Breakthrough cases: What we know right now

For the past few months, we’ve been watching the vaccines and variants race in real time. With every new case, the coronavirus has the opportunity to mutate—and many scientists agree that it will inevitably mutate into a viral variant capable of outsmarting our current vaccines.

How will we know when that happens? Through genomic surveillance, examining the structure of coronavirus lineages that arise in the U.S. and globally. While epidemiologists may consider any new outbreak a possible source of new variants, one key way to monitor the virus/variant race is by analyzing breakthrough cases—those infections that occur after someone has been fully vaccinated. 

In May, the CDC changed how it tracks breakthrough cases: the agency now only investigates and reports those breakthrough cases that result in hospitalizations or deaths. I wrote about this in May, but a new analysis from COVID Tracking Project alums and the Rockefeller Foundation provides more detail on the situation.

A couple of highlights from this new analysis:

• 15 states regularly report some degree of information about vaccine breakthroughs, some including hospitalizations and deaths.
• Six states report sequencing results identifying viral lineages of their breakthrough cases: Nebraska, Arkansas, Alaska, Montana, Oregon, and Washington.
• Washington and Oregon are unique in providing limited demographic data about their breakthrough cases.
• Several more states have reported breakthrough cases in isolated press briefings or media reports, rather than including this vital information in regular reports or on dashboards.
• When the CDC stopped reporting breakthrough infections that did not result in severe disease, the number of breakthrough cases reported dropped dramatically.
• We need more data collection and reporting about these cases, on both state and federal levels. Better coordination between healthcare facilities, laboratories, and public health agencies would help.

Vaccine breakthrough cases are kind-of a data black box right now. We don’t know exactly how many are happening, where they are, or—most importantly—which variants they’re tied to. The Rockefeller Foundation is working to increase global collaboration for genomic sequencing and data sharing via a new Pandemic Prevention Institute.

Luckily, there is a lot we do know from another side of the vaccine/variant race: vaccine studies have consistently brought good news about how well our current vaccines work against variants. The mRNA vaccines in particular are highly effective, especially after one has completed a two-dose regimen. If you’d like more details, watch Dr. Anthony Fauci in Thursday’s White House COVID-19 briefing, starting about 14 minutes in.

New research, out this week, confirmed that even the one-shot Johnson & Johnson vaccine works well against the Delta variant. The company reported that, after a patient receives this vaccine, blood antibody levels are high enough to beat off an infection from Delta. In other words, people who got the J&J shot do not need to rush to get a booster shot from an mRNA vaccine (a recent debate topic among some experts).

Again, we’ll need more genomic surveillance to carefully watch for the variant that inevitably does beat our vaccines. But for now, the vaccinated are safe from variants—and getting vaccinated remains the top protection for those who aren’t yet. 

More variant reporting

• National numbers, September 17September 17, 2023
  For the second week in a row, available data suggest that the current COVID-19 surge may be turning around, or at least heading for a plateau. But there’s still a lot of coronavirus going around—and this will likely remain true through the winter respiratory virus season.
• New data on BA.2.86 suggest the fall booster may work wellSeptember 10, 2023
  Since BA.2.86 emerged a couple of weeks ago, scientists around the world have been racing to evaluate this variant. Several teams posted data in the last week, and the news is promising: while BA.2.86 does have an advantage over past variants, the lab findings suggest that vaccines (including the upcoming boosters) and past infections provide protection against it.
• Wastewater surveillance is crucial for tracking new variants, BA.2.86 shows usSeptember 3, 2023
  This week, the health department in New York City, where I live, announced that they’d identified new variant BA.2.86 in the city’s wastewater. I covered the news for local outlet Gothamist/WNYC, and the story got me thinking about how important wastewater surveillance has become for tracking variants.
• Variant Q&A: Why scientists are concerned about BA.2.86, and which questions they’re still investigatingAugust 27, 2023
  Last week, I introduced you to BA.2.86, a new Omicron variant that’s garnered attention among COVID-19 experts due to its significant mutations. We’ve learned a lot about BA.2.86 since last Sunday, though there are many unanswered questions to be answered as more research is conducted.
• BA.2.86 is the latest variant to watch; send me your questionsAugust 20, 2023
  Last week, several variant experts that I follow on Twitter started posting about a new SARS-CoV-2 variant, first detected in Israel. They initially called it Omicron BA.X while waiting for more details to emerge about the sequence; it’s now been named BA.2.86.