What does the term “breakthrough infection” really mean with the COVID-19 vaccines?

Recently, the news has been flooded with reports of COVID-19 “breakthrough infections.” These are COVID-19 infections that occur in properly immunized individuals who have had both doses of one of the mRNA COVID-19 vaccines. Much has been made of an article from Israel documenting “breakthrough infections” which has undermined confidence that the vaccine could protect people from this virus.

No vaccine is perfect, and the Israeli article showed that (as expected) less than 5% of individuals who were properly immunized got clinically infected with COVID-19. Of those, 40% had serious immune problems that may have prevented the vaccine from working. This is what is expected and represents true “breakthrough infections.” The vaccine is still remarkably effective, and most of these folks did not get seriously ill or die.

As is usual, the situation is much more confusing in the news and has been mixed up with whether the vaccines work against the newer, “delta variant” of COVID-19. I attached two articles, one in the Atlantic and another in the Wall Street Journal, that highlight the fact that “breakthrough infections” in individuals who are fully vaccinated are not common, and that this does not indicate that the delta variant has outwitted the vaccine.

Most of the “breakthrough infections” that have been reported in the general news are not clinical COVID-19; instead they are documentation of virus in the nose of vaccinated people using the polymerase chain reaction (PCR). PCR amplifies the genetic material from the virus up to 30 million times, so it can detect a very small amount of virus that’s present. Most of the individuals who are positive by PCR have been identified not because they are sick and looking for treatment, but rather because they were being screened routinely for virus. This is particularly true of individuals who were getting on cruise ships or who were with the Olympic basketball players.

Reinforcing the efficacy of the mRNA COVID-19 vaccines, even in the presence of the delta variant, over 96% of the individuals that have been hospitalized with the delta variant and 99% of those who have died recently from COVID are individuals who are not fully vaccinated or have immune problems so that they can’t be effectively immunized. This suggests that even now in the U.S., when the COVID delta variant virus is present, the vaccines are still fully effective in preventing clinical illness from COVID 19. These hospitalizations and deaths are not because of vaccine “breakthrough.”

Hospitalizations from COVID-19 are NOT associated with the presence of delta variant virus in a region.

Another marker of the vaccine’s efficacy against COVID-19 delta is the percentage of individuals who get hospitalized with delta variant virus compared with its presence in the surrounding area. Analyses showed that hospitalization rates from COVID-19 are not associated with percentages of delta variant in the area. So, the delta variant is not escaping immune control and uniquely causing more severe illness and hospitalizations (although it may be possible that it’s easier to transmit in non-immunized individuals, which is why it has spread so fast).

Finally, I keep hearing statements from young adults saying that they believe it would be “better and safer to get infected with COVID than to take the vaccine.” This is, quite honestly, insane. While most young people do not die from COVID, they have the possibility of developing long term COVID or complications at a much higher rate than suffering any adverse event from the mRNA vaccines. And God help them if they are pregnant when they get infected as they could easily die or lose their baby. Reinforcing this, every physician and nurse I know who is considering getting pregnant has taken the vaccine!

I have also heard that the rare autoimmune problems with the Johnson & Johnson vaccine have deterred people from being immunized. At this point in the United States, you do not have to get the J&J vaccine! You can walk into almost any pharmacy any day of the week and get either the Moderna or Pfizer vaccines, which have not been associated with autoimmune side effects. 

Finally, for individuals who have gotten a single dose of the vaccine and missed their return visit, the data now show that you can come back up to six months later and get a booster shot of the vaccine and have it be helpful in protecting you from COVID-19.

Regardless of what you hear, the bottom line hasn’t changed. If you want to end this pandemic, if you want to protect yourself and protect those around you who may have immune problems or are too young to get the vaccine, you need to get vaccinated. At this point there’s simply no reason not to do it.

Published by jbakerjrblog

Immunologist, former Army MD, former head of allergy and clinical immunology at University of Michigan, vaccine developer and opinionated guy.

3 thoughts on “What does the term “breakthrough infection” really mean with the COVID-19 vaccines?

    1. It is possible, but because immunize folks shed less virus the probability is low. However, given the increased infectivity of the delta variant most of the time people will err on the side of quarantining anyone who is virus positive regardless of vaccine status.


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