Black Friday and Cyber-Monday bring more surprises from COVID

The news this weekend about a new variant "Omicron" has fueled speculation about up coming events in the world of pandemics.  Truly, no one knows much about it yet.  It will require about two weeks to gather meaningful data about Covid Omicron.

Fortunately the WHO and the nations of the world are not taking any chances, based upon the original outbreak in December 2019.  Poor communications, delays in lockdowns and the unavailability of a vaccine contributed to the fiasco in early 2020. Viral immunologists are already making plans to develop a new vaccine based upon early samples from already infected patients.  The affected countries, U.K. South Africa, Botswana and other countrie have been quarantined until these issues are determined.

The World Health Organization reports

Much of the previous tests, and treatments probably will be unchanged

Current knowledge about Omicron 

Researchers in South Africa and around the world are conducting studies to better understand many aspects of Omicron and will continue to share the findings of these studies as they become available.  

Transmissibility: It is not yet clear whether Omicron is more transmissible (e.g., more easily spread from person to person) compared to other variants, including Delta. The number of people testing positive has risen in areas of South Africa affected by this variant, but epidemiologic studies are underway to understand if it is because of Omicron or other factors.  

Severity of disease: It is not yet clear whether infection with Omicron causes more severe disease compared to infections with other variants, including Delta.  Preliminary data suggests that there are increasing rates of hospitalization in South Africa, but this may be due to increasing overall numbers of people becoming infected, rather than a result of specific infection with Omicron.  There is currently no information to suggest that symptoms associated with Omicron are different from those from other variants.  Initial reported infections were among university students—younger individuals who tend to have more mild disease—but understanding the level of severity of the Omicron variant will take days to several weeks.  All variants of COVID-19, including the Delta variant that is dominant worldwide, can cause severe disease or death, in particular for the most vulnerable people, and thus prevention is always key. 

Effectiveness of prior SARS-CoV-2 infection 

Preliminary evidence suggests there may be an increased risk of reinfection with Omicron (ie, people who have previously had COVID-19 could become reinfected more easily with Omicron), as compared to other variants of concern, but information is limited. More information on this will become available in the coming days and weeks. 

Effectiveness of vaccines: WHO is working with technical partners to understand the potential impact of this variant on our existing countermeasures, including vaccines. Vaccines remain critical to reducing severe disease and death, including against the dominant circulating variant, Delta. Current vaccines remain effective against severe disease and death.   

Effectiveness of current tests: The widely used PCR tests continue to detect infection, including infection with Omicron, as we have seen with other variants as well. Studies are ongoing to determine whether there is any impact on other types of tests, including rapid antigen detection tests.  

Effectiveness of current treatments:   Corticosteroids and IL6 Receptor Blockers will still be effective for managing patients with severe COVID-19. Other treatments will be assessed to see if they are still as effective given the changes to parts of the virus in the Omicron variant.  

 China has not reported cases of the Omicron variant, nor have Brazil, or Russia.

Expert Newsletters - MashupMD: A Tribute to Omicron

SARS-COVID 2 is not the same as Inluenza.

Lung autopsies of COVID-19 patients reveal treatment clues

SARS-CoV-2 prevents lung tissue repair, regeneration.

Colorized scanning electron micrograph of a cell infected with a variant strain of SARS-CoV-2 virus particles (blue), isolated from a patient sample. NIAID

What

Lung autopsy and plasma samples from people who died of COVID-19 have provided a clearer picture of how the SARS-CoV-2 virus spreads and damages lung tissue. Scientists at the National Institutes of Health and their collaborators say the information, published in Science Translational Medicine, could help predict severe and prolonged COVID-19 cases, particularly among high-risk people, and inform effective treatments.

Although the study was small—lung samples from 18 cases and plasma samples from six of those cases—the scientists say their data revealed trends that could help develop new COVID-19 therapeutics and fine-tune when to use existing therapeutics at different stages of disease progression. The findings include details about how SARS-CoV-2, the virus that causes COVID-19, spreads in the lungs, manipulates the immune system, causes widespread thrombosis that does not resolve, and targets signaling pathways that promote lung failure, fibrosis and impair tissue repair. The researchers say the data are particularly relevant to caring for COVID-19 patients who are elderly, obese, or have diabetes—all considered high-risk populations for severe cases. Study samples were from patients who had at least one high-risk condition.

The study included patients who died between March and July 2020, with time of death ranging from three to 47 days after symptoms began. This varied timeframe allowed the scientists to compare short, intermediate, and long-term cases. Every case showed findings consistent with diffuse alveolar damage, which prevents proper oxygen flow to the blood and eventually makes lungs thickened and stiff.

They also found that SARS-CoV-2 directly infected basal epithelial cells within the lungs, impeding their essential function of repairing damaged airways and lungs and generating healthy tissue. The process is different from the way influenza viruses attack cells in the lungs. This provides scientists with additional information to use when evaluating or developing antiviral therapeutics.

Israeli Study Shows How COVID-19 Immunity Wanes over Time – NIH Director's Blog

The winter holidays are approaching, and among the many things to be grateful for this year is that nearly 200 million Americans are fully vaccinated for COVID-19. That will make it safer to spend time with friends and family, though everyone should remain vigilant just to be on the safe side. Though relatively uncommon, breakthrough infections are possible. That’s why the Centers for Disease Control and Prevention (CDC) recommends booster shots for several at-risk groups, including folks 65 years and older, those with underlying medical conditions, and people whose occupations place them at high risk of exposure.

One of the main studies providing the evidence for CDC’s recommendation was recently published in the New England Journal of Medicine [1]. It found that vaccine-induced immunity, while still quite protective against infection and severe illness from COVID-19, can wane after several months.

The study is yet another highly informative report from Israel, where public health officials launched a particularly vigorous national vaccination campaign in December 2020. More than half of adult Israelis received two doses of the Pfizer vaccine within the first three months of the campaign. By May 2021, Israel had extremely small numbers of confirmed COVID-19 cases—just a few dozen per day.

But the numbers crept back up in June 2021. The rise also included a substantial number of breakthrough infections in vaccinated individuals. The vast majority of those cases in June—98 percent—were caused by the emerging Delta variant.

Researchers led by Yair Goldberg, Technion-Israel Institute of Technology, Haifa, wondered whether this resurgence of COVID-19 could be fully explained by the rise of the more infectious Delta variant. Or, they wondered, did the waning of immunity over time also play a role?

To find out, the researchers looked to over 4.7 million fully vaccinated Israeli adults, more than 13,000 of whom had breakthrough infections from July 11 to 31, 2021 with SARS-CoV-2. The researchers looked for an association between the rate of confirmed infections and the time that had passed since vaccination. Without any significant waning of immunity, one shouldn’t see any difference in infection rates among people who were fully vaccinated at the earliest opportunity versus those vaccinated later.

The results were clear: the rate of confirmed COVID-19 infection revealed a slow but steady waning of immunity over time. Among individuals 60 years or older who were fully vaccinated last January, the number of confirmed breakthrough infections was 3.3 per 1,000 people during the three weeks of the study. Those who were vaccinated in February and March had lower infection rates of 2.2 per 1,000 and 1.7 per 1,000, respectively. The data revealed a similar pattern in those aged 40 to 59 and those aged 16 to 39.

An important question is whether these breakthrough infections were serious enough to require hospitalization. While such cases were much less common, more than 400 of those with confirmed COVID-19 breakthroughs went on to develop severe illness. And, again, the data show a similar pattern of waning immunity. The rate of severe COVID-19 among adults 60 years of age or older who were fully vaccinated in January was 0.34 cases per 1,000 persons. The rate of severe illness dropped to 0.26 cases per 1,000 among those vaccinated in February and 0.15 cases per 1,000 for those vaccinated in March. The researchers report that the number of severe COVID-19 cases among the younger fully vaccinated groups were too small to draw any conclusions.

While the Delta variant surely has played a role in the resurgence of COVID-19 in recent months, these findings suggest that waning immunity also is an important factor. Understanding these dynamics is essential for making critical policy decisions. In fact, these data were a key factor in the decision by the Israeli Ministry of Health in July 2021 to approve administration of COVID-19 booster shots for individuals who’d been vaccinated at least 5 months before.

Back in the U.S., if you were among those who got your vaccine on the early side—good for you. If it’s been more than six months since your original shots, and if you are in one of the risk groups, you should consider a COVID-19 booster shot to remain optimally protected in the months ahead. I’ll be getting my Moderna booster this week. While you’re at it, consider getting your annual flu shot taken care of, too. The CDC guidelines state that it’s perfectly OK to get your COVID-19 and flu shots at the same time.

What about it?  WAI

Steve White says:

November 9, 2021 at 11:04 am

I am not against the vaccines or boosters, but I think the numbers the Director is citing from this study indicate the media and CDC have given out very misleading information. Instead of saying “In Israel, 1 in 300 people who got vaccinated in January have gotten infected” – a number which I think CDC knows will not scare people enough – and indeed, their own experts believed was not scary enough (they may not have had all the data available now but they certainly knew breakthroughs were rare when they advised on boosters) – to really push boosters, we are given horror stories about significantly reduced protection.

Stories about breakthroughs, which probably get some people running for their boosters, and others saying :Heck with it, what is the point?” Or other rationalizations.

Maybe they should have said, “breakthrough are so rare, and so unlikely to be severe, that we do not think boosters are really needed for most healthy people” -or something similar to that. Oh, wait …

Or, how about “while there is extra protection from getting a booster, for those who were already infected, the rate of reinfection is very low in either case” ?

I am not even going into the extremely low rate of severe illness among children, and the strong possibility they are better off with natural immunity – remember, the human race, and for that matter, all our ancestor mammalian races, presumably, have dealt with viruses from other species for millions of years. Think about this deeply – maybe we’ve evolved so that children strongly tend to not get severely ill, and tend to get lifelong protection, when exposed to novel viruses. Old folks who are no longer breeding – anything can happen to them – just what we see with this thing so far – and maybe giving kids vaccines, which will protect against one variant (the one they were designed to stop) very well, closely related variants less effectively, and other variants maybe not at all, will set them up to be more vulnerable for the coming variants, than kids who caught the first, apparently least virulent, variant, and now have some immunity to every vulnerable part of it.

Israeli Study Shows How COVID-19 Immunity Wanes over Time – NIH Director's Blog

Novavax has been granted its first emergency use authorisation in Indonesia for COVID-19 vaccine NVX-CoV2373, and expects other regulators in India, the Philippines and other countries to follow suit in the coming weeks.

Third world nations have been short changed during the 4 months that the pandemic spread throughout the world.  Many nations have even donated millions of doses of vaccines produced in their own countries. Canada recently agreed to donate several million dollars to the United Nations fund for distributing covid vaccines to those less developed nations.

Indonesia has applied for an emergency authorization for it's vaccine, NVX-COV2373. Nations in their own regional market place, including India. and the Phillipines will also join their effort.  These three nations may pool their resources to produce vacccines for many millions of people.  Local sources for vacccine will eliminate the challenges of distribution,  such a refrigeration, spoilage, and transportation.

Indonesia falls into that category as it has a fragmented healthcare system, despite universal access,  which is amplified by the geographical hurdles associated with being an archipelago with 275 million people spread across 6,000 islands. Initial shipments into the country are expected to begin “imminently,” said Novavax.

The vaccine is the first based on recombinant protein to be approved anywhere in the world, and has the key advantage over many of the currently approved jabs as it can be stored at regular refrigeration temperatures. That makes it well suited to distribution in countries where healthcare delivery is more challenging.

Recombinant protein is produced by recombinant DNA using bacteria (E.Coli) as a manufacturing process. E.coli  is the manufacturing plant for recombinant DNA and in turn. recombinant proteins

Why is E. coli used for transformation?

Other cell types including mammalian cells,  yeast, insect cells, or other eukaryocytic cells could be used. E. coli is a preferred host for protein production due to its rapid growth and the ability to express proteins at very high levels. Bacterial conjugation can be used to transfer large DNA fragments from one bacterium to another.

The following references explain in further the use of recombinant DNA/Protein for the manufacture of other Covid 19 vaccines.

Rather than using messenger RNA (m-RNA) to produce a 'spike protein' from the corona virus, the Indian Covid vaccine is manufactured as an inactive viral particle.

Covax information

1. Center for Systems Science and Engineering, Johns Hopkins University. COVID-19 Dashboard. [Accessed 15 Nov 2020.]

2. World Health Organization. DRAFT landscape of COVID-19 candidate vaccines, 12 November, 2020. https://www.who.int/publications/m/item/draft-landscape-of-covid-19-candidate-vaccines.

3. World Health Organization. WHO Concept for fair access and equitable allocation of COVID-19 health products. Final working version 9 September 2020. Geneva, Switzerland: World Health Organization, 2020. https://www.who.int/publications/m/item/fair-allocation-mechanism-for-covid-19-vaccines-through-the-covax-facility.

4. Emanuel EJ, Persad G, Kern A, et al. An ethical framework for global vaccine allocation. Science 2020;369:1309-12. 10.1126/science.abe2803  [PubMed] [CrossRef] [Google Scholar]

5. COVAX. Commitment Agreements, September 30, 2020. https://www.gavi.org/sites/default/files/covid/pr/COVAX_CA_COIP_List_COVAX_PR_30-09.pdf.

6. Gavi, the Vaccine Alliance. COVAX, the ACT-Accelerator Vaccines Pillar: Insuring Accelerated Vaccine Development and Manufacture, 2020. https://www.gavi.org/sites/default/files/covid/COVAX-Pillar-background.pdf.

7. Gavi COVAX Facility. Over US$ 2 billion raised to support equitable access to COVID vaccines with additional US$ 5 billion needed in 2021. Press release, 13 November 2020. https://www.gavi.org/news/media-room/over-us-2-billion-raised-suppor

Novavax gets first authorisation for its COVID-19 jab -