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Here’s how scientists are designing vaccines that can ditch the fridge | Science | AAAS



Most vaccines require refrigeration to keep from going bad. The messenger RNA vaccines for COVID-19 require freezing temperatures.

Here’s how scientists are designing vaccines that can ditch the fridge

From the cutting-edge vaccines for COVID-19 to the decades-old ones for poliovirus, most vaccines need to be kept cold to survive the trip from factory to patient. But that poses a major hurdle to even routine immunizations in countries like Mali or Bangladesh, where up to 90% of health facilities lack adequate refrigeration. To solve this problem, some researchers are working toward a radical goal: vaccine formulations that don’t have to be kept cold. Significant hurdles remain, but many scientists are optimistic that 10 years from now vaccination campaigns won’t be quite so hampered by the heat.

“I think we are at the limit of how many people we can vaccinate using [refrigerated supply chains],” says Asel Sartbaeva, a chemist at the University of Bath who is working on a molecular “cage” to make multiple vaccines temperature stable. “And this is where we come in.”

Most vaccines include biomolecules or weakened forms of pathogens that start to fall apart above—or below—certain temperatures. Even when the formulas are freeze-dried or suspended in solutions to improve stability, many still require refrigeration between 2°C to 8ºC, the temperature of a regular fridge. When vaccines don’t have to be kept cold, the results can change the world: A freeze-dried smallpox vaccine that was stable for months at high temperatures was essential for eradicating the global scourge in the 1970s. Even incremental improvements can make a big difference: MenAfriVac, a meningitis vaccine that can now be kept without refrigeration for 4 days, cut costs in half during a 2011 vaccination campaign in Chad.

Scientists have different strategies for creating vaccines that can beat the heat, ranging from modified chemical solutions to new methods of delivery. Which strategy works best depends largely on the vaccine’s active ingredient: RNA, DNA, live or inactivated virus or bacteria, or bits of the pathogen like peptides or proteins.

Protein-based vaccines, which are relatively stable, are “low-hanging fruits,” says Maria Bottazzi, a microbiologist who co-directs the Texas Children’s Hospital Center for Vaccine Development. But other types, like live attenuated viral vaccines, are especially susceptible to changes in temperature. Diverse approaches are necessary, she says: “There’s no silver bullet.”

But there are silica cages. That’s what Sartbaeva used to stabilize proteins in the common vaccine for diphtheria, tetanus, and pertussis (DTP). Because the DTP vaccine is made of proteins from each of the disease-causing microbes, it needs to be kept at 2°C to 8ºC. Sartbaeva, whose previous research focused on the structure of porous silicate materials, thought silica might be able to create a protective molecular cage around the vaccine’s proteins, preventing them from unfolding in the heat.

Over the next few years, Sartbaeva and colleagues developed a process in which reactive silica molecules are mixed with the proteins. Attracted to the biomolecules’ positively charged regions, the silica comes together in a network that precisely matches the proteins’ contours. “The cool thing about silica is that it’s quite malleable,” allowing for a perfect fit, Sartbaeva says.

Her group’s silica cages stabilized diphtheria and tetanus proteins for at least 1 month at room temperature and 2 hours at 80ºC, she and her colleagues reported last year in Nature Scientific Reports. When injected into mice, the caged proteins provoked an immune response; the uncaged proteins were duds. But several challenges remain before clinical trials are in sight: proving the method can stabilize all the proteins in the DTP vaccine at once and simplifying the process needed to dissolve the silica before the vaccine is injected.

Another approach is the “Fruit Roll-Up” method. Maria Croyle, a pharmacist at the University of Texas, Austin, encased live adenovirus—a vector used in multiple vaccines, including Johnson & Johnson’s COVID-19 vaccine—within a solid film of sugars and salts with a texture similar to the popular snack. The film can be dissolved under the tongue or inside the cheek to administer the vaccine, or even reconstituted and injected. The film kept an adenovirus-based vaccine for Ebola stable at room temperature for 36 months, Croyle and colleagues reported last year in Science Advances. When reconstituted from the film and inhaled, the 3-year-old viruses protected primates from a lethal dose of Ebola.

The researchers add that by altering the mix of sugars and salts in the film, the method could work for other vaccines and therapeutics, including influenza vaccines. Croyle, who is also chief scientific officer of the biomedical startup Jurata Thin Film, says her colleagues there want to start clinical trials for a vaccine using the film within 12 to 18 months, once they determine how to scale up manufacturing. Michigan Technological University chemical engineer Caryn Heldt calls the film a “very promising technology” for multiple vaccine platforms. Bottazzi agrees, and says she’s considering testing the formulation with some vaccine prototypes.

Meanwhile, refrigeration-dependent messenger RNA vaccines—like those developed by Moderna and the Pfizer/BioNTech collaboration for COVID-19—present their own challenges. Some scientists have turned to a tried-and-true approach used with other vaccines: freeze-drying. Once a vaccine is freeze-dried, says Drew Weissman, an immunologist at the University of Pennsylvania, “It’s essentially stable forever. … The big challenge is the cost.”

New manufacturing techniques could help, but freeze-drying is a slow and expensive process, and it doesn’t work for every vaccine. Just this month, however, Pfizer started clinical trials on a freeze-dried version of its vaccine designed to be stable at regular refrigerator temperatures; currently, it has to be stored at about –20ºC. Results are expected at the end of May.

Another strategy: Alter the lipid nanoparticles that surround the vaccines’ RNA molecules; it is these nanoparticles that are responsible for the vaccines’ ultracold storage requirements. Seattle-based HDT Bio recently took this tack, inventing a nanoparticle that can be shipped in regular refrigerators, then combined with RNA just before injection, says Amit Khandhar, the company’s chief of formulations. The approach doesn’t entirely eliminate the need for refrigeration, and the more stable formulation does not provoke as much of an immune response, Weissman says. But the world may soon know how well it performs in the wild: A vaccine candidate for COVID-19 using the company’s nanoparticles is about to start clinical trials in India.

To avoid cold storage entirely, another option is to use DNA instead of RNA. DNA, the more stable of the two nucleic acids, “could be sitting in a warehouse at room temperature for months,” says Deborah Fuller, a microbiologist at the University of Washington, Seattle, who helped design the HDT Bio vaccine. DNA vaccines have not had much clinical success despite years of research, Fuller says, though a number of DNA vaccines for COVID-19 are in clinical trials.

But even if technical hurdles are overcome, getting temperature-stable formulations to market requires “aligning all the stars,” for manufacturers and regulators, Bottazzi says. Encouraging drug developers to spend millions of dollars on new formulations is no easy task. Incentives are rare, especially when it comes to reformulating existing vaccines, says Jason Hallett, a chemist at the Future Vaccine Manufacturing Research (FVMR) Hub at Imperial College London who works on temperature-stable vaccine formulations using liquid salts. Under current regulations, “It is more cost effective to improve the cold chain than it is to eliminate the cold chain,” he says.

Yet the enormous resources that countries have poured into COVID-19 vaccine research could change the outlook for temperature-stable formulations, says Benjamin Pierce, operations manager at the FVMR Hub. A temperature-stable vaccine may not come in time for the current pandemic, he says, but as the world prepares for the next one, “eliminating the cold chain will absolutely be a priority.”

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Git commands data scientists use on a day-to-day basis | by Varshita Sher | Apr, 2021 | Towards Data Science




Git commands data scientists use on a day-to-day basis | by Varshita Sher | Apr, 2021 | Towards Data Science

Git commands data scientists use on a day-to-day basis

For scenarios like reviewing a local PR copy, bringing back a messed up file, or removing a file as part of PR.

Terms and Terminology

Scenario 1

Scenario 2

Scenario 4

Scenario 5

Scenario 6

Scenario 7

Scenario 8

Scenario 9

Scenario 10

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Scientists tracking coronavirus variants struggle with global blind spots | Science | AAAS




Scientists tracking coronavirus variants struggle with global blind spots | Science | AAAS

A passenger being tested for COVID-19 at Johannesburg’s international airport in January. A coronavirus variant of concern that arose in South Africa has spread around the world.

Scientists tracking coronavirus variants struggle with global blind spots

Science’s COVID-19 reporting is supported by the Heising-Simons Foundation.

Last month, Gytis Dudas was tracking a concerning new coronavirus variant that had triggered an outbreak of COVID-19 in his native Lithuania and appeared sporadically elsewhere in Europe and in the United States. Exploring an international database of coronavirus genomes, Dudas found a crucial clue: One sample of the new variant came from a person who had recently flown to France from Cameroon. A collaborator, Guy Baele of KU Leuven, soon identified six more sequences from people in Europe who had traveled in Cameroon. But then their quest to pinpoint the variant’s origins hit a wall: Cameroon had uploaded a total of only 48 genomes to the global sequence repository, called GISAID. None included the variant.

With dogged legwork, Baele and Dudas, an evolutionary biologist at the Gothenburg Global Biodiversity Centre, learned another team had gathered as-yet-unpublished sequences from a COVID-19 outbreak among staff at a great ape program in the Central African Republic—near the Cameroonian border. Six people there carried the new variant.

Baele, Dudas, and their colleagues reconstructed the variant’s evolutionary tree and geographic spread, and concluded that the new variant most likely arose in Cameroon, as they reported in a preprint on 8 May. They note that the variant carries a suite of mutations seen in other “variants of concern” that are more infectious or dangerous.

“It looked like the typical thing that should raise all red flags,” says Sebastien Calvignac-Spencer, an evolutionary biologist at the Robert Koch Institute whose team sequenced samples from the ape station. But Cameroon and neighboring countries, where the team inferred the variant might already be prevalent, had been blind to it.

The researchers say the story of this variant, designated B.1.620, holds a warning for the world: “The sequencing effort in Cameroon and other African countries is not enough,” says co-author Ahidjo Ayouba, a biologist at the French National Research Institute for Sustainable Development at the University of Montpellier. He is traveling to his native Cameroon next month to set up the country’s first next-generation sequencer. The emergence of new variants with deleterious mutations in countries with no regular sequencing “may become an alarming norm,” the researchers caution in the paper.

It is not just Africa. Of 152 countries for which data were available as of 10 May, 100 had uploaded sequence data for less than 1% of their reported cases to GISAID (see map, below). Among those, 51 countries, including large nations such as India, Indonesia, Russia, and Brazil, had uploaded sequences for less than 0.1% of cases. Ten wealthy nations accounted for 82% of the more than 1.4 million sequences in GISAID’s database. “We are working to change that,” says Frank Konings, leader of the World Health Organization’s (WHO’s) Virus Evolution Working Group. 

Most countries with scarce sequencing also currently have little or no access to vaccines, and some have severe outbreaks. As the virus replicates unchecked, those regions can become breeding grounds for new mutants, which can then spread around the world. India, for example, is coping with a world-leading surge of cases. On 11 May, WHO labeled the new variant B.1.617, which arose in India and has spread to dozens of countries, a variant of concern. “Where the pandemic is currently unchecked is where we can expect that variants are on the rise,” Dudas says. “It would be much more interesting to sequence the last 1000 cases in the Central African Republic than the next 100,000 cases in Germany.”

A patchy picture

Sequencing of the pandemic coronavirus is minimal in most countries around the world, so scientists often have little insight into emerging new variants. 


Globally, the obstacles to systematic surveillance are daunting. State-of-the-art sequencers cost $335,000, and local scientists must be trained to use them. Many areas lack the roads and refrigeration needed to speedily transport samples. In India, “The issue is sampling: Somebody has to collect and ship the samples and provide the clinical data. That takes some time,” says Anurag Agrawal, director of the Council of Scientific and Industrial Research’s Institute for Genomics and Integrative Biology in New Delhi. And costly sequencing reagents need to be continually imported.

“We ordered … reagents [from a U.S. company] in November [2020]. They are arriving now!” says Senjuti Saha, a microbiologist at the Child Health Research Foundation in Dhaka, Bangladesh. “This is not an exception, rather it’s the rule.”

Saha is nonetheless pleased with a multilab effort that has allowed the country to scale up sequencing to 0.2% of 777,000 identified cases. “I don’t think [that number is] great,” she says. “But it was zero before. And we have never done this before.”

The effort is already paying off, most recently on 8 May, when two Bangladeshi patients who recently returned from India were found to be carrying B.1.617. Two days later, after a long meeting with scientists, Bangladeshi officials tightened quarantine at the border.

Other countries face geographical challenges. In December 2020, Brazilian scientists identified P.1, now a variant of concern globally, during a massive outbreak in Manaus, the capital of Amazonas state. But sequencing coverage is poor in places like the neighboring rainforest state of Acre and in Brazil’s northeast, says Ana Vasconcelos, a computational biologist at the National Laboratory for Scientific Computing in Petrópolis, Brazil. She says just 25 genomes have been uploaded from Acre. She enlisted colleagues there to provide 100 samples, then found there was no dry ice, needed for transport. She finally received the samples yesterday, with the help of a French nongovernmental organization, the Mérieux Foundation.

Some experts have suggested nations aim to sequence virus from 5% of cases, but others say such goals are wrongheaded. “The world is getting too obsessed with numbers,” says Tulio de Oliveira, a computational biologist and director of KRISP, the KwaZulu-Natal Research and Innovation Sequencing Platform at the University of KwaZulu-Natal, Durban. For example, he and South African colleagues identified the variant of concern that originated in South Africa soon after it arose, by strategically sampling regions fighting outbreaks rather than by boosting sampling evenly around the country.

De Oliveira and a huge team of other African scientists have now turned sparse sequence data in Africa into a big picture of how the virus has evolved within the continent. In a preprint posted yesterday, based on nearly 9000 sequences collected in 33 African countries, they found that SARS-CoV-2 likely arrived in multiple African countries with travelers, mainly from Europe. Travel restrictions initially kept case counts in check. But then, the virus evolved into several concerning variants. “Although distorted by low sampling numbers and blind-spots,” the authors write, “the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new variants.”

That’s true worldwide, Calvignac-Spencer says. “It’s not really possible that we go on being so selfish with genomic surveillance, with vaccines,” he says. “It’s not understanding our own best interests.”

This content was originally published here.

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Physicians, scientists believe doctors’ group deserves Nobel Prize for finding ‘most powerful COVID-19 killer known to science’




June 1, 2021 (LifeSiteNews) – The “miraculous” drug Ivermectin has proved to be incredibly effective at both preventing and treating COVID-19, yet it has been subject to widespread suppression and misinformation from global health bodies in an apparent attempt to promote financial revenue over saving the lives of millions.

In a recent article, New York Times best-selling author and journalist Michael Capuzzo detailed the manner in which Ivermectin came to be used to treat COVID-19, and simultaneously subjected to global censorship despite its incredibly high success rate at treating the virus. The May 2021 issue of Mountain Home contains Capuzzo’s detailed report, following the actions of doctors in the Front Line COVID-19 Critical Care Alliance (FLCCC). 

Ivermectin is “what the world desperately needs now,” according to Dr. Pierre Kory, one of the founding members of the FLCCC. But although the desperate need is present, governing health bodies apparently seem intent on ensuring that the drug is not known, Capuzzo reveals. 

FLCCC formation and the miracle drug Ivermectin 

However, the FLCCC is not promoting Ivermectin based on a hunch or without medical qualifications to support them. The five-man team of Dr. Paul Marik, Dr. Joseph Varon, Dr. Gianfranco Umberto Meduri, Dr. Jose Iglesias, and Dr. Kory has “nearly 2,000 peer reviewed papers and books and over a century of bedside experience in treating multi-organ failure and severe pneumonia-type diseases” between them. 

Dr. Marik spent the early days of COVID-19 at Sentara Norfolk General Hospital treating patients with the virus, and developing a treatment protocol as early as January 2020. The FLCCC then realized in March 2020 that the coronavirus itself does not directly kill a person but rather overpowers the body with a “vast viral graveyard,” which then attacks the body, causing organ inflammation and blood clotting. They developed the MATH+ protocol for treating COVID, composed of Methylprednisolone, Ascorbic Acid (Vitamin C), Thiamine (Vitamin B1), and the blood thinner Heparin. 

As Capuzzo wrote, while the approach was strongly recommended against by health bodies throughout the world, it was subsequently made the “global standard of hospital care,” courtesy of later studies. Their first COVID-19 preventive protocol, the first of its kind, was “centered” on the use of the “miracle drug” Ivermectin.

“It’s therapeutic nihilism to say that doctors can do nothing,” Marik said. “Supportive care is no care at all.”

Early censorship

The FLCCC’s MATH+ protocol treatment was hailed as eminently successful by medics around the world, who wrote to thank the FLCCC doctors, who were fast becoming “heroes of the pandemic.” In order to spread the good news of the medical success, Emmy Award-winning publicist Joyce Kamen and former CBS News correspondent Betsy Ashton devoted themselves to contacting TV news anchors, scientists, public health experts, “every governor and member of Congress, President Trump, Dr. Anthony Fauci, and, when the time came, President-elect Biden.” All ignored the successful treatment. 

“People are dying needlessly. We’ve cracked the code of the coronavirus,” said Marik.

The censorship was a foreshadow of things to come.

Ivermectin vindicated

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Then in October, Marik came across studies from Latin America demonstrating the effectiveness of Ivermectin. The incredibly effective drug was described by Marik as “one of the safest drugs ever given to humanity,” with more than 3.7 billion doses given over 40 years. Australian research had earlier discovered that Ivermectin not only blocked the development of RNA viruses such as the Zika virus, influenza, West Nile virus, and Avian flu, but also lethally attacked COVID, wiping out “essentially all viral material by 48 hours.”

Ivermectin “basically obliterates transmission of this virus. If you take it, you will not get sick,” testified Dr. Kory before the Senate Homeland Security Committee in December 2020. He pointed to “mountains of data,” which had emerged in the past few months, backing up his claims. 

These mountains were composed at the time of 27 studies, 16 of which were randomly controlled trials, with “miraculous” results. (Now there are 56 trials, with 28 randomly controlled trials.) People with COVID who took Ivermectin were “far more likely” to get better at home and did not need hospitalization, while those already ill in hospitals did not end up the intensive care units. 

In fact, six of the studies presented results showing that Ivermectin’s efficacy at reducing the risk of developing COVID was a staggering 92.5 percent. Dr. Hector Carvallo, professor of medicine at the University of Buenos Aires, conducted a real world trial of the drug, giving Ivermectin to 788 doctors and health-care workers in three different centers, with a control group of 407 medical staff who were not given Ivermectin. Out of the control group, 236 people became “ill with COVID,” and the 788 treated with Ivermectin recorded no infections. 

Brazilian states with cities that took up Ivermectin protocols similarly “show a much greater drop” in cases than others, with disparities of more than 60 percent between neighboring areas, according to analysis linked by Kory. A subsequent study by a Brazilian-led team reported “a reduction of 31.5 to 36.5 percent in viral shedding” and 70 percent to 73 percent shorter symptom duration for patients treated with regimens that included the drug.

This was mirrored in Peru and India, as thousands, even millions, were given the drug, with COVID cases and deaths plummeting as a result. Dr. Andrew Hill, senior WHO investigator for potential COVID-19 treatments, also provided corroboration, stating that Ivermectin reduced COVID mortality by 81 percent.

A deafening silence of global censorship

However, Capuzzo reported that Kory and the FLCCC team have faced global censorship in their attempts to enlighten doctors and politicians to the truth about Ivermectin. 

“Only big randomized controlled trials by big pharma/big academic medical centers are accepted by big journals, while others are rejected,” he declared. In order to escape the “media/social media censorship,” a treatment must be a big drug recommended by a large public health agency. 

“This leaves you with a system where the only thing that’s considered to have sufficient evidence or proven efficacy is essentially a big new pharmaceutical drug,” he continued.

Kory’s powerful Senate testimony garnered a huge amount of views on YouTube, upward of 8 million, before it was deleted for “misinformation” about COVID-19. YouTube also removed the video from Republican Wisconsin Senator Ron Johnson’s channel as well as other clips from the December 2020 Senate hearing. 

In Argentina, Ivermectin-promoting Dr. Carvallo noted that “as soon as our reports were published … resistance appeared in the horizon.” He said his team faced pressure from “many doctors who worked for the pharmaceutical industry, because this was a very, very cheap treatment.”

Then in England, Dr. Tess Lawrie, a prominent independent medical researcher evaluating drugs for the World Health Organization and the U.K.’s National Health Service (NHS), attempted to promote the drug, only to face similar censorship. 

Having studied all of the reports that Kory cited, she called the evidence “consistent and unequivocal,” and promptly sent a high-level multi-study review to NHS leaders, U.K. politicians, and Prime Minister Boris Johnson, stating that Ivermectin should be “adopted globally and systematically for the prevention and treatment of COVID-19.” Three months later, she has heard nothing, and instead been “batted .. away with waffle.”

Social media also weighed in on the censorship. Twitter removed a January 12, 2021 tweet from the Brazilian Ministry of Health that urged people to “request early treatment” for COVID-19, i.e. Ivermectin. Twitter accused the message of “spreading misleading and potentially harmful information.”

Then the Slovakian Ministry of Health announced on Facebook it would being using Ivermectin, which caused Facebook to remove the post and the entire page. 

Even the so-called modern arbiters of truth, fact-checkers, attacked Kory’s “mountains of data,” when after he presented all the evidence from the many successful randomized trials to the Associated Press (AP), the AP wrote, “False. There’s no evidence Ivermectin has been proven a safe or effective treatment against COVID-19.”

The drug was blacklisted by medical agencies, health bodies, and media the world over, and emphasis placed solely on the much-hyped, hastily developed, experimental COVID injections.

Did President Trump receive Ivermectin?

A particularly poignant point made, but fleetingly in the article, is related to former President Donald Trump and his own connection to Ivermectin. 

Capuzzo makes the groundbreaking claim that Trump was treated with Ivermectin while undergoing treatment for his own diagnosis of COVID-19 at Walter Reed Hospital. Capuzzo wrote that Trump’s use of the drug went “unreported by the press, though it may well have saved the president’s life while he was instead touting new big pharma drugs.”

Capuzzo is alone in making this revelation and provides no reference for his information. 

However, the weight of his claim is not to be ignored, given his hard-earned credentials as a six-time-nominated Pulitzer journalist and a New York Times best-selling author. 

Commenting on the matter, LifeSite co-founder and president Steve Jalsevac suggested that Capuzzo’s claims could indeed be true, and had suspected that the President must have received either Hydroxychloroquine or Ivermectin, since Regeneron and Remdesivir, both of which Trump received, would not have been effective enough to cause such a dramatic improvement in his condition. 

Jalsevac previously questioned why Trump was not receiving Hydroxychloroquine, since it had been proved to be both effective and safe in treating COVID-19. 

Given the censorship that the FLCCC reported in its attempts to promote Ivermectin, it is perhaps not surprising that any news of Trump receiving the drug should be equally censored, and news of the incident only revealed in a publication of comparatively small readership. 

Why such blacklisting of Ivermectin?

Given the widespread censorship of Ivermectin’s success that Capuzzo describes, along with his claim that Trump received Ivermectin but was completely ignored by the media, the question rises as to why such censorship is being enacted.

Writing to Dr. Marik, Dr. Carvallo summarized the reason for the censorship: “I am afraid we have affected the most sensitive organ on humans: the wallet … ”

What then is the connection between the wallet and Ivermectin? Ivermectin’s parent drug company Merck owned the patent, but it expired in 1996. Consequently, Ivermectin can be found for a price measured in cents or dollars, rather than hundreds or thousands. 

In contrast, Gilead-produce Remdesevir, the “only anti-viral treatment for hospitalized COVID-19 patients approved by the NIH COVID-19 Treatment Guidelines Panel,” costs $3,000 per dose. Remdesevir has been shown to have no mortality benefit for COVID patients. As noted by The Washington Post, “Remdesivir may not cure coronovirus, but it’s on track to make billions for Gilead.”

The same is seen with the COVID experimental injections. Drugs are only granted Emergency Use Authorization provided that “there are no adequate, approved, and available alternatives” for the drugs being authorized. Vaccine companies have received billions in funding in order to produce the experimental drugs, something that would not have occurred had Ivermectin been publicly known and promoted as the effective treatment which the FLCCC has shown it to be. 

A censorship-free global promotion of Ivermectin would mean the loss of the billions in funding and the EUA awarded to the vaccines – vaccines that are rapidly being followed by adverse effects in their hundreds of thousands, and deaths in the thousands.

In fact, Merck recently warned against Ivermectin being used for COVID; a point that Philippine Dr. Agbayani called a conflict of interest, since Merck is currently making a rival medicine for COVID-19, having received $356 million from the United States to do so, and which will be marketed at $3,000, according to Capuzzo. 

“Our little Ivermectin has so many big enemies. It’s David versus 10 Goliaths,” declared Dr. Kory.

This content was originally published here.

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