Scripps Research tracks new COVID-19 variants with daily reports on Outbreak.info

 The Center for Viral Systems Biology (CViSB) at Scripps Research is tracking the prevalence of new variants of SARS-CoV-2—the virus behind the COVID-19 pandemic—and making this information publicly available to drive global research efforts. The daily situation reports appear on Outbreak.info, a website created by the same team in early 2020, shortly after the emergence of COVID-19. The new reports add to the website’s rich data on the coronavirus, providing a standardized hub of information on viral mutations.

“For researchers to stay updated on information needed to fight the pandemic, it’s imperative that they have access to open source tools and the latest scientific data,” says Alaa Abdel Latif, research programmer on the CViSB team. “Especially now that several variants of the coronavirus are circulating in the United States, we saw the importance for a standardized hub of information about known mutations and any others that may surface.”

Demand for mutation data is high among health researchers, as some coronavirus variants in the U.S. have shown to be significantly more transmissible than others. This includes the B.1.1.7 variant first identified in the UK in early December 2020. According to a new study by Scripps Research and collaborators, this variant is expected to become the dominant form of the virus as early as March.

Initially, CViSB created the situation reports as a tracking tool to analyze the mutations found in their lab's sequencing samples. The lab of Scripps Research Professor Kristian Andersen, PhD, who is also a director of CViSB, has been sequencing high volumes of virus samples from the San Diego area in partnership with other local teams—and notably, sequenced the first known B.1.1.7 variant in California.

“But given the growing concerns about emerging SARS-CoV-2 variants, we started applying it to analyze mutations found across the United States,” Latif says.

And though some of the data may be too sophisticated for a non-scientist to understand, the team expects that many members of the public will also find the dashboard a welcome resource for reliable, updated information.

The dashboard includes daily situation reports for mutations and lineages, which are series of mutations. Using data generated from the GISAID organization, which promotes rapid sharing of virus data, these reports track the number of sequences detected, locations where sequences have been detected, and prevalence over time at global, national and state levels. The dashboard also includes mutation maps for easy comparison between lineages.

“Thanks to global scientific efforts to sequence SARS-CoV-2, an unprecedented number of viral genomes are being produced and deposited to the GISAID database every day,” says Karthik Gangavarapu, a graduate student and computational scientist with CViSB. Gangavarapu says the situation reports are a natural extension of Outbreak.info, giving the world a way to track the virus and stay updated on changes as they occur—and giving researchers an edge in breaking ground in the COVID-19 pandemic.

The new SARS-CoV-2 Mutation Situation Reports and the Outbreak.info website are a result of efforts from the laboratories of Andersen, Andrew Su, PhD, and Chunlei Wu, PhD, with contributions from many other members of the CViSB team. Outbreak.info is supported by the National Institute for Allergy and Infectious Diseases, National Center for Data to Health and Centers for Disease Control and Prevention.  

About the Center for Viral Systems Biology

The Center for Viral Systems Biology uses genomics, bioinformatics, computational biology, and other areas of research to investigate attributes of pathogenic viruses that determine the outcomes of human disease. The research center is located in Scripps Research in La Jolla, California, and is supported by the National Institute of Allergy and Infectious Diseases. Learn more at https://cvisb.org

https://www.scripps.edu/news-and-events/press-room/2021/20210217-outbreakinfo-mutations.html

SARS-CoV-2 B.1.1.7 and B.1.351 Spike variants bind human ACE2 with increased affinity

 Muthukumar Ramanathan, Ian D. Ferguson, Weili Miao, Paul A. Khavari

doi: https://doi.org/10.1101/2021.02.22.432359

This article is a preprint and has not been certified by peer review [what does this mean?].

PDF: https://www.biorxiv.org/content/10.1101/2021.02.22.432359v1.full.pdf

Abstract

SARS-CoV2 being highly infectious has been particularly effective in causing widespread infection globally and more variants of SARS-CoV2 are constantly being reported with increased genomic surveillance. In particular, the focus is on mutations of Spike protein, which binds human ACE2 protein enabling SARS-CoV2 entry and infection. Here we present a rapid experimental method leveraging the speed and flexibility of Mircoscale Thermopheresis (MST) to characterize the interaction between Spike Receptor Binding Domain (RBD) and human ACE2 protein. The B.1.351 variant harboring three mutations, (E484K, N501Y, and K417N) binds the ACE2 at nearly five-fold greater affinity than the original SARS-COV-2 RBD. We also find that the B.1.1.7 variant, binds two-fold more tightly to ACE2 than the SARS-COV-2 RBD.

Competing Interest Statement

The authors have declared no competing interest.

https://www.biorxiv.org/content/10.1101/2021.02.22.432359v1

Reassessing COVID-19 Vaccine Deployment in Anticipation of a US B.1.1.7 Surge: Stay the Course or Pivot?

 Michael Osterholm, PhD, MPH Angela Ulrich, PhD, MPH Cory Anderson, MPH Eric Topol, MD Bruce Gellin, MD, MPH Ruth Berkelman, MD Marc Lipsitch, DPhil Kristine Moore, MD, MPH

COVID-19: The CIDRAP Viewpoint 

February 23, 2021

Introduction 

The SARS-CoV-2 B.1.1.7 variant, which is more transmissible and virulent than previously circulating strains, threatens to reverse the current downward COVID-19 trends in the United States (US) and could lead to a significant surge in cases in the next 4 to 12 weeks (CDC 2021a)(PHE 2021a)(Walensky et al 2021). Whether the surge will occur in the US remains uncertain; however, evidence from countries such as Ireland, Israel, Portugal, and the United Kingdom (UK) suggest surges driven by the B.1.1.7 variant occur when initial widespread transmission of the variant is documented throughout a country. Since the B.1.1.7 variant is now widespread in the US and the proportion of COVID-19 cases caused by this variant are increasing rapidly in areas such as Florida and California, a major peak in cases, hospitalizations, and deaths in the near future remains a strong possibility. In the US, the variant is 35% to 45% more transmissible, and its frequency is doubling every week and a half (Washington et al 2021). According to a model from the Centers for Disease Control and Prevention (CDC), B.1.1.7 is expected to become the dominant variant in many states in March 2021 (Galloway et al 2021). If the US experiences a surge similar to that seen in the UK, one could expect to see unprecedented healthcare demand of 175,000 to 193,000 hospitalizations per day (COVID Tracking Project 2021)(PHE 2021b)—far surpassing the US peak of 132,474 individuals hospitalized with COVID-19 set in early January. Thus, the immediate goal of public health policy should be to reduce the likelihood of a significant escalation in severe COVID-19 infections, hospitalizations, and intensive care that could compromise the ability of the healthcare system to provide adequate healthcare services and to minimize preventable suffering and deaths. While we need to continue to strive for equity in our vaccination program, we also recognize that above all, age is the strongest risk factor for COVID-19–related severe disease, hospitalization, and death. Adults 65 years Report 7: Reassessing COVID-19 Vaccine Deployment in Anticipation of a US B.1.1.7 Surge: Stay the Course or Pivot? 3 and older constitute a risk group with significant morbidity and mortality and produce the greatest COVID-19 burden on the healthcare system. In the event of a surge in cases, the vast majority of hospitalizations and deaths will occur in this age-group. In the US, nearly half of all COVID-19 hospitalizations and 80% of COVID-19 deaths are among those 65 and older (CDC 2021b)(CDC 2021c). Compared with 5- to 17-year-olds, older individuals had a 35-fold, 55-fold, and 80-fold increase in hospitalizations among individuals ranging from 65 to 74 years, 75 to 84 years, and 85 years and older, respectively, and a 1,100-fold, 2,800-fold, and 7,900-fold increase in deaths (CDC 2021d). While the current US distribution of vaccines is a critical development in preventing and controlling COVID-19, doses will be limited for the next several months. Supply will likely remain limited throughout some, if not all, of a B.1.1.7-related surge. To date, approximately 43 million people in the US have received at least one dose of vaccine (CDC 2021e). Even with the nearly 84 million Americans who have had COVID-19 (CDC 2021b), we are far short from reaching a herd immunity threshold, with an estimated 65% of the US population remaining susceptible to infection. To maintain healthcare capacity during a B.1.1.7 surge, we have a time-limited period to strategically target vaccination to those at highest risk of hospitalization and death before the surge arrives.

https://www.cidrap.umn.edu/sites/default/files/public/downloads/cidrap-covid19-viewpoint-report7.pdf

World Economic Forum Tweets 'Lockdowns Improving Cities,' Then Deletes

 If there was any doubt that economic lockdowns supposedly inspired by the Covid pandemic are the peak in globalist propaganda, it disappeared not so "quietly" once and for all at 5:48am ET on Saturday, when the globalist organization which recently unleashed such lunatics as Klaus Schwab, best known for revealing the endgame with his book COVID-19: The Great Reset, deleted a that "Lockdowns are quietly improving cities around the world."

Remarkably, the WEF’s propaganda tweet - which was was accompanied by a video showing deserted streets and silent factories, that noted a record drop in carbon emissions and linked to an article claiming that silent cities contributed to better detection of minor earthquakes (because millions of workers losing their jobs is clearly less important than being able to measure the next M2 quake to the 8th significant digit) - survived just a few hours following a barrage of mockery and outraged comments.

Just before 6am ET on Saturday, the WEF finally deleted the tweet, admitting in a subsequent highly ratioed tweet that "lockdowns aren’t “quietly improving cities” around the world" despite still insisting that the restrictions have been “an important part of the public health response to Covid-19.”

By this point, however, social media was  in a full blown frenzy over the WEF's admission that covid lockdowns are just peak propaganda  - one which has the complicit participation of all Silicon Valley tech giants - and sparked en even louder response from an outraged non-Davos audience.

The concession message looked like the WEF was actually “doubling down on [its] idiocy” instead of trying to do some damage control, former British MEP Martin Daubney wrote

At the same time, the peasants demonstrated remarkable insight accusing the WEF of being "the hidden enemy of the people, worldwide. The unelected force that look to dominate our lives by influencing Governments all over the globe. It needs shutting down."

Some were furious that the propaganda arm of globalists had a "RIGHT TO RULE and DECIDE WHAT IS FAIR, EQUITABLE and REASONABLE" and warned that the crowd was coming for the WEF:

Others quickly saw through the propaganda flip-flopping, and straight to the heart of the WEF's agenda, one of spreading "global socialism" which will make lives for billions of people a nightmare which making a handful of virtue signaling uber-globalists (who arrive in Davos on their private jets even as they parade with how green they are) richer than ever:

Yet others had even more direct suggestions for the WEF:

At the end, the catastrophic gaffe left a huge dent on what little was left of the the globalist group's reputation, and many users argued that it should just shut up:

But most importantly, the tweet confirmed once again that what until now was a "conspiracy theory" pursued with rabid fervor by such tech giants as Google, Amazon and Twitter, was fact:

Hours later, as the WEF's catastrophic fiasco spread virally across the world, the WEF decided to triple down on its peak idiocy, and instead of just forgetting all about the matter decided that it's best to engage with random twitter economists, and blame it all on "a working human being who made a mistake."

https://www.zerohedge.com/economics/propaganda-crash-world-economic-forum-tweets-lockdowns-improving-cities-then-deletes

Tech Teladoc's virtual visits reach 3M during Q4 as revenue grows to $383M

 Teladoc's 2020 revenue reached $1.1 billion as virtual care visits continued to soar.

The telehealth giant reported it delivered 10.6 million virtual visits last year, up 156% from 2019. The company's U.S. paid membership hit 51.8 million, up about 41% from 36.7 million users in 2019.

Teladoc, one of the nation's top telehealth providers, reported 3 million total virtual visits during the fourth quarter, up 139% from 1.2 million visits in the fourth quarter of 2019.

Fourth-quarter revenue came to $383 million, up 145% from $156 million in the same period in 2019.

"2020 was a transformational year for Teladoc Health and for the role of virtual care within the broader healthcare industry," Teladoc CEO Jason Gorevic said during a fourth-quarter and full-year 2020 earnings call Wednesday.

"We delivered needed healthcare to millions of consumers in the midst of the coronavirus pandemic and completed two significant acquisitions that together, under Teladoc Health, are defining a new category of whole person virtual care. Taken together, we dramatically accelerated our mission to empower all people everywhere to live their healthiest lives by transforming the healthcare experience," he said.

Teladoc completed its massive $18.5 billion acquisition of Livongo in October, and, combined with its acquisition of InTouch Health last year, the company's value proposition in the marketplace is only getting stronger, he said.

"As virtual care shifted to become a consumer expectation in 2020, Teladoc Health not only met the rapidly growing demand, but we transformed our company to define a new category of whole-person virtual care,” Gorevic said. “By accelerating our mission to transform the health care experience, we exceeded our fourth-quarter and full-year 2020 expectations and see strong momentum across our global business in 2021 as the market embraces the breadth and depth of our unique capabilities.”

The company's fourth-quarter revenue beat Wall Street estimates of $378 million for the quarter.

Earnings per share in the quarter came to a loss of 27 cents, which missed the Wall Street estimate of a loss per share of 24 cents.

The company onboarded a record 15 million new paid members in 2020. And, over the last 18 months, Teladoc added 25 million paid members and 11 million members with BFO access.

Teladoc is making significant investments to integrate its products and services following the Livongo deal, Gorevic said. "We see a tremendous opportunity for a new integrated behavioral health product that combines the capabilities of both Livongo and Teladoc. This innovative offering will pair the highly scalable, personalized self-directed digital care programs of Livongo's myStrength platform with access to the expertise and convenience of Teladoc's virtual network of clinicians. With this integrated offering, we will create a new digital front door to behavioral healthcare, further breaking down barriers to mental health by allowing consumers to find the right care at the right time, increasing access and improving outcomes," he said.

Out of its $383 million quarterly revenue, revenue from subscription access fees came to $283 million, up 188% from the prior year's quarter, while total visit-fee revenue increased 80% to $53 million.

Total international revenue of $34 million grew 16% versus the prior year. 

However, the company grew its sizable net losses during the quarter due to $58 million in transaction costs related to the Livongo deal.

Growth in specialty visits has been particularly strong, led by growth in behavioral health, which experienced visit growth of over 500% in 2020 as the growth in visits accelerated throughout the course of the year, the company reported.

Teladoc reported a loss of $394 million in the fourth quarter, which grew from a net loss of $19 million during the same quarter a year ago. Net loss was $485 million for full-year 2020 compared to $99 million for full-year 2019.

Teladoc Chief Financial Officer Mala Murthy said the company expects full-year 2021 revenue to be in the range of $1.95 billion to $2 billion, representing growth of 78% to 83% over the prior year.

"Our confidence in that strong revenue growth is underpinned by first, continued growth in utilization, particularly among noninfectious disease-related visits such as hypertension, lower back pain, anxiety and depression. During the fourth quarter, approximately 75% of our volume was related to noninfectious diseases, up from 50% in the fourth quarter of last year as our visit mix continues to diversify, a trend that has continued into the new year," Murthy said.

"We've also seen tremendous growth in new registrations over the past year with newly registered individuals growing at twice the rate of new member additions," she said.

First-quarter 2021 total revenue is expected to be in the range of $445 million to $455 million, and total U.S. paid membership should be in the range of 51 million to 52 million members.

Total visits are expected to reach between 2.9 million and 3.1 million.

Murthy said total revenue for full-year 2021 will be in the range of $1.95 billion to $2 billion. Total U.S. paid membership is expected to rise to 52 million to 54 million members.

Teladoc expects visits to increase to between 12 million and 13 million, Murthy said.

https://www.fiercehealthcare.com/tech/teladoc-s-virtual-visits-reach-3m-during-q4-as-revenue-grows-to-383m

Cyberattack on Universal Health Services in September cost $67M last year

 Universal Health Services ended the last year with a $308.7 million profit in the fourth quarter of 2020, it reported in its latest quarterly earnings.

The King of Prussia, Pennsylvania-based health system giant reported earnings of $3.06 per diluted share were up from $254.2 million, or $2.79 a share, during the fourth quarter of 2019. That income was on revenue of $3.1 billion in the fourth quarter of 2020, up 6.6% from $2.9 billion in the fourth quarter of 2019.

The health system's fourth-quarter results included a favorable impact from about $151.4 million, or $1.76 per diluted share, from an approximately $200 million federal relief grant. 

However, they also included a hit of $42.1 million, or 49 cents per diluted share, in the fourth quarter resulting from costs associated with a massive IT breach in September. The attack forced UHS to suspend access to all IT applications related to its operations in the U.S. as it realized on backup processes including offline documentation. Certain patient activity, including ambulance traffic and elective procedures at acute care hospitals, were diverted to competitor facilities, officials said.

They also incurred a "significant incremental labor expense, both internal and external, to restore information technology operations" as quickly as possible. Certain administrative functions such as coding and billing were delayed into December 2020, which had a negative impact on operating cash flows during the fourth quarter of 2020.

In all, the health system said the breach cost an estimated $67 million in pretax dollars in 2020, largely in the form of lost operating income from the related decrease in patient activity as well as increased revenue reserves associated with billing delays.

"Immediately after the incident, we worked diligently with our information technology security partners to restore our information technology infrastructure and business operations as quickly as possible," officials said in a statement. "In parallel, we began investigating the nature and potential impact of the security incident and engaged third-party information technology and forensic vendors to assist. No evidence of unauthorized access, copying or misuse of any patient or employee data has been identified to date."

UHS officials said they believe they are entitled to recover the majority of the financial impact resulting from the cyberattack through their commercial insurance coverage. 

UHS posted a $944 million profit, or $10.99 per diluted share, for the year ending Dec. 31, up from $814.9 million, or $9.13 per share, in 2019. That was on revenues of $11.6 billion in 2020, up 1.6% from $11.4 billion for full-year 2019.

The health system held its fourth-quarter and year-end earnings call Friday at 9 a.m. ET.

https://www.fiercehealthcare.com/hospitals/universal-health-services-tops-308m-profit-q4

J&J vaccine rollout 'marred by production problems'

Johnson & Johnson’s Covid-19 vaccine supplier Catalent had to resort to checking vials by hand for two weeks, one of the production problems that have contributed to the US government being set to receive millions fewer doses than it expected this month. 

Catalent, which also fills vaccine vials for Moderna, suffered a setback in the US when tuning up its automated visual verification line, which makes checks on vials, according to people familiar with the matter.  J&J on Saturday received US emergency approval for its single shot after advisers to the Food and Drug Administration voted unanimously to endorse it. The company has said it will deliver 4m doses immediately, fewer than the 10m the US government originally expected. 

Catalent, a New Jersey-based contract manufacturer, moved staff from other parts of the company to complete the vital checks manually. Mike Riley, president of Catalent Biologics, North America, said it was on track to meet its vaccine production commitments to all customers, including Moderna and J&J.  

 “Short-term variations are normal when initiating new production processes to rapidly increase the supply of safe, high-quality vaccines,” he said. “We are moving as quickly as possible, and we will not make any compromises on safety.”

 Recommended Covid-19 vaccines Africa will pay more for Russian Covid vaccine than ‘western’ jabs Other manufacturing problems may have also delayed production. J&J had to scale up its vaccine substance manufacturing from a small facility to a large one in the Netherlands, and another large factory in the US, run by contract manufacturer Emergent Biosolutions. 

This technology transfer, while far faster than usual, took longer than hoped for, according to a different person familiar with the matter.  J&J said that it had been “working around the clock” to expand manufacturing around the world. It said it was confident it would meet its targets for the US, of 100m by June 2021, and the EU, which has ordered 200m doses in 2021.  He noted it was adding capacity to fill vials with its recent agreement with Sanofi Pasteur. 

 “To accelerate production and expand capacity, we have entered into agreements with established manufacturers,” he said. “As all of these sites come online, our supply is expected to increase throughout the year.”

 Earlier this week, Jeff Zients, the White House coronavirus co-ordinator, said the initial increase in J&J’s production was slower than it would have liked.  

 “When we got here five weeks ago, we learned that J&J was behind on manufacturing, and our team has been working with them since. And, yeah, I think they’re in a better place now,” he said. 

https://www.ft.com/content/b5ba2702-3bad-4f10-9d80-00eb3d48d802