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Archive for the ‘SARS-CoV-2’ Category


Mechanistic link between SARS-CoV-2 infection and increased risk of stroke using 3D printed models and human endothelial cells

Reporter: Adina Hazan, PhD

 

Kaneko, et al.  from UCLA aimed to explore why SARS-CoV-2 infection is associated with an increased rate of cerebrovascular events, including

  • ischemic stroke and
  • intracerebral hemorrhage

While some suggested mechanisms include an overall systemic inflammatory response including increasing circulating cytokines and leading to a prothrombotic state, this may be only a partial answer. A SARS-CoV-2 specific mechanism could be likely, considering that both angiotensin-converting enzyme-2 (ACE2), the receptor necessary for SARS-CoV-2 to gain entry into the cell, and SARS-CoV-2 RNA have been reportedly detected in the human brain postmortem.

One of the difficulties in studying vasculature mechanisms is that the inherent 3D shape and blood flow subject this tissue to different stressors, such as flow, that could be critically relevant during inflammation. To accurately study the effect of SARS-CoV-2 on the vasculature of the brain, the team generated 3D models of the human middle cerebral artery during intracranial artery stenosis using data from CT (computed tomography) angiography. This data was then exported with important factors included such as

  • shear stress during perfusion,
  • streamlines, and
  • flow velocity to be used to fabricate 3D models.

These tubes were then coated with endothelial cells isolated and sorted from normal human brain tissue resected during surgery. In doing so, this model could closely mimic the cellular response of the vasculature of the human brain.

Surprisingly, without this 3D tube, human derived brain endothelial cells displayed very little expression of ACE2 or, TMPRSS2 (transmembrane protease 2), a necessary cofactor for SARS-COV-2 viral entry.

Interestingly,

  • horizontal shear stress increased the expression of ACE2 and
  • increased the binding of spike protein to ACE2, especially within the stenotic portion of the 3D model.

By exposing the endothelial cells to liposomes expressing the SARS-CoV-2 spike protein, they also were able to explore key upregulated genes in the exposed cells, in which they found that

  • “binding of SARS-CoV-2 S protein triggered 83 unique genes in human brain endothelial cells”.

This included many inflammatory signals, some of which have been previously described as associated with SARS-COV-2, and others whose effects are unknown. This may provide an important foundation for exploring potential therapeutic targets in patients susceptible to cerebrovascular events.

Overall, this study shows important links between the

  • mechanisms of SARS-CoV-2 and the
  • increase in ischemic events in these patients. It also has important implications for
  • treatment for SARS-CoV-2, as high blood pressure and atherosclerosis may be increasing ACE2 expression in patients, providing the entry port for viral particles into brain endothelia.

SOURCE:

https://www.ahajournals.org/doi/10.1161/STROKEAHA.120.032764

Other related articles published in this Open Access Online Scientific Journal include the following:

The Impact of COVID-19 on the Human Heart

Reporters: Justin D. Pearlman, MD, PhD, FACC and Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2020/09/29/the-impact-of-covid-19-on-the-human-heart/

 

SAR-Cov-2 is probably a vasculotropic RNA virus affecting the blood vessels: Endothelial cell infection and endotheliitis in COVID-19

Reporter: Aviva Lev-Ari, PhD, RN – Bold face and colors are my addition

https://pharmaceuticalintelligence.com/2020/06/01/sar-cov-2-is-probably-a-vasculotropic-rna-virus-affecting-the-blood-vessels-endothelial-cell-infection-and-endotheliitis-in-covid-19/

 

Diagnosis of Coronavirus Infection by Medical Imaging and Cardiovascular Impacts of Viral Infection, Aviva Lev-Ari, PhD, RN  Lead Curator – e–mail: avivalev-ari@alum.berkeley.edu

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Mysteries of COVID Smell Loss

Reported : Irina  Robu, PhD

When Covid-19 patients have smell loss it tends to be sudden and severe. They are usually don’t have a blocked, stuffy or runny nose – most people with coronavirus can still breathe freely.  Since the epidemy started in march, an estimated of 80 percent of people with COVID-19 have experience smell disturbances in addition to loss of taste and the ability to smell chemical irritants. Research has shown that smell loss is common in people with COVID-19 disease, the reason why researchers and doctors have recommended to use a diagnostic test to determine if a patient has COVID-19.

Yet, the mystery is how the new coronavirus robs patients of their senses. During the early days of the epidemic, physicians and researchers thought that COVID related loss of smell might signal that the virus makes its way into the brain through the nose, where it can do the most severe damage. According to Sandeep Robert Data, a neuroscientist at Harvard Medical School, the research data showed that the primary source is the in the nose, but more specifically in the nasal epithelium. It looks like the virus attacks the cells responsible for registering odors rather than attacking neurons directly.  

It is well known that  olfactory neurons do not have angiotensin-converting enzyme 2 (ACE2) receptors, which permit the virus entry to cells, on their surface. But sustentacular cells, which provide support for  olfactory neurons are scattered with the receptors. These cells preserve the important  balance of salt ions in the mucus that neurons rest on on to send signals to the brain. If that balance is disturbed, it could lead to a closure of neuronal signaling and loss of smell.

The sustentacular cells correspondingly deliver the metabolic and physical support necessary to keep the fingerlike cilia on the olfactory neurons wherever receptors that detect odors are disturbed. Nicolas Meunier, a neuroscientist at the Paris-Saclay University in France determined that disruption of the olfactory epithelium might explain the loss of smell. Yet, it remains unclear if the damage done by the virus or because it invades immune cells.

Since COVID-19 doesn’t cause nasal congestion, researchers have found a few clues about the loss of smell. Taste receptor cells, which detect chemicals in the saliva and sends signals to the brain do not have ACE receptors. They don’t necessarily  get infected by COVID-19, but other support cells in the tongue carry the receptor.

Researchers determined that more clues on  to how the virus obliterates smell. However, some patients have seen that after five months the ability to smell has returned but not as great as expected. That news is welcomed for patients that have suffered loss of smell due to the COVID-19 virus, yet apprehensions about long term loss of smell is a large cause of concern.

SOURCE

https://www.scientificamerican.com/article/mysteries-of-covid-smell-loss-finally-yield-some-answers1/

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Allocation and Prioritization of Vaccine Dose Administration Schedules: Cover more people or Adhere to Immunization Protocol

Curators:

This curation has four parts:

Part 1:

Waiting on the Covid booster would allow more people to be vaccinated sooner.

  • By Michael Segal, MD, PhD

Part 2:

Expert Opinion by Clinical Authority in Practice of Cardiac Imaging:

  • The Voice of Dr. Justin D. Pearlman, MD, PhD, FACC

Part 3:

Expert Opinion by Scientific Authority in Population Biology

  • The Voice of Prof. Marcus W. Feldman, PhD

Part 4:

Summary

  • The Voices of Prof. Stephen J. Williams, PhD and Aviva Lev-Ari, PhD, RN

Introduction

Aviva Lev-Ari
@AVIVA1950

We agree the protocol should not be changed

Quote Tweet

Pearl Freier
@PearlF
FDA’s Peter Marks explained why the 2 dose regimen for Pfizer/BioNtech vaccine shouldn’t be changed to 1 dose in attempt to reach more patients while there’s limited supply. Aside from 95% effectiveness w/ 2 dose regimen based on clinical data, he said no one knows how long 1/n

Pearl Freier
@PearlF

Replying to

1 dose would be effective for & no one knows if only given 1 dose if patient would get an immune response that “would just dwindle” “And we know that can happen because we know already that people who get very mild covid-19 tend to lose their immune responses pretty quickly.” 2/n

Pearl Freier
@PearlF

We need to make sure that those who get the vaccine regimen are people who know they’ve gotten that protection [95% effective]. Because that’s something we know, whereas the other [1 dose] is conjecture. And I would hate for people to change their behavior on the basis of 3/n

Pearl Freier
@PearlF

one dose of vaccine where we don’t know what’s really happening.” Peter Marks/FDA said (6 min mark) youtube.com/watch?v=uePet5 (
Research!America Alliance Member Meeting with Dr. Peter Marks
With several COVID-19 vaccine candidates under FDA review, Dr. Peter Marks, Director of FDA’s Center for Biologics Evaluation and Research (CBER), joined us …
youtube.com

 (she/her/hers)

@lisabari

Replying to

It will be really interesting to learn more about the immune response from J&J’s one dose regimen.

Pearl Freier
@PearlF

I think they’re expecting data from J&J in January

Part 1:

Waiting on the Covid booster would allow more people to be vaccinated sooner.

By Michael Segal, MD, PhD

https://www.wsj.com/articles/a-shot-instead-of-two-at-saving-lives-11607643152

A Shot (Instead of Two) at Saving Lives

Waiting on the Covid booster would allow more people to be vaccinated sooner.

By Michael Segal

Dec. 10, 2020 6:32 pm ET

Recent days brought good news and bad news about coronavirus vaccines. The developments could add up to months of delay in getting most Americans inoculated. But there’s a way to make use of the good news to speed up herd immunity.

The bad news is that in July the U.S. passed up an opportunity to secure by June 2021 more than 100 million doses of the Pfizer vaccine, now expected to receive emergency-use authorization in the next few days. Instead, officials followed a balanced-portfolio strategy that reserved as many as 300 million doses of the AstraZeneca vaccine, whose prospects are unclear.

The good news is that the Pfizer and Moderna vaccines performed at the upper end of expectations, with 95% efficacy after two doses. And intriguingly, Pfizer’s submission to the Food and Drug Administration shows that the efficacy of the vaccine in preventing disease had largely kicked in by two weeks after the first dose, and there was no dramatic increase in efficacy after the booster was given three weeks later.

The protocol in Pfizer’s clinical trial was to give all participants two doses. The FDA is likely to approve this protocol, and standard procedure is to prescribe a drug according to protocol. But we are in a pandemic and supplies of vaccine are inadequate. There’s an alternative: vaccinating as many people as possible with a first dose and waiting on the booster until supplies are plentiful.

The Pfizer study wasn’t designed to put a number on first-dose efficacy, but the data in Pfizer’s “cumulative incidence curves” suggest at least 75% efficacy for two weeks after one dose. The question is whether to use the 100 million doses on 50 million people, of whom two doses would protect roughly 47.5 million, or to give one dose each to 100 million people and protect at least 75 million.

States have the authority to allocate vaccines as they choose, but they’re unlikely to deviate from the study protocol unless a federal authority—whether the Centers for Disease Control and Prevention or a coronavirus “czar”—suggests this as an option.

Even under such an approach, some essential personnel—such as doctors and nurses who work directly with coronavirus patients and health aides who work in multiple nursing homes—should get two doses as soon as possible, given their high-risk role in the pandemic response.

The U.S. will have more than these 100 million doses of the Pfizer vaccine. Some will come from Moderna, and the federal government could use the Defense Production Act to snatch some Pfizer doses that the company contracted to sell to other countries. Even so, supply will be constrained at first, and officials need to think clearly and flexibly about how to allocate the limited doses that will be available soon.

Harvard epidemiologist Michael Mina expressed his disappointment with society’s decision making during the pandemic: “I’m just astounded by the dysfunction, the willingness to just stay the course as hundreds of thousands of people die, and the unwillingness to innovate in literally any way.” Here’s a simple innovation that could save many lives.

Dr. Segal is a neurologist and neuroscientist.

Copyright ©2020 Dow Jones & Company, Inc. All Rights Reserved. 87990cbe856818d5eddac44c7b1cdeb8

Appeared in the December 11, 2020, print edition.

Part 2:

Expert Opinion by Clinical Authority in Practice of Cardiac Imaging:

The Voice of Dr. Justin D. Pearlman, MD, PhD, FACC

From: Justin MDMEPhD <jdpmdphd@gmail.com>

Date: Saturday, December 12, 2020 at 10:40 PM

To: “Aviva Lev-Ari, PhD, RN” <AvivaLev-Ari@alum.berkeley.edu>

Subject: Re: I NEED YOUR EXPERT OPINION on Mickey Segal’s WSJ op-ed on vaccine dose allocation

Michael Segal proposes off-label use of the Pfizer 2-injection Covid-19 vaccine, based on data that suggested “75% protection at 2 weeks.” There was no controlled study reported of any sustained benefit from the single injection beyond 2 weeks, because those who received a first injection of vaccine received the designed booster at 2 weeks. Dr. Segal suggests it would be irresponsible to use the medication in the manner designed and tested. Instead, he could have proposed a study to determine the duration and degree of benefit from a single dose injection. However, one might argue that could delay the release of an effective regimen for the possibility that his proposed 1 dose regimen might be adequate for some, and possibly for more than the two weeks observed. Even if his guess is correct on both counts, both in his guess that the partial benefit at two weeks might be adequate and that it might last longer than the observed two weeks, it could still be deemed irresponsible to impose his guess for obvious reasons. His guess might be wrong, and could deprive many of the regimen that was validated as effective. Diverting an effective validated regimen to a guess could put many in harms way who would have been protected by the designed 2 dose regimen. He admits to low confidence in his recommendation when he proposes that essential workers should get the validated 2-dose regimen. Why does his recommendation stop there – why not propose a quarter dose to 4 times as many, or 1/8 dose to 8 times as many? Why apply the argument just to the two-dose regimen? He could also guess that a half dose of the single injection successful vaccines might be adequate. The motivation to second guess supply choices and doses is understandable, but it is not sound, as it is just a guess, not a validated regimen.

In addition, he also argues for 20-20 hindsight in the government distributing funds to mulitiple vaccines, instead of disproportionate purchase from Pfizer. Trials are limited in size, and further data will be collected on those vaccinated. Balanced investment may save more lives, not fewer, depending on those outcomes.

On Sat, Dec 12, 2020, 8:20 PM Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu> wrote:

Dear Dr. Pearlman,

Please send me 1/2 –1 page as a Critic of 

  • Mickey Segal’s WSJ op-ed on vaccine dose allocation, below

Part 3:

Expert Opinion by Scientific Authority in Population Biology

The Voice of Prof. Marcus W. Feldman, PhD

From: Marcus W Feldman <mfeldman@stanford.edu>

Date: Sunday, December 13, 2020 at 6:52 PM

To: “Aviva Lev-Ari, PhD, RN” <AvivaLev-Ari@alum.berkeley.edu>

Subject: Re: Mickey Segal’s WSJ op-ed on vaccine dose allocation

RE Segal’s note:

We need more details on the longer term efficacy of the one-dose regimen. Once we have such data, the question of whether 100 million one-dose treatments will be more protective of the population than 50 million two-dose treatments can be addressed. The question of how many hospitalizations and/or deaths would be avoided by going straight to the one-dose regimen can’t be answered. Both approaches leave unanswered whether the transmission of the virus from a vaccinated person is reduced. I would estimate that we need 300 million 2-dose treatments to vaccinate all under 16 year olds.

On Dec 13, 2020, at 1:56 PM, Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu> wrote:

Dear Prof. Feldman,

Please send me 1/2 –1 page as a Critic of 

  • Mickey Segal’s WSJ op-ed on vaccine dose allocation, below

Part 4:

Summary

The Voices of Prof. Stephen J. Williams, PhD and Aviva Lev-Ari, PhD, RN

The Voice of Prof. Stephen J. Williams, PhD

In light of just approved Moderna vaccine, AstraZenaca & JNJ forthcoming vaccine and the approved Pfizer BioNTech coverage should be over 200 million in US, making rationing of second booster shot unnecessary.  However, there is still a concern among the developing and underdeveloped nations that access to these vaccines will be restricted.

The following curation are articles related to this matter from the AAAS and CDC.

CDC advisory panel takes first shot at prioritizing who gets the first shots of COVID-19 vaccines
By Jon CohenDec. 1, 2020 , 8:25 PM
Science’s COVID-19 reporting is supported by the Pulitzer Center and the Heising-Simons Foundation.

Health care workers and elderly people living in long-term care facilities should receive top priority for COVID-19 vaccines in the United States if, as expected, one or more becomes available next month in limited supply. That’s what a group that advises the U.S. Centers for Disease Control and Prevention (CDC) on such fraught issues decided today in a near-unanimous vote.

After hearing detailed presentations from CDC scientists who explained the rationale for this specific prioritization scheme, the Advisory Committee on Immunization Practices (ACIP) voted 13 to one to support their proposal. Under the scheme, the first phase of vaccination, known as 1a, would begin with about 21 million health care workers and about 3 million adults who live in long-term care facilities. As spelled out in the 4-hour-long virtual meeting, these groups are at highest risk of becoming seriously ill or dying from COVID-19, and protecting them first, in turn, reduces the burden on society.

“I agree strongly with the decision of the committee,” says Stanley Perlman, a veteran coronavirus researcher and clinician at the University of Iowa who advised ACIP but is not part of it. “The discussions were incredibly thoughtful with everyone recognizing that we needed to make difficult choices. Of course, these allocation issues will become irrelevant once there are enough doses of useful vaccines.”

‘Just beautiful’: Another COVID-19 vaccine, from newcomer Moderna, succeeds in large-scale trial
By Jon CohenNov. 16, 2020 , 7:00 AM
Science’s COVID-19 reporting is supported by the Pulitzer Center and the Heising-Simons Foundation.

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Now, there are two. Another COVID-19 vaccine using the same previously unproven technology as the vaccine from Pfizer and BioNTech, the U.S. and German companies that reported success on 9 November, appears to work remarkably well. And this time, the maker, U.S. biotech Moderna, is releasing a bit more data to back its claim than the other two companies.

An independent board monitoring Moderna’s 30,000-person vaccine trial met on Sunday and reported to the company and U.S. government health officials that only five people in the vaccinated group developed confirmed cases of COVID-19, whereas 90 people who received placebo shots became ill with the disease. That’s an efficacy of 94.5%, the company reported in a press release this morning. Although the clinical trial measurement may not translate into an equally high level of real-world protection, the success indicates the vaccine is Iikely more than effective enough to stop the pandemic if it can be widely distributed.

“That efficacy is just beautiful, and there’s no question about the veracity of it either,” says Lawrence Corey, a virologist at the Fred Hutchinson Cancer Research Center who co-led the clinical trials network that is testing the vaccine.

Moderna’s COVID-19 vaccine ready to ship pending FDA approval -U.S. health chief

Source: https://www.reuters.com/article/health-coronavirus-usa-azar-idUSKBN28R265?taid=5fdc062c54859c0001437b9b&utm_campaign=trueanthem&utm_medium=trueanthem&utm_source=twitter

WASHINGTON (Reuters) – U.S. Health and Human Services Secretary Alex Azar on Thursday said nearly 6 million doses of Moderna Inc’s experimental COVID-19 vaccine were poised to ship nationwide as soon as it secures Food and Drug Administration approval. Azar, in an interview on CNBC, said federal health officials had allotted 5.9 million doses to send to the nation’s governors, who are managing each state’s distribution. “We’re ready to start shipping this weekend to them for rollout Monday, Tuesday, Wednesday of next week. We’re ready to go,” he said. An FDA panel of outside advisers is weighing the safety and effectiveness of Moderna’s vaccine candidate at a meeting on Thursday. The agency will weigh the committee’s conclusions in making its approval decision.

The strategy seems to have been produce multiple vaccines from multiple sources which reduce the strain on manufacturing of required doses.
However, many underdeveloped nations as well as developing nations are worried about the nationalism of access to these vaccines.  Please read below:

Abstract

The 2030 Agenda for Sustainable Development (AfSD) has the vision to leave no one behind, particularly low-income countries. Yet COVID-19 seems to have brought up new rules and approaches. Through document and critical discourse analysis, it emerges that there has been a surge in COVID-19 vaccines and treatments nationalism. Global solidarity is threatened, with the USA, United Kingdom, European Union and Japan having secured 1.3 billion doses of potential vaccines as of August 2020. Vaccines ran out even before their approval with three candidates from Pfizer-BioNTech, Moderna and AstraZeneca having shown good Phase III results in November 2020. Rich countries have gone years ahead in advance vaccines and treatments purchases. This is a testimony that the 2030 AfSD, especially SDG 3 focusing on health will be difficult to achieve. Low-income countries are left gasping for survival as the COVID-19 pandemic relegates them further into extreme poverty and deeper inequality. The paper recommends the continued mobilisation by the World Health Organisation and other key stakeholders in supporting the GAVI vaccine alliance and the Coalition for Epidemic Preparedness Innovations (COVAX) global vaccines initiative that seeks to make two billion vaccine doses available to 92 low and middle-income countries by December 2021.

Others have voiced their concerns on this matter:

 

Reserving coronavirus disease 2019 vaccines for global access: cross sectional analysis

From: Anthony D So 1 2Joshua Woo 2 BMJ2020 Dec 15;371:m4750. doi: 10.1136/bmj.m4750.

Abstract

Objective: To analyze the premarket purchase commitments for coronavirus disease 2019 (covid-19) vaccines from leading manufacturers to recipient countries.

Design: Cross sectional analysis.

Data sources: World Health Organization’s draft landscape of covid-19 candidate vaccines, along with company disclosures to the US Securities and Exchange Commission, company and foundation press releases, government press releases, and media reports.

Eligibility criteria and data analysis: Premarket purchase commitments for covid-19 vaccines, publicly announced by 15 November 2020.

Main outcome measures: Premarket purchase commitments for covid-19 vaccine candidates and price per course, vaccine platform, and stage of research and development, as well as procurement agent and recipient country.

Results: As of 15 November 2020, several countries have made premarket purchase commitments totaling 7.48 billion doses, or 3.76 billion courses, of covid-19 vaccines from 13 vaccine manufacturers. Just over half (51%) of these doses will go to high income countries, which represent 14% of the world’s population. The US has reserved 800 million doses but accounts for a fifth of all covid-19 cases globally (11.02 million cases), whereas Japan, Australia, and Canada have collectively reserved more than one billion doses but do not account for even 1% of current global covid-19 cases globally (0.45 million cases). If these vaccine candidates were all successfully scaled, the total projected manufacturing capacity would be 5.96 billion courses by the end of 2021. Up to 40% (or 2.34 billion) of vaccine courses from these manufacturers might potentially remain for low and middle income countries-less if high income countries exercise scale-up options and more if high income countries share what they have procured. Prices for these vaccines vary by more than 10-fold, from $6.00 (£4.50; €4.90) per course to as high as $74 per course. With broad country participation apart from the US and Russia, the COVAX Facility-the vaccines pillar of the World Health Organization’s Access to COVID-19 Tools (ACT) Accelerator-has secured at least 500 million doses, or 250 million courses, and financing for half of the targeted two billion doses by the end of 2021 in efforts to support globally coordinated access to covid-19 vaccines.

Conclusions: This study provides an overview of how high income countries have secured future supplies of covid-19 vaccines but that access for the rest of the world is uncertain. Governments and manufacturers might provide much needed assurances for equitable allocation of covid-19 vaccines through greater transparency and accountability over these arrangements.

The Voice of Adina Hazan, PhD

I have a few issues with the proposal and the asserted outcomes:

The author suggests that back in July 2020 “the U.S. passed up an opportunity to secure by June 2021 more than 100 million doses of the Pfizer vaccine…[by] follow[ing] a balanced-portfolio strategy”. By stating that the U.S. “passed up an opportunity” at that time when all available evidence could not indicate which vaccine would prove successful is taking a “hindsight is 2020” approach. Instead, an all-or-nothing portfolio in July 2020 for one vaccine over another would have been at best unwise and at worst could have passed up the “right” vaccine.

In addition, the author’s core suggestion is that every person in America and the world needs the vaccine at the same time, aka as soon as possible. Considering the incredibly striated outcomes of patients that contract COVID-19, this is not the case. We know that males up until 85 years old with have a much worse prognosis than women, for example1. In addition, all data suggests that the lowest risk group is children, with a death rate in the U.S. of 0.1%1. Trying to vaccinate all children with a vaccine whose long-term effects are, at this time, unknown, for a disease with such a low death rate is not urgent and may warrant waiting for more evidence. Instead of trying to inoculate everyone as fast as possible, the two-dose approach that is currently implemented ensures that those most at risk receive the maximum protection, instead of leaving them at higher risks even after vaccination. In this way, the vaccine will do what it was originally intended to do: protect the most vulnerable immediately, and in turn begin to alleviate the strain on the overall population as a result of this disease.

  1. S. CDC website (Deaths by Age Group, 12/18/2020)

The Voice of Aviva Lev-Ari, PhD, RN

  • I recommand to adhere to administration protocol.
  • I agree with Dr. Joel Jertock:

It is very clear that the current COVID vaccination protocols call for two shots, three weeks apart, for maximum protection.

Limiting personnel to a single shot, “to spread the available vaccines further” just means wasting those doses.  It is similar to taking an antibiotic for only 5 days instead of the recommended 10 days, “to make the pills last longer.”

References on Vaccine Development 

Development of Medical Counter-measures for 2019-nCoV, CoVid19, Coronavirus

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COVID-19 T-cell immune response map, immunoSEQ T-MAP COVID for research of T-cell response to SARS-CoV-2 infection

Reporter: Aviva Lev-Ari, PhD, RN

 

Read our latest blog | T cells: Understanding Exposure and Immunity to COVID-19 by Adaptive Co-Founder and CSO, Harlan Robins. Read here

Watch the video

T cells are the adaptive immune system’s first responders to any virus, circulating in the blood to detect and quickly multiply to attack the virus, often before symptoms appear. Adaptive Biotechnologies’ unique MIRA Technology and immunoSEQ Technology has enabled us to create a comprehensive view of the T-cell response to SARS-CoV-2 infection. This data has been made public as part of the ImmuneCODE Initiative in order to help propel drug, vaccine, and clinical trial research. We are launching immunoSEQ T-MAP COVID with the tools to study and analyze the COVID-19 T-cell immune response map.

SARS-CoV-2-specific Antigen-TCR sequence-level data
Quantitative sequence level data for TCR repertoires for SARS-CoV-2 specific antigens
Monitor immunologic response to SARS-CoV-2 infection or vaccine
Track COVID-19 specific TCR sequences longitudinally
Dive into Patient, Population, or Cohort-level data
Determine TCR clones shared between cohorts & those that are Public vs Private clones

 

Learn more about the science behind the ImmuneCODE database in our first publication (Nolan et al.) and to discover initial COVID-19 data insights, read our recently updated pre-print publication (Snyder et al.)

A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2

Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels

End-to-end solution; from experimental design to publication ready data

SARS-CoV-2-specific TCR repertoire sequences & antigen data

✔  Validated TCR-antigen data from over 70 MIRA experiments

✔  In vivo identified SARS-CoV-2-specific TCR sequences

✔  TCR-Antigen sequence level data with the PCR, bias-controlled, reproducible immunoSEQ Assay

Data analysis through the immunoSEQ Analyzer or Computational Biology Services

✔  Explore SARS-CoV-2-specific TCR-Antigen sequence data in the immunoSEQ Analyzer

✔  Compare your COVID-19 samples against our COVID-19 samples to identify public vs private clones

✔  Computational Biology Services for COVID-19 data and Metadata analysis

Comprehensive COVID-19 TCR-Antigen sequence database

✔  Providing you a comprehensive view of SARS-CoV-2-specific antigen and TCR level data

✔  Database will constantly be updated with new findings and TCR-Antigen sequence data

 

Check out the publications below to learn how researchers are propelling their COVID-19 research by leveraging immunoSEQ T-MAP COVID and the ImmuneCODE COVID-19 database

Analysis of SARS-CoV-2 specific T-cell receptors in ImmuneCode reveals cross-reactivity to immunodominant Influenza M1 epitope

 

Watch our video, about how the immunoSEQ Technology and immunoSEQ T-MAP COVID can be used to better understand the immune response to SARS-CoV-2 infection.

 

Ready to learn more about how our immunoSEQ T-MAP COVID service can help you propel your research forward? Contact us below to speak with one of our experts.

SOURCE

https://ww2.adaptivebiotech.com/immunoseq-TMAP-COVID?utm_source=genomeweb&utm_medium=email&utm_campaign=dailynews

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The complication of Pfizer’s Vaccine Distribution’s Plan

Reporter : Irina Robu, PhD

Even though Pfizer announcing the development of safe and effective vaccine is cause for celebration, scientists and public experts face  the challenge of how to quickly make millions of doses of the vaccine and getting them to hospitals, clinics and pharmacies. But Pfizer distribution of vaccines rely on a network of companies, federal and state agencies and on the ground health workers in the midst of a pandemic that is spreading at a high rate in United States.

Before Pfizer can begin shipping its vaccine, federal and state governments must inform Pfizer of how many doses are needed along with syringes, needles and other supplies needed to administer the vaccine. In addition, employees at the locations should be trained to store and administer the vaccine and to ensure that after people are vaccinated, they return for a second dose.

The complication of Pfizer’s vaccine is that it has to be stored at minus 70 degree Celsius until before it is injected.  Pfizer is making the vaccine at facilities in Kalamazoo, Mich., and Puurs, Belgium. The doses distributed in the United States will mostly come from Kalamazoo. When they receive emergency authorization from FDA, Pfizer will send limited doses to large hospitals, pharmacies and other vulnerable groups. At the same time, nine other candidates are also in the final stage of testing.

In Kalamazoo, vaccines will go into vials, vi will go into trays (195 vials per tray) and the trays will go into specially designed cooler-type boxes (up to five trays per box).The reusable boxes, each toting between 1,000 and 5,000 doses and stuffed with dry ice, are equipped with GPS-enabled sensors. Pfizer employees will be able to monitor the boxes’ locations and temperatures as FedEx and UPS transport them to hospitals and clinics nationwide.

The minute Pfizer coolers reach their destinations, hospitals or pharmacies will have a few alternatives of  how to store the vaccine. The easiest option is using ultracold freezers, but they can stash the trays in conventional freezers for up to five days. The destinations can keep the vials in the cooler for up to 15 days as long as they replenish the dry ice and don’t open it more than twice a day.

The chief executives at Pfizer and BioNTech suggest that Pfizer is able to produce up to 50 million doses per year and only half of those will go to US. But since two doses are needed for each person, only 12.5 million doses can be vaccinated.

The other challenge is distributing the vaccine in rural areas, where if not administering the doses fast enough it can go bad. Even though Pfizer has developed and tested an effective vaccine, figuring out how to distribute it is the hardest challenge Pfizer will face.

SOURCE

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12/5/2020

Regeneron’s Covid Antibody coktail has been cleared for emergency use by the FDA. The emergency authorization for REGN-COV2, a combination of monoclonal antibodies casiriviamb and imdevimab, marks the second for the antibody therapy. The first emergency authorization was given to Eli Lily’s bamlanivimab.

The difference that REGN-COV2 is a concoction of several drugs, whereas Lilly’s treatment contains only one drug, the two emergency authorizations  are almost identical. They treat both for mild-to-moderate COVID-19 patients at least 12 years of age who are not hospitalized but are at high risk for progressing to severe COVID-19.

SOURCE

https://www.fiercepharma.com/pharma/regeneron-following-lilly-s-footsteps-wins-fda-emergency-nod-for-covid-19-antibody-cocktail


Regeneron’s new antibody cocktail drug, REGN-COV2

Reporter : Irina Robu, PhD

Regeneron,  leading biotechnology company using the power of science to bring new medicines to patients in need answered quickly to the COVID-19 pandemic and found an antibody cocktail  as the pandemic numbers increase in the U.S. The antibody cocktail, also known as REGN-COV2 antibody combination therapy is an investigational medicine, and its safety and efficacy have not been fully evaluated by any regulatory authority.

REGN-COV2 is being studied in four ongoing late-stage clinical trials: two Phase 2/3 trials for the treatment of hospitalized and non-hospitalized COVID-19 patients, Phase 3 RECOVERY trial of hospitalized COVID-19 patients in the UK, and a Phase 3 trial for the prevention of COVID-19 in uninfected people who are at high-risk of exposure to a COVID-19 patient. The Phase 3 prevention trial is being jointly conducted with the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH).

The company expects approval from FDA on its antibody cocktail and expect to have 2.4-gram doses ready for about 80,000 patients at the end of November and 200,000 doses at the beginning of January.  At the same time, Regeneron partnered with Roche to expand its capacity further by increasing its manufacturing capacity.

Regeneron come in COVID-19 research early this year as the outbreak was in its early stages, testing hundreds of virus-neutralizing antibodies in mice and seeing how they compared with antibodies from human survivors of the novel coronavirus.

SOURCE

https://www.fiercepharma.com/manufacturing/regeneron-predicts-300-000-covid-19-cocktail-doses-ready-by-january-and-substantially

 

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Detecting SARS-COV-2 antibodies in serum and plasma samples

Reporter: Irina Robu, PhD

Convalescent plasma therapy is a possible treatment under investigation where antibodies from recovered patients are transfused to current COVID-19 patients with the intent to help them fight the infection and buy time until their immune system can produce antibodies. Yet, not all recovered patients have the same quantity of antibody titers suitable for such transfusions. In some patients it will minimize the severity of the disease length.

The U.S. Food and Drug Administration authorized convalescent plasma therapy for patients with coronavirus disease 2019 and it permitted to be used during the pandemic because there is no approved treatment for COVID-19. The donated blood is processed to remove cells, leaving behind liquid and antibody.   

Companies like Forte Bío are developing instruments such as Octet HTX Instrument, Octet RED384 Octet RED96e Instrument and Octet K2 Instrument to detect SARS-COV-2 antibodies in serum and plasma samples. The Octet technology allows quantification with high resolution comparable to an HPLC . The instrument utilizes BLI enabling label-free detection for protein quantitation and kinetic characterization at unmatched speed and throughput. The instrument can  measure up to 96 samples simultaneously allowing both unlimited characterization capacity for various applications and custom assay tailoring to maximize analytical throughput or sensitivity and preventing bottlenecks. 

 How are antibodies tested ?

  1. Immobilize a virus protein such as the receptor binding domain (RBD) of the SARS CoV-2 spike protein.
  2. Dip the coronavirus biosensor into diluted patient plasma or serum samples.
  3. Block the biosensor with non-relevant serum or blocking buffer if needed to prevent non-specific binding.

Even the researchers believe that the risk to donors is low, there are additional risks such as allergic reactions, lung damage, difficulty breathing or infections such as HIV, hepatitis B and Donated blood must be tested for safety prior to administering to patients.

What to expect ? It is up to the doctor treating the patient, if convalescent plasma therapy is an option.  Even though data from clinical trials suggest that convalescent plasma may diminish the severity or duration of the COVID19, more research is needed to determine if convalescent plasma therapy is an effective treatment.

SOURCE

https://www.fortebio.com/covid19research19research

https://www.medrxiv.org/content/10.1101/2020.07.17.20156281v1

 

Other related articles were published in this Open Access Online Scientific Journal including the following:

https://pharmaceuticalintelligence.com/2020/05/18/race-to-develop-antibody-drugs-for-covid-19

https://pharmaceuticalintelligence.com/2020/05/18/race-to-develop-antibody-drugs-for-covid-19

 

 

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Why Do Some COVID-19 Patients Infect Many Others, Whereas Most Don’t Spread the Virus At All?

Guest Reporter: Jason S Zielonka, MD

One of the key parameters in COVID-19 pandemic epidemiology has been to define the spread metrics, basically identifying how a host spreads the virus to uninfected individuals. The pattern of spread can impact how and which preventative measures such as social distancing and hand washing can impact spread patterns. In particular, two metrics, the average number of new patients infected by each host (the reproduction number, R) and a factor representing the tendency to cluster (the dispersion factor, k) can be used to describe and model the spread of a virus quite well. Higher values of R mean more people are infected by a single host, i.e, the disease is more contagious; lower values of k mean that a host infects a larger number of new patients, i.e., the disease is more clustered.

The reproduction number, R, for SARS-CoV-2, without social distancing, is about 3. But this is an average, taken over an aggregate of patients. For most individuals, R is zero, i.e., most patients do not transmit the virus to others. For comparison, SARS and MERS, both coronaviruses, had R > 3 and the 1918 influenza pandemic had R >> 3. So what determines viral spread and how can we use that information to treat and eradicate SARS-CoV-2?

In 2005, by modeling the Chinese SARS outbreak and comparing the model to the real-world data, Lloyd-Smith and co-authors were able to determine that SARS had a k of about 0.16. MERS, in 2012, was estimated to have k around 0.25; the 1918 pandemic, by contrast, had a k of 1, meaning it had very little cluster effect. The current modeling indicates that k for SARS-CoV-2 is not conclusive, but it appears higher than k for either SARS or MERS.

This work has provided insights into some of the factors influencing cluster spread, which can be controlled in a more specific way than quarantining an entire population. There will be individual variance, but we know that people are particularly infectious over a certain time period; that certain activities are more conducive to droplet formation and wider spread, and that being outdoors rather than in confined and noisy indoor locations leads to less spread. This can all lead to better, faster and more tolerable approaches to either future pandemics or to a recurrence of SARS-CoV-2.

SOURCE

https://www.sciencemag.org/news/2020/05/why-do-some-covid-19-patients-infect-many-others-whereas-most-don-t-spread-virus-all

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From AAAS Science News on COVID19: New CRISPR based diagnostic may shorten testing time to 5 minutes

Reporter: Stephen J. Williams, Ph.D.

 

 

 

 

 

 

 

 

 

A new CRISPR-based diagnostic could shorten wait times for coronavirus tests.

 

 

New test detects coronavirus in just 5 minutes

By Robert F. ServiceOct. 8, 2020 , 3:45 PM

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

 

Researchers have used CRISPR gene-editing technology to come up with a test that detects the pandemic coronavirus in just 5 minutes. The diagnostic doesn’t require expensive lab equipment to run and could potentially be deployed at doctor’s offices, schools, and office buildings.

“It looks like they have a really rock-solid test,” says Max Wilson, a molecular biologist at the University of California (UC), Santa Barbara. “It’s really quite elegant.”

CRISPR diagnostics are just one way researchers are trying to speed coronavirus testing. The new test is the fastest CRISPR-based diagnostic yet. In May, for example, two teams reported creating CRISPR-based coronavirus tests that could detect the virus in about an hour, much faster than the 24 hours needed for conventional coronavirus diagnostic tests.CRISPR tests work by identifying a sequence of RNA—about 20 RNA bases long—that is unique to SARS-CoV-2. They do so by creating a “guide” RNA that is complementary to the target RNA sequence and, thus, will bind to it in solution. When the guide binds to its target, the CRISPR tool’s Cas13 “scissors” enzyme turns on and cuts apart any nearby single-stranded RNA. These cuts release a separately introduced fluorescent particle in the test solution. When the sample is then hit with a burst of laser light, the released fluorescent particles light up, signaling the presence of the virus. These initial CRISPR tests, however, required researchers to first amplify any potential viral RNA before running it through the diagnostic to increase their odds of spotting a signal. That added complexity, cost, and time, and put a strain on scarce chemical reagents. Now, researchers led by Jennifer Doudna, who won a share of this year’s Nobel Prize in Chemistry yesterday for her co-discovery of CRISPR, report creating a novel CRISPR diagnostic that doesn’t amplify coronavirus RNA. Instead, Doudna and her colleagues spent months testing hundreds of guide RNAs to find multiple guides that work in tandem to increase the sensitivity of the test.

In a new preprint, the researchers report that with a single guide RNA, they could detect as few as 100,000 viruses per microliter of solution. And if they add a second guide RNA, they can detect as few as 100 viruses per microliter.

That’s still not as good as the conventional coronavirus diagnostic setup, which uses expensive lab-based machines to track the virus down to one virus per microliter, says Melanie Ott, a virologist at UC San Francisco who helped lead the project with Doudna. However, she says, the new setup was able to accurately identify a batch of five positive clinical samples with perfect accuracy in just 5 minutes per test, whereas the standard test can take 1 day or more to return results.

The new test has another key advantage, Wilson says: quantifying a sample’s amount of virus. When standard coronavirus tests amplify the virus’ genetic material in order to detect it, this changes the amount of genetic material present—and thus wipes out any chance of precisely quantifying just how much virus is in the sample.

By contrast, Ott’s and Doudna’s team found that the strength of the fluorescent signal was proportional to the amount of virus in their sample. That revealed not just whether a sample was positive, but also how much virus a patient had. That information can help doctors tailor treatment decisions to each patient’s condition, Wilson says.

Doudna and Ott say they and their colleagues are now working to validate their test setup and are looking into how to commercialize it.

Posted in:

doi:10.1126/science.abf1752

Robert F. Service

Bob is a news reporter for Science in Portland, Oregon, covering chemistry, materials science, and energy stories.

 

Source: https://www.sciencemag.org/news/2020/10/new-test-detects-coronavirus-just-5-minutes

Other articles on CRISPR and COVID19 can be found on our Coronavirus Portal and the following articles:

The Nobel Prize in Chemistry 2020: Emmanuelle Charpentier & Jennifer A. Doudna
The University of California has a proud legacy of winning Nobel Prizes, 68 faculty and staff have been awarded 69 Nobel Prizes.
Toaster Sized Machine Detects COVID-19
Study with important implications when considering widespread serological testing, Ab protection against re-infection with SARS-CoV-2 and the durability of vaccine protection

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Tiny biologic drug to fight COVID-19 show promise in animal models

Reporter : Irina Robu, PhD

A research team at University of Pittsburg School of Medicine identified an antibody component that is 10 times smaller than a full-sized antibody. Their research published in Cell, indicates that the drug, Ab8 based on it is effective in mice and hamsters. The research was started by screening a library of about 100 billion antibody fragments to identify candidates that bound tightly to the spike protein on SARS-CoV-2’s surface, which the virus uses to enter and infect human cells.

A typical antibody consists of two heavy chains and two light chains. The chosen molecule is the variable domain of the heavy chain of an immunoglobulin, which is a type of antibody. The heavy chain variable domain is essential for binding with an antigen. Ab8 was created by fusing the variable, heavy chain domain with part of the immunoglobulin tail region, giving it immune functions but doing so with a molecule that’s about half the size of a full immunoglobulin.

The smaller size of the antibody can improve the therapeutic efficacy for infectious diseases and can be delivered through inhalation. Their research showed that Ab8 completely neutralized SARS-CoV-2 in lab dishes. The drug developed showed that inhibited the virus in lung tissue in animal body even at the lowest dose 2 mg/kg as compared to untreated controls.

The research team is looking to determine the drug effect in hamsters, which were reported to have better clinical signatures of COVID-19. And the hamsters that got the drug display less severe pneumonia that did the control animals. Drugs with alternative administration routers could provide additions to the first wave of COVID-19 therapies and vaccines.

What is more important, Ab8 does not appear to bind to human cells which is a good sign that it won’t have negative side effects.

SOURCE

https://www.fiercebiotech.com/research/small-sized-biologic-against-covid-19-shows-promise-animal-models

 

 

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