Author: Kevin Homer, MD

Kevin Homer has practiced anatomic and clinical pathology at a community hospital in Texas since 1994.

Breakthrough

As more Americans are receiving COVID vaccinations, there are reports of COVID occurring in individuals who have been fully vaccinated. Can this really happen?

Yes, you may still become sick from a SARS-CoV-2 infection even if more than two weeks have passed since your final vaccine injection. “Breakthrough” is the term for this type of infection, and many state health departments have reported breakthrough infections. According to current CDC reports, over 50 million Americans have been fully vaccinated, accounting for 15.1% of the total U.S. population, yet 7-day rolling averages for new COVID-19 cases and hospital admissions for COVID are up 6.7% and 2.6% respectively.

We know that breakthrough infections occur with other vaccines. In years past, many patients were admitted to the hospital for flu even though they received a flu vaccine earlier in the season. We may be seeing a similar phenomenon with the COVID vaccine. Furthermore, we still do not know whether most breakthrough infections are caused by the original SARS-CoV-2 virus, or one of the emerging variants. It is possible that vaccine is less effective against one or more variants.

We have a lot to learn about breakthrough infections, but this much is clear: the pandemic is not over, and the vaccine is not a panacea. While vaccine may provide an added layer of protection against dying from COVID, it does not prevent contraction of disease. For now we must continue to do what we know keeps us safe: mask in public and keep apart, even if you have received a vaccine.

2021 COVID-19 Testing Vaccine

New Variant Classification

Last week the CDC revised its classifying terminology for SARS-CoV-2 variants. To have clarity in our thoughts and debates, we must be precise in our language. Poor decisions often descend from muddled and incomplete understandings. I know that readers of these posts strive to be current in models of understanding and language, so they will not be caught flatfooted in conversation and reasoning. That’s why I summarize the essential points here.

There are now three types of SARS-CoV-2 variants: Variants of Interest, Variants of Concern and Variants of High Concern. I will discuss the definitions, lists of variants and their characteristics in reverse order.

Variants of High Concern. Variants of high concern are those SARS-CoV-2 variants that cannot be detected by tests, are not treatable by current therapies or for which natural or vaccine induced immunity offers no protection. Any one of those three criteria is enough to place the variant on the High Concern list. Scary stuff. The good news is that there are no variants on this list. At least not yet.

Variants of Concern. Variants of Concern have reduced detection by tests, reduced response to therapy, reduced immune protection, greater transmissibility, or more severe disease. Again, any one of these criteria is enough to land a variant on this list. The bad news is that the number of variants on this list has exploded since the last time I wrote about it. In addition to the B.1.1.7 variant first detected in the UK last fall, four other variants have been added to the list:

These Variants of Concern have all been identified in the United States. The B.1.427/429 Variants of Concern are most prevalent in the western United States, now responsible for more than half of infections in California. The B.1.1.7 Variant of Concern is most prevalent in New Jersey and Florida, approaching 10% of the new viral infections there. Click here to view the current numbers and distribution in the United States. To see worldwide cases of COVID-19 caused by variants, click here. These maps are updated at least weekly.

Variants of Interest. Variants of Interest are being watched closely because they have the potential to become Variants of Concern based in the mutations within the variant, even though they don’t fulfill criteria to be a Variant of Concern based on observation. This may be because the variant is too new or because too few of the instances of the variant exists to make meaningful observations. The current Variants of Interest and their potential, but not observed, effects are listed below:

Like the Variants of Concern, all the Variants of Interest are currently present in the United States.

There are a number of other variants which have been identified and named, but which have not yet been classified as a Variant of Interest, Variant of Concern, or Variant of High Concern. Expect the members of these variant classification lists to change and shift as more becomes known about variants.

2021 COVID-19 Vaccine

New Guidance for the Fully Vaccinated

Post author By Kevin Homer, MD
Post date March 9, 2021
No Comments on New Guidance for the Fully Vaccinated

Yesterday, the CDC published new guidance for fully vaccinated individuals. In this article, we will summarize the key points of this new guidance.

First, we must understand what it means to be fully vaccinated. The full effect of vaccine-induced immunity takes about 2 weeks, so an individual is considered fully vaccinated 14 days after the final vaccine injection. The final vaccine injection is the second dose of the Pfizer or Moderna vaccine, or the single dose of the Janssen vaccine.

Last month, the CDC issued guidance lifting the quarantine requirements for fully vaccinated individuals following a COVID exposure, provided they remain asymptomatic. Previously, this permission expired after 90 days. Yesterday, the CDC affirmed its previous guidance, but lifted the 90-day expiration. According to current CDC guidance, there is no longer an outer time-limit for the benefit of vaccine-induced immunity. This is bound to change; we will follow closely.

To the removal of quarantine requirement, the CDC also added two additional liberties yesterday: (1) fully vaccinated individuals may visit indoors with other fully vaccinated individuals without wearing masks or social distancing, and (2) fully vaccinated individuals may visit with unvaccinated people from a single household who are at low risk for COVID-19 without wearing masks or social distancing.

Other COVID precautions remain in force for fully vaccinated individuals, including masking and social distancing in public except in the specific situations mentioned above. If symptoms develop, fully vaccinated individuals should follow the same quarantine and testing recommendations of unvaccinated individuals.

2021 COVID-19 Vaccine

New Vaccine

There were a couple of big changes in the COVID vaccine landscape last week. On Thursday, February 25, the FDA reissued its EUAs for the Pfizer and Moderna COVID-19 vaccines, revising portions of their original EUAs. On Saturday, February 27, the FDA issued a new EUA for the Janssen COVID-19 vaccine, commonly known as the Johnson and Johnson vaccine. Lots of news, too much for one blog. Let’s address the important information one bite at a time, starting with the Janssen vaccine.

Like all other COVID-19 vaccines, the Janssen vaccine has not been approved for use by the FDA. Instead, these vaccines are authorized for use in the U.S. This authorization is based on the FDA’s authority to make unapproved products available during an emergency when “there are no adequate, approved, and available alternatives.” As stated in the EUA letter issued February 27, 2021, “It is an investigational vaccine not licensed for any indication.” This means that clinical trails on vaccine safety and effectiveness have not been completed. Expect comprehensive analysis of clinical trials this summer at the earliest.

However, the Janssen vaccine differs from the other two vaccines in important ways. First, it is not an mRNA vaccine. Rather, it is a recombinant vector vaccine. This vaccine is made by inserting genetic code for a protein of the target into a harmless virus (the “vector”). When injected, this harmless virus presents the target proteins to the immune system, causing formation of antibodies, in this case antibodies to the spike proteins on the SARS-CoV-2 capsule. This technology is not entirely new. Manufactured (or “recombinant”) genetic code has been used to synthesize proteins for vaccines for nearly a decade. Recombinant flu vaccines received FDA approval in 2013. You may have received a recombinant flu vaccine in recent years. The difference between recombinant protein vaccine and viral vector vaccines has to do with where the antigenic proteins are made–either in your body (viral vector) or outside your body (recombinant protein). The harmless virus (the “viral vector”) cannot replicate within your body, so the effect is the same.

There are more differences. According to data submitted to the FDA, the Janssen vaccine is less effective preventing moderate to severe COVID-19 than the Moderna and Pfizer vaccines. The Janssen vaccine requires only one doses compared to the two doses required by Moderna and Pfizer. Storage of the Janssen vaccine is easier to accomplish than the other two. Vaccines features are compared as follows:

	Pfizer	Moderna	Janssen
Vaccine Technology	mRNA	mRNA	Recombinant Vector
FDA Approval	No	No	No
Effective rate	95%	95%	66%
Minimum Age	16 years	18 years	18 years
Doses	2	2	1
Storage	-70°C	-70°C	Refrigerated
Time between doses	3 weeks	1 month	Not applicable

Current comparison among authorized COVID-19 vaccines.

There is another difference. In its reissued EUA, the FDA has required Pfizer to disclose post-authorization adverse events in its fact sheet to health care providers. We will discuss that next time.

2021 COVID-19

Vaccine and Quarantine

On February 10, the CDC updated quarantine guidance for vaccinated individuals exposed to COVID-19, giving some people a get out of jail free card.

Text

Description automatically generated

According to the new guidance, individuals who received their second FDA authorized mRNA vaccine injection between 14 and 90 days ago need not quarantine after exposure to COVID-19 provided they are symptom free.

An exposure is still defined as an encounter of more than 15 minutes and less than 6 feet with someone infected by SARS-CoV-2 when one or both individuals are not wearing a mask. Provided that there is no fever or other indications of upper respiratory infection in the exposed individual, quarantine is not necessary for those who received both doses of either the Pfizer or Moderna vaccine more than two weeks before the exposure. However, vaccinated individuals should monitor for symptoms (i.e., take daily temperatures) for 14 days after exposure, and should quarantine immediately if symptoms (i.e., fever) develop. This reduced quarantine requirement does not apply to individuals who complete a vaccination series which has not receive an EUA from the FDA, such as vaccines approved in countries outside the United States.

If it has been more than two weeks since you completed a vaccine series, then you benefit from reduced quarantine requirements after exposure. But you don’t get to party like it’s 2019! You may still be able to spread the virus to others, so you must still mask and social distance in public. Furthermore, no one knows how long vaccine-induced immunity will last.

The CDC maintains that natural immunity—immunity from infection—lasts for at least 90 days. It may last longer, but the CDC is still unwilling to say so. Since the CDC’s new quarantine exemption also expires after 90 days, it seems reasonable to infer that 90 days may be the outer limits of immunity, whether from previous infection or vaccination. We may hope that it’s longer, but so far, the CDC has not said so.

So what does all this mean? If it has been more than two weeks since you completed Pfizer or Moderna vaccination series, you have a get out of quarantine jail free card—you don’t have to quarantine after a potential exposure if you are symptom free. However, a vaccination does not make you special in any other way. You must monitor for symptoms for 14 days after exposure. You must quarantine immediately if you have symptoms. You must continue to mask and keep apart in public. In other words, even if you have completed a vaccination series, you don’t have this card:

At least not yet.

2021 Philosophy Science

Shouldna Taken That Shot

It was a heady time to be a scientist. Albert Einstein was still alive, and his special and general theories of relativity changed our understanding of the universe. Quantum physics predicted space travel and limitless energy. We had a brand-new theory of gravity, of space-time, of waves and particles, and of the atom. Vaccines had nearly wiped smallpox off the earth. We had penicillin, saving many lives and limbs. Science, it seemed, could conquer all. So, when your doctor said you needed a shot to prevent a miscarriage, you took an injection without question.

DES (diethylstilbestrol) is a synthetic estrogen created by Sir Charles Dodd in 1938. Cheap and easy to produce, pharmaceutical companies marketed DES for prevention of menopause symptoms in women. In 1947, the FDA approved DES for use to prevent miscarriages, and such use was advocated by an article published in the American Journal of Obstetrics and Gynecology. American obstetricians enthusiastically embraced the new drug as a cure for one of the most unhappy outcomes in their profession. Although some physicians questioned its effectiveness, DES continued to be commonly prescribed in the United States to women with threatened miscarriages until 1971.

That’s when a bombshell was published in the New England Journal of Medicine. The daughters of women who received DES during pregnancy had an unignorably high rate of clear cell adenocarcinoma of the vagina, an extremely rare tumor in women whose mothers had not received DES. That’s right—a drug manufactured and sold in the United States, approved by the FDA, prescribed as intended by licensed physicians—caused a rare cancer in young women. And not just clear cell adenocarcinoma. The daughters of women who received DES during pregnancy have higher rates of breast cancer, abnormal cells on their pap smears, anatomic defects in their reproductive organs, trouble getting pregnant, and problems during pregnancy. And not just the daughters—the sons too have increased rates of benign tumors and structural defects in their reproductive organs. Even the mothers are affected. Women who received DES during pregnancy have an increased risk of breast cancer. Does it stop there? Research is currently ongoing on the third generation, the grandchildren of women who received DES during pregnancy.

Clear cell adenocarcinoma of the vagina.

Although it’s not a story my profession likes to tell, the lessons of the DES tragedy must never be lost. Before we accept the opinions of experts, we must be mindful of the limitations of science. Before we are swept along with the crowd, we must recognize the possibility of unintended consequences. Before we act on conventional wisdom, we must think; think with our own brains, and make up our own minds. We must ask questions, critically examine data, and make judgements by what we know from experience. We must all be scientists now.

2021 Blood Donation

We Have No Bananas

When Texas freezes over, most everything closes. That includes blood collection centers, which were closed for 5 days this week. I’m writing to encourage you to donate blood. If you’re a bottom-line person, you can skip this blog, find a donation site, and sign-up to give blood by clicking here.

For those of you still with me, this is what I saw at the grocery store last night:

There were no bananas. What does that have to do with blood donation? Read on; I’ll tell you.

Blood has four parts. First, there are the red cells which carry oxygen to the tissues in your body. Oxygen is the fuel that makes cells go. Without oxygen, cells get cold and die. When people bleed, they lose these fuel-carriers, and their body goes on the biologic version of rolling blackouts, shunting blood towards essential internal organs at the expense of less vital parts like fingers and toes. The second part of blood are white cells. These are the infection fighting cells of your immune system. Like first responders, white cells are carried by blood to the front lines of battle, where they protect you from invasion. Third, blood contains platelets which are little bits of larger cells that act like the Fix-A-Flat you put in bicycle tires. Platelets circulate in the blood looking for holes to plug, helping slow down or stop bleeding. The fourth part of blood is plasma, the liquid part. Plasma contains proteins, hormones, antibodies, clotting factors, and all the other stuff that needs to be carried from one part of your body to another.

Most people have all four parts of blood in excess, but the blood center will test before collection to make sure you will not miss the unit you donate. The unit you give is divided into three parts, so every donation helps three different people. The collected red cells are separated into one bag, the platelets into another bag, and the plasma into a third bag. The white cells collected are not used.

Red cells are like milk. They must be refrigerated, and they expire after about a month (up to 42 days). Plasma is like frozen vegetables. Once frozen, plasma can be stored for a year. But platelets are like bananas. They are stored at room temperature, and they are only good for five days. So when Texas freezes over, we run out of bananas, and we run out of platelets.

Blood bank inventories are slim during the first part of the year. After the holidays, people don’t feel like donating blood. That’s understandable, but our hospital blood banks suffer critical shortages as a result. This year is no exception; blood banks were dealing with critical shortages before the freezing weather. But two massive winter storms this week have reduced blood inventories to nearly nothing. That’s why your urgent action is needed.

There is no substitute for donated blood. There are no synthetic red cells or platelets, and there is no substitute for human plasma when it is needed. To have blood products available when you or your family need it, you must make blood available to your neighbors today. Please, your community needs your blood. Find a donation site, and sign-up to give blood by clicking here.

2021 COVID-19 Science Vaccine

mRNA Vaccines

To understand how mRNA vaccines work, we must first have a basic understanding of cells and genetics. Zzzzzzz. Wait! Before you go to sleep, we’re going to make this really short and really simple. Cells are bags of jelly—jellybeans, so to speak—and in those jellybeans is a kernel called a nucleus. DNA lives in the nucleus, and like the cell’s hard drive, DNA stores and preserves the cell’s genetic code. Genetic code is a series of nitrogen bases strung together to form nucleic acid. There are only four possible bases, so just like computer code is a series of 1’s and 0’s, genetic code is a series of A’s, T’s, G’s, and C’s, each letter standing for a different nitrogen base. DNA is arranged in two complimentary stands—the famous double helix of Watson and Crick—to create code redundancy like mirrored hard drives that protect your data in case of a crash.

When the genetic code needs to be accessed, a specific portion of the DNA untwists, exposing a segment of code which is copied onto a new strand of messenger RNA (mRNA). Unlike DNA, RNA is only a single strand of nucleic acid and much less stable. The mRNA floats into the cell jelly, the cytoplasm, where ribosomes attach and move along the strand, coupling together amino acids as they go. Every sequence of three bases on the mRNA, known as a codon, codes for a specific amino acid. For example, GCA codes for alanine, CAA codes for glutamine, and so on. There are 20 different amino acids, each with its own codon or codons (some have more than one). Put together according to the sequence of bases on the mRNA, the amino acid chains become a protein. Out of the trillions of possible amino acid combinations, the proteins formed by your genetic code define the shape of your nose, the length of your bones, the complexion of your skin and everything else that makes you you. Once the right number of proteins have been made, the mRNA disintegrates into the cytoplasm of the cell. The process starts again in the nucleus, and a new protein is created as called for by the cell.

What if mRNA could be injected directly into cytoplasm without first being created in the nucleus? Then the cell’s machinery could create a protein that wasn’t part of the cell’s genetic code. That’s exactly the hypothesis behind mRNA vaccines. After the vaccine delivers mRNA into the cytoplasm of muscle cells in the arm, those cells begin forming the protein coded by the mRNA in the vaccine—in the case of COVID vaccines, one of the spike proteins known to exist on the SARS-CoV-2 viral capsule—and those proteins make their way to the surface of the cell where the immune system forms antibodies which are memorized by the body for future use. How cool is that!

Various companies have been working on mRNA vaccines for over a decade, but none made it to production until the pandemic demanded rapid vaccine development. Although never been used on a large scale before, mRNA vaccine technology is appealing for several reasons:

Molecular sequencing systems makes creation of mRNA almost as easy as writing a computer script.
Once sequenced, mRNA can be mass produced easily and cheaply.
There is no danger from viable pathogens in the vaccine production.
There are no infectious agents or toxins injected into the vaccine recipient.
Once the delivery system is perfected, vaccinations for many different pathogens can be created by simply altering the mRNA sequence, making it possible for vaccines to respond quickly to emerging viral variants.

Before we anoint mRNA vaccines as our pandemic savior, we should first listen to voices urging caution about this new technology. For example, in a recent New England Journal of Medicine publication, Dr. Mariana Castells and Dr. Elizabeth Phillips note that the incidence of anaphylaxis, a serious, sometimes fatal allergic reaction, associated with the Pfizer SARS-CoV-2 mRNA vaccine is “10 times as high as the incidence reported with all previous vaccines, at approximately 1 in 100,000, as compared 1 in 1,000,000.” Why? And moreover, what are our expectations of vaccination? Do vaccines prevent COVID or simply reduce COVID complications? How long will immunity last? Who should NOT get the vaccine? Answers to these and other questions are not readily apparent, not because of a failure of diligence, but because there has simply not been enough time to collect, compile and analyze the data that will eventually yield answers.

The Center for Evidence Based Practice at the University of Pennsylvania recently published a review of the adverse effects of mRNA vaccines. Among their findings are the following:

There are no specific guidelines for use of messenger RNA (mRNA) vaccines or contraindications to mRNA vaccines.
No large trials of any mRNA vaccine have been completed yet.
The only evidence on safety of mRNA vaccines comes from small phase I and phase II trials of SARS-CoV-2 vaccines, with follow-up typically less than two months.
Systemic adverse events such as fatigue, muscle aches, headache, and chills are common
The rate and severity of adverse events appears to be higher for the second dose of vaccine than for the first.
Higher vaccine doses appear to increase the rate and severity of adverse events.
Larger trials of SARS-CoV-2 vaccines are in progress, with results expected in mid-2021.
There is not sufficient evidence to support any conclusions on the comparative safety of different mRNA vaccines.
Direct evidence on the comparative safety of mRNA vaccines and other vaccines is lacking.

Clearly, mRNA vaccines offer an attractive, promising alternative to other vaccine technology, especially when a new vaccine is needed quickly. However, it is a new technology associated with risks of the unknown. Many unanswered questions remain, demanding a sober examination of the evidence for and against vaccine safety. Since the risk-to-benefit ratio from taking a COVID vaccine varies individually, I urge individual decisions, not collective ones. The Infectious Diseases Society of America recently published a comprehensive FAQ on vaccine safety which you may find to be a valuable great resource for making an individual decision.

Although paved with good intentions, the early path of new technologies is frequently littered with unintended consequences. Next time, I will tell a story of good intentions that ended tragically for many.

2021 COVID-19

The Latest about Variants

The CDC recently released new information about the variants of SARS-CoV-2, updating information previously released.

Although SARS-CoV-2 mutates frequently, about once every two weeks, most mutations do not result in a clinically different virus. However, three variants have emerged which are being watched closely.

B.1.1.7 is the first variant of concern which emerged in the UK last December and is now present in at least 70 countries, including the United States. This variant is associated with a fifty percent higher transmission rate, which means it may soon be the dominant form of the virus. There is emerging data that suggests this form of the virus is also associated with a higher death rate.

B.1.351 emerged in South Africa and has spread to other countries, including the United States. There is data that suggests that the Moderna mRNA-1273 vaccine currently used in the US may be less effective against this variant.

P.1 has been found in Japan and Brazil. As of late January, this variant is known to exist in the United States. There is data suggesting this variant may be less susceptible to immunity acquired either by previous infection or by vaccination.

All three variants are concerning because of mutations in the spike proteins in the virus. These proteins are significant because they are responsible for the binding of virus to cells in the back of the nose, the first step in infection. They are also significant because antibodies in the human immune system work by recognizing these spike proteins. Whether these antibodies come from natural immunity (i.e., previous infection), induced immunity (i.e., vaccination) or convalescent plasma, altered spike proteins may allow viral particles to slip past this line of protection.

Since we’ve talked a lot about vaccination recently, now may be the time to discuss how COVID vaccines work. We will pick up there next time.

2021 COVID-19

The Mask Clinic

Face coverings, N95 masks, respirators, and P99 masks—how do we make sense of this confusing alphabet soup?

Standard face coverings do not have a rating. They made from cloth or paper, and they usually resist fluids. But they leak. Air comes in around the sides–anyone who has worn a mask (and who hasn’t?) knows this. Nevertheless, mask usage is key to protecting you from exposure to SARS-CoV-2, the virus that causes COVID-19. However, there are more infectious organisms that require a rated mask for protection. One such organism is Mycobacterium tuberculosis, the organism that causes tuberculosis. Another such organisms may be the B.1.1.7 variant of SARS-CoV-2, the variant of concern, which has a transmission rate fifty percent greater than standard SARS-CoV-2.

Rated masks have a letter prefix, either N, R, or P, followed by a number, usually 95, 99 or 100. The letter refers to how resistant the mask is to oil, and the number refers to the percentage of airborne particles filtered by the mask.

Mask Type	Airborne Particles Filtered	Resistance to Oil
N95	At least 95%	No
N99	At least 99%	No
N100	At least 99.97%	No
R95	At least 95%	Somewhat
P95	At least 95%	Strong
P99	At least 99%	Strong
P100	At least 99.97%	Strong

These masks are held snuggly around the face by elastic bands or straps around the head that eliminate the gaps between the skin and the mask. Note that “KN95” masks do not meet U.S. standards, and often have bands that loop over the ears and not over the head. Don’t let the word “respirator” confuse you: respirator is just another name for a rated mask. All the masks in the table above are also known as respirators. For protection against most respiratory organisms, an “N” mask is adequate since resistance to oil is not necessary.

So what level of protection is needed? Standard face coverings are adequate protection against SARS-CoV-2 exposure if worn properly by all individuals interacting at distances less than six feet, but an N95 mask is needed to provide adequate respiratory protection against tuberculosis. At 2 microns long, tuberculosis organisms are much larger than SARS-CoV-2 particles which measure 0.1 microns or less. Still, I believe that N95 masks also provide adequate protection against COVID, even when unmasked, infected individuals are nearby because of the experience of collectors at the test collection centers run by the laboratories where I work. These collectors use an N95 mask and a face shield for respiratory protection, and none has become infected at work despite collecting thousands of positive swabs.

How does an N95 mask work? In addition to forming a tight seal on the face around mouth and nose, N95 masks are made from material with pore sizes between 0.1 and 0.3 microns in diameter.

“But wait!” you might say, “You said that a SARS-CoV-2 virus particle is 0.1 microns or less. What keeps the virus from slipping through?” The spread of SARS-CoV-2 virus is on respiratory droplets. These droplets are 5-10 microns in diameter, much larger than the pore size of the masks, keeping most viral particles out of the nose of the mask wearer.

What about the coming B.1.1.7 variant of SARS-CoV-2? I want to be very clear: the FDA does not recommend the general use of an N95 or higher rated mask for COVID-19 prevention. Although N95 masks protect against SARS-CoV-2, there continues to be supply shortages of these masks. Therefore, the FDA recommends that their use be reserved for health care providers. However, as we discussed last time, there may soon be a time that this recommendation changes. It is possible that an N95 mask will be required to protect against the B.1.1.7 variant because of its higher transmission rate.

So what other new information is there about the SARS-CoV-2 variants? We will discuss the latest information about variants next time.

Share this:

Share this:

Share this:

Share this:

Share this:

Share this:

Share this:

Share this:

Share this:

Share this: