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A new study has found that the Novaplex SARS-CoV-2 Variant I, II, and IV real-time PCR assays (from Seegene Technology) can reliably detect SARS-CoV-2 in patient samples and identify known variants of interest and concern. Results from the PCR assays were comparable to those from the “gold standard” spike gene Sanger sequencing method. Researchers were also able to successfully streamline testing and reduce cost and turnaround time by processing samples without extracting RNA for testing. Their findings appear in The Journal of Molecular Diagnostics, published by Elsevier.
“Real-time PCR (RT-PCR) methodology for variant detection is accessible, rapid, simpler, and accurate compared to traditional sequencing,” said lead investigator Ping Ren, PhD, Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA. “Combining an extraction-free processing method with RT-PCR technology can help laboratories without sequencing capabilities track circulating variants and investigate variant-dependent effects on treatment efficacy and disease severity.”
The I, II, and IV assays are designed to detect genetic mutations associated with the alpha, beta, delta, and epsilon variants of SARS-CoV-2. At the time of the study, the omicron variant had not yet emerged. RNA was extracted from each sample for testing by the Novaplex RT-PCR assays and Sanger sequencing. The samples were also directly tested without extraction of RNA by the Novaplex assays.
Of the 156 samples processed with RNA extraction, the RT-PCR assays identified 109 variants. The results were 100% in agreement with the Sanger sequencing test. The RNA extraction-free method was 91.7% as sensitive as the traditional RNA extraction method. In samples with a lower viral load, the extraction-free RT-PCR assays did not detect some mutations, presumably because of lower nucleic acid concentrations in the original samples.
“A major limiting factor for molecular SARS-CoV-2 assays is the shortage of RNA extraction reagents,” explained co-lead author Marisa C. Nielsen, PhD, Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA. “Conventional extraction remains a time-consuming aspect of molecular diagnosis of SARS-CoV-2. Recent CDC guidance recommends sequencing only for cases with a cycle threshold (Ct) value lower than 28, which indicates a higher viral load, because sequencing is less reliable in samples with lower viral loads.”
“Although lower sensitivity was observed with the extraction-free method, it still represents a viable alternative,” Dr. Nielsen added. “Spike sequencing is still necessary for detecting new variants.”
RT-PCR assays can be tailored to include additional representative genes as different variants emerge and allow for more accessible variant detection and monitoring to inform public health and treatment decisions. While not included in this study, assays are now available to identify omicron-specific mutations.
“Determining the SARS-CoV-2 variant in individual patient samples can help guide treatment since some variants are more resistant to current treatment regimens,” Dr. Ren observed. “However, the potential impact extends beyond individual patients and into the public health realm. It is important to track variant spread as part of public health surveillance because of variant-dependent transmission, disease severity, and treatment decisions.
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Materials provided by Elsevier. Note: Content may be edited for style and length.

Faculty from the Departments of Microbiology, Medicine Genetics and Genomic Sciences, and Pathology and Molecular Cell-Based Medicine at the Icahn School of Medicine at Mount Sinai play key roles in a National Institutes of Health (NIH) program set up to provide a real-time risk assessment of variants of SARS-CoV-2, the virus that causes COVID-19. The program, called SARS-CoV-2 Assessment of Viral Evolution (SAVE) and described in a paper published March 31 in Nature, assesses how the variants might affect transmission, virulence, and resistance to both disease-induced (convalescent) and vaccine-induced immunity.
The SAVE program was established by the National Institute of Allergy and Infectious Diseases (NIAID), part of NIH, in January 2021 to address the global public health threat caused by increasing SARS-CoV-2 genomic diversity and the emergence of viral variants that jeopardize the protective antiviral immunity following infection or vaccination. It uses a coordinated approach to identify and curate data about these variants, their impact on immunity, and their effects on vaccine protection.
“Collaborative science and open sharing of results in near real-time amongst an international team of scientists has defined the SAVE program and has facilitated rapid prioritization, reagent development, testing, and assessment of SARS-CoV-2 variants,” said Florian Krammer, PhD, Mount Sinai Professor of Vaccinology at Icahn Mount Sinai, Co-Chair of the SAVE program’s In Vitro group and co-corresponding author of the paper. “The SAVE program serves as a template for response to not only SARS-CoV-2 variants but for other emerging pathogens.”
The SAVE program is composed of an international team of scientists with expertise in virology, immunology, vaccinology, structural biology, bioinformatics, viral genetics, and evolution. It was formed as a critical data-generating component for the U.S. Department of Health and Human Services’ SARS-CoV-2 Interagency Group (SIG) and to facilitate rapid data-sharing with global partners and the scientific community. Each team member is responsible for key contributions ranging from curation of viral mutations, bioinformatics analysis, development of novel reagents, assay development and testing, in vitro characterization, and in vivo model development to countermeasure testing.
The SAVE program is divided into three working groups: (1) Early Detection and Analysis group; (2) In Vitro group; (3) In Vivo group. The Early Detection group uses public databases and analysis tools to curate and prioritize emerging SARS-CoV-2 variants. The In Vitro group evaluates the impact of SARS-CoV-2 variants on humoral and cell-mediated immune responses using in vitro assays. The In Vivo group uses small and large animal models to test vaccine efficacy, and define immune mechanisms and correlates of protection.. Collaborative efforts between the Early Detection geneticists and evolutionary biologists, and the In Vitro group of virologists/immunologists allow for rapid determination of relationships between viral evolution and neutralization sensitivity. In turn, these results enable the In Vivo team to assess and evaluate protection provided by vaccination and/or previous infection in animal studies.
The emergence of the B.1.1.529 variant (Omicron, which includes BA.1, BA.1.1 and BA.2), which contains more than 30 mutations in the spike protein, threatened to reduce the effectiveness of clinically approved COVID-19 monoclonal antibody therapies and infection- and vaccine-induced immunity to the virus. The SAVE program rapidly responded by generating plasmids and spike protein, identifying the first Omicron cases (BA.1) in New York City, isolating, propagating, and distributing authentic Omicron viral stocks, sharing reagents, performing binding and neutralization assays, and evaluating virus infection across different animal models. The data from these studies were rapidly shared with government agencies and submitted as manuscripts on pre-print servers to inform the wider scientific community.
Icahn Mount Sinai faculty members who are key to this effort include: Harm van Bakel, PhD — Serves as a member of the Early Detection and Analysis group. His lab leverages data they generated as part of the Mount Sinai Pathogen Surveillance Program, as well as data from public repositories to identify and prioritize novel emerging variants for isolation and further characterization. Adolfo García-Sastre, PhD, and Michael Schotsaert, PhD- Lead the In Vivo efforts through the Global Health and Emerging Pathogens and Tisch Cancer Institutes at Icahn Mount Sinai. Their labs have set up SARS-CoV-2 animal infection models and have vaccinated animals available that can be used to test efficacy against variants of concern as soon as they emerge. Viviana Simon, MD, PhD — Serves as a member of the In Vitro group and oversees the charachterization of disease-causing viral variants cultured from samples collected from patients seeking care at the Mount Sinai Health System. Florian Krammer, PhD — Serves as co-chair of the In Vitro group. In addition, the Krammer laboratory provides critical insights into how well sera from COVID-19 vaccinated individuals continues to neutralize variants.”As is described in the paper, there are many critical and time-sensitive components that are involved in a successful response to emerging variants,” said Viviana Simon, MD,PhD, Professor of Microbiology and Medicine and faculty member of the Global Health and Emerging Pathogens Institute at Icahn Mount Sinai, and a member of the In Vitro group of the SAVE program. “Partnerships like the SAVE program must continue to include scientists from around the world to ensure that variants are rapidly identified and characterized so that we can effectively counter the constant threat emerging pathogens pose against global public health.”
“All Mount Sinai members of the SAVE program want to emphasize the major role that institutional support and collaborations with other Icahn Mount Sinai groups have played in our ability to participate in the SAVE program. This would have not been possible without the biosafety supervision of Randy Albrecht and the support from the institution in expanding our biocontainment capabilities, as well as without collaborations with many clinical and basic research colleagues at Mount Sinai,” said Adolfo Garcia-Sastre, PhD, Director of the Global Health and Emerging Pathogens Institute and member of the In Vivo group of the SAVE program. “And of course we do not want to forget our young members of our group, the research assistant professors, instructors, postdoctoral students, doctoral students, lab supervisors, technicians, andpre-doctroal students, who participated in the studies of the SAVE program. We could not do anything without them.”
The NIAID grants that supported funding of this work at Mount Sinai include: HHSN272201400008C, 75N93021C00014, 75N93019C00051.

Researchers at the Yale Cardiovascular Data Science (CarDS) Lab have developed an artificial intelligence (AI)-based model for clinical diagnosis that can use electrocardiogram (ECG) images, regardless of format or layout, to diagnose multiple heart rhythm and conduction disorders.
The team led by Dr. Rohan Khera, assistant professor in cardiovascular medicine, developed a novel multilabel automated diagnosis model from ECG images. ECG Dx © is the latest tool from the CarDS Lab designed to make AI-based ECG interpretation accessible in remote settings. They hope the new technology provides an improved method to diagnose key cardiac disorders. The findings were published in Nature Communications on March 24.
The first author of the study is Veer Sangha, a computer science major at Yale College. “Our study suggests that image and signal models performed comparably for clinical labels on multiple datasets,” said Sangha. “Our approach could expand the applications of artificial intelligence to clinical care targeting increasingly complex challenges.”
As mobile technology improves, patients increasingly have access to ECG images, which raises new questions about how to incorporate these devices in patient care. Under Khera’s mentorship, Sangha’s research at the CarDS Lab analyzes multi-modal inputs from electronic health records to design potential solutions.
The model is based on data collected from more than 2 million ECGs from more than 1.5 million patients who received care in Brazil from 2010 to 2017. One in six patients was diagnosed with rhythm disorders. The tool was independently validated through multiple international data sources, with high accuracy for clinical diagnosis from ECGs.
Machine learning (ML) approaches, specifically those that use deep learning, have transformed automated diagnostic decision-making. For ECGs, they have led to the development of tools that allow clinicians to find hidden or complex patterns. However, deep learning tools use signal-based models, which according to Khera have not been optimized for remote health care settings. Image-based models may offer improvement in the automated diagnosis from ECGs.
There are a number of clinical and technical challenges when using AI-based applications.
“Current AI tools rely on raw electrocardiographic signals instead of stored images, which are far more common as ECGs are often printed and scanned as images. Also, many AI-based diagnostic tools are designed for individual clinical disorders, and therefore, may have limited utility in a clinical setting where multiple ECG abnormalities co-occur,” said Khera. “A key advance is that the technology is designed to be smart — it is not dependent on specific ECG layouts and can adapt to existing variations and new layouts. In that respect, it can perform like expert human readers, identifying multiple clinical diagnoses across different formats of printed ECGs that vary across hospitals and countries.”
This study was supported by research funding from the National Heart, Lung, and Blood Institute of the National Institutes of Health (K23HL153775).
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Materials provided by Yale University. Original written by Elisabeth Reitman. Note: Content may be edited for style and length.

An implant little bigger than a grain of rice, put gently in place alongside a strategically placed blood vessel, could replace much bulkier devices that stimulate nerves.
Rice University engineers in collaboration with a host of Texas Medical Center institutions have published the first proof-of-concept results from a yearslong program to develop tiny, wireless devices that can treat neurological diseases or block pain. The nerve stimulators require no batteries and instead draw both their power and programming from a low-powered magnetic transmitter outside the body.
The MagnetoElectric Bio ImplanT — aka ME-BIT — is placed surgically and an electrode is fed into a blood vessel toward the nerve targeted for stimulation. Once there, the device can be powered and securely controlled with a near-field transmitter worn close to the body.
The team led by Jacob Robinson and Kaiyuan Yang of the Rice Neuroengineering Initiative and the George R. Brown School of Engineering and Sunil Sheth of the University of Texas Health Science Center’s McGovern Medical School successfully tested its technology on animal models and found it could charge and communicate with implants several centimeters below the skin.
The implant detailed in Nature Biomedical Engineering could replace more invasive units that now treat Parkinson’s disease, epilepsy, chronic pain, hearing loss and paralysis.
“Because the devices are so small, we can use blood vessels as a highway system to reach targets that are difficult to get to with traditional surgery,” Robinson said. “We’re delivering them using the same catheters you would use for an endovascular procedure, but we would leave the device outside the vessel and place a guidewire into the bloodstream as the stimulating electrode, which could be held in place with a stent.”
The ability to power the implants with magnetoelectric materials eliminates the need for electrical leads through the skin and other tissues. Leads like those often used for pacemakers can cause inflammation, and sometimes need to be replaced. Battery-powered implants can also require additional surgery to replace batteries.

Though the number of epidemiologists in state health departments surged during the pandemic, the Centers for Disease Control and Prevention reported on Thursday that states were still far short of the public health workforces that officials said they needed.The report, based on a survey from early 2021 of state epidemiologists from all 50 states and the District of Columbia, reinforced broader concerns that public health workers across the country are less equipped to respond to a pandemic now than they were at the beginning of 2020.Even as the number of state epidemiologists grew, especially in fields like the Covid-19 response, staffing in general infectious diseases, chronic diseases, and maternal and child health declined, the C.D.C. said. Epidemiologists are responsible for tracking disease, developing responses, investigating health threats and studying public health services and health care.And although the number of state epidemiologists grew by 23 percent from 2017 to 2021, to a total of 4,136 positions, fewer states said in 2021 that they had the resources to fully monitor population health issues and to investigate and diagnose hazards that could affect people.In all, state officials said they needed another 2,196 epidemiologists to provide basic public health services, the survey found.“The Covid-19 response has strained the U.S. public health system,” the C.D.C. report said. “Workforce and capacity needs remain unmet.”The federal government has poured money into public health response activities during the pandemic, including $7.66 billion from the American Rescue Plan Act in 2021, the C.D.C. said. It is not clear how states’ public health needs or staffing levels had changed since the survey was conducted in 2021.The C.D.C. warned that public health needed predictable levels of funding over longer periods.Public health was often underfunded and neglected even before the pandemic. A combination of unpredictable funding, reduced authority to impose health orders and staffing problems have made the work of state and local public health departments all the more difficult.Funding for epidemiology was fragile, the C.D.C. reported. In 2021, epidemiology activities relied on federal money for 85 percent of their budgets, but states were unsure how long that money would last: 39 percent of the federal money was designated for Covid-19 work over limited time periods.The C.D.C. report tracked epidemiology positions only in state health departments, and not in other state agencies.Among the fields in which states reported being the shortest-staffed were genomics, mental health, oral health and occupational health.

By revealing the structure of a protein used by bacteria to pump out antibiotics, a research team designed an early-stage therapeutic that sabotages the pump and restores the effectiveness of antibiotics.
Led by researchers from New York University, NYU Grossman School of Medicine, and NYU Langone’s Laura and Isaac Perlmutter Cancer Center, the new study used advanced microscopy to “see” for the first time the structure of NorA, a protein that the bacterial species Staphylococcus aureus uses to pump out widely used antibiotics before they can kill them.
Efflux pumps represent one mechanism by which S. aureus has evolved resistance to fluoroquinolones, a group of more than 60 approved antibiotics that includes norfloxacin (Noroxin), levofloxacin (Levaquin), and ciprofloxacin (Cipro). Fluoroquinolones are now ineffective against some drug-resistant bacterial strains, including methicillin-resistance S. aureus (MRSA), a major cause of death among hospitalized patients when infections become severe, the researchers say. For this reason, the field has sought to design efflux pump inhibitors, but early attempts have been hindered by side effects.
“Instead of trying to find a new antibiotic, we hope to make the most widely used antibiotics over the last few decades, rendered ineffective by bacterial resistance, highly effective again,” says first study author Doug Brawley, PhD. He completed his doctoral thesis in the laboratories of senior authors Nate Traaseth, PhD, a professor in the Department of Chemistry at New York University, and Da-Neng Wang, PhD, a professor in the Department of Cell Biology at NYU Grossman School of Medicine.
Antibodies to the Rescue
Published online March 31 in the journal Nature Chemical Biology, the study builds on advances in antibody technology development in recent years. Invading bacteria trigger the body’s immune system to make many slightly different antibodies, proteins shaped to attach to and neutralize specific invaders.

Colon cancer is one of the most common types of cancer. Particularly in advanced stages of disease, the treatment still largely relies on traditional chemotherapy. The new generation of cancer treatments, so-called immunotherapies, has only been effective in a small subgroup of colon cancers. TU Dresden scientists led by Prof. Sebastian Zeissig have now identified proteins that are promising targets for new immunotherapies against colon cancer. Their results also underline the central role of intestinal bacteria in the development of colon cancer. The study was published in the journal Immunity on March 31, 2022.
Our bodies can naturally clear cancerous cells. Every day our immune system may detect mutated cells in our bodies and destroy them. Once in a while though, cancerous cells can find a way to hide from the immune system. The cells develop molecular signals that block immune cells from recognizing them as a threat. This, among other strategies, allows cancer cells to multiply and grow into tumors. Understanding the molecular mechanism of this process allowed for the development of new cancer treatments, the so-called immunotherapies. These treatments can unleash the patient’s immune system to target the tumor and limit its growth.
Unfortunately, current immunotherapies are not effective for all types of cancers. Most cases of colon cancer, one of the most commonly diagnosed type of cancer, do not respond to these treatments. Now, a team of researchers from TU Dresden described a new pathway that lets colon cancer hide from the immune system. Their results provide a potential first step towards the development of a new generation of immunotherapies.
How Colon Cancer Hides from the Immune System
Inhibition of immune cells is carried out by special signals present on the surface of cancer cells. “These signals are known as checkpoint proteins,” says Prof. Sebastian Zeissig from the University Hospital Dresden and the Center for Regenerative Therapies Dresden (CRTD) at TU Dresden who led the research team. Current immunotherapies use drugs called checkpoint inhibitors to target a small set of known checkpoint proteins. Unfortunately, this approach had only a very limited impact on colon cancer growth. “This raised the question of whether there are other checkpoint proteins that may represent more promising targets for immunotherapy in colon cancer,” says Dr. Kenneth Peuker, author of the study.
Researchers analyzed colon cancer samples and looked for signal proteins present in tumor cells but not in the healthy tissue. Two proteins caught their attention. CB7H3 and B7H4 were present in large number in colon cancer cells while almost undetectable in the healthy tissue.

Men with high blood pressure have a biased recognition of other people’s anger, as shown in a new study.
Hypertension is a disease. However, in the majority of cases, there is no clear medical explanation, referred to as “essential hypertension.” Could psychological factors play a role? In this context, Konstanz biological health psychologists Alisa Auer and Professor Petra Wirtz conducted a study in male participants over several years together with colleagues from Konstanz (Germany) and Switzerland. The researchers wanted to better understand the psychobiosocial mechanisms in hypertension, since previous work in this area has left many questions open.
In an article published in the Annals of Behavioral Medicine on 22nd March 2022, they show that compared to a healthy control group, men with essential hypertension more often recognized angry expressions when they looked into the faces of others. In addition, this anger recognition bias seems to contribute to blood pressure increases over time if someone tends to frequently and intensively experience anger. This tendency is called “trait anger.”
Recognition of mixed emotions
In their study in 145 hypertensive and normotensive men, researchers presented different pictures of people who were angry. However, the pictures did not just display anger alone, but combined anger with one of three other emotions: fear, happiness, and sadness. The background for this approach is that, in everyday life, people’s faces rarely show just one emotion. Mixed emotions are more prevalent. Each of the computer-morphed pictures showed two emotions with varying affect intensities. Participants were asked which emotion they saw in the pictures.
“Hypertensive men recognized anger more often than any other emotion,” Alisa Auer says. “So, they overrated anger displayed in other people’s faces as compared to our healthy control group.” Petra Wirtz adds: “Overrating anger displayed by other persons seems to affect whether high ‘trait anger’ contributes to blood pressure increases over time.” Hence, interpersonal factors seem to play a role in essential hypertension. The expectation of associations between hypertension and social aspects was one of the reasons why the study was supported by the Cluster of Excellence “Centre for the Advanced Study of Collective Behaviour.”
Improving treatment of essential hypertension
Auer and Wirtz hope that their results will be examined and confirmed by other researchers. “Then, a next step would be to offer people with essential hypertension a more targeted support,” says Alisa Auer, who is currently completing her doctorate in Psychology. Auer is thinking of “therapeutic treatments that address a person’s perception of social environments in order to protect them from other people´s anger.”
Such therapeutic interventions would be important, because blood pressure lowering medication only treats the consequences of hypertension, but does not address potential causes. In addition, hypertension is one of the major risk factors for cardiovascular disease. In 2020, as in previous years, the Federal Statistical Office (Destatis) listed cardiovascular disease as the leading cause of death in Germany. “338,001 deaths, or more than one third of all deaths (34%), can be attributed to cardiovascular disease,” Destatis reports. Cardiovascular disease is especially deadly for older people: 93% of those who died of cardiovascular disease were 65 years or older.
What about women? The researchers hope that future studies will include women. Since women may possibly differ in their emotion recognition from men and as fewer women suffer from hypertension, the study initially focused on men.
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Materials provided by University of Konstanz. Note: Content may be edited for style and length.

When they’re prepared for transport, apples and other fruits are often treated with a fungicide to prevent spoilage and extend shelf life. The practice preserves freshness, but it may be a double-edged sword: They may help select and boost the transmission of pathogenic yeasts that are multi-drug resistant. A study published this week in mBio, an open-access journal of the American Society for Microbiology, offers new evidence for that idea.
Previous studies have examined the effect of fungicides on the human pathogen Aspergillus fumigatus, said mycologist Anuradha Chowdhary, M.D., Ph.D, at the University of Delhi, but the new work focuses on drug-resistant strains of Candida auris, a pathogenic yeast that spreads quickly in hospitals and has been isolated from nature. Fungicides used in agriculture may inadvertently select the drug resistant fungi, Chowdhary said.
She and her collaborators screened the surfaces of 84 fruits, representing 9 different tree fruit types, for pathogenic C. auris and other yeasts. The fruits were collected in 2020 and 2021 from areas of northern India and included 62 apples — 20 picked in orchards and 42 purchased from a market in Delhi. Each fruit species hosted at least 1 type of yeast.
The scientists focused on the apples. They found drug-resistant strains of C. auris on a total of 8 apples (13%) and used whole genome sequencing to identify 16 distinct colonies. The apples included 5 ‘Red Delicious’ and 3 ‘Royal Gala’ varieties. All 8 of those apples had been stored before purchase, and none of the freshly-picked apples hosted C. auris.
The group found other Candida strains on the packed apples, said microbiologist Jianping Xu, Ph.D, at McMaster University in Hamilton, Ontario. Xu co-led the study with Chowdhary.
C. auris is resistant to many drugs. It was first identified in 2009 in Japan, and since then it has emerged in or spread to all inhabited continents. Researchers have been investigating how the pathogen originates and spreads. “We still don’t really understand the forces that drive the simultaneous emergence of multiple distinct genetic clusters of C. auris,” Xu said. A study led by Chowdhary and Xu published last year in mBio was the first to isolate C. auris from a natural environment, the marshes and sandy beaches of a natural coastal ecosystem in the Andaman Islands, India.
The new findings suggest the apples could be a selective force for the pathogen, and help it to spread. Although the study focused on fruits collected from northern India, Xu pointed out that the spread of C. auris is not an Indian-specific phenomenon. It’s a global menace: In 2019, the Centers for Disease Control and Prevention identified C. auris as 1 of 5 pathogens that pose an urgent threat to public health worldwide. To figure out how to respond to the pathogen’s threat to humans, researchers need to know how it travels through other natural systems.
“When we look at human pathogens, we tend to look at what’s immediate to us,” Xu said. “But we have to look at it more broadly. Everything is connected, the whole system. Fruit is just 1 example.”
Fungi are an important part of the environment, and Chowdhary said the new study shows how the environment, animals and humans are all connected — the central tenet in the concept of One Health. “The One Health concept warrants continuous efforts and our attention in preventing the transmission of infections,” she said.
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Materials provided by American Society for Microbiology. Note: Content may be edited for style and length.