Monthly Archives: July 2022

Early in 2020, Austria began decoding the Sars-CoV-2 genome from wastewater samples from wastewater treatment plants. These analyzes are now part of the National Epidemic Surveillance. They reflect the diverse dynamics in astonishing detail and precision, according to a report by a team led by Andreas Bergthaler of CeMM, Med-Uni Vienna and Innsbruck researchers in the Nature Biotechnology journal. At the moment, with the exception of BA.5, fairly little happens with variants.

In Austria, researchers from the University of Innsbruck, the Technical University of Vienna and the Medical University of Innsbruck have developed analyzes of viruses in wastewater in the early stage of the epidemic. As a result, the ministries of education and health established a national monitoring system for the sewage treatment plant. Samples were taken from about 100 wastewater treatment plants across Austria regularly in order to have an overview of the local infection process and circulating variables. But at the end of the school year, the so-called school website monitoring was gradually abolished. At the moment, the monitoring of the 24 largest sewage treatment plants in Austria, funded by the Ministry of Health, is still in place their catchment area covers about half of the population.

For the current study, the scientists used sequencing and analysis data from a total of 3,413 wastewater samples from more than 90 municipal catchment areas and wastewater treatment plants, which were taken between December 2020 and February 2022. Using specially developed software, the first authors, Fabian Oman From the Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences (AW) and Rudolf Markt from the Institute of Microbiology at the University of Innsbruck, from the spatio-temporal frequency determination of virus variants from wastewater samples. This data was then compared to records of more than 311,000 individual cases, that is, confirmed infections, along with infection epidemiologists at the Agency for Health and Food Safety (AGES).

The results will confirm for the first time worldwide that wastewater analyzes provide a highly accurate overview of the pandemic situation in an entire country and reflect the spread of virus variants in the population. For every week and every gathering area where a particular variant has occurred at least once, according to the Epidemiological Reporting System, we see a corresponding signal in wastewater in 86 percent of samples from the same week. Conversely, in about three percent of wastewater samples we see escaped variants of the existing system, Oman says.

The researchers emphasize that the data obtained from wastewater analyzes will provide a basis for prediction of newly emerging variables and facilitate the calculation of reproductive advantage for questionable variables. Another advantage is that the infection process can be recorded in people who do not have symptoms or who do not use the test presentation. Overall, the study shows that wastewater-based epidemiology can support public health at the national level and specifically benefit countries without extensive individual surveillance, the researchers wrote. In addition, it also shows the potential of wastewater analytics in order to improve global surveillance of other infectious diseases in the future.

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According to the study: Wastewater analyzes provide an accurate overview of the variables of Covid 19 - Socialpost

The US Food and Drug Administration made arecommendationlast week that vaccine manufacturers should make a booster dose of COVID-19 vaccine that targets the omicron variant -- specifically, BA.4 and BA.5 subvariants. BA.5, the most contagious version of the virus to date, now makes upthe majorityof COVID-19 cases in the US and seemslikely to leadto another summer surge of COVID-19 cases ahead of the anticipated fall or winter booster rollout.

The current advice for this summer is the same: Get the booster shots you're eligible for. (For everyone 50 and older, that means two boosters.) But the question at hand for health regulators was whether vaccine-makers should continue to use their original primary vaccine formulas (which will probably stay the same for the time being) for boosters, or if they should create a vaccine that targets omicron, which has been dominant worldwide for months and keeps mutating into more contagious versions of itself.

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While there's still the chance we could be dealing with a whole new variant come fall or winter (you can never underestimate COVID-19), the FDA decided boosters targeting BA.5 should be the way forward.

The US government is expected to roll out vaccine boosters based on need: the most at-risk will be eligible for a new booster first. And the vaccines based on earlier strains of the virus that causes COVID-19 (also called "ancestral" strains) are still protective against severe disease and death from omicron the most important function of vaccination in general. On Tuesday, the FDA authorized another primary vaccine based on an ancestral strain of COVID,called Novavax.

While the details are being tested and ironed out, here's what we know about the fall COVID-19 vaccine strategy.

Both BA.4 and BA.5 are considered part of the "original" omicron variant (BA.1) family. They're newer versions of the virus that causes COVID-19. BA.5 quickly overtook the conversation on BA.4/BA.5 because of its extreme contagiousness, and it's now the dominant variant in the US. In a late June post, Dr. Eric Topol, professor of molecular medicine, called BA.5 "the worst version of the virus that we've seen."

While more time and research is needed to see what effect they have in the US (which has already experienced a high number of cases this late spring and summer), BA.5 is thought to whittle away much of the infection protection people got prior sickness, even with other omicron variants.

Omicron caused such a huge number of cases last winter because it was the most contagious variant to date, evading some infection protection from prior illness and effectiveness of the vaccines. The fact that newer versions of omicron are proving to be even more contagious isn't a big surprise, as this is the path COVID-19 has taken over the last two and half years.

Read more abouteverything we know about BA.5.

Specifically, the FDA is asking for abivalent(two-component) vaccine booster, which will include the BA.4/BA.5 spike protein in addition to an older strain. The FDA doesn't make vaccines, so the agency will likely authorize individual vaccine types as companies create and test them, as it did for the original COVID-19 vaccines and booster doses.

The vaccines currently authorized or approved only use older or "ancestral" strains of the virus. These vaccines still provide good protection against severe disease and death, but the effectiveness against infection is becoming more limited as the virus keeps mutating.

At a White House COVID-19 Response Teambriefing Tuesday, Dr. Ashish Jha said that if the timeline goes accordingly, he expects the first people to be eligible will start getting vaccinated in October, with other people becoming eligible in November or December.

But there is no authorized booster yet, so an exact timeline isn't available right now.

Moderna and Pfizer had both been working on boosters that target the general omicron variant. With the FDA's request to target omicron's newest strains, they will need to switch lanes to meet their target, hopefully in time for fall.

Novavax which justreceived FDA authorization for its primary two-dose vaccine also said it'sspeeding up workon a formula specifically targeting the new versions of omicron.

Pfizer announced last month that it struck a deal with the US government to provide more doses including ones that are adapted for omicron, pending FDA authorization.

The information contained in this article is for educational and informational purposes only and is not intended as health or medical advice. Always consult a physician or other qualified health provider regarding any questions you may have about a medical condition or health objectives.

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New COVID Vaccine for Fall? What to Know About the FDA's Plans - CNET

Thu, 07/14/2022 - 14:22pm | By: Ivonne Kawas

According to recent estimates reported to the Center for Disease Control and Prevention, cases of Lyme disease have rapidly increased in the United States to more than 476,000 annually, and healthcare-related costs exceed $1 billion annually.

Most cases of Lyme disease in the U.S. are due to the spirochete bacteria Borrelia burgdorferi sensu stricto transmitted by bite of a black-legged tick Ixodes scapularis.

A research paper recently published in the International Journal of Molecular Sciences by researchers at The University of Southern Mississippi (USM) opens up a new area of study: to explain the functional role of MicroRNAs (miRNAs)in tick biology and tick-pathogen-host interactions.

miRNAs, a small non-coding RNA molecule that contains 19-25 nucleotides in length that regulate posttranscriptional gene expression, are predicted to have a role in tick immunity and can aid scientists in understanding the process of how the disease is developed.

The lead author of this study, Dr. Deepak Kumar, postdoctoral researcher in USMs Center for Molecular and Cellular Biosciences, and collaborators published new insights in the paper titled: Identification of microRNAs in the Lyme Disease VectorIxodes scapularis, as they examined the potential of manipulating the novel class of tick miRNAs.

The team of researchers note that miRNAs have tremendous potential to regulate cellular processes, including immune pathways within the tick to control bacterial, parasitic, and viral infections; however, there has been limited data on differentially expressed miRNAs in the black-legged tickafter infection withthe spirochete bacteria.

In the study, they identified that miRNAs differentially expressed in Borrelia burgdorferi-infected ticks. They explain that the potential of manipulating the novel class of tick miRNAs in the context of Borrelia transmission will likely aid in developing tick-borne pathogen control strategies that can pave the way to prevent or treat the infection.

Collaborators included Latoyia Downs, graduate student in USMs School of Biological, Environmental, and Earth Sciences; Dr. Monica Embers, associate professor of microbiology and immunology division of immunology at Tulane National Primate Research Center; and professors in USMs Center for Molecular and Cellular Biosciences Dr. Alex Flynt and Dr. Shahid Karim.

The researchers sequenced, assembled, and annotated tick miRNAs, a key informative dataset enabling insights into molecular adaptations of Borrelia burgdorferi to survive in Ixodes scapularis. The team added >254 new and novel miRNAs to the existing database.

Tick-borne diseases are rising due to climatic changes and are predicted to increase, said co-author Dr. Karim. The increase in tick-borne diseases is a significant threat to public health in the absence of preventive measures. The field of tick miRNAs is primarily neglected and unexplored. This work is the tip of the iceberg, as it opens up a new avenue to exploit the full potential of miRNAs in ticks.

The International Journal of Molecular Sciencesis an international,peer-reviewed, open access journal providing an advanced forum for biochemistry, molecular and cell biology, molecular biophysics, molecular medicine, and all aspects of molecular research in chemistry, and is published semimonthly online by MDPI. Its affiliates include The Australian Society of Plant Scientists (ASPS), Epigenetics Society, European Calcium Society (ECS), European Chitin Society (EUCHIS), Spanish Society for Cell Biology (SEBC) and others.

The research was published in a special issue of the journal, Molecular Biology of Disease Vectors. Read the paper.

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Ticks and Lyme Disease: USM Researchers Co-Author Paper That Examines microRNAs in Ticks - The University of Southern Mississippi

Alexander Spira, MD, PhD, FACP: The education that we need to provide is really for providers more than anybody else. I haven't had many issues with payers in terms tests. It's great you have all these targets, but you can't treat them with a targetable therapy if you don't test for the target. It sounds simple, but there's a lot of data published through US Oncology Research, which I'm part of. The MYLUNG study showed that, as of a couple of years ago, we are still only doing about 70%75% of testing [for EGFR in patient with non-small cell lung cancer], and those drugs have been around forever. We need to test early and test often. All patients in the United States have access to this testing. There are other countries [where it is] more challenging for cost reasons. Everybody in the United States currently has access to testing; it's just a matter of the timing. I'm a community-based oncologist, and it's been harder for the community to uptake [testing] because it's more fragmented. There are multiple hospitals, multiple oncology labs, multiple provider groups vs an academic center where it's one-size-fits-allyou go to one system, and it's all there. 90% of patients get phenomenal care and are treated outside academic medical centers, but we need to keep moving the dial further.

Joshua Sabari, MD: For payers, it's important to understand that this is a complicated and complex disease. Broad panel NGS [next generation sequencing] is a must and needs to be reimbursed because if not, we can't identify the alteration to match the patient to the best possible therapy. When you look at precision medicine, it's come under a lot of fire. Are we really improving survival for our patients and quality of life? In the EGFR space, we're talking about survival in the 38-, 39-month range compared with what we've seen with standard chemotherapy, which is about a year and a half. We've added value to our patients. Payers need to understand how important matching patients to the correct targeted therapy is. When you look at small differences between individual agents, that's when it becomes more difficult of a discussion. If you have a drug that has a 5% improvement in response and a negligible 1 month-or-so improvement in progression-free survival, does that calculate into a better therapy? That's more of a debate in economic circles. For me and my patients, I use the best medication that has the best activity efficacy, as well as the best safety profile because we want to enhance patient quality of life. We know that stage 4 advanced non-small cell lung cancer is treatable, but it's not curable, right? The goal of all systemic therapies is to decrease symptomsto treat symptoms related to the cancer, but also extend life, with a focus on quality of life.

Martin Dietrich, MD, PhD: The education we needthis is affecting the oncology community, from the clinical aspect to the patient, to payers and other stakeholders in the spaceis [providing] the best possible outcomes for patients with the least amount of adverse effect burden [at the most reasonable cost]. The key to accomplishing this is evidence-based medicine with a precision medicine approach. [Planning] out the individual steps for patients upfront is important, and that's by the investment upfront in a next generation sequencing panel. This is oftentimes done by both liquid- and tissue biopsy-based assessments synchronously. We optimize outcomes for patients, see the sequence of events happening, and everybody must understand that this is not an optional step for the identification. When we look at KRAS, there is an understanding of what KRAS biology signifies, with both on label and clinical trial options. There are 4 treatment opportunities. Those are interesting for additional therapies, both in the first line and later line settings, while we use it more in the single agent setting currently. There's nobody here uninterested in understanding the presence of these molecular mutations and exploiting them for patients' benefit.

This transcript has been edited for clarity.

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Educating Payers and Providers on Advanced NSCLC With Mutations - AJMC.com Managed Markets Network

Toy company Mattel is delving into its vaults toreintroduce brandsthat havent been seen in decades, like Big Jim and Pulsar. Should Barbie be worried?

Today in health care, Anthony Fauci announced plans to retire from government after a career spanning seven administrations. Well look at what hes saying and when he plans to step down.

Welcome to Overnight Health Care, where were following the latest moves on policy and news affecting your health. For The Hill, werePeter Sullivan andJoseph Choi. Subscribe here.

The Fauci era may be coming to an end in the foreseeable future.

Anthony Fauci, President Bidens chief medical adviser, said Monday he plans to retire by the end of Bidens term in office.

Fauci said the National Institute of Allergy and Infectious Diseases (NIAID), where he is the director, had the best people in the country to carry out his vision.

The Brooklyn-born immunologist has served as director of the NIAID since 1984, most notably working on HIV-AIDS research before becoming a leading health authority during the COVID-19 pandemic, earning both praise and derision from the public and lawmakers.

Fauci has advised seven presidents on public health issues. His working relationship with former President Trump was famously fraught during the COVID-19 pandemic, as Fauci often had to counter unfounded claims made by the president.

Read more here.

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The Hills Future of Health Care 2022,Tuesday, July 19 at 8 a.m. ET Washington, D.C., or On-Demand

The pandemic has highlighted the pitfalls and potential within our health care system. Join policymakers and health experts for a comprehensive discussion on advancing access, the pursuit of health equity and resetting the care paradigm across the U.S. Featuring:Dr. Anthony Fauci, CMS Administrator Chiquita Brooks-LaSure, AMA president Dr. Jack Resneck, Dr. Mark McClellanand more.RSVP today

The rise of the BA.5 variant is spurring new calls for funding for an Operation Warp Speed 2.0 to accelerate development of next-generation COVID-19 vaccines that can better target new variants.

The BA.5 subvariant of omicron that now makes upthe majority ofU.S. COVID-19 cases is sparking concern because it has a greater ability to evade the protection of current vaccinesthan past strains of the virus did.

Pfizer and Moderna are working on updated vaccines that target BA.5 that could be ready this fall, but experts say that by the time they are ready, a new variant very well could have taken hold.

The promising alternatives:

The obstacle: There is ongoing research on these next-gen vaccines, but unlike in 2020, when the federal governments Operation Warp Speed helped speed the development of the original vaccine, there is less funding and assistance this time.

COVID-19 funding that could help develop and manufacture new vaccines more quickly has been stalled in Congress for months.

Theres no Operation Warp Speed,said Eric Topol, professor of molecular medicine at Scripps Research.Soits moving very slowly. But at least its moving.

Read more here.

IDAHO GOP REJECTS ABORTION EXCEPTION

Idahos Republican Party on Saturday adopted language to their platform that supports the criminalization of abortion in all cases, rejecting an amendment that would have supported allowing a person to get an abortion to save their life.

Delegates at the states GOP convention in Twin Falls approved changes to the partys platform that went further than existing language classifying abortion as murder from the point of conception. The new language backs criminalization of all abortions in Idaho,according to the Idaho Capitol Sun.

Scott Herndon, who is running unopposed for a state Senate seat, proposed the amendment, which he called a declaration of the right to life for preborn children.

Herndon said even in the cases where a persons life is endangered, doctors should not be giving priority to the person over the unborn child.

We will never win this human rights issue, the greatest of our time, if we make allowances for the intentional killing of another human being, Herndon said, according to the Capital Sun.

Read more here.

HOSPITAL SYSTEM PLANS TO DENY LGBT WORKERS FERTILITY COVERAGE

A Catholic hospital system operating 15 hospitals and another 132 facilities in Illinois and Michigan has adopted a policy to cover fertility treatment only for workers in opposite-sex marriages.

Illinois-based OSF HealthCare, which has more than 24,000 health care workers, changed the language of its fertility treatment policy to explicitly refer to opposite sex-couples, according todocuments reviewed by Bloomberg Law, meaning employees who are in same-sex marriages would not be covered.

The policy could be illegal under federal laws prohibiting discrimination based on sexual orientation.

It would also would likely run afoul of the 2020 U.S. Supreme Court case Bostock v. Clayton County, which ruled an employer cannot discriminate against an individual based on their sexual orientation, as it would violate Title VII of the 1964 Civil Rights Act.

OSF HealthCare is owned by the Sisters of the Third Order of St. Francis, a Roman Catholic organization in Peoria, Ill.

Read more here.

Legislative battles over abortion access are heating up in the House and Senate as Democrats look to raise pressure on Republicans.

A round of bills aimed at protecting abortion access that were introduced byDemocrats were considered on Capitol Hill last week, leading to the first instances of lawmakers butting heads over such legislation since the Supreme Court overturned Roe v. Wade last month.

Though the bills are unlikely to pass in the evenly divided Senate, where they would require bipartisan support to overcome the legislative filibuster, Democrats arepushing for action in the aftermath of the courts decision andseekingto get GOP members of Congress on the record objecting to legislation on the issue in an apparent attempt to paint Republicans as going to extremes to stop abortions.

Targeted legislation:The House on Friday passed a bill 223-205 that would protect out-of-state travel for abortion services, with three Republicans Reps. Brian Fitzpatrick (Pa.), Adam Kinzinger (Ill.) and Fred Upton (Mich.) joining Democrats in voting for the measure.

It is absolutely important to get Republicans on the record to how far they will go to restrict a womans right, Rep.Judy Chu(D-Calif.) told The Hill. Are they really saying that women should not be allowed to travel to another state to get a medical procedure?

President Biden has previously called on voters to elect more pro-abortion rights lawmakers when the Womens Health Protection Act failed to pass in a Senate vote earlier this year.

We actually need to do all things, Chu said of the multiple approaches Democrats are taking to protect abortion access. There have been marches and demonstrations and rallies all across America on a continuous basis for these three weeks. We need to do that and we also need to point to the elections.

Read more here.

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Health Care Fauci to retire from government after five decades - The Hill

Penn Medicine: $9 Million to Advance Study of Technology that Illuminates Lung Cancer Tumors

Building on Penn Medicines years of research and use of imaging technology that illuminates tumor tissuehelping clinicians more easily detect and remove itthe Perelman School of Medicine at the University of Pennsylvania has received a five-year, $9 million research grant from the National Cancer Institute (NCI) to push the field forward, particularly for lung cancer patients.

This technology, intraoperative molecular imaging (IMI), is based on fluorescent beacon molecules that target and bind themselves to tumor cells, essentially making them glowand allowing doctors to more easily distinguish cancer from healthy tissue. Penn researchers with the Center for Precision Surgery in the Abramson Cancer Center, along with colleagues at other institutions, will use the research grant to study and improve IMI technology for non-small-cell lung cancers (NSCLC). Often related to smoking, NSCLCs are the most common form of lung cancer; they are diagnosed in more than 200,000 people in the United States every year and can be life threatening.

This funding gives us a tremendous opportunity to further evaluate this important technology and with the goal being to improve outcomes for patients, said principal investigator Sunil Singhal, the William Maul Measey Professor in Surgical Research and chief of thoracic surgery, and director of the Center for Precision Surgery in the Abramson Cancer Center. We aim to develop this technology even further and to study it in additional clinical trials to help improve surgical identification and removal of tumors.

Dr. Singhal has helped pioneer the research and development of IMI use in lung cancer surgery. Among other achievements, he led the first large, multi-institutional randomized clinical trial of the technology for lung cancer. To date, studies have shown that IMI can significantly improve surgeons ability to remove tumors, while sparing other healthy tissue. The fluorescent beacon molecules used in IMI are normally infused into the patient hours or days before surgery. They bind to cell-surface receptors, such as folate receptors, which are particularly abundant on cancer cells. The light the beacons emit is typically in the near-infared range, allowing for visualization detection of tumor cells up to about two centimeters below the tissue surface, depending on the tissue type. Tissue tagged with these fluorescing beacons can be imaged in real-time, during surgery, with relatively inexpensive and portable equipment. Data from additional clinical trials have shown it also has the potential to help doctors detect tumorsfor example, following a positive or ambiguous X-ray findingduring non-surgical inspections of patients lungs via bronchoscopy, when doctors use a scope to investigate the passages in a persons lungs.

The new grant-funded research project aims to develop improved beacon molecules for NSCLC and imaging equipment to go with it, then test them in clinical trials. Collaborating researchers include Purdue Universitys Philip Low, professor of chemistry and biochemistry, who will help develop new beacon molecules; the University of Illinois Urbana-Champaigns Shuming Nie, a professor of bioengineering; and Viktor Gruev, a professor of electrical and computer engineering, who will develop sensitive near-infrared cameras. Johnson & Johnsons Bruce Rosengard will also help develop miniaturized chips for bronchoscopic detection of the light emitted from the tumor-homing beacons. The clinical trials of the new technology will be conducted at Penn Medicine, led by Dr. Singhal and Edward Delikatny, a professor of radiology and director of translational research at the Center for Precision Surgery.

Complete resection is the best outcome for patients, and the goal in this program is to improve the chances of achieving that without unnecessary tissue removal, said Ronald DeMatteo, the John Rhea Barton Professor of Surgery and chair of the department of surgery at Penn.

Link:
Penn Medicine: $9 Million to Advance Study of Technology that Illuminates Lung Cancer Tumors - UPenn Almanac

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Credit: University of Missouri

COLUMBIA, Mo. -- As new Omicron subvariants of COVID-19 continue to sweep across the United States, researchers at theUniversity of Missourihave identified specific mutations within the virus spike protein that help Omicron subvariants evade existing antibodies humans have from either vaccines or previous COVID-19 infections. These mutations help explain why some people are continuing to test positive for the coronavirus, which, like most viruses, continues to evolve.

The findings can help developers of COVID-19 treatments and vaccines consider which parts of the virus to target going forward to produce the most effective outcomes.

Kamlendra Singh, a professor in the MU College of Veterinary Medicine and Christopher S. Bond Life Sciences Center principal investigator, collaborated with Saathvik Kannan from Hickman High School in Columbia and MU undergraduate student Austin Spratt, to analyze protein sequences from more than 10 million Omicron-related coronavirus samples collected since November 2021 from around the world. Singh, Kannan and Spratt haveworked togetherto analyze protein sequences from COVID-19 samples since 2020, including the identification of specific mutations for bothDeltaandOmicronvariants.

Throughout the pandemic, the virus has continued to get smarter and smarter. Even with vaccines, it continues to find new ways to mutate and evade existing antibodies, Singh said. Omicron now has more than 130 sublineages, and they have been here for quite a while. We are now just finally able to detect them and differentiate among them with this research. Previous variants, including Alpha, Beta, Gamma and Delta, contributed to many of the mutations occurring now with these Omicron variants. So our research shows how the virus has evolved over time with new mutations.

Singh said that as the pandemic progresses, new variants and their sublineages will continue to evolve going forward. Additionally, investigators are beginning to see individuals infected with a combination of two variants, such as Delta and Omicron variants simultaneously.

Vaccinated individuals or those that have previously tested positive may have the antibodies for one variant but not necessarily for any of the other variants, Singh said. The various mutations may seem like only subtle differences, but they are very important.

Singh said that similar to the influenza virus, the coronavirus is likely never going to vanish from society, but new vaccines can be developed to target the virus most up-to-date version. However, with how rapidly the coronavirus has been mutating, the vaccines may become less effective over time.

The ultimate solution going forward will likely be the development of small molecule, antiviral drugs that target parts of the virus that do not mutate, Singh said. While there is no vaccine for HIV, there are very effective antiviral drugs that help those infected live a healthy life, so hopefully the same can be true with COVID-19.

Recently, Singh, who has tested positive for COVID-19 multiple times himself, helped develop CoroQuil-Zn, a supplement that can be taken while infected with COVID-19 to help reduce ones viral load. The supplement, which is currently being used by patients in India, southeast Asia and Great Britain, is awaiting FDA approval for use in the United States.

I am proud of my teams efforts, as we have identified specific mutations for various variants throughout the pandemic, and it feels good to be contributing to research that is assisting with the situation, Singh said. We will continue to help out, as there will surely be new variants in the future.

Complex mutation pattern of omicron BA.2: Evading antibodies without losing receptor interactions was recently published in theInternational Journal of Molecular Sciences. Funding for the study was provided by the National Institute of Allergy and Infectious Diseases, the National Strategic Research Institute at the University of Nebraska, and the Christopher S. Bond Life Sciences Center.

International Journal of Molecular Sciences

Meta-analysis

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Complex mutation pattern of omicron BA.2: Evading antibodies without losing receptor interactions

16-May-2022

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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Express News Service

NEW DELHI: BA.5, the new fast-moving Omicron sub-variant, fuelling widespread Covid-19 wave globally, is not expanding or spiking hospitalisation rate in India so far.

According to the US Centers for Disease Control and Prevention (CDC), an estimated 65 percent of coronavirus variants in the US last week were of the fast-spreading BA.5 sub-lineage.

Good at evading past immune protection from vaccination or earlier infection, BA.4 and BA.5 were first identified in March, and the World Health Organisation (WHO) started tracking them in April. By May-June, this most transmissible sub-variant took over the world and caused spikes in countries like South Africa, the UK, Europe and Australia.

However, in India, the sub-variant along with BA.4 has not caused a spike or increase in hospitalisation rate, the way it dominates globally.

Speaking with this newspaper, Dr N K Arora, head of the Covid-19 Working Group of the National Technical Advisory Group on Immunisation (NTAGI), said in India, the BA.2 variant is still dominant.

In India, BA.2 is still 85 percent. BA.4 and BA.5 are not expanding the way it is happening worldwide. The two Omicron sub-variants are less than 10 percent in the country, he said.

In May, India reported its first BA.5 in Telangana when an 80-year-old man in Hyderabad tested positive for the sub-variant, as per the Indian SARS-COV-2 Genomics Consortium (INSACOG). The octogenarian was fully vaccinated.

What is worrying is that, like the Delta variant, which created havoc in India and other parts of the world, BA.5 also affects the lungs. Earlier, Omicron was described as mild with symptoms of cold or flu.

BA.5 is different, according to a study published in medRxiv, a Yale and British Medical Journal that publishes studies not yet certified by peer review. The study said that the sub-variant is shifting back to the lower respiratory tract - at least in animal models, with a potential increase in disease severity and infection within lung tissue.

The researchers referenced another May preprint study that found BA.5 and close relative BA.4 replicate more efficiently in the alveoli of human lungs than so-called stealth Omicron, BA.2.

BA.5 not only gives the virus greater antibody evasion potential but concurrently has changed [where it tends to accumulate], along with an increased transmission potential in the community, Australias Kirby Institute authors said.

As BA.5 can infect cells more like Delta than the previous Omicron family of variants, a top US scientist has referred to the new sub-variant as Deltacron - a Delta-Omicron hybrid.

According to Dr Eric Topol, a professor of molecular medicine at Scripps Research and founder and director of the Scripps Research Translational Institute, the term Deltacron is more appropriate for BA.5, even though the subvariant isnt a true hybrid.

The technical lead on Covid-19, Maria Van Kerkhove, has also said that "BA.5 has a growth advantage over the other sublineages of Omicron that are circulating.

However, she said there is no evidence that BA.5 is more dangerous than other Omicron variants. But stressed that spikes in cases could put health services under pressure and risk more people getting long Covid.

Original post:
BA.5 fuelling Covid wave globally, but the Omicron sub-variant is less than 10 percent in India - The New Indian Express

Friday, July 15, 2022

A diagnostic panel developed by researchers in Purdue Universitys College of Veterinary Medicine will enable its Animal Disease Diagnostic Laboratory (ADDL) to screen for 22 different vector-borne pathogens in a single test. The panel, designed to be used on cats and dogs, is the only test of its kind and will soon be available to clients of the ADDL.

Dr. Becky Wilkes, associate professor of molecular diagnostics in the colleges Department of Comparative Pathobiology, and head of the ADDLs Molecular and Virology sections, developed the methodology using next generation sequencing (NGS), a process that can sequence large amounts of DNA more economically than other techniques. First commercially available in the mid-2000s, NGS technology has been used to sequence the human genome and track foodborne outbreaks and infectious disease transmission.

Dr. Wilkes novel approach of incorporating NGS as an everyday diagnostic tool will facilitate more accurate identification of a wider range of pathogens in a single test through rapid sequencing of the pathogens DNA. Polymerase chain reaction testing (PCR), the current industry standard, can only test for three or four pathogens at a time in a single test and it only gives a fluorescent signal that pathogens are detected; it cannot sequence their DNA.

Were using a targeted NGS method to specifically identify vector-borne pathogens such as those transmitted through the bite of a mosquito, flea or tick, Dr. Wilkes said. Multiple pathogens can be found within the same tick and sometimes co-infections go undiagnosed because were not looking for all the organisms that could be there.

Diagnosing vector-borne diseases in dogs can be difficult because there are many different disease-causing agents that can be transmitted from an insect bite and the clinical signs caused by these agents often overlap. Patients can also initially present with non-specific signs, such as fever and lethargy.

For the NGS panel, Dr. Wilkes developed specific primers short single-stranded DNA fragments for each organism of interest, ensuring the primers would be specific for each pathogen. She then collaborated with Thermo Fisher Scientific to finalize the assay design, ensuring the primers wouldnt interact with each other or amplify genetic material from the dog or cat.

The primers target specific DNA segments in the pathogens of interest. This results in amplification of these pathogen-specific sequences if present in the sample. When pathogens are present, they make up less than 1% of the sample. The majority of the sample is made up of host genetic materials. NGS provides sequences for everything in the sample, including pathogens and the host genetic materials. The targeted NGS approach enhances the sequences of the pathogens of interest to make them easier to detect. Once the targeted DNA is sequenced, it can be compared to information in the GenBank database, an annotated collection of all publicly available DNA sequences, to confirm its identification as a pathogen.

As I researched NGS, I was amazed by the amount of data it generates, Dr. Wilkes said. In the past, you could only sequence one piece of DNA at a time, which could be 1,000 base pairs. Thats the process originally used to sequence the human genome. It took 13 years and $3 billion. With NGS, you can generate the same information in a matter of days. Its use as a diagnostic tool for pathogen detection was untested when I started working with targeted NGS. That motivated me to conduct this research to see if NGS could be used to create a targeted diagnostic panel that would be affordable for the veterinary community.

In a recent canine necropsy case at the Purdue Small Animal Hospital, Dr. Viju Pillai, a resident in anatomic pathology, suspected the dog had been infected with Rocky Mountain spotted fever, a relatively rare tick-borne zoonotic disease caused by the bacterium Rickettsia ricketsii. The ADDL doesnt have a standalone PCR for that organism and previously would not have been able to conduct a test onsite. A sample would have been sent out for PCR testing at another lab.

The NGS panel developed by Dr. Wilkes confirmed Dr. Pillais suspicion that the case was Rocky Mountain spotted fever. As the panel becomes more widely used, faster diagnosis of less common diseases will aid veterinarians in developing appropriate treatment plans for their patients.

Most tick-borne diseases are bacterial and can be treated with doxycycline, Dr. Wilkes said. But there are a few vector-borne diseases that are caused by parasites, and in those cases doxycycline wouldnt work. These organisms are less commonly tested for, and if they are missed it can delay proper treatment.

Earlier diagnosis and treatment is especially critical when the animal is infected with a zoonotic disease one that can spread to humans such as West Nile virus, Lyme disease, Rocky Mountain spotted fever or malaria. Although the initial panel targets vector-borne pathogens in cats and dogs, NGS technology can be applied to panels for a range of illnesses affecting a variety of species.

The method were launching is going to change the way we do diagnostics, said Dr. Kenitra Hendrix, director of the ADDL and clinical associate professor of veterinary diagnostic microbiology. We will no longer be limited to picking and choosing a few pathogens to determine whether or not they are present in the sample. Well be able to select these panels based on the syndrome the animal has which will give us a better understanding of all the potential causes of the disease.

Last year, the ADDL conducted 107,332 tests. Implementation of the NGS testing platform, which requires state-of-the-art equipment and specific lab expertise, will expand the ADDLs ability to fulfill its mission of providing accurate and reliable animal diagnostic services and consultations to its clients, which include veterinarians, animal health officials, livestock producers and animal owners. Future panels might be developed for diseases that spread through livestock, such as pigs and poultry.

Its a lengthy and expensive process to validate the panels, Dr. Hendrix said. So we need to be strategic about implementing tests that will be most useful to our clients, but the opportunities are limitless. Dr. Wilkes is a leading expert in molecular diagnostics for infectious diseases for animals. We are very fortunate to have her here at Purdue developing these diagnostic panels.

The research was funded by the American Kennel Club (AKC) Canine Health Foundation, which awarded Dr. Wilkes a $103,000 grant to develop the comprehensive vector-borne targeted NGS panel. Dr. Jobin Kattoor, postdoctoral research associate in the Department of Comparative Pathobiology, assisted Dr. Wilkes in validating the vector-borne panel. Through parallel sequencing, the panel will incorporate testing for additional infectious diseases that may cause gastrointestinal, respiratory, reproductive, dermatologic, or neurological signs in dogs and cats.

Dr. Wilkes was recently invited to present her research at a meeting of the Flat-Coated Retriever Society of America whose members were amazed at the number of organisms that can be detected with a single test.

The vector-borne testing is only part of this panel, Dr. Wilkes said. The panel is validated for 22 vector-borne pathogens, but it contains many more. It is capable of detecting basically all known pathogens in dogs and cats. That is what we are working toward.

Click here for more information about the comprehensive vector-borne targeted NGS panel.

Writer(s): Kat Braz | pvmnews@purdue.edu

Originally posted here:
Purdue's first-of-its-kind vector-borne disease panel screens for 22 different pathogens in a single test - Purdue University