Part 2: Delta Variant Dominance in the U.S. and Unvaccinated Vulnerability
The Now Dominant Delta Variant Begins Surging in Unvaccinated Communities
This piece is a follow-up to the article Delta Variant Dominance in the U.S. which had the following key points:
- Genomic sequencing data and weekly growth rates were used to estimate when the Delta variant would become the dominant strain
- Being fully vaccinated provides high levels of immune protection although lower than previous strains (e.g., Pfizer: 93% against Alpha, 88% against Delta) and much lower if partially vaccinated (e.g., Pfizer and AstraZeneca only 33% against Delta)
- U.K. data shows most COVID cases largely amongst those unvaccinated
- Early and preliminary data shows Delta, in comparison to the original wild-type that started the pandemic, has increased levels of transmissibility by nearly 4 times, increased severity around 3.3 times, and increased immune escape that reduces previous immune protection
- The United States remains largely vulnerable to Delta due to low vaccination rates in many counties and states that are affected by access, trust, and misinformation
- Recommendations include increasing genomic testing, testing the fully vaccinated to increase data on variants of concern that could evade immunity and increase data on secondary infections, increase ventilation in buildings, and recommending of quality masks (e.g., N95s)
Caveats: Prevalence numbers are only estimates due to a very small percentage of COVID tests being sequenced across the country and lag in reporting data. Additionally, studies on severity cited in this article continue to be early and in large part preliminary and studies are ongoing to provide greater details on transmissibility, immune escape, and severity. Vaccine breakthrough infections reported to CDC are likely underreported since national surveillance relies on passive and voluntary reporting.
Big Picture
As of June 22, the latest genomic sequencing data shows the Delta variant (B.1.617.2, first identified in India) has become the dominant strain in the United States. Nationally, cases have plateaued and we are seeing localized increases in certain states that had reached dominance earlier and surges within many of their counties. These surges are largely happening in counties with low vaccination rates with the overwhelming amount of cases and hospitalizations happening amongst those who are unvaccinated which further supports the mounting evidence that being fully vaccinated offers high levels of protection against the Delta variant. With early and preliminary data continuing to show an increase in transmission, severity, and immune escape, the World Health Organization has recommended all individuals, including those fully vaccinated, to continue wearing masks as it expects Delta to become the global dominant strain. The characteristics of the Delta variant and the current absence of protection protocols that include indoor high-quality mask recommendations put those without vaccine protection at risk, including children under 12 and those who are immunocompromised. The United States is at a pivotal point where it can actively slow the growth of Delta through increased clear communication, implementing protection protocols, and accelerating vaccination initiatives built on trust.
ETA of Delta Dominance Reached
On June 22, we reached the bottom of declining cases and an estimated prevalence of 56% in the United States. The latest figures, as of June 28, can be noisy due to fewer samples but currently estimate us at 64% prevalence.
This bottom of declining cases is obvious with the plateau over the last week and the beginning of an increase in cases nationally.
We had previously seen this change in trajectory upwards when the U.K. reached the bottom of their declining cases on the same day it reached dominance of the Delta variant, May 18, and has experienced an increase in cases ever since.
Although it may take some weeks to know the exact date the Delta strain became dominant, approximating the June 22nd date when we were at 56% prevalence, we can see that we had a higher percentage of our population fully vaccinated, 44.98%, compared to 30.74% in the U.K., more than a 14% difference. Whereas for the share of people who had received at least one dose of a vaccine, the U.S. was 53.11% compared to 54.48% in the U.K., putting the U.S. about 1% behind.
While the fully vaccinated rate appears to be a comparative advantage relative to our moment of the Delta variant becoming dominant compared to the U.K., it leaves nearly 55% of the U.S. population short of full protection from vaccinations and almost 47% without any vaccination protection. At scale, this number of people is significant when we look at the United States having about 5x the population than that of the U.K.
The decreasing trend of our national vaccination rates provides another challenge in closing the gap to increase immune protection against the Delta variant. Current rates of the daily count of fully vaccinated people are at a record low not seen since January when we first rolled out vaccines to a limited group of health care workers and long-term care residents and staff.
Updated Vaccination Rates
The U.S.’s vulnerability to the Delta variant becomes even clearer when we begin to look at the vaccination rates at the county levels.
CDC data shows that 90% percent of U.S Counties have less than 50% of their populations fully vaccinated, less than 1% of counties have more than 70% of their populations fully vaccinated, and there are over one 1,000 counties with less than 30% of their populations fully vaccinated.
While we have fully vaccinated rates as high as 71% in some counties we have other counties with rates low as around 9%.
Cases in States Increasing
At the state level, we start to see larger vulnerabilities that extend to a regional level when we look at the area that makes up Missouri, Kansas, Oklahoma, and Arkansas as well as the western region of Nevada, Utah, and Wyoming. Just today, July 1, Nebraska and Mississippi were added to the orange tier.
Taking a closer look at the states of Missouri, Kansas, Oklahoma, and Arkansas, each one is dominant with the Delta variant and current fully vaccinated rates are 39%, 42 %, 38%, and 34%, respectively.
Taking a look at their daily new cases we begin to see an increase and infection rates above 1 which indicates cases are increasing at an exponential rate. The lowest infection rate is Kansas with a rate of 1.02 and out of the four has the highest rates of fully vaccinated individuals.
Cases in Counties Surging
Missouri became dominant with the Delta variant on May 30 and currently is second in the United States in cases per capita (second to Nevada). Taking a look at Counties in Missouri, we see many areas surging with daily new cases well above that of the overall state. Looking closer at Green County, it has nearly 3x the rate of daily new cases compared to the state, 38.2 compared to 13.3.
Currently, Greene County’s positive test rate is at 14.2% and they are estimated to have used up 93% of their ICU capacity.
Steve Edwards, the head of the local health system, Cox Health, said in an interview on June 21,
“We began to get news of the Delta variant about 5 weeks ago, maybe 3–4 weeks ago it was about 10% of isolates that were sequenced and as of last week it appeared to be 90%.”
On June 29, Cox Health had confirmed diverting 23 patients to other hospitals in St. Louis and Kansas City, signaling that it had reached capacity. The hospital system put out the following statement:
“Many factors are different today than they were a few months ago. During the last COVID-19 surge, CoxHealth employees were joined by hundreds of traveling nurses and respiratory therapists who were dedicated to caring for COVID-19 patients. Unfortunately, there now is a limited number of those individuals available. This reality is compounded by the fact that COVID-19 patients take a great deal of concentrated attention and specific expertise, requiring more staffing than other units.”
Breakthrough Cases
A breakthrough case is considered to be a person who tests positive for SARS-CoV-2 after becoming fully vaccinated (i.e., ≥14 days after completing all doses). While vaccines remain highly effective, breakthroughs are expected because vaccines are not 100% effective. The Delta variant’s increase of immune escape will help us understand the WHO’s recent recommendation to have everyone, including those fully vaccinated, to continue wearing masks.
A recent report by the CDC outlines the following breakthrough figures:
- 10,262 SARS-CoV-2 reported vaccine breakthrough infections, 6,446 (63%) occurred in females, and the median patient age was 58 years
- Preliminary data shows 2,725 (27%) vaccine breakthrough infections were asymptomatic, 995 (10%) patients were known to be hospitalized, and 160 (2%) patients died (median age was 82 years) and among the 995 hospitalized patients, 289 (29%) were asymptomatic or hospitalized for a reason unrelated to COVID-19
- Sequenced data showed a majority of cases were Alpha (B.1.1.7) and did not find Delta (B.1.617.2) amongst these breakthroughs
In light of immune escape from Delta that has decreased vaccine effectiveness from 93% to 88%, we can estimate the risk of breakthrough cases increases by 70% with Delta cases above that of Alpha, a risk ratio of 1.7.
There are different factors that can determine the risk of a breakthrough infection like an individual’s immune response to the vaccines, viral load exposure by amount and time, and the virus’s ability to bind to the ACE2 receptor which this study suggests the Delta variant has improved its ability to do which reduces the amount of exposure one would need for potential transmission.
This now puts the WHO’s recommendation on masking into context. Since breakthrough cases include those who could potentially be infectious and in combination with the increased levels of transmissibility, the precaution of wearing masks for everyone, including those fully vaccinated, will help to reduce community transmission of the Delta variant and substantially in areas with low vaccination numbers.
Age Groups
One thing we are noticing from the UK data is that more cases are among younger demographics which aligns greatly with their lower vaccination rates compared to older demographics.
With similar trends here in the United States, we can expect a similar uptick in cases amongst the unvaccinated which include younger demographics.
Taking a longer timeframe, we see how the age groups who have increased their fully vaccinated rates have dropped in cases compared to groups that remained comparatively low or unvaccinated.
The current surges in counties like Green County, MO supports what we are seeing from the UK figures. Steve Edwards of COX Health shares the types of patients they are seeing in the hospital.
“We are seeing younger patients, we are seeing them sicker… almost always the breakthrough infections are patients that are asymptomatic infection and nothing more severe than a cold… I think we had one patient with a break through infection that had COVID pneumonia and that patient’s immune system was severly compromised, so a unique case.”
When we look at overall data in the U.K., we see cases overwhelmingly amongst those who are unvaccinated.
The charts below paint the picture of case numbers and hospitalizations in stark contrast between those who are unvaccinated and those who are partially and fully vaccinated.
Long COVID
A largely neglected impact of this pandemic is the serious health outcomes of Long COVID for many survivors. One study by Fair Health finds, “Of patients who had COVID-19, 23.2% had at least one post-COVID condition 30 days or more after their initial diagnosis with COVID-19.” The symptoms can include fatigue, shortness of breath, “brain fog”, sleep disorders, fevers, gastrointestinal symptoms, anxiety, and depression. A study published in JAMA shares that “approximately 80% of hospitalized patients with COVID-19 report persistent symptoms several months after infection onset.” The study goes on to find that eight months after mild COVID, one in ten people still have at least one moderate to severe symptom that they perceive to have a negative impact on their work, social, or home life. Funding has recently been increased to research Long COVID but as Michael Saag, M.D., an infectious disease doctor and researcher at the University of Alabama at Birmingham shared with NIH, “as with any new disease, there are many unanswered questions about Long COVID.” However, we do know that taking preventative measures against SARS-CoV-2 is our best chance against Long COVID.
Vaccines Work
On June 29, Maryland’s Secretary of Health recently announced that since May 10 unvaccinated people make up 97% of cases, 89% of hospitalizations, and 89% of deaths. Maryland currently has one of the leading fully vaccinated rates in the country with 56% fully vaccinated and 62% with at least one dose.
In Australia, there was a superspreader event where we see another indication of the vaccines’ effectiveness and the level of transmissibility of the Delta variant where a group of 30 people attended a party and the only people who didn’t test positive for COVID were the 6 who were vaccinated, all the other 24 unvaccinated people tested positive.
Moderna is now starting to release some early and preliminary data on a study showing “a modest reduction in neutralizing titers against the Delta (2.1-fold).” While this is good news and high effectiveness is expected because Moderna is an mRNA vaccine similar to Pfizer-BioNTech, the caveat is that the sample size was 8 people and more studies are ongoing to provide more data (please check back to this section for updates on vaccine data).
What’s Next?
We have experienced record level decreases in cases and now the United States is in a pivotal moment where it will determine what outcomes the Delta variant will have in our communities. The challenges we face of low vaccination rates across the country threaten local and regional hospital systems that will impact both COVID patients that won’t be able to get care as well as non-COVID patients who will not be able to go to the hospital or will avoid it altogether to prevent risk of exposure. Additionally, the high levels of transmission put vulnerable groups who are unable to get vaccinated like children under 12 and the immunocompromised at great risk. One county, Los Angeles, has already implemented WHO’s mask recommendations in light of Delta’s increase in cases and hopefully more local counties and states will follow. Delta is increasing quickly in areas with high prevalence and low vaccination rates, leaving the possibility of these localized surges turning into regional hot spots if both protection protocols are not implemented and vaccination rates do not quickly increase. Proactively communicating early and clearly to get ahead of misinformation to address the impacts of the Delta variant on vaccines, spread, and illness will be helpful in helping people understand the benefits of vaccines and other protection protocols. It’s important to emphasize that there are tools that can make a difference in controlling outbreaks like increasing genomic testing, implementing quality mask recommendations for indoor use, increasing ventilation, and testing the fully vaccinated after exposure to improve data on vaccine effectiveness against new variants and increase data on secondary infections. We have all the tools necessary to prevent these localized surges from becoming regional hot spots, let’s use them quickly.
Follow-up publication: Part 3: Delta Variant Hot Surge Summer in the U.S.
