Many of the questions below have received updates, but a few highlights include:
Views on the current surge due to the Omicron variant are becoming more polarized with some claiming it is more mild, particularly in light of high vaccination coverage in many areas of the country, while many businesses, schools, and healthcare providers are gravely concerned about how Omicron will impact their settings. While many employers and employees are experiencing pandemic fatigue, it is likely that COVID-19 will continue after the current Omicron surge.
The US is better prepared to respond to Omicron than we were to the original SARS-CoV-2 variant in January 2020, and to the subsequent emergence of the Delta variant. The mRNA platform can adjust vaccine formulations to incorporate new variants, genomic sequencing has increased globally with improved information-sharing between partners, many governments and decision-makers now understand the importance of early action, rapid tests are becoming more widely accessible, there are two very promising antiviral pills to treat COVID-19, and we have vastly greater knowledge of the SARS-CoV-2 virus. Preparing for novel variants and an eventual shift towards endemicity are not mutually exclusive, in fact, PHC believes they are both necessary in any comprehensive response prevention and mitigation plan.
While many people may have “pandemic fatigue”, the critical lesson we have learned from the last few years is that drawing down important prevention and mitigation measures can and has led to resurgence in cases, hospitalization and death.
The CDC updated and shortened the recommended isolation and quarantine period for the general population from 10 days to 5 days following a positive test result, provided that the individual is asymptomatic or symptoms are resolving and they can remain masked for another 5 days when around other people outside their household. Below, we describe PHC’s perspective on this update.
A UK Health Security Agency study supports a 7 day self-isolation with 2 negative antigen tests 24 hours apart. By 7 days, 1 in 6 (16%) were still infectious compared to 5 days where 1 in 3 (33%) were still infectious. In addition, a recent Harvard study looking at Omicron’s infectious period in samples of NBA players, staff, arena staff, and others affiliated with the NBA showed that at day 5 from testing positive, 30-50% of individuals were still infectious.
Despite efforts by health institutions to increase Omicron testing and sequencing, test availability remains scarce, especially for at-home rapid tests. Delays for lab test results are increasing. In recent promising news, 8 home tests per person per month are covered by insurance and households can now request up to 4 at-home rapid COVID-19 tests from the Government at no cost. Tests will ship in 1-2 weeks, and can be found here.
PHC believes CDC's recent guidance was not based on sufficient public health science for Omicron but on the need to maintain workforces in the short-term. This shortened isolation period may backfire, though, with more infections based on early Omicron data suggesting the infectious period is longer than 5 days for nearly half of those tested. PHC strongly urges organizations to require a negative rapid test in order to exit isolation after 5 completed days.
Omicron is widespread in the U.S. There are immediate steps we can take to protect lives and livelihoods. We know the layers of defense, or “Swiss cheese” model, that work to slow the spread of COVID-19:
The Omicron variant probably did not evolve from the Delta variant, rather it likely pre-dates the Delta variant. We can tell this because the mutations in Omicron’s genome can serve as a molecular clock, allowing an estimation of when it evolved from an existing strain of SARS-CoV-2. That molecular clock suggests it evolved around June of 2020.
As global sequencing to detect Omicron increases, missing links in the recent Omicron family tree may be detected, including from older frozen specimens. This may help fill in the gaps in our knowledge of where and when it emerged.
Most countries and territories have confirmed Omicron cases (source 1, source 2). As predicted, Omicron cases are exploding globally and in the U.S.
Wastewater surveillance (testing of wastewater from toilets, showers, sinks, etc. for molecular / RNA analysis) has identified unprecedented levels of Omicron. The identification of cases through wastewater surveillance, followed by positive Omicron cases demonstrates the ability for wastewater to be an early indicator of disease spread and detection. This U.S. map shows where SARs-CoV-2 has been identified in wastewater across the United States. Boston and some areas of California show signs of decreased levels of virus in wastewater – a sign that the virus may begin to trend downwards in those particular areas.
Although the UK and some US states and cities are beginning to see declines in newly reported cases, Omicron cases will continue to rise globally, due to both rapid spread and to improvement in Omicron detection in countries. For countries with less robust sequencing capabilities, as the saying goes, “absence of evidence is not evidence of absence."
Omicron is currently the dominant variant in the U.S., currently accounting for ~99.5% of new cases in the U.S. In January, the daily count of new COVID-19 cases (including both Delta and Omicron) reached >1 million – the highest case count the U.S. has experienced. Currently, the U.S. has the highest number of daily new cases relative to all other countries. Cases in the U.S. have risen faster, in part due to robust testing and sequencing efforts to detect the new variant. Hospitalizations are also surging in many areas of the U.S., and many states are implementing crisis standards of care.
NewsNodes Omicron Tracker
As U.S. sequencing continues to increase, we will continue to see evidence of the dominance of this variant within the United States. The precipitous growth of cases in the U.S. is due to both rapid spread and to sequencing efforts “catching up” with the cases that have already been circulating and eluding prior detection.
Early information suggests the mode of transmission for Omicron is the same as prior variants, meaning it is mainly spread through air and droplets (breathing, singing, talking, coughing, sneezing). A recent pre-peer reviewed study analyzed differences in viral environmental stability between various SARS-COV-2 strains. On plastic and skin surfaces, Alpha, Beta, Delta, and Omicron variants exhibited more than two-fold longer survival than the original strain and maintained infectivity for more than 16 hours on skin surfaces. The high environmental stability of these variants could potentially lead to contact spread but further data is needed to determine if this is a viable mode of transmission.
Omicron will have identical modes of transmission as previous COVID-19 variants. This is another reason why we are not in the same situation as February 2020, because we now know how COVID-19 is spread and know how to implement layers of protection to stop / slow the spread.
Omicron has a higher transmissibility (R0) than that of prior variants.
Exponential community spread of Omicron is rising across Europe and the United States. The underlying attributes of Omicron that enable it to spread quickly (higher R0, significant immune escape of antibodies formed by the vaccine or previous infection, or both) are still being determined. The U.K. reports that the risk of reinfection of the Omicron wave is 16-fold higher than during the Delta wave, bolstering the evidence for significant immune evasion.
A question we are asking is, “How long did it take for countries to report confirmed cases of different variants?” This is an imperfect and rough proxy for speed of international spread, but a useful comparison especially for Delta and Omicron. Despite substantially reduced air travel, relative to before the pandemic, the speed at which Omicron has been reported by countries is substantially faster than any previous variant.
A global surge in Omicron cases has already led to significant staffing shortages and disruption to public and private institutions. Businesses should implement prevention and mitigation measures to limit the disruption to global supply chains, business continuity, and healthcare access.
The analysis below shows the rate at which each variant was publicly reported as a confirmed case by a country. It is important to recognize that many factors are at play here, including the amount of testing, genomic sequencing capacity (how fast will they detect it?), political will to publicly share confirmed cases as soon as they are detected, etc.
*Note: For Delta, the curve above shows the number of days since it was detected in the 3rd country. We excluded two early outlier countries where Delta was detected in samples far before it started to spread widely.
Incubation period is the time from virus/pathogen exposure (“infection”) to the start of symptoms. Infectious period is the time when a person can spread the virus to another person. Data from recent outbreaks of Omicron demonstrate that the incubation period of Omicron may be as short as 3-5 days (compared to 5-7 days for Delta and 7-14 days for the original strain).
Generation time (also known as generation interval) is the time from infection-to-infection, or the time between infection of a primary case and its subsequent infection of a secondary case. This is a really important number in determining the rate of spread. Very preliminary estimates of generation time are between 3-5 days, meaning Omicron is spreading very quickly.
A Norwegian study from an Omicron outbreak suggests that the time between virus exposure and symptom onset/positive test was 3-4 days, with a range up to 8 days.
The incubation period will likely be ~3-5 days and the infectious period will likely be ~6-14 days. Note, this does not include immunocompromised persons who become chronically infected.
Virulence is the severity or degree of harm of a disease. We are learning more about Omicron’s virulence as case numbers rise.
A study from the CDC, the White House, and Kaiser reports that when compared with Delta, people testing positive for the Omicron variant have a 53% lower risk of symptomatic hospitalization, 74% lower risk of ICU admission, a 91% lower risk of death, and a 70% decrease in hospital length of stay if hospitalized.
Of note, patients diagnosed with the Omicron variant in this study were more likely to be between the ages of 20-39 years and less likely to be older adults and young children than patients diagnosed with the Delta variant in the same population. While the decrease in severity of Omicron held true across all demographics in the study when compared to Delta, it is important to remember we do not yet have enough data to say if Omicron will be less severe for the most at-risk populations (i.e. immunocompromised, older adults, young children).
The ZOE COVID study in the UK reports the top five symptoms associated with Omicron infection are runny nose, headache, fatigue, sneezing, and sore throat. This information was obtained from review of cases in the London area, where the case rate is higher than any other region in the UK.
Omicron will probably have equal or lower severity (virulence) compared to Delta across all demographic groups. However, given our prediction that prior infection with COVID-19 (natural immunity) will likely offer poor protection against Omicron, we suspect that the hospitalization rate (a percentage of positive cases that are hospitalized) and case fatality rate (a percentage of positive cases that result in death) in the unvaccinated could be similar to Delta. It is indisputably clear that the overall number of hospitalizations are climbing rapidly and PHC predicts the impacts of this will grow, causing systemic impacts to essential workforces and services, especially the U.S. health system.
We cannot afford to have a bad flu season, or even a “normal” flu season, on top of COVID-19, given both Omicron and Delta have the potential to severely stress healthcare systems, cause hospital bed and medical supply shortages, and drain already exhausted healthcare workers. Everyone with access should get their influenza vaccine, as soon as possible, to protect themselves, their loved ones, our healthcare system, and our economy.
Omicron underscores the fact that global HIV treatment and control, particularly in under-resourced countries, is a matter of global health security. Untreated HIV leads to an immunocompromised host, enabling COVID-19 to continue replicating and mutating within that host for up to six months. The inability of the host’s immune system to clear the virus creates an internal microcosm of molecular evolution. This is analogous to how many multi-drug resistant tuberculosis (TB) cases arise.
Globally, the capacity to detect, treat and prevent many other infectious diseases has suffered as the world mustered resources to stop the COVID-19 pandemic. Cases of regularly occurring but deadly diseases such as malaria and tuberculosis have increased since the COVID-19 pandemic has begun; our ability to efficiently protect people from COVID-19 will indirectly improve public health capacity to respond effectively to other important diseases.
The U.S. FDA has issued a statement about the impact of SARS-CoV-2 mutations on the performance of COVID-19 molecular tests: The FDA acknowledges that mutations in the viral genome can result in changes to viral proteins and therefore have an effect on the performance of molecular tests. Specific EUA-authorized tests whose performance might be impacted by mutations associated with the Omicron variant have been identified and the recommendation from the FDA is to avoid using these specific tests until the ability of the tests to detect Omicron can be validated.
In the interim, the FDA has identified molecular tests that have been successful in identifying patterns that may be associated with the Omicron variant, specifically, a phenomenon called S gene target failure (SGTF), which produces a noticeably different signal in test results (essentially a clue that is left behind after a portion of the analysis fails). By running these specific molecular tests (e.g., “TaqPath” PCR from Thermo Fisher), a laboratory can indicate a suspected Omicron case.
A pre-peer review print of a study comparing rapid simultaneous nasal rapid antigen testing (BinaxNOW™) and RT-PCR testing found the sensitivity of a single antigen test was 95.2% (95% CI 92-98%); 82.1% (95% CI 77-87%) and 65.2% (95% CI 60-71%) for Ct threshold of < 30, < 35 and no threshold, respectively. Comparisons between BinaxNOW™ and RT-PCR from oral cheek swabs to nasal swabs found the oral cheek specimen was significantly less sensitive than nasal swab; indicating the BinaxNOW rapid test continues to be a very useful diagnostic during the omicron surge and oral (throat or cheek swab) should not replace nasal swabs due to significantly reduced sensitivity compared to nasal swabs.
With the proliferation of free and subsidized rapid tests in the US similar to the UK, PHC believes more routine testing will facilitate earlier identification of cases for isolation and better exposure management towards bringing down case rates.
The UK Government announced that there is no impact on rapid test sensitivity to Omicron, based on laboratory data, however, there is emerging evidence from a real-world study indicating that several rapid tests that use nasal swabs may fail to detect some Omicron cases in the first days of infection. One preliminary explanation is that in the beginning of an Omicron infection, the virus may be more prominent in the throat as opposed to the nose.
This US study comparing the test results of PCR and a particular rapid antigen test dispels any concerns that antigen tests will not work against Omicron.
Some rapid tests target the nucleocapsid protein, not the spike protein, and thus are likely to remain effective against Omicron. Currently, no rapid COVID-19 test manufacturers (either antigen or molecular) have confirmed a decline in efficacy for the Omicron variant. The UK has also been using an alternative type of test (lateral flow rapid antigen tests) and found similar sensitivity to detect Omicron compared to Delta.
There is a low probability that the currently available rapid antigen tests will lose efficacy based on a mutation preventing them from detecting the viral antigens. However, if the location where the virus primarily grows in the body shifts away from the nasal area, then there may not be enough virus collected on a nasal swab alone for the test to detect. While not yet officially recommended by rapid test manufacturers, swabbing the back of one's throat and nose may improve the test's ability to detect Omicron infections.
PHC predicts there is moderate risk that rapid molecular tests may have reduced efficacy based on the mutations found in the Omicron variant (i.e. some rapid molecular tests may not appropriately detect COVID-19 infections in a person that contracts the Omicron variant).
It is clear that vaccine effectiveness against disease caused by Omicron is lower than effectiveness against the Delta variant, but protection against hospitalization and death remains strong. While vaccine effectiveness is generally lower with Omicron, new cases are increasing more sharply among unvaccinated individuals, meaning it is ever important to get fully vaccinated
Numerous studies (study 1, study 2, study 3, study 4, study 5, study 6) have compared how effective various combinations of natural and/or vaccine-induced immunity were against variants of SARS-CoV-2, including Omicron. People who had received two vaccine doses had low to no ability to neutralize Omicron (meaning there was almost no protective effect from two vaccine doses against Omicron). Omicron’s reinfection rate was five times higher than Delta’s, which suggests low levels of residual immunity from prior infection with other variants.
However, a report from the UK Health Security Agency shows that getting the booster vaccine produced a moderate amount of neutralization (i.e. protection) against Omicron, and confirmed that a booster dose is more effective against the Omicron variant than 2 doses alone. Additionally, a study from a large health system in South Africa reports that the vaccine’s (Pfizer, 2-doses) ability to prevent hospitalization was reduced from 93% against delta to 70% against Omicron, further exemplifying the need for a booster.
This table is from a U.K. technical briefing that describes vaccine effectiveness against hospitalization for Omicron. This shows a significant increase in protection from Omicron hospitalization after a 3rd dose (booster).
Scientists at the Walter Reed Army Institute have announced a vaccine that protects against all variants of SARS-CoV-2, including those in the past. It has passed phase 1 trials, but must still pass phase 2 and 3 trials.
We believe Omicron is going to have a meaningful reduction in vaccine efficacy, however the magnitude is yet to be determined. These early antibody neutralization studies are concerning, but it is not straightforward to translate a reduction in antibody neutralization into a reduction in overall vaccine efficacy; there are many other factors in play. Lab tests are one data point, and how the variant behaves out in the wild and up against the full landscape of our complex human immune system is another.
Note that the world is now a mixed bag of different immunity profiles because of different vaccines and different variants.
We correctly predicted that being fully vaccinated (which PHC defines as inclusive of a booster dose), combined with natural immunity from a past infection, affords the best protection against the Omicron variant. This prediction was based on the very high efficacy of booster shots, which help generate a robust immune response even beyond what the initial vaccine generated. Booster shots not only trigger strong B-cell response (the cells that make antibodies), but also trigger strong T-cell response, creating immune protection against many different flavors of COVID-19 variants regardless of specific spike protein mutations. As a precaution, vaccine manufacturers are already pursuing mRNA vaccines that will target the new changes to the spike protein in Omicron. However, vaccine development will take months.
The most pressing global priority is to vaccinate the entire world against COVID-19, prioritizing vulnerable populations and under-resourced nations. It is not enough to make vaccines “available;” efforts to operationalize culturally appropriate vaccine messaging and distribution must accompany that availability.
Governments should highly encourage and push for people to get their booster shots given the effectiveness of boosters in comparison to two doses of vaccine.
The United States is lagging behind many other countries in the percentage of people who have received booster vaccines. It is critical that the U.S. increases public messaging surrounding the positive impact that boosters play in the resistance against Omicron and future variants.
On December 21, Israel approved a fourth dose of a COVID-19 vaccine for persons over 60 years and healthcare providers.
Numerous governing bodies will begin to reclassify “fully vaccinated” as including a booster vaccine. Additionally, we anticipate heightened efforts from the G20 to further global vaccination campaigns.
Taking a long-term view, it is not realistic to think that the entire world can be vaccinated or boosted against a new variant every 9-12 months. Indeed, we have not even achieved global vaccination yet with our current vaccines. We predict that in the next 1-2 years there will be promising developments toward a vaccine that covers most variants and whose protection lasts longer than 6 months.
Vaccine manufacturers and research laboratories are currently assessing vaccine efficacy against Omicron. Thanks to critical work on rapid mRNA vaccine development earlier in the pandemic, and how the mRNA platform was constructed, vaccine manufacturers report they will be able to adjust the vaccines for new mutations, if necessary, in a matter of months. On January 4,2022, the CDC updated their recommendation for when many people can receive a booster shot, shortening the interval from 6 months to 5 months for people who previously received the Pfizer-BioNTech COVID-19 vaccine.
On Dec. 8, 2021 Pfizer announced in a press release findings from their preliminary testing: 3 doses of the Pfizer COVID-19 vaccine neutralizes the Omicron variant, while 2 doses show “significantly reduced neutralization titers”. This means that only 2 doses likely provides less protection against Omicron.
Pfizer also “continues to develop a variant-specific vaccine against Omicron in case it is needed with the aim to induce high levels of protection against disease as well as a prolonged protection” with first batches anticipated by March 2022.
On December 20, Moderna announced that the authorized booster dose and a higher dose demonstrated a 37-fold and 83-fold increase in the antibodies that neutralize the SARS-CoV-2 virus. This is incredible validation of the benefit and importance of a booster dose, and specifically of the Moderna vaccine.
Laboratory assays show nearly all of the monoclonal antibody treatments used to prevent severe disease have reduced efficacy against the Omicron variant. However, other treatments have been introduced to treat Covid-19, like Paxlovid, an antiviral pill. It has been FDA approved in the US to treat COVID-19 and reduces hospitalization and fatality rates.
A recent study indicates that Omicron remains largely sensitive to eight of the most important anti-SARS-CoV-2 treatments, including remdesivir and molnupiravir (antiviral medications).
Current mRNA vaccines coupled with booster shots will continue to provide the best protection against Omicron while Omicron-specific vaccines are being developed.
In the near future, patients with COVID-19 may need to have their virus sequenced (viral genotyping) to determine if a monoclonal antibody will be effective or not, based on which variant they have. Different treatments for different variants is a very real possibility.
In the US, mask requirements on airplanes, trains, buses, and other modes of transportation will remain through March 18th. This date is likely a placeholder and can be extended as it has been in the past based on the state of the pandemic. Additionally, new testing and quarantine requirements (i.e. requirement for proof of negative COVID-19 test for all air passengers boarding a flight from a foreign country to the U.S.) have been put in place for international travelers including both vaccinated and unvaccinated persons.
Since US public health is implemented on a state or more regional level, , we see variability across jurisdictions where airports are located in terms of additional quarantining or testing guidelines. For example, Los Angeles County is now offering free rapid COVID-19 tests to international travelers arriving at the LAX international terminal and advising to test in the days following arrival or should you become symptomatic.
US travel bans have not been shown to be effective if only limited to specific countries. If all travel shuts down or is incredibly limited overall as opposed to measures directed at specific routes or countries (i.e. Taiwan, Hong Kong, Australia, and China), we do see more short-term favorable outcomes. Yet, none of these countries have remained COVID free even with incredibly aggressive travel, testing, and quarantine policies. If novel variants continue to emerge, there may be additional travel restrictions, but we believe other interventions such as greater access to free tests and more stringent vaccination requirements are public health interventions that are easier to implement into the population.