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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Dudas, an evolutionary biologist at the Gothenburg Global Biodiversity Centre, learned another team had gathered as-yet-unpublished sequences from a COVID-19 outbreak among staff at a great ape program in the Central African Republic—near the Cameroonian border.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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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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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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Is Malcolm Turnbull the only Liberal who understands economics and climate science – or the only one who’ll talk about it?




Darren England/AAP

Yesterday, former Liberal prime minister Malcolm Turnbull was unceremoniously dumped as chair of the New South Wales government’s climate advisory board, just a week after being offered the role. His crime? He questioned the wisdom of building new coal mines when the existing ones are already floundering.

No-one would suggest building new hotels in Cairns to help that city’s struggling tourism industry. But among modern Liberals it’s patently heresy to ask how rushing to green light 11 proposed coal mines in the Hunter Valley helps the struggling coal industry.

Coal mines in the Hunter are already operating well below capacity and have been laying off workers in the face of declining world demand for coal, plummeting renewable energy prices and trade sanctions imposed by China. The problem isn’t a shortage of supply, but an abundance.

The simple truth is building new coal mines will simply make matters worse, especially for workers in existing coal mines that have already been mothballed or had their output scaled back.

coal mine in the Hunter Valley
Turnbull has called for a moratorium on new coal mines in the Hunter Valley, such as the one pictured above.
Dean Lewins/AAP

It gets worse. Once an enormous, dusty, noisy open cut coal mine is approved, the agriculture, wine, tourism and horse breeding industries – all major employers in the Hunter Valley – are reluctant to invest nearby. While building new coal mines hurts workers in existing coal mines, the mere act of approving new coal mines harms investment in job creation in the industries that offer the Hunter a smooth transition from coal.

The NSW planning department doesn’t have a plan for how many new coal mines are needed to meet world demand. Nor does it have a plan for how much expansion of rail and port infrastructure is required to meet the output of all the new mines being proposed.

Read more:
Forget about the trade spat – coal is passé in much of China, and that’s a bigger problem for Australia

That’s why my colleagues and I recently called for a moratorium on new coal mines in the Hunter until such plans were made explicit. Just as you wouldn’t approve 1,000 new homes in a town where the sewerage system was already at capacity, it makes no sense to approve 11 new coal mines in a region that couldn’t export that much coal if it tried.

But if there’s one thing that defines the debate about coal in Australia, its that it makes no sense.

Just as it made no sense for then-treasurer Scott Morrison to wave a lump of coal around in parliament in 2017, it makes no sense for right-wing commentators to pretend approving new mines will help create jobs in coal mining. And it makes no sense for the National Party to ignore the pleas of farmers to protect their land from the damage coal mines do.

Scott Morrison with a lump of coal to Question Time in 2017.
Scott Morrison took a lump of coal to Question Time in 2017.
Lukas Coch/AAP

On the surface, Turnbull’s support for a pause on approving new mines while a plan is developed is old-fashioned centrism. It protects existing coal workers from new, highly automated mines, it protects farmers and it should make those concerned with climate change at least a bit happy. Win. Win. Win.

But there’s no room for a sensible centre in the Australian coal debate. And when someone even suggests the industry might not be set to grow, its army of loyal parliamentary and media supporters swing into action.

Labor’s Joel Fitzgibbon said Turnbull “wants to make the Upper Hunter a coal-mine-free zone”. The Nationals’ Matt Canavan suggested stopping coal exports was “an inhumane policy to keep people in poverty”. The head of the NSW Minerals Council suggested 12,000 jobs were at risk.

But of course, the opposite is true. Turnbull’s proposal to protect existing coal workers from competition from new mines would save jobs, not threaten them. He didn’t suggest coal mines be shut down tomorrow, or even early. And, given existing coal mines are running so far below capacity, his call has no potential to impact coal exports.

Read more:
Labor politicians need not fear: Queenslanders are no more attached to coal than the rest of Australia

Coal workers
Opening new coal mines won’t help save the jobs of existing coal workers.
Dan Himbrechts/AAP

Predictably, the Murdoch press ran a relentlessly misleading campaign in support of the coal industry and in opposition to their least favourite Liberal PM. But surprisingly, the NSW government rolled over in record time.

While the government might think appeasing the coal industry will play well among some older regional voters, they must know such kowtowing is a gift to independents such as Zali Steggall, and a fundamental threat to inner-city Liberals such as Dave Sharma, Jason Falinski and Trent Zimmerman.

The decision to dump Turnbull might have bought NSW Premier Gladys Berejiklian some respite from attacks from the Daily Telegraph. But such denial of economics and climate science will provide no respite for existing coal workers in shuttered coal mines or the agriculture and tourism industry that is looking to expand.

No doubt the National Party are pleased with their latest scalp. But it must be remembered this is the party that last year wanted to wage a war against koalas on behalf of property developers. Such political instincts might help the Nationals fend off the threat from One Nation in regional areas but it does nothing to retain votes in leafy Liberal strongholds that deliver most Liberal seats.

Read more:
Aren’t we in a drought? The Australian black coal industry uses enough water for over 5 million people

The Conversation

Richard Denniss is the Chief Economist of The Australia Institute. He was a senior strategic advisor to Australian Greens Leader Senator Bob Brown and Chief of Staff to Senator Natasha Stott-Despoja, former Leader of the Australian Democrats.

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