Publisher Health

The human body is an incredibly designed machine, and mechanical processes such as those in the lymphatic system play major roles in maintaining healthy tissue and organs.
Donny Hanjaya-Putra is an assistant professor whose work lies at the intersection of engineering and medicine. He studies the lymphatic system — the part of the immune system that rids the body of toxins and other unwanted materials. He looks at how to restore dysfunctional lymphatic networks, which are associated with a wide range of diseases, including cancer, cardiovascular disease, diabetes, neurological conditions and metabolic syndromes.
Now Hanjaya-Putra and his team — bioengineering doctoral student Laura Alderfer, along with Elizabeth Russo, a 2019 graduate; Adriana Archilla, a student from Syracuse University; and Brian Coe, class of ’19 — have demonstrated how extracellular matrix stiffness affects lymphatic vessel function.
The team is combining this knowledge with polymer science and mechanical engineering to build new lymphatic cord-like structures, which help restore normal behavior to dysfunctional lymphatic systems and allow the body to fight the disease.
“Cells can sense mechanical stimuli, such as matrix stiffness, and this activates certain genes to promote lymphatic formation,” said Hanjaya-Putra. “We used hydrogels made from hyaluronic acid (a natural sugar molecule) to enhance the cell-binding motif with appropriate mechanical stimuli (matrix stiffness) in a 2D model of lymphatic vessels and successfully stimulated new lymphatic vessel formations.”
The team has published its findings in The FASEB Journal of the Federation of American Societies for Experimental Biology.
This type of research is only possible, Hanjaya-Putra said, because of advances in imaging and stem cell biology.
“Traditionally, medical students spent hours studying the cardiovascular system, but not as much emphasis was placed on the lymphatic system,” said Hanjaya-Putra. “The reason, in large part, was due to the difficulty in visualizing lymphatic vessels, which are transparent.
“Recent advances have allowed us to use specific cell markers to distinguish between blood endothelial cells and lymphatic endothelial cells, so we can now see and study these very important networks in vitro and in vivo.”
Hanjaya-Putra and his team are now developing hydrogels that can be implanted under the skin to promote wound healing as well as gels that can be injected into the body at the site of injury.
Alderfer, the lead author on the FASEB article, was awarded a Fulbright U.S. Student Program Grant to study at the University of Helsinki. She will be studying lymphatic vessel formation in vivo in wound and cardiac injury models with Kari Alitalo, a global leader in the research of lymphatic vessels and translational cancer biology.
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Physicists on the hunt for a rarely seen magnetic spin texture have discovered another object that bears its hallmarks, hidden in the structure of ultra-thin magnetic films, that they have called an incommensurate spin crystal.
A team from the University of Warwick reports the findings in the journal Nature Communications, which could offer new possibilities for technologies such as computer memory and storage.
The researchers initially set out to find a Skyrmion, a whirling magnetic spin texture theorised to exist in particular magnetic materials and that are of great interest to physicists due to their unique properties and potential for a new generation of energy efficient data storage. To find them, scientists look for abnormal behaviour of the Hall effect; this causes electrons moving through a conducting material to behave differently, measured as resistivity.
To induce this effect, the team created samples by combining an extremely thin film of a ferroelectric material, lead titanate, with another thin film of a ferromagnet, strontium ruthanate. These layers are atomically flat, a mere five to six unit cells (3 nanometres) thick.
The ferroelectric layer induces an electric field that warps the atomic structure of the ferromagnet, breaking its symmetry. Using atomical precision electron microscopy, they measured this symmetry breaking, and were also able to separately measure the electrical resistivity of the material and confirmed the presence of features akin to the Topological Hall effect, as would be expected for a Skyrmion.
Then the researchers used Magnetic Force Microscopy to examine the topology of the material’s atomic structure, which formed a lattice based on rectangles — not hexagons, as they would expect. Within this lattice are magnetic domains where Skyrmions would be found as individual, isolated particles. Instead, these domains formed more like beads on a string or necklace, with beads that never quite form a perfect circle.
Lead author Sam Seddon, a PhD student in the University of Warwick Department of Physics, said: “Once you make careful examination of the images, you realise, actually, this doesn’t present like a Skyrmion at all.
“A Skyrmion causes its own complicated Hall effect and when similar-looking effects are observed it is often treated as a signature of the Skyrmion. We’ve found a very ordered domain structure, just as a Skyrmion lattice would form, however they are simply chiral and not topologically protected. What this shows with real-space imaging evidence is that you don’t need a topological domain to cause a Hall effect of this kind.”
Ferroelectric and ferromagnetic materials are important for technologies such as computer memory and storage. For example, materials very similar to lead titanate are often used for the computer memory in the electronic systems in cars, due to their robustness and ability to operate at extreme temperatures.
Co-author Professor Marin Alexe from the University of Warwick said: “There is interest in these types of interfaces between ferroelectric and ferromagnet materials, such as for new types of computer memory. Because ferroelectric polarisation can be switched permanently, this modifies a quantum effect in a ferromagnet and that might give us direction for materials for the next quantum computers. These will need stable materials which work at extreme temperatures, are low-power consumption, and can store information for a long time, so all the ingredients are here.
“Topology is the translation of certain mathematical concepts into real life and is now at the core of new discoveries in physics. At the University of Warwick we have an extraordinary and advanced infrastructure which allows us to tackle a problem from theoretical point of view, to looking at atomic structure, right up to looking into functional properties at extreme temperatures and fields, especially magnetic fields. We are able to offer foundations for engineers to develop new technologies from.”
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An aggressive type of brain cancer, glioblastoma has no cure. Patients survive an average of 15 months after diagnosis, with fewer than 10% of patients surviving longer than five years. While researchers are investigating potential new therapies via ongoing clinical trials, a new study from Washington University in St. Louis suggests that a minor adjustment to the current standard treatment — giving chemotherapy in the morning rather than the evening — could add a few months to patients’ survival.
The study appears online in the journal Neuro-Oncology Advances.
Average overall survival for all patients in the study was about 15 months after diagnosis. Those receiving the chemotherapy drug temozolomide in the morning had an average overall survival of about 17 months post diagnosis, compared with an average overall survival of about 13½ months for those taking the drug in the evening, a statistically significant difference of about 3½ months.
“We are working hard to develop better treatments for this deadly cancer, but even so, the best we can do right now is prolong survival and try to preserve quality of life for our patients,” said co-senior author and neuro-oncologist Jian L. Campian, MD, PhD, an associate professor of medicine at the School of Medicine. “These results are exciting because they suggest we can extend survival simply by giving our standard chemotherapy in the morning.”
Co-senior authors Joshua B. Rubin, MD, PhD, a professor of pediatrics and of neuroscience at the School of Medicine, and Erik D. Herzog, PhD, the Viktor Hamburger Distinguished Professor and a professor of biology in Arts & Sciences, developed a collaboration to study circadian rhythms and their effect on glioblastoma. Rubin and Herzog published studies in which they analyzed mouse models of glioblastoma and found improved effectiveness for temozolomide when given in the morning.
“In my lab, we were studying daily rhythms in astrocytes, a cell type found in the healthy brain,” Herzog said. “We discovered some cellular events in healthy cells varied with time of day. Working with Dr. Rubin, we asked if glioblastoma cells also have daily rhythms. And if so, does this make them more sensitive to treatment at certain times? Very few clinical trials consider time of day even though they target a biological process that varies with time of day and with a drug that is rapidly cleared from the body. We will need clinical trials to verify this effect, but evidence so far suggests that the standard-of-care treatment for glioblastoma over the past 20 years could be improved simply by asking patients to take the approved drug in the morning.”
In the current study, the researchers — led by co-first authors Anna R. Damato, a graduate student in neuroscience in the Division of Biology & Biomedical Sciences, and Jingqin (Rosy) Luo, PhD, an associate professor of surgery in the Division of Public Health Sciences and co-director of Siteman Cancer Center Biostatistics Shared Resource — also observed that among a subset of patients with what are called MGMT methylated tumors, the improved survival with morning chemotherapy was more pronounced. Patients with this tumor type tend to respond better to temozolomide in general. For the 56 patients with MGMT methylated tumors, average overall survival was about 25½ months for those taking the drug in the morning and about 19½ months for those taking it in the evening, a difference of about six months, which was statistically significant.

A Penn Medicine patient with a genetic form of childhood blindness gained vision, which lasted more than a year, after receiving a single injection of an experimental RNA therapy into the eye. The clinical trial was conducted by researchers at the Scheie Eye Institute in the Perelman School of Medicine at the University of Pennsylvania. Results of the case, detailed in a paper published today in Nature Medicine, show that the treatment led to marked changes at the fovea, the most important locus of human central vision.
The treatment was designed for patients diagnosed with Leber congenital amaurosis (LCA) — an eye disorder that primarily affects the retina — who have a CEP290 mutation, which is one of the more commonly implicated genes in patients with the disease. Patients with this form of LCA suffer from severe visual impairment, typically beginning in infancy.
“Our results set a new standard of what biological improvements are possible with antisense oligonucleotide therapy in LCA caused by CEP290 mutations,” said co-lead author Artur V. Cideciyan, PhD, a research professor of Ophthalmology. “Importantly, we established a comparator for currently-ongoing gene editing therapies for the same disease, which will allow comparison of the relative merits of two different interventions.”
In an international clinical trial led at Penn Medicine by Cideciyan and Samuel G. Jacobson, MD, PhD, a professor of Ophthalmology, participants received an intraocular injection of an antisense oligonucleotide called sepofarsen. This short RNA molecule works by increasing normal CEP290 protein levels in the eye’s photoreceptors and improving retinal function under day vision conditions.
In a 2019 study published in Nature Medicine, Cideciyan, Jacobson, and collaborators found that injections of sepofarsen repeated every three months resulted in continued vision gains in 10 patients. The eleventh patient, whose treatment was detailed in the latest Nature Medicine paper, received only one injection and was examined over a 15-month period. Prior to treatment, the patient had reduced visual acuity, small visual fields, and no night vision. After the initial dose, the patient decided to forgo the quarterly maintenance doses, because the regular dosing could lead to cataracts.
After a single injection of sepofarsen, more than a dozen measurements of visual function and retinal structure showed large improvements supporting a biological effect from the treatment. A key finding from the case was that this biological effect was relatively slow in uptake. The researchers saw vision improvement after one month, but the patient’s vision reached a peak effect after month two. Most striking, the improvements remained when tested over 15 months after the first and only injection.

Infants born by cesarean section have a relatively meager array of bacteria in the gut. But by the age of three to five years they are broadly in line with their peers. This is shown by a study that also shows that it takes a remarkably long time for the mature intestinal microbiota to get established.
Fredrik Bäckhed, Professor of Molecular Medicine at Sahlgrenska Academy, University of Gothenburg, has been heading this research. The study, conducted in collaboration with Halland County Hospital in Halmstad, is now published in the journal Cell Host & Microbe.
Professor Bäckhed and his group have previously demonstrated that the composition of children’s intestinal microbiota is affected by their mode of delivery and diet. In the current study, the researchers examined in detail how the composition of intestinal bacteria in 471 children born at the hospital in Halmstad had developed.
The first fecal sample was collected when each child was a newborn infant. Thereafter, sampling took place at 4 months, 12 months, 3 years and 5 years. The scientists were thus able to follow the successive incorporation of various bacteria into the children’s gut microbiota.
At birth, the infant’s intestine has already been colonized by bacteria and other microorganisms. During the first few years of life, the richness of species steadily increases. What is now emerging is a considerably more detailed picture of this developmental trajectory.
One key conclusion is that the intestinal microbiota forms an ecosystem that takes a long time to mature. Even at 5 years of age, the system is incomplete. The maturation process can look very different from one child to another, and take varying lengths of time.

The governor is expected to sign the law, which would make New Mexico the 16th state to permit recreational use.New Mexico was set to become the 16th state to legalize recreational marijuana after the Legislature passed a bill on Wednesday, joining a national movement to rethink antidrug laws that are increasingly seen as impediments to racial justice and the economy.Gov. Michelle Lujan Grisham, a Democrat, said she would sign the bill, which would also expunge the criminal records of people who possessed marijuana for personal use. She said in a statement that workers, entrepreneurs and the government would benefit from the new industry, creating jobs and tax revenue.“And those who have been harmed by this country’s failed war on drugs, disproportionately communities of color, will benefit from our state’s smart, fair and equitable new approach to past low-level convictions,” she said.The bill passed on the same day that New York State legalized recreational marijuana. Lawmakers in both states said they were motivated to produce a legal, tax-revenue-generating industry that formerly operated underground, and to end arrests for low-level offenses.Under the New Mexico law, people over 21 would be permitted to have up to two ounces of marijuana, and individuals could have six plants at home, or up to 12 per household. Sales would begin no later than April 2022 and be taxed at 12 percent, eventually rising to 18 percent, plus gross receipts taxes.The industry will be regulated by the state and produce an estimated $20 million in revenue for the state in 2023, plus $10 million for local governments, according to a fiscal analysis cited by The Albuquerque Journal.New Mexico’s measure is part of a growing consensus in the United States in favor of marijuana decriminalization, with 91 percent of Americans in 2019 supporting legal medical or recreational use, according to the Pew Research Center. Voters in Arizona, Montana, New Jersey and South Dakota opted to legalize recreational marijuana in November, while Mississippi and South Dakota became the 34th and 35th states to allow medical marijuana.The New Mexico bill passed over Republican objections, but not all were opposed to legalization; some just clashed over the details, including how the industry would be taxed, licensed and regulated.Supporters, including Emily Kaltenbach, senior director for resident states and New Mexico for the Drug Policy Alliance, hailed the passage of the law.“Today’s passage of the cannabis legalization and expungement package will ensure equitable opportunities for farmers and other small businesses, and long overdue justice — including automatic expungement — for those with past cannabis arrests or convictions,” she said in a statement.About 100 prisoners will have their sentences reconsidered under the new law, according to The Associated Press.

The risk is low that scientists could pass coronavirus to North American bats during winter research, according to a new study led by the U.S. Geological Survey. Scientists find the overall risk to be 1 in 1,000 if no protective measures are taken, and the risk falls lower, to 1 in 3,333 or less, with proper use of personal protective equipment or if scientists test negative for COVID-19 before beginning research.
The research specifically looked at the potential transmission of SARS-CoV-2, which is the type of coronavirus that causes COVID-19, from people to bats. Scientists did not examine potential transmission from bats to people.
“This is a small number, but the consequences of human-to-bat transmission of coronavirus are potentially large,” said USGS scientist Evan Grant, an author of the new rapid risk assessment. “The virus has not been identified in North American bats, but if it is introduced, it could lead to illness and mortality, which may imperil long-term bat conservation. It could also represent a source for new exposure and infection in humans.”
“These are hard risks for wildlife managers and other decision makers to weigh as they consider whether and how to allow researchers to study bats in their winter colonies,” continued Grant.
Bats provide natural services that people value; for example, previous USGS studies found that bats save the U.S. agriculture industry more than $3 billion per year by eating pests that damage crops, reducing the need for pesticides. Yet they are often erroneously portrayed as menacing creatures at Halloween and in horror movies. They are also under duress from white-nose syndrome, a disease that has killed millions of bats in North America.
The origin of SARS-CoV-2 is not confirmed, but studies indicate the virus likely originated from similar viruses found in bats in the Eastern Hemisphere.

There is no singular way to respond to heartache or sorrow. Find the strategy that works best for you.We are all grieving right now.Perhaps you’re one of the millions who has lost a loved one to the brutalities of Covid-19, or maybe you’re grieving another kind of loss: missed time with family and friends, a postponed wedding, a former job. Many of us have also grieved circumstances or deaths unrelated to the coronavirus — each made even more difficult in the context of a pandemic.Every loss deserves to be acknowledged and addressed. So we gathered advice from bereavement experts and asked people who have recently experienced grief to tell us how they are finding peace.There are a wide variety of strategies. But it’s important to acknowledge that many people “don’t have the luxury of attending fully to grief and mourning,” said Therese A. Rando, the clinical director of the Institute for the Study and Treatment of Loss in Warwick, R.I. “That’s one of the most insidious things about the pandemic.”If you’re running on adrenaline and still living in survival mode, start small and see if one of the methods below might be helpful to you, too.Lean on your virtual community“In initial stages of bereavement, many grievers find the most helpful resource to be other supportive people,” said Sherry Cormier, a psychologist and bereavement trauma specialist in Edgewater, Md. “This is because grief can feel like abandonment, and because it can feel isolating.”Finding this kind of support in person can be a challenge during the pandemic, but video chats with helpful friends or family are often useful substitutes for get-togethers, she added.Online resources like Grieving.com and Grief Healing Discussion Groups offer moderated group discussion forums, and the websites National Covid-19 Day and Modern Loss have additional resources for people who need support.What people tend to find most helpful during the grieving process is “acknowledgment, and an ongoing invitation to share their experiences,” said Rebecca Soffer, the co-founder and chief executive of Modern Loss. “This has become all the more urgent as grieving people have had to endure the process in relative isolation for more than a year.”Online religious services can also provide a sense of community.Elizabeth Sanford, 58, who lives in Atlanta, said she started listening to the morning prayers of a monastery in Cumbria, England, a few months after her father died and the country went into lockdown. She watches nearly every morning on Facebook Live at 3 a.m., which is when she now tends to wake up.“It’s like getting a hug,” she said. “The bells ring. The guided imagery helps me cry. The prayers bring peace.”Finally, keep an eye out this spring for a new online guide with nearly 80 websites pertaining to grief during the pandemic. The guide, which is being curated by Camille B. Wortman, an expert on grief and a professor emeritus of psychology at Stony Brook University in New York, will cover topics as varied as how to process feelings of guilt or lack of closure; how to explain death to a child; and how to help those who are mourning.Learn something new“It’s hard to be grieving actively when you are learning something new,” Dr. Cormier said. “It’s stimulating to our brain, and it takes our mind off of our struggle.”Whether you start volunteering, foster a pet or take up a hobby, you are giving yourself a mental break from grieving, the experts said.That was the case for Allyn Young, 43, who lives in Manhattan. After her father died of Covid in December, she said, she became “obsessed with horses.”She started reading books about horses, following horse rescues on Instagram and watching a documentary series that described how horses are used for therapy.“I had no idea!” she said. “Right now I’m trying to get in touch with the stables around N.Y.C. to take lessons and volunteer. My newfound and totally random excitement at the idea of petting a horse has been bringing me joy.”Mark Seaman, 51, a cake decorator who lives in Chicago, said he became sad and fearful when his husband started suffering from serious health problems in December of 2019. A few months later Mr. Seaman began teaching himself to crochet by watching a how-to video on the website Craftsy, and started to feel more at ease.“The repetitive nature of the activity distracted me so fully from the reality of the pandemic that the world was experiencing that I felt calm,” Mr. Seaman said.Explore podcasts and booksMany people who are in the depths of grief find inspiration and connection while listening to podcasts, Dr. Cormier said.In “Everything Happens,” Kate Bowler, a professor at Duke Divinity School, talks with people about what they’ve learned in dark times; “Terrible, Thanks for Asking” is hosted by Nora McInerny, an author who asks people to share their complicated and honest feelings about how they are actually doing; and “Unlocking Us,” with Brené Brown, a research professor at the University of Houston, aims to reveal the “messiness of what it means to be human.”Then there are books — far too many examples to mention here, including “Finding Meaning: The Sixth Stage of Grief” by David Kessler (2019); and “It’s OK That You’re Not OK: Meeting Grief and Loss in a Culture That Doesn’t Understand” by Megan Devine (2017).Dr. Cormier has also written a book, “Sweet Sorrow: Finding Enduring Wholeness After Loss and Grief” (2018), based in part on her own experience with cumulative grief. In the span of six years, she lost her father, husband, mother and sister.“I really get what people are going through. I get the heartbreak. I get the wanting to stay under the covers all day,” she said.If you have young children or teenagers, there are a variety of books and films that can help them cope with loss, too. And check out these articles about how to talk with children about death and how to help children with pandemic grief.Speak with a grief counselor, religious leader or other professionalKristin Taylor, 39, of Oak Park, Ill., who lost her mother to pancreatic cancer in November, had tried it all: meditation, talking with friends who lost their parents, long walks, writing in a journal and yoga. “Nothing helped too much,” she said.Then she started speaking with a grief counselor once a week.“I feel I have a place to not only openly weep and mourn without burdening another person, but I also now have someone to help me sort out the trauma I experienced while caregiving and witnessing an aggressive and ruthless cancer take over my mother’s body,” Ms. Taylor said.A November survey of more than 800 U.S. adults who lost someone to Covid-19 found that two-thirds of the respondents were suffering from debilitating levels of grief, a type of mourning that can disrupt a person’s ability to live life normally.If you are using drugs or alcohol to cope, or if you are having trouble functioning, it’s important to speak with a professional, said Sherman A. Lee, an associate professor of psychology at Christopher Newport University in Newport News, Va., and one of the authors of the study. Dr. Lee’s website, The Pandemic Grief Project, offers a short test that people can use to assess their level of distress: A score of seven or higher suggests that additional assessment or treatment is needed.The demands of the pandemic have made it even more difficult for some people to find a mental health provider, however, especially one who takes insurance.Psychology Today maintains a large list of providers that you can filter by location, insurance, specialty or other criteria. But if you can’t find a provider who is accepting new patients, ask the providers you contacted or your primary care provider for referrals.Online therapy services may also be worth exploring if you need to speak with someone quickly.Get activeSayrah Garrison, 47, a licensed clinical social worker and dance teacher, is grieving the death of her mother-in-law, and missing her family’s California home now that they have moved across the country to New Jersey to be closer to her father-in-law. In March, she found a “grief dancer” workshop, rooted in the meditative 5Rhythms movement practice, to be cathartic and enlightening.“I realized how much I actually missed our home in Oakland and how much I missed my regular students and the incredibly healing dance spaces we shared together,” she said.Aerobic exercise may also release mood-elevating endorphins, the chemicals that can help you feel relaxed and happy after a workout.Yoga is another option that helps strengthen your body and build flexibility, while offering an added spiritual component that can be calming in times of stress.Tania Bunik of Minneapolis, Minn., 55, said the Down Dog yoga app, which she uses every day, helped preserve her mental health during a time of chaos by giving her the space to do something therapeutic for herself.“It allows you to tailor your yoga session by the amount of time you have, the pace, the background music, the areas of your body you want to work on,” she said. “It gave me a sense of control because I had choices.”Spend time in natureSeveral people who are grieving told us that they have found it relaxing to take walks in nature; nurture their garden; or simply sit outside and observe.“I was determined to make our backyard a nature sanctuary with a lot of beautiful flowers in the gardens, a bird bath and feeders,” said Carol Struve, 70, an artist and retired nurse who lives in Kingston, N.Y. Last year, Ms. Struve fractured her sternum, mourned the deaths of three older relatives and then grappled with a uterine cancer diagnosis.“I restored the vintage, rusty patio furniture and bought a new umbrella for the table,” said Ms. Struve, who spent many afternoons making drawings of the flowers and gardens. “This helped me find my way through the cancer diagnosis and surgery, along with the support of my therapist and friends.”If you don’t have easy access to a scenic spot, watching tranquil scenes on video can also be soothing. Dr. Wortman said that she and her husband take about 15 minutes a day to watch nature videos featuring scenic landscapes and animals.It is easy and comforting, she added, and “it shows you that there’s still beauty in the world.”

SharecloseShare pageCopy linkAbout sharingimage copyrightGetty ImagesPfizer says its vaccine is preventing 91% of coronavirus cases in the six months after people are immunised.And a separate study shows even people in their 80s and 90s are producing impressive levels of antibodies after receiving both doses of the vaccine. Only 63% of them, however, also produce the T-cells that help maintain those antibodies in the longer term.And the crucial question of how long the protection from the vaccine lasts remains unanswered. Pfizer analysed data from 46,000 people on the original clinical trial, exactly six months after their second dose.It also looked at 800 trial participants in South Africa and concluded the vaccine was equally effective against the variant identified there – despite laboratory studies suggesting people’s antibodies were less effective at attacking this variant. “The high vaccine efficacy observed through up to six months following a second dose and against the variant prevalent in South Africa provides further confidence in our vaccine’s overall effectiveness,” chairman and chief executive officer Albert Bourla said. Brazil variantSeparate research by the University of Birmingham looked at what happened to the immune systems of 100 80- to and 96-year-olds.Blood samples showed high levels of antibodies able to effectively neutralise the original coronavirus.Against the variant identified Brazil, however, they were 14 times less effective.Although, the researchers were confident those who had received the Pfizer vaccine would still be protected against the Brazil variant because their levels of antibodies were so high.Coronavirus factoriesHowever, only 63% of people in this age group produced a detectable T-cell response. “It is not clear what that means for clinical protection in the longer term,” one of the researchers, Dr Helen Parry, said.T-cells can kill the cells in the body that have been hijacked and turned into coronavirus factories. But they also help maintain levels of antibodies over time. “That’s something we’ll keep an eye on very closely,” researcher Prof Paul Moss said. OXFORD JAB: What is the Oxford-AstraZeneca vaccine?GLOBAL SPREAD: How many worldwide cases are there?VACCINE: When will I get the jab?NEW VARIANTS: How worried should we be?COVID IMMUNITY: Can you catch it twice?

Genome sequencing of thousands of SARS-CoV-2 samples shows that surges of COVID-19 cases are driven by the appearance of new coronavirus variants, according to new research from the School of Veterinary Medicine at the University of California, Davis published April 1 in Scientific Reports.
“As variants emerge, you’re going to get new outbreaks,” said Bart Weimer, professor of population health and reproduction at the UC Davis School of Veterinary Medicine. The merger of classical epidemiology with genomics provides a tool public health authorities could use to predict the course of pandemics, whether of coronavirus, influenza or some new pathogen.
Although it has just 15 genes, SARS-CoV-2 is constantly mutating. Most of these changes make very little difference but sometimes the virus becomes more or less transmissible.
Weimer and graduate student DJ Darwin R. Bandoy initially analyzed the genomes of 150 SARS-CoV-2 strains, mostly from outbreaks in Asia prior to March 1, 2020, as well as epidemiology and transmission information for those outbreaks. They classified outbreaks by stage: index (no outbreak), takeoff, exponential growth and decline. The ease of transmission of a virus is set by the value R, or reproductive number, where R is the average number of new infections caused by each infected person.
They combined all this information into a metric called GENI, for pathogen genome identity. Comparing GENI scores with the phase of an epidemic showed that an increase in genetic variation immediately preceded exponential growth in cases, for example in South Korea in late February. In Singapore, however, bursts of variation were associated with smaller outbreaks that public health authorities were able to quickly bring under control.
20,000 virus samples
Weimer and Bandoy then looked at 20,000 sequences of SARS-CoV-2 viruses collected and from February to April 2020 in the United Kingdom and compared them with data on cases.
They found that the GENI variation score rose steadily with the number of cases. When the British government imposed a national lockdown in late March, the number of new cases stabilized but the GENI score continued to rise. This shows that measures such as banning gatherings, mask mandates and social distancing are effective in controlling spread of disease in the face of rapid virus evolution.
It could also help explain “superspreader” events when large numbers of people get infected in a single incident where precautions are relaxed.
Weimer said he hopes that public health authorities will take up the approach of measuring virus variation and linking it to the local transmission rate, R.
“In this way you can get a very early warning of when a new outbreak is coming,” he said. “Here’s a recipe for how to go about it.”
Parts of the work previously appeared online as a preprint. Bandoy is sponsored by the Philippine California Advanced Research Institute.
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