How much does the Delta variant change the pandemic?


On July 27, the US Centers for Disease Control and Prevention (CDC) revised its public guidance to encourage indoor mask-wearing among all individuals in areas where they have identified higher transmission of SARS-CoV-2, the virus that causes COVID-19. The guidance also recommends mask wearing for all students and staff in K-12 schools. The CDC made this recommendation for all Americans, regardless of COVID-19 vaccination status.

In Maine, the Mills administration dutifully incorporated this guidance into their own, recommending Mainers begin wearing masks again in high-transmission counties. Ironically, when this guidance was announced, two Maine counties fit that description: York and Piscataquis. The following morning, those counties were back in the green and only Waldo county was considered to have high transmission. On Sunday, Kennebec and Somerset were added to that list. It’s anyone’s guess to where it goes next.

Why would public health officials reverse weeks of working mask-wearing guidance, especially as emergency-use vaccines for COVID-19 have been broadly available for those who want one? The rationale: the rise of the Delta variant.

On the day following the new CDC guidance, Dr. Anthony Fauci, a leading federal public health official, described the emergence of the Delta variant as having “changed the entire landscape.” He mentioned that this significant policy change was in response to “clear” and “compelling” data that showed vaccinated and unvaccinated people infected with the Delta variant carry a similar level of virus in their respiratory pathways. 

At the time of Fauci’s comments, public awareness of this new batch of data was not fully known, but the following day, the Washington Post reported on an internal slideshow document from CDC accounting their current understanding of the Delta variant. 

Citing data from a recent outbreak in Provincetown, Massachusetts, CDC notes there was “no difference in mean Ct values in vaccinated and unvaccinated cases.” Ct refers to the “cycle threshold” count used by PCR testing to understand the amount of virus contained in a particular sample. While data on this outbreak does not outline how many of those cases were from the Delta variant, the same slide cites other “passive surveillance” data from around the country showing the Ct value of the average Delta breakthrough case is 3 cycles less than for the Alpha variant and the initial strain out of Wuhan known as the ancestral or “wild-type” strain.

Additional evidence cited which show patients infected with the Delta variant carry more virus than those infected with previous lineages comes from Guangdong, China. National Public Radio cited this study to support the claim that Delta-infected people have “1,000 times more copies of the virus” in their respiratory tracts as compared to previous cases. In that study, researchers observed that patients infected with the Delta variant indeed carry a higher viral load, peaking about four days from first positive versus six days for earlier strains. They found that the overall duration of infection is shorter among Delta-infected patients, but did not consider patients’ vaccination status.

The specific methodology of this study, indeed of the latest change in CDC guidance, relies on the acknowledgement that lower cycle threshold (Ct) of PCR-positive tests mean higher viral loads. This is exactly how the Guangdong study works. The researchers tested subjects daily and found that it took fewer days from exposure to see a positive result for patients infected with the Delta variant. Noting that “samples with Ct value above 30 (<6×105 copies/mL viruses) never yield an infectious isolate in-vitro,” the researchers set the maximum Ct value at 30, and found Delta patients to trigger a positive PCR test result earlier in their infection, compared to Alpha and wild-type SARS-CoV-2. Given this information, they concluded that “the Delta variant could be more infectious during the early stage of the infection.”

Curiously, the connection between Ct values and viral load is exactly why Maine Policy Institute submitted a Freedom of Access Act (FOAA) request for the PCR cycle threshold data from Maine CDC, so that we may better understand the scope of the outbreak over time in terms of active, infectious cases. As many know, the predominant PCR test run by Maine CDC amplifies to 45 cycles, more than 32,000 times more sensitive than the threshold for positive tests determined by the Guangdong study authors. Clearly, Ct data is useful in determining current, active infections; Maine CDC must provide this crucial public information as quickly as possible.

Maine officials like Dr. Nirav Shah have done their part to warn about the increasing prevalence of Delta in the state, but with similarly lax scientific evidence. While diagnostic tests like PCR are used to identify currently infected people, in order to determine the specific viral strain carried by the infected patient, those samples must be sent to a more advanced laboratory for genetic sequencing.

On July 23, Maine CDC published its weekly genomic testing report, which found that the Delta variant made up 47.6% of samples run in the month of July. To the detriment of better public understanding, media and state reports of this data ignored its tiny sample size. The report only contains the first seven days of July, within which only 21 samples were sequenced, all at the same lab. Of those, only 16 contained Variants of Concern (VOC) such as Delta, or other Variants of Interest (VOI), a lesser category of variants that public health officials are watching. Thus, only 10 out of 21 samples sequenced were the Delta variant, leading to a staggering percentage of samples collected in July.

In the following report released on July 30, the total number of samples sequenced in July (through the 14th) was only 61, of which 54 were VOC or VOI. In total, 37 were found to be the Delta variant, or 60.7% of all July samples. Normally, between 250 and 800 samples are sequenced in a given month.

Moreover, a quick check of NextStrain, a database cited in the genomic sequencing report, shows that Delta variant strains (B.1.617.2 & AY.3) account for only about 30% of samples sequenced in the most recent survey. It remains unclear why this figure is so far off of Maine CDC’s reporting. In that NextStrain breakdown, the Iota and Alpha variants still make up 27% and 18% of samples sequenced in Maine, respectively.

The Maine CDC genomic sequencing report also mentions that “Variants of Concern have increased severity of disease based on hospitalization and case fatality rates,” yet this claim is not substantiated in the report, and is not repeated in federal CDC information about known variants. As far as data show, while the Delta variant is more contagious, its virulence, or ability to cause more severe disease than initial strains, is less clear. The assertions made to support the claim appear in the “leaked” CDC slideshow document which references a preprint paper from Singapore citing studies showing higher mortality and hospitalization risks for previous VOC from early 2021.

We’re told that if you’re not vaccinated, you could be spreading new variants to others and not even know it. Based on the CDC’s latest reports, the same can be said of vaccinated people; it is why the CDC reinstated its face mask guidance for vaccinated individuals. Given this reality, is it fair to call this a “pandemic of the unvaccinated,” as Biden administration officials and media have in recent weeks? Data show that those who received a shot are at substantially lower risk of SARS-CoV-2 infection, and at an even lower risk of serious COVID-19 illness and death, regardless of the viral strain identified.

Instead of seeing these data as good news, using it to drive optimism that has sadly waned over the last few months, media and public health officials used them to reflexively take a step backward and drive yet another wave of fear. Public health messaging must be more consistent with current scientific understanding of these new products. Vaccines which completely stop the spread of SARS-CoV-2 were never part of the deal. While the prospect of variants which escape vaccine protection might be frightening, early data from Israel still show 93% vaccine effectiveness at preventing severe illness and death. This must be taken into account with one’s own age, health status and risk profile in order to assess the real change in risk due to prevalence of the Delta variant.

We must remember that CDC is not a scientific body, it is a public health agency, first and foremost. Its job is to provide guidance based on reviewing scientific data, but it is also known to be extremely risk-averse. For instance, CDC currently does not recommend anyone eat a hamburger cooked less than well-done. They won’t even concede that eating a medium-rare steak is a justifiable risk. 

At some point, if we want to continue living in a society which values individual freedom and choice, we must learn to make personal decisions by weighing the risks and benefits. The best that public health agencies can offer is data so that citizens have the information needed to make a rational calculation of risk.

In a report published by Maine Policy last summer, we argued for a public health policy that places trust in people. If a certain policy recommendation is effective, government health experts should be able to make their case like everyone else in the scientific community, through a robust debate of the evidence. Broad mandates will (and have shown to) simply turn more people against the wishes of authorities.

Our focus should be—as Maine Policy has argued from the outset—on preventing severe illness and death, especially for those who are especially vulnerable to this virus and thus carry a higher risk. Data have and continue to show the greatest factors leading to severe disease are old age and underlying health conditions such as hypertension, diabetes, and obesity. The risks to healthy people younger than 40 is very different than for those over 60 who may have other complications.

Without controlling for overall health factors or vaccination status (since Maine CDC does not publicly provide this information) Maine’s COVID-19 data as of July 29 show that those 60 or older are 135 times more likely to die from COVID-19 than that of those who are under 60. By using 40 to 49 year olds as the reference group—since Maine’s median age is around 45 years old—data show the case-fatality risk for Mainers in their 60s is more than 9 times greater than this reference group. In fact, the risk for those in their 70s is more than 38 times greater, and more than 106 times greater for those 80 and older, than people in their 40s. While the overall case-fatality rate in Maine is around 1.27%, it is nearly 11% for Mainers over 70.

An analysis of Maine CDC data charts the percentage of total cases and the case-fatality rate of each age group. While Mainers under 60 make up more than 90% of those who caught the disease, compared to those 60 and older, they are at a much lower risk of dying from it. Even though Mainers 70 and older make up just under 11% of the population and about 9.5% of total cases, they account for more than 80% of deaths from COVID-19 statewide.

The emergence of the Delta variant has not changed these data whatsoever. What should be troubling is that Mainers 80 and older have about equal risk of catching COVID relative to their share of the population. This means that Governor Mills’ broad mandates and restrictions did not succeed in protecting them. Instead, the governor and her administration implemented indiscriminate lockdown orders, warning that all were at risk, that the virus is “attacking babies, teenagers, Millennials, and seniors alike.” This is an obvious falsehood, yet it has been repeated by Mills and her department heads over many months.

Even as the Delta variant becomes more prevalent, data overwhelmingly suggest that the vaccines still provide high protection against severe illness from the virus, no matter the variant thus far.

Broad availability of the vaccines and the significant uptake among the elderly and vulnerable has shown to be an effective way to protect against the most severe outcomes. Even though there are many media reports of breakthrough cases, as of July 23, less than 600 had been reported across Maine. Considering the more than 816,000 who have been fully vaccinated for COVID-19, this puts the rate of breakthrough cases well below 0.1%.

Ultimately, public health officials should take a long look in the mirror to determine who is to blame for their messaging missteps. Likely more and more citizens will be taking back responsibility for their health and well-being as government guidance becomes more tedious and reactionary. After the last 18 months, this can only be a step in the right direction.