Why did the CDC change its breakthrough case reporting?

Earlier this month, the CDC made a pretty significant change in how it tracks breakthrough cases. Instead of reporting all cases, the agency is only investigating and collecting data on those cases that result in hospitalizations or deaths.

In case you need a refresher: “breakthrough cases” are those infections that occur after a patient is fully vaccinated (including both doses, if applicable, and the two-week waiting period after a final dose). These cases are rare—like, one in ten thousand rare. As I wrote back in April, it’s important to contextualize any reporting on these cases with their incredible rareness so that we hammer home just how effective the vaccines are.

But just because breakthrough cases are rare doesn’t mean we shouldn’t pay attention to them. In fact, it’s critical to pay attention to these cases in order to monitor precisely how well our vaccines are working—and how new variants may threaten the protections those vaccines provide.

As The Atlantic’s Katherine J. Wu explains:

Breakthroughs can offer a unique wellspring of data. Ferreting them out will help researchers confirm the effectiveness of COVID-19 vaccines, detect coronavirus variants that could evade our immune defenses, and estimate when we might need our next round of shots—if we do at all.

As I’ve discussed in past variant reporting, numerous studies have demonstrated that the vaccines currently in use in the U.S.—especially the Pfizer and Moderna vaccines—work well against all variants. That includes variants of concern, such as B.1.617 (from India), B.1.351 (from South Africa), and P.1 (from Brazil). But the vaccine efficacy rates for some of these variants are lower than that stellar 95% we saw in Pfizer and Moderna’s clinical trials. And some common therapeutic drugs don’t work well for patients infected with variants, too.

As a result, scientists are concerned that, while the vaccines are working well now, they might not work well forever. Whenever the coronavirus infects a new person, it has the opportunity to evolve. And that continued evolution must be monitored. The first coronavirus variant able to evade our vaccines may emerge in a foreign country with a raging outbreak—but it may also emerge here in the U.S. Closely monitoring all breakthrough cases will help us find that dangerous variant.

(Of note: A new, potentially-concerning variant was identified just last night in Vietnam; WHO scientist Maria Van Kerkhove described it as an offshoot of the variant from India, B.1.617, with “additional mutation(s).”)

With that in mind, let’s unpack the CDC’s reporting change. When the vaccine rollout started, the agency was investigating all breakthrough cases that came to its attention—including those in patients with only mild symptoms, or with no symptoms at all. According to an agency study released this past Tuesday, the CDC identified 10,262 such breakthrough cases from 46 U.S. states and territories between January 1 and April 30, 2021.

Keep in mind: By April 30, about 108 million Americans had been fully vaccinated. Dividing 10,262 by 108 million is where I got that “one in ten thousand” comparison I cited earlier. As I said: very rare.

Starting on May 1, however, the CDC changed its strategy. Now, it is only tracking breakthrough cases that result in severe illness for patients, leading to hospitalization and/or death. The CDC says that this choice is intended to focus on “the cases of highest clinical and public health significance” rather than tracking down asymptomatic cases.

In its May 25 report, CDC scientists said that 27% of the breakthrough cases identified before May 1 were asymptomatic. 10% of the infected individuals were hospitalized, though almost a third of those patients were hospitalized for a reason unrelated to COVID-19. Only 160 patients (less than 2% of the breakthrough cases) died.

We need to take these numbers with a grain of salt, though, because the CDC has likely undercounted the true number of asymptomatic cases. Both clinical trials and studies on vaccine effectiveness in the real world have suggested that those people who get infected with COVID-19 after completing a vaccination regime are more likely to have mild symptoms, or no symptoms at all.

Plus, the CDC is recommending that vaccinated Americans don’t need to get tested before traveling, if they have come into contact with someone known to have COVID-19, or for many of the other reasons that many of us got tested this past year. (The agency is still recommending that fully vaccinated people get tested if they’re experiencing COVID-19 symptoms, though.)

As I wrote at Slate Future Tense last month, such guidelines are likely to drive down the number of COVID-19 tests conducted across the U.S. And this trend seems to be happening, so far: PCR tests dropped from their winter surge levels this spring, and are now dropping again. (Antigen and other rapid tests may be getting used more, but we don’t have any comprehensive data on them.)

With that drop in testing—combined with the overall challenge of identifying asymptomatic COVID-19 cases outside of dedicated studies—it would be pretty damn hard for the CDC to track down all breakthrough cases. The agency’s focus on more serious cases instead may thus be considered a conservation of resources, directing research efforts and care to those Americans who get seriously ill after vaccination.

But “a conservation of resources” is also a nice way of saying, the CDC made a lazy choice here. The agency has poured money into genomic surveillance over the past few months, sequencing over 20,000 cases a week (compared to a few thousand cases a week before Biden took office). In recent weeks, the Biden administration has announced renewed funding for public health and similar commitments to prioritizing scientific research. If the CDC wants to find and sequence breakthrough cases in order to identify vaccine-busting variants, there should be nothing stopping the agency.

Or, as epidemiologist Dr. Ali Mokdad told the New York Times: “The C.D.C. is a surveillance agency. How can you do surveillance and pick one number and not look at the whole?”

Out of those 10,262 cases that the CDC reported this week, only 5% had sequence data available—but the majority of those sequined cases were variants of concern, including B.1.1.7 and P.1. At The Atlantic, Wu reported that epidemiologists in some parts of the country are seeing more breakthrough cases tied to concerning variants, while others are seeing breakthrough case sequences that match the overall infections in the community.

To me, this high level of unknowns and uncertainties mean that we need more breakthrough case reporting and sequencing, not less. And we need a national public health agency that commits to true surveillance, so that we aren’t flying blind when the coronavirus inevitably evolves beyond our current defenses.

(P.S. Shout-out to Illinois, the one state that reports its own breakthrough case data.)

More vaccine reporting

  • Cash incentives for vaccination have little impact
    While politicians at all levels have praised cash incentives, research has shown that this strategy has little impact on actually convincing Americans to get vaccinated. A recent investigation I worked on (at the Documenting COVID-19 project and the Missouri Independent) provides new evidence for this trend: the state of Missouri allocated $11 million for gift cards that residents could get upon receiving their first or second vaccine dose, but the vast majority of local health departments opted not to participate in the program—and a very small number of gift cards have been distributed thus far.
  • Vaccines aren’t enough: What Biden can do about Omicron
    This past Monday, President Biden said in a speech, “We’re throwing everything we can at this virus, tracking it from every angle.” Which I, personally, found laughable. The U.S.’s anti-COVID strategy basically revolves around vaccines, and it’s not sufficient for stopping new surges.
  • Omicron variant: What we know, what we don’t, and why not to panic (yet)
    On Thanksgiving, my Twitter feed was dominated not by food photos, but by news of a novel coronavirus variant identified in South Africa earlier this week. While the variant—now called Omicron, or B.1.1.529—likely didn’t originate in South Africa, data from the country’s comprehensive surveillance system provided enough evidence to suggest that this variant could be more contagious than Delta, as well as potentially more able to evade human immune systems.
  • COVID source callout: CDC’s breakthrough case data
    The CDC has not updated its breakthrough case data since September. A full two months ago.
  • Boosters for all adults: Why eligibility expanded, and what it means for you
    On Friday morning, the FDA authorized booster shots of Pfizer’s and Moderna’s COVID-19 vaccines for all adults in the U.S., six months after their first two doses. The CDC’s vaccine advisory committee voted to support this expanded booster eligibility that afternoon, and CDC leadership signed off on it a few hours later.

26 thoughts on “Why did the CDC change its breakthrough case reporting?

  1. My understanding from listening to “this week in virology” is that its unlikely any of the vaccines will results in sterilizing immunity, so one would expect there to be asymptomatic cases if you test enough. However there should be very few cases of any kind of illness. I agree that reporting only severe cases is a mistake…it could be making the vaccines look better than they are, and in particular one wants to know what mutations the breakthru cases are (that is the ones that result in illness)..

    Again, my understanding is that its likely that most people will have a robust t-cell response to virtually every variant that has a spike protein that is reasonable similar to the one used in the vaccine. T cells bind to chopped pieces of the spike, not the whole spike. Antibodies on the other hand are more easily evaded by changes since there are only a limited number of places on spike that result in antibodies. so you get infected, but your body quickly clears the infection…hence virtually everyone should be asymptomatic. The part I still don’t understand is that one needs IgA in the lung mucus to prevent infection, and I don’t see how the vaccine results in anything other than IgG. It would be great if someone could better explain. Or I just have to hope TWIV covers it at some point.

    I may not have this all correct, so I encourage any experts to correct it. I think its critical the more people start understanding the virus “life” cycle (for lack of a better term) and the general mechanics of how our immune system combats them. Otherwise everything is just a statistical black box where it really difficult to figure out what factors matter.

Leave a Reply