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January 2021

Increasingly Contagious And Lethal CoV-2 Variants Are Popping Up Around The World

In September, the UK noticed a coronavirus variant that has a surprising number of genome mutations, including eight point mutations in the spike protein, which is the viral antigen targeted by most of the vaccines. In just a couple of months, the variant became the prevalent cause of COVID-2 in the UK, meaning that it spreads faster than other iterations of the virus. It also has been found in a few pockets in the US and is expected to become the dominant strain here by March. It appears that the variant is 30-50% more infectious in all age groups (down from the early 70% estimate in December). Fortunately, all indications are that the two mRNA vaccines being rolled out by Pfizer and Moderna are effective against the variant (expect two more vaccines based on different technology platforms soon, from AstraZeneca and J&J).

The bad news is that British public health officials just warned that the virus variant is just not more contagious, it also is 30-40% more lethal. Out of 1000 60-year old patients infected with the UK variant, 13-14 would be expected to die, compared to 10 deaths in patients infected with the previous virus. This warning was based on four separate UK studies.

Related, but not identical, viral variants also have appeared in South Africa and in Brazil. These variants also seem to be more contagious and, not surprisingly, share some of the same spike protein mutations as the British variant. There is no word, yet, on the lethality of these variants. However, three lab studies in South Africa have raised concerns that their variant might be resistant to the current vaccines. Pfizer studies found that their vaccine protects well against the British variant, but the South African variant seems to be more resistant to the two vaccines currently in use. It too has quickly become the dominant virus strain in that country and has been found in 22 other countries. It has not yet been found in the US, but give it time.

These new virus variants that are more contagious and more lethal are appearing in countries where a significant percentage of people have already built some immunity to the original CoV-2 strain. This raises concern that our immune responses can provide natural selection pressure that favors virus variants that avoid the specificity of our immune response. In other words, our immune systems and the vaccines might be driving the emergence of more contagious and deadly forms of the virus. If so, this would necessitate adapting the vaccines to meet the variants and establishing a regular vaccine schedule with continually changing vaccines like we do now for the flu virus.

The CEO of BioNTech, the German biotech company that spent a decade developing the mRNA vaccine platform used in Pfizer’s vaccine, said it would take only six weeks to design a new vaccine specific for new variants in the spike protein. The platform is in place and all they would need to do is swap out the spike protein mRNA for the new variant sequence. Then it would take some time to produce the new vax and get it into arms. But, again, that is similar to what we do each year for the new flu strains that pop up annually.

Hopefully, the new vax technology will let us develop new vaccines as fast as the virus mutates.

The race is on. Bet on the new vax technology, which I earlier christened, BioX.

400,000 Total COVID-19 Deaths In A Year

Shortly after Thanksgiving, I wrote in these pages how the post-turkey surge moved COVID-19 to the top cause of death in the US. I reported that the disease was killing more than 14,000 people a week, above the ~12,000 killed weekly by the former top killers, heart disease and cancer.


It is getting grimmer: Now the CDC estimates that 92,000 people will die from the disease in the next three weeks. That is almost 31,000 deaths a week, more than double the death rate in early December. And, a study just published in the Proceedings of the National Academy of Sciences reported that the average life expectancy in the US in 2020, dropped by more than a year. The study was conducted by researchers from Princeton and the University of Southern California using data from the Institute for Health Metrics and Evaluation.

If the pandemic didn’t take place, the study authors note that a person born in 2020 would, on average, live to about 79 years. The virus shaved almost 1.22 years off of that average life span. Black and Latino populations were projected to suffer significantly greater declines in life expectancy compared to White populations.  Reduced life expectancy among minorities was projected to be about triple that for White populations: life expectancy is projected to be 0.73 years lower for the White population, 2.26 years lower for the Black population, and 3.28 years lower for Latinos.

While 400,000 deaths is very tragic, it is a mere drop in the bucket compared to the many more COVID-19 patients who suffer long term, or even permanent morbidity. More on that later.

Shifting Topics: From June to November, Public Health England, tested thousands of healthcare workers in the UK. They reported that out of 6,614 healthcare workers who tested positive for COVID-19 antibodies, there were 44 reinfections. That is a good rate of protection against reinfection, but the reinfection rate still is surprisingly high.

This means that even though you had the virus or even were vaccinated, you might still be able to pass it on. What should you do?

  • Still get the shot.
  • Still mask up.
  • Still socially distance.
  • Still wash your hands.

In other words, be a good neighbor.

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More Than Half CoV-2 Transmission Comes From People Without COVID-19 Symptoms

The Journal of the American Medical Association just reported that 59% of new CoV-2 infections are likely caused by infected people who do not show COVID-19 symptoms. This conclusion is based on the results of a decision analytical model that assessed the spread from pre-symptomatic, never-symptomatic and symptomatic people infected with CoV-2. 35% of viral transmission came from pre-symptomatic people, and 24% from people who never develop symptoms.  

This means that until the vaccines are widely disseminated, identifying and isolating people with COVID-19 will be much less effective at controlling the spread of the virus than previously thought. Effective control of the disease still requires social isolation measures such as wearing face masks indoors, distancing from others, hand hygiene, and limiting indoor contact with other people.

The Lesson Behind The Long Recovery From COVID-19 For A Young Physician Assistant

This is an update to a story published on March 10, 2020 by MedPageToday. You can read the original piece here.

In March, James Cai, a physician assistant and New Jersey's first COVID-19 patient, made headlines for warning the country that even young, healthy 32-year-olds like himself were vulnerable to the virus. He came down with the disease in early March and was admitted to the hospital on March 3. Because the disease was so new, he was worried that he wasn't getting the right treatment at the hospital, so he took his case to Twitter.

In the beginning, he was treated like he had a serious case of the flu. He received high-flow oxygen, chloroquine, and lopinavir/ritonavir (Kaletra), and was one of the first patients to receive remdesivir under compassionate use approval. He was able to connect with Chinese physicians who had experience with the disease, and a Chinese-American doctor translated the Chinese protocols into English for Cai's New Jersey doctors.

He was discharged on March 21, but still needed supplemental oxygen -- especially at night. A month after his discharge he went back to work as a physician assistant, but only virtually and half-time. But even by mid-summer, Cai was still seeing impairments in his oxygen saturation and activity levels. His O2 saturation was 97% during the day, which is good, but it dropped to 90% when he lay down to sleep, necessitating the oxygen supplement. He tired very easily and was unable to run and exercise like he did before. Through that time, he was taking dual anticoagulant therapy of Xarelto and aspirin.

In late summer, things started to look up. On August 21, he confirmed that he could sleep through the night without oxygen, but the results of his latest chest CT showed permanent fibrotic lung damage in his left lower lung. As of December, he was still testing positive for coronavirus antibodies.

We still do not know why some people, especially young, healthy people can be so hard hit by the virus while others are not. Why did Cai become so ill and suffer permanent lung damage, while a couple of my nearly 70 year old friends caught it and had milder, temporary symptoms? It will be a while before we understand this.

This story also illustrates the folly of just looking at mortality numbers when assessing COVID risk. The death rate for COVID-19  is low, about 1% or less of people who get infected die from the disease, so some folks cite that low death risk and take a cavalier approach and avoid social restrictions designed to slow the virus spread. By focusing on that simple statistic, they ignore the fact that COVID is now the leading cause of death in the US by far and has killed 10 times the number of people who are killed by seasonal flu. The devastating 1918 Spanish flu also had a very low death rate, but in just 24 weeks, it killed more people around the world than were killed in the 10 years of WWI and WWII combined!

And those people who cherry pick their statistics to justify their careless behavior ignore the greater number of people like Cai who survive the disease, but suffer long term and even permanent health problems. Is it really worth the risk of permanent lung damage to exercise your freedom to not wear a mask?

Some People Worry About The Vaccines Because They Were Developed So Quickly

A poll published by Gallup in early August found that 35% of surveyed Americans would decline a Covid-19 shot offered to them at no cost. I have seen other studies that say 50% of Americans will not get the vaccine. And on social media sites I have seen discussion and comments about why folks are so reticent to get the vaccine. Let me address the concerns.

1) Problem: People will not take a vaccine pushed out by Trump. Nancy Pelosi and Chuck Schumer are the more prominent members of this cadre. Answer: Well, Trump has had nothing to do with the vaccine development. The two leading vaccines now available are based on RNA vaccine technology that is a decade old. In other words, the technology was being developed way before Trump had presidential aspirations. Also, the Pfizer vaccine was developed in the UK using technology from a German biotech company and was developed without any US dollars. Trump did set up Operation Warp Speed to produce and disseminate a vaccine quickly, but the Pfizer vaccine’s share of that initiative is only a four star Army general, Gus Parna, who is overseeing the enormous logistics of getting a few hundred million people vaccinated. Trump’s fingerprint on all that is negligible.

2) Problem: The vaccine was rolled out too fast for comfort. Answer: As I wrote above, the RNA vaccines are based on technology platforms that are at least a decade old. All the companies needed to do was take a short CoV-2 genome sequence and add it to that well developed platform then test it. With a raging pandemic, the vax testing went quickly—when several thousands of people get infected every day, the results of a test vaccine come quickly. Similar vaccines were being developed for the earlier coronaviruses, SARS and MERS, but both of those pandemics fizzled out before enough data about the vaccines could be collected. Those platforms were repurposed to accommodate the SARS-CoV-2  virus. During the several months of testing, tens of thousands of people were given the vaccines and adequate efficacy and safety data were rapidly gathered. Since the vaccines were approved, a few million people around the world have been vaccinated and that larger sample simply confirms the data from the clinical trials. The vaccines are safe and effective.

Keep in mind, every year we roll out new flu vaccines in just a few months and they are safe. This vaccine has been adequately tested.

3) Problem: The RNA vaccines can alter your cellular DNA. Answer: Total bull scat. There is no way that the short stretch of the virus’ RNA genome that is used in the two leading vaccines can interfere with cell DNA. That is biologically impossible. Having said that, let me elaborate. There is a family of RNA viruses, called lentivirus, that can mess with your DNA. The lentivirus family includes HIV, human T cell leukemia virus, and several animal viruses that cause cancer. However, the unique thing about lentiviruses is that their genome carries a gene that encodes the enzyme, reverse transcriptase, which copies RNA into DNA allowing it to insert randomly into cellular genomes. Two of my science mentors and friends, David Baltimore and Howard Temin, shared the Nobel Prize for discovering reverse transcriptase. Most RNA viruses, like flu and coronaviruses do not express reverse transcriptase, so they do not affect cellular genomes. It is biologically impossible for the Pfizer and Moderna vaccines to alter your cells’ DNA.

4) Problem: The vaccines will infect you with the virus. Answer: Balderdash! The RNA vaccines are not produced using any living microorganism. A short stretch of DNA is tethered to insoluble beads and used to produce copies of a short RNA sequence that will produce the viral spike protein. The insoluble DNA templates are easily separated from the RNA that remains in solution, and the RNA is then encapsulated in lipid nanoparticles. That is what is injected. After injection, the lipid nanoparticles fuse with lipid cell membranes to empty the encapsulated RNA into the cells. Then normal cell machinery takes over producing the spike protein, which generates an immune response and immune memory that protects you from subsequent infection. The vaccine RNA is gone in about two days.

5) Problem: We need several years of data to be assured of the safety of the vaccine. And we do not know how the vaccine will interact with other drugs many people take. Answer: Wrong. Vaccines are not drugs and do not interact with drugs you might take. And since vaccines are just one or two shots, and not taken chronically like drugs, long term problems are not a concern. I challenge any naysayer to name one long term health problem caused by vaccines.

6) Problem: Vaccines cause allergic reactions. Answer: Some do, but that risk is nothing compared to the risk of serious consequences of getting the disease that the vaccine prevents. The FDA and other regulatory agencies weigh these risk factors and the vaccines that are approved come out way on top. Such reactions can occur with any vaccine, but are extremely rare—about one per 1 million doses.

There have been very few allergic problems with the CoV-2 vaccines and that problem has been linked to polyethylene glycol (PEG), a component of the lipid nanoparticles that carry the RNA sequence. PEGs are also used in everyday products such as toothpaste and shampoo as thickeners, solvents, softeners, and moisture carriers, and they have been used as a laxative for decades. So, most of us have been exposed to PEGs, but very few of has have a problem with them.

Endnote: As published in these pages in late October, there are several examples of vaccine production errors that led to tragic consequences. In 1955, the Salk polio vaccine was rushed into production just hours after it was approved. This was an inactivated virus, which means that live virus was grown, then killed, then injected. Some lots from one of the manufacturers, Cutter Laboratories, were not fully inactivated and some patients received injections of live virus leading to tragic results. Similar production errors have led to people being infected with live measles virus, and respiratory syncytial virus. In 1976, an H1N1 flu that was similar to the 1918 Spanish flu reached pandemic stage and we rushed out a vaccine that was associated with a spike in the very rare Guillaume Barre disease (GBD), which is a type of paralysis. It is thought that the rushed vaccine somehow caused the small, but significant spike in the disease in fewer than 500 patients across the country. It is not known how the vaccine was related to GBD.

Note: your humble blogger was a college student and working in a hospital physical therapy department at the time, and worked with two GBD patients.

Those problems using inactivated virus vaccines are very rare and have not arisen in over 40 years. Since the CoV-2 RNA vaccines do not use any live microorganisms, this will not be a problem with the vaccines.

I will willingly get mine as soon as it is offered. How about you?