings a tech background to Ultima—his PhD is in applied physics, not the biological sciences. He founded Ultima in 2016 after serving as founder, president, and CEO at Fulfil Solutions, a manufacturer of custom automation robotics systems. At Ultima, his goal is to “unleash the same relentless scaling in sequencing” that was used to drive down the cost of computing power and transform modern life.
“Ultima is the real deal, with good technology,” Raymond McCauley, cofounder and Chief Architect at BioCurious, and Chair of Digital Biology at Singularity Group, told Singularity Hub. “They’ve been working on an Illumina killer for years.”
“We designed our new sequencing architecture to scale beyond conventional technologies, and are excited to soon make the UG 100, our first instrument using this architecture, commercially available to more customers,” said Gilad Almogy, PhD (above), Ultima Genomics’ founder and CEO, in a press release. “In the future, we aim to continuously improve our technology, further drive down costs, and increase the scale of genomic information to improve patient outcomes.” At $100/sequence, whole genome sequencing may well become commonly available to improve precision medicine diagnostics and clinical laboratory testing. (Photo copyright: Ultima Genomics.)
TechCrunch reported that Ultima’s UG100 sequencing machine and software platform can perform a complete sequencing of a human genome in about 20 hours, with precision comparable to existing options, but does so at a far lower cost per gigabase (Gb), equal to one billion base pairs.
According to the Ultima Genomics website, its breakthroughs include:
An open substrate that creates a massive, low-cost reaction surface that delivers many billions of reads while avoiding costly flow cells and complicated fluidics.
Novel scalable chemistry that combines the speed, efficiency, and read lengths of natural nucleotides with the accuracy and scalability of endpoint detection.
A revolutionary sequencing hardware that uses spinning circular wafers that enable efficient reagent use, zero crosstalk, and ultra-high-speed scanning of large surfaces.
“We may be on the brink of the next revolution in sequencing,” Beth Shapiro, DPhil, an evolutionary molecular biologist at the University of California, Santa Cruz (UCSC), told Science. Shapiro is a professor of ecology and evolutionary biology and an HHMI Investigator at UCSC and Director of Evolutionary Genomics at the UCSC Genomics Institute.
Ultima Genomics maintained a low profile since its founding six years ago. But that changed in May when it announced it had raised $600 million from multiple investors, including:
Affordable Genomics Will Lead to ‘Millions of Tests per Year’
Exact Sciences’ Chairman and CEO Kevin Conroy—whose Wisconsin-based molecular diagnostics company recently entered into a long-term supply agreement for Ultima Genomic’s NGS technologies—believes low-cost genomic sequencing will improve cancer screening and disease monitoring.
“Exact Sciences believes access to differentiated and affordable genomics technologies is critical to providing patients better information before diagnosis and across all stages of cancer treatment,” Conroy said in a press release. “Ultima’s mission to drive down the cost of sequencing and increase the use of genomic information supports our goal to provide accurate and affordable testing options across the cancer continuum. This is particularly important for applications like cancer screening, minimal residual disease, and recurrence monitoring, which could lead to millions of tests per year.”
GEN pointed out that Ultima’s 20-hour turnaround time is fast and its quality on par with its competitors, but that it is Ultima’s $1/Gb price (noted in the preprint) that will set it apart. That cost would be a fraction of Illumina’s NextSeq ($20/Gb) and Element Biosciences’ AVITI ($5/Gb).
Almogy told TechCrunch that Ultima is working with early access partners to publish more proof-of-concept studies showing the capabilities of the sequencing technique, with broader commercial deployment of the technology in 2023. Final pricing is yet to be determined, he said.
If the $100 genome accelerates the pace of medical discoveries and personalized medicine, clinical laboratory scientists and pathologists will be in ideal positions to capitalize on what the executives and investors at Ultima Genomics hope may become a revolution in whole human genome sequencing and genomics.
As demand for DTC at-home genetic testing increases among consumers and healthcare professionals, clinical laboratories that offer similar assays may want to offer their own DTC testing program
Things are happening in the direct-to-consumer (DTC) medical laboratory testing market. Prior to the pandemic, the number of consumers interested in ordering their own diagnostic tests grew at a rapid rate. The SARS-CoV-2 outbreak, however, and the need for consumers to access COVID-19 tests, caused DTC test sales to skyrocket.
One company benefiting from the DTC trend is New York City-based LetsGetChecked. In March, it announced its acquisition of Veritas Genetics which included that company’s Veritas Intercontinental business division. No purchase price was disclosed.
LetsGetChecked describes itself as a “virtual care company that allows customers to manage their health from home, providing direct access to telehealth services, pharmacy, and [clinical] laboratory tests with at-home sample collection kits for a wide range of health conditions,” according to the company’s LinkedIn page.
“Through these acquisitions, LetsGetChecked will leverage the power of whole genome sequencing to launch a full lifecycle of personalized healthcare, delivering the most comprehensive health testing and care solution on the market,” said Peter Foley, Founder and CEO of LetsGetChecked in a press release.
“By integrating Veritas Genetics’ and Veritas Intercontinental’s capabilities with LetsGetChecked’s scalable diagnostic and virtual care infrastructure, we are able to turn comprehensive genetic insights into practical recommendations and lifestyle changes, guided by clinical experts,” he added.
“Our mission to deliver the benefits of whole genome sequencing to millions of individuals continues as part of the LetsGetChecked family. I am particularly excited about the opportunity to combine genetic testing with the broad spectrum of virtual and at-home care models offered by LetsGetChecked. I expect these acquisitions will change the future of personalized healthcare as we know it,” said geneticist George Church, PhD, co-founder of Veritas Genetics, and Professor of Health Sciences and Technology at Harvard and MIT, in a press release. (Photo copyright: Wyss Institute at Harvard University.)
Leveraging the Power of Whole Genome Sequencing
To date, LetsGetChecked claims it has delivered nearly three million at-home direct-to-consumer tests and served more than 300 corporate customers with testing services and biometric screening solutions since its founding in 2015.
The company focuses on manufacturing, logistics, and lab analysis in its CAP-accredited, CLIA-certified laboratory in Monrovia, Calif., as well as physician support, and prescription fulfillment. The DTC company’s products include at-home tests for women’s health, men’s health, basic wellness, sexual health, and SARS-CoV-2 testing.
Veritas Genetics also was a DTC testing company co-founded by internationally-known geneticist George Church, PhD. In 2016, the company announced it would deliver a whole human genome sequence (WGS) for just $999—breaking the $1,000 cost barrier for whole genome sequencing.
“There is no more comprehensive genetic test than your whole genome,” Rodrigo Martinez, former Veritas Chief Marketing and Design Officer, told CNBC. “So, this is a clear signal that the whole genome is basically going to replace all other genetic tests. And this [price drop] gets it closer and closer and closer.”
That market strategy did not succeed. By the end of 2019, the company announced it would cease operations in the United States but continue operations in Europe and Latin America. It has sought a buyer for the company since that time. Now, almost three years later, LetsGetChecked will become the new owner of Veritas Genetics.
Veritas’ primary product, myGenome was launched in 2018 as a whole genome sequencing and interpretation service to help consumers improve their health and increase longevity. The myGenome test screens for and provides insight on many hereditary diseases such as cancer, cardiovascular disease, and neurological disorders. It also provides observations on more than 50 personal traits and ancestry information.
In addition to bringing whole genome sequencing abilities to its test offerings for consumers, LetsGetChecked hopes the acquisitions will create new testing capabilities such as pharmacogenomics, cancer and viral screenings, and maternal fetal screenings.
“By integrating Veritas Genetics’ and Veritas Intercontinental’s genetics offering with our scalable virtual care infrastructure, we are able to leverage the power of whole genome sequencing to launch a full lifecycle of personalized healthcare, which has always been our goal,” Foley told MobiHealthNews.
Veritas Genetics and Veritas Intercontinental will continue to operate under the LetsGetChecked family of companies.
BioIQ also Acquired by LetsGetChecked
In early May, LetsGetChecked also acquired diagnostic testing and health improvement technology company BioIQ, which will continue to operate as a wholly-owned subsidiary.
BioIQ offers at-home tests, health screenings, and vaccinations to consumers. The company’s products include:
Heart health panel,
Lipid panel,
Respiratory panel,
Prevention panel, and
Wellness panel.
Individual tests offered by BioIQ include:
A1C,
COVID-19,
Hepatitis C test and
Sexually transmitted diseases.
BioIQ also offer e-vouchers for health screenings and vaccinations at participating retail pharmacies, clinical laboratories, and physician’s offices.
“The future of healthcare is in providing high-quality at-home diagnostics and care that comprehensively serve an individual’s health needs throughout their whole life,” said Foley in a press release about the BioIQ acquisition. “With this acquisition, LetsGetChecked gains a trusted partner with an extensive knowledge base and a breadth of experience in serving health plans and employer markets to deliver healthcare solutions at scale.”
These acquisitions by LetsGetChecked demonstrate how genetic testing companies are pivoting to new strategies. Clinical laboratories that perform genetic testing will want to monitor how these partnerships unfold in the future as healthcare consumers and providers continue to embrace at-home genetic testing.
Screening and analysis of ocean samples also identified a possible missing link in how the RNA viruses evolved
An international team of scientists has used genetic screening and machine learning techniques to identify more than 5,500 previously unknown species of marine RNA viruses and is proposing five new phyla (biological groups) of viruses. The latter would double the number of RNA virus phyla to 10, one of which may be a missing link in the early evolution of the microbes.
Though the newly-discovered viruses are not currently associated with human disease—and therefore do not drive any current medical laboratory testing—for virologists and other microbiologists, “a fuller catalog of these organisms is now available to advance scientific understanding of how viruses evolve,” said Dark Daily Editor-in-Chief Robert Michel.
“While scientists have cataloged hundreds of thousands of DNA viruses in their natural ecosystems, RNA viruses have been relatively unstudied,” wrote four microbiologists from Ohio State University (OSU) who participated in the study in an article they penned for The Conversation.
The OSU study authors included:
Ahmed Zayed, PhD, research scientist, Dept. of Microbiology, OSU.
Matthew Sullivan, PhD, Professor of Microbiology and Director of the Center of Microbiome Science at OSU.
“RNA viruses are clearly important in our world, but we usually only study a tiny slice of them—the few hundred that harm humans, plants and animals,” explained Matthew Sullivan, PhD (above), Director, Center of Microbiome Science, in an OSU news story. Sullivan led the OSU research team. “We wanted to systematically study them on a very big scale and explore an environment no one had looked at deeply, and we got lucky because virtually every species was new, and many were really new,” he added. (Photo copyright: University of Ohio.)
RNA versus DNA Viruses
In contrast to the better-understood DNA virus, an RNA virus contains RNA instead of DNA as its genetic material, according to Samanthi Udayangani, PhD, in an article she penned for Difference Between. Examples of RNA viruses include:
One major difference, she explains, is that RNA viruses mutate at a higher rate than do DNA viruses.
The OSU scientists identified the new species by analyzing a database of RNA sequences from plankton collected during a series of ocean expeditions aboard a French schooner owned by the Tara Ocean Foundation.
“Plankton are any aquatic organisms that are too small to swim against the current,” the authors explained in The Conversation. “They’re a vital part of ocean food webs and are common hosts for RNA viruses.”
The team’s screening process focused on the RNA-dependent RNA polymerase (RdRp) gene, “which has evolved for billions of years in RNA viruses, and is absent from other viruses or cells,” according to the OSU news story.
“RdRp is supposed to be one of the most ancient genes—it existed before there was a need for DNA,” Zayed said.
The RdRp gene “codes for a particular protein that allows a virus to replicate its genetic material. It is the only protein that all RNA viruses share because it plays an essential role in how they propagate themselves. Each RNA virus, however, has small differences in the gene that codes for the protein that can help distinguish one type of virus from another,” the study authors explained.
The screening “ultimately identified over 44,000 genes that code for the virus protein,” they wrote.
Identifying Five New Phyla
The researchers then turned to machine learning to organize the sequences and identify their evolutionary connections based on similarities in the RdRp genes.
“The more similar two genes were, the more likely viruses with those genes were closely related,” they wrote.
The technique classified many of the sequences within the five previously known phyla of RNA viruses:
But the researchers also identified five new phyla—including two dubbed “Taraviricota” and “Arctiviricota”—that “were particularly abundant across vast oceanic regions,” they wrote. Taraviricota is named after the Tara expeditions and Arctiviricota gets its name from the Arctic Ocean.
They speculated that Taraviricota “might be the missing link in the evolution of RNA viruses that researchers have long sought, connecting two different known branches of RNA viruses that diverged in how they replicate.”
In addition to the five new phyla, the researchers are proposing at least 11 new classes of RNA viruses, according to the OSU story. The scientists plan to issue a formal proposal to the International Committee on Taxonomy of Viruses (ICTV), the body responsible for classification and naming of viruses.
Studying RNA Viruses Outside of Disease Environments
“As the COVID-19 pandemic has shown, RNA viruses can cause deadly diseases. But RNA viruses also play a vital role in ecosystems because they can infect a wide array of organisms, including microbes that influence environments and food webs at the chemical level,” wrote the four study authors in The Conversation. “Mapping out where in the world these RNA viruses live can help clarify how they affect the organisms driving many of the ecological processes that run our planet. Our study also provides improved tools that can help researchers catalog new viruses as genetic databases grow.”
This remarkable study, which was partially funded by the US National Science Foundation, will be most intriguing to virologists and microbiologists. However, clinical laboratories also should be interested in the fact that the catalog of known viruses has just expanded by 5,500 types of RNA viruses.
