Delta Plus Omicron
The Simple Story
In July, 2021, I cobbled together a short summary of the newly emerging Delta variant of the SARS-COV-2 virus, relying on the wonderfully clear Tomas Pueyo in his Unchartered Territories article. This January, 2022, I add similar information on the new variant of concern, Omicron, and include a couple of theories of how this latest version of the virus may have evolved. Let me briefly summarize where we are with the SARS-COV-2 variants.
Mutations:
Since coming out of Wuhan China in late 2019, SARS-COV-2 has made its way through millions of people and undergone thousands of mutations. Most mutations that are still with the virus can be considered “neutral” but a few will change the virus’s ability to operate in its host. Through mutation, a virus can become more or less lethal, more or less transmissible, adhere differently to different types of cells (lung versus nasal passages, for example), and acquire other selective advantages and disadvantages to its survival.
Variants of Concern:
Today, variants of concern branching out from the original Wuhan version of the SARS-COV-2 virus are the following:
Alpha (B.1.1.7 originating in the UK in September 2020),
Beta (B.1.351 originating in South Africa in October 2020),
Gamma (B.1.1.281 originating in the Manaus area of Brazil in early 2020—also known as P.1)
Delta (B.1.617 originating in India in late 2020).
Omicron (B.1.1.529 originating in South Africa in November of 2021)
The first three variants are genetically related in that they have the same “eek” (E484K) mutation (and other linked mutations) that makes evading the human immune system easier for the virus and thus more deadly for the host. Originally, public health scientists were more worried about these variants but became increasingly concerned about Delta due to its greater transmissibility. Delta does not have the “eek” and related mutations, but won out across the globe in 2021 because its mutations made it more transmissible.
In November of 2021 a new variant emerged and rapidly replaced Delta. This variant, named Omicron, turns out to be even more contagious and transmissible than Delta and has won out over the other variants.
Transmissibility:
According to Pueyo, the original virus from Wuhan China had an R0 of ~2.71. Alpha, the “English variant,” which caused a spike around the world in late 2020, turned out to be about 60% more infectious—and Delta another 60% more infectious yet, putting Delta’s R0 at about 8. Thus, with the Delta variant, each person infected, on average, passes the virus on to 8 others (in normal situations without mitigation). Omicron is more infectious yet. It’s R0 has been estimated as 10 or more.
Incubation Period:
And, the incubation period for Omicron is shorter than for previous variants: the Wuhan original was 5 days from exposure to symptoms, Delta was 4 days, and Omicron now is 3 days.
Herd Immunity:
If we assume an R0 of 8 and a vaccine effectiveness of 90% against transmission, you need at least 90% of the population immune through vaccination or prior infection in order to reasonably protect the naive, unvaccinated (without mitigation). No country was close to that in July during the Delta surge. By January, 2022, with Omicron surging and highly contagious, even infecting the vaccinated (these are called breakthrough cases), communities are likely to get close to herd immunity quickly through widespread infection, but not without a cost to health and lives (see more below).
Note that if the virus continues to mutate significantly, complete herd immunity may never be reached. New vaccine formulations would have to keep up with new mutations and, importantly, people must avail themselves of vaccination. While a reasonable degree of herd protection can be expected from Omicron, plus prior immunity (through vaccination and/or prior infection), the virus may never completely disappear and can become endemic.
Fatality:
From studies out of the University of Toronto, it looked like the risk of death with Delta was twice that of the original Wuhan variant. The short explanation is: “viruses that tend to win do so because they reproduce faster. Such a virus will grow faster inside a person, and will make that person more infectious, faster. It may also kill that person faster.” While Omicron appears less virulent, we are not sure about its case-fatality rate. US estimates will be coming soon as data accrues.
Viral Load:
You may have heard that the viral load of Delta was as much as 1,000 times higher than that of the original variant. How could this be? The answer is that Delta, replicating faster, reaches a higher viral load earlier (at a given time after infection compared to the original variant). Remember, the growth of a virus is geometric! Viral load is measured in laboratory settings using tissue samples that are exposed to the virus, then counting the number of viruses that accrue after a certain amount of time. It appears that Omicron replicates even faster than Delta when measured in bronchial tissue but slower than Delta when measured in lung tissue.
Vaccination Efficiency: Breakthrough transmissions of people vaccinated:
A vaccine’s efficacy of, say, 90% means that 10% of vaccinated people will get the disease if adequately exposed. These are considered “breakthrough transmissions.” Last July, the CDC released a study of holiday revelers in Provincetown Massachusetts who had congregated in tight settings over several days. Among the revelers who were fully vaccinated, a disturbing number became infected with the Delta variant. This was the nation’s first wake-up call that vaccination does not guarantee full protection of infection. According to epidemiologists, however, breakthrough numbers were probably within the range predicted by vaccine efficiency, and infections that did break through were mostly mild.
The rate of breakthrough infections during the Delta surge in a nationwide study released just days after the Provincetown study found the rate of reported breakthrough cases among fully vaccinated people to be extremely low, ranging from 0.01 percent in Connecticut to 0.29 percent in Alaska.
Such low breakthrough rates, unfortunately, are not the case with Omicron.
Breakthrough Transmissions with Omicron:
Some researchers say now that Omicron is so contagious that virtually everyone will eventually be getting it, previously infected or not, symptomatic or not, vaccinated or not. Fortunately, a growing body of evidence suggests that Omicron is less virulent than earlier variants. As with earlier variants, but presumably even more so, many infections will be asymptomatic and go unnoticed.
Vaccination, however, is still highly efficacious in preventing severe disease. Among vaccinated individual compared to the “naive” unvaccinated (naive here means no prior infection with SARS-COV-2), Omicron infections are both less severe and less lethal (see references below). Interestingly, immunity through prior infection with earlier SARS-COV-2 variants may be even more efficacious against Omicron than currently available vaccines, recent studies suggest.
Where Did Omicron Come From?
Omicron has a large number of mutations, more that 50, half of which affect the spike protein. Omicron is most similar to the original Wuhan version of the SARS-COV-2 virus and does not seem to have branched from Alpha, Beta, Gamma, or Delta. A plausible theory of Omicron’s emergence is that it evolved inside an immune-compromised person who had an early, protracted COVID-19 infection of the original Wuhan virus. Another theory proposes that Omicron may have evolved in mice who were infected in 2020 with the Wuhan virus, then—skipping over Alpha, Beta, Gamma and Delta—jumped back to humans in late 2021.
The Surge:
If you have been following the story of Omicron you will know that a steep surge in cases is well underway. Surges in hospitalizations are following, although fewer severe outcomes are both expected and observed. New data out of Kaiser Permanente in Southern California confirm far less virulence of Omicron over Delta, fewer severe cases and fewer deaths. With less severe disease in patients and a better ability by medical teams to manage infections after two years of lessons learned, it makes sense that outcomes would be improved over other surges.
Unless hospitals and medical personnel become overwhelmed!
Right now, the US has more people with COVID in hospitals than at any other time during the pandemic. Many cases are incidental, that is, persons are hospitalized for other reasons but test positive for COVID. For example, in New York state the proportion of cases in the hospital that are incidental is currently estimated as 43%. These cases, however, still need infectious disease isolation and appropriate care to contain the spread of the virus.
Our Task Now:
As in the beginning of the pandemic, our task now is to flatten the curve so that we don’t all get COVID at once and overwhelm our health care system. If overwhelm does occur, however, the surge is likely to be of a short duration as herd immunity kicks in due to so many infections. To get through this period it will be good to keep up personal mitigations we all are familiar with by now. A recent report using cell phone data provides excellent, hard evidence that social distancing works. Masks work in theory and have been confirmed in a smattering of studies (though clinical trials are impossible to conduct with masks for ethical and logistical reasons). Lockdown works but could be avoided if people, especially the vulnerable, do their best to stay away from crowded situations, mask up, keep distance from others, ventilate rooms, and otherwise take personal responsibility until Omicron peaks in the next couple of weeks and is on its way down.
