COVID-19 Situation Report
Editor: Alyson Browett, MPH
Contributors: Clint Haines, MS; Natasha Kaushal, MSPH; Amanda Kobokovich, MPH; Christina Potter, MSPH; Matthew Shearer, MPH; Marc Trotochaud, MSPH; and, Rachel A. Vahey, MHS.
BA.2 OMICRON SUBVARIANT The BA.2 subvariant of the SARS-CoV-2 Omicron variant of concern (VOC) is increasing in prevalence, but questions remain regarding whether it results in more severe disease. The Omicron VOC spans multiple subvariants, including the main B.1.1.529 lineage and the BA.1 and BA.2 sublineages. When Omicron emerged in the US, the rapid increase in prevalence was predominantly due to the B.1.1.529 and BA.1.1 lineages, which combined to account for nearly 99% of US cases the week of January 29. Since that time, the BA.2 lineage prevalence has increased from an estimated 0.8% to 3.8% of US cases, approximately doubling each of the past 2 weeks. The increase in prevalence indicates that BA.2 is more transmissible than the other Omicron lineages, possibly 30% more. Notably, genomic surveillance for the BA.2 lineage is difficult, because it does not result in the S-gene target failure (SGTF) in PCR-based assays, which has been used to track other VOCs—including Omicron—without requiring genomic sequencing. The BA.2 lineage has not yet taken off in the US, but the next several weeks will provide important information regarding the potential for a second Omicron surge.
Research is ongoing to better characterize protection against the BA.2 subvariant from vaccination, booster doses, and prior infection. Like the original Omicron variant, BA.2 is less susceptible to SARS-CoV-2 vaccines than previous VOCs, but booster doses can increase the vaccine effectiveness against symptomatic COVID-19 disease to 74%. The BA.2 lineage also appears to evade antibodies generated in response to prior infections with earlier strains, including the Alpha and Delta VOCs. There is some evidence that BA.2 is able to reinfect individuals who were previously infected with the BA.1 lineage, although the combination of prior infection and vaccination appears to provide moderate protection. Researchers in Denmark recently conducted a study to evaluate reinfection with the BA.2 lineage. Out of a sample of 187 reinfection cases (within 20-60 days), 47 were the result of BA.2 infection following infection with the BA.1 lineage. Conversely, a recent study by the UK government found “no detected sequence-confirmed BA.2 reinfection following a BA.1 infection at any interval.”
The data on disease severity for the BA.2 lineage are mixed. Some countries where BA.2 has become more prominent are exhibiting declining trends in daily COVID-19 mortality, such as the UK, whereas Denmark is exhibiting an increasing trend. Through the use of animal models, researchers have identified more extensive damage to lung tissue in hamsters infected with the BA.2 lineage compared to BA.1, but this may not necessarily hold true for humans. A study in South Africa found similar disease severity among patients infected with the BA.1 and BA.1 subvariants, and US CDC Director Dr. Rochelle Walensky indicated that “there is no evidence that the BA.2 lineage is more severe than the BA.1 lineage.” Evidence also indicates that the BA.2 subvariant exhibits strong resistance to many monoclonal antibody treatments, including sotrovimab, which is currently being used to treat patients infected with the Omicron variant. The lack of an effective treatment option could impact disease severity and mortality.
MENTAL HEALTH Results from the largest cohort study to date on the impact of acute COVID-19 on mental health were published February 16 in The BMJ. The cohort consisted of 153,848 individuals who survived 30 days after initial SARS-CoV-2 infection, and 2 control groups: 5.6 million individuals who did not have recorded SARS-CoV-2 infection and 5.8 million historical control individuals pulled from pre-pandemic data. All of the data came from a US Department of Veterans Affairs database. Overall, the study found that people who had COVID-19 were 60% more likely to experience subsequent mental health problems than people who never had the disease. Individuals who had COVID-19, even mild cases, had a 41% increased risk of developing sleep disorders, 39% increased risk of developing depression, 38% increased risk of heightened stress levels, 35% increased risk of developing anxiety, 34% increased risk of developing an opioid use disorder, and 80% higher risk of developing other cognitive symptoms, such as “brain fog.” Limitations of the study include that it was performed before vaccines were widely available and that the population primarily included older white men, although controlling for race, gender, and age found no difference in risk.
Growing evidence indicates that SARS-CoV-2 infection has the potential to impact nearly every organ system, including the nervous system. The exact mechanism behind the observed increase in mental health risks after SARS-CoV-2 infection is currently unclear, but one hypothesis suggests that the virus can enter the brain and damage areas responsible for mood and emotional regulation. An association between acute COVID-19 and long term increases in mental health disorders raises the likelihood that a wave of mental health symptoms could occur in the near future, given that nearly 425 million people worldwide have had COVID-19. The National Health Service (NHS) in England recently warned that millions of patients face dangerously long wait times for mental health services. Concerns are rising that a lack of investment in mental health care infrastructure could lead to an increase in suicide, self-harm, and eating disorders. Mental health services historically have been neglected worldwide, but they will need an increase in funding and attention if we want to be prepared for the coming increase in patient needs.
FOURTH VACCINE DOSE Questions about the necessity of a second SARS-CoV-2 vaccine booster, or fourth dose, arose shortly after announcements regarding the importance of an initial booster. Several new studies attempting to shine a light on the durability of vaccine-mediated immunity provide evidence that a 3-dose regimen of mRNA-based vaccines—possibly only 2 doses—may be able to protect most people against severe COVID-19 disease for months or even years. Evidence for possibly lengthy protection from vaccination includes an increase in neutralizing antibody diversity, T cells that can recognize the Omicron variant, and germinal center activation for up to 15 weeks post-vaccination. Leading immunologists have stated that fourth or fifth doses of the vaccine might lead to diminishing returns for the majority of the population when compared to 3 doses. However, a fourth vaccine dose may still be necessary for certain populations, including older and immunocompromised individuals.
Several nations have begun offering fourth vaccine doses to specific populations or openly discussing that possibility. Many health officials in the US have agreed that it is too early to officially recommend a fourth vaccine dose, but the US FDA is continually examining emerging data to determine if and when another booster may be necessary. If a fourth dose does appear to be warranted, for all age groups or only older adults, experts say it likely would be recommended in the fall to coincide with annual flu shots and the rise of respiratory virus transmission. Additional considerations include whether the vaccine should be reformulated for novel variants. Other nations are moving forward with plans to provide fourth doses to certain populations, including the UK, Italy, South Korea, Sweden, and Israel. While fourth doses of SARS-CoV-2 vaccine may be necessary for certain populations, it is critical to ensure that populations in low- and middle-income countries (LMICs) are not left behind. Vaccine equity must be addressed now so the world can be prepared for future pathogens with pandemic potential.
VACCINES IN AFRICA Egypt, Kenya, Nigeria, Senegal, South Africa, and Tunisia will be the first 6 countries in Africa to receive the technology needed to produce SARS-CoV-2 mRNA vaccines, WHO Director-General Dr. Tedros Adhanom Ghebreyesus announced February 18 at an event held at the European Union-African Union summit in Brussels. The technical information and training will come from the global mRNA technology transfer hub established by the WHO last year in Cape Town, South Africa, in order to expand mRNA vaccine manufacturing—for COVID-19 and other diseases in the future—to low- and middle-income countries (LMICs). As a hub partner, South Africa's Afrigen Biologics announced earlier this month that it has developed a version of the Moderna vaccine using publicly available information. While the EU is supporting the effort, the bloc received criticism at the summit for continuing to block a proposal at the World Trade Organization (WTO) for a temporary waiver of the TRIPS Agreement. South Africa President Cyril Ramaphosa, who has accused Europe of hoarding the vaccines, called on the EU to drop its opposition to a waiver, saying it is a matter of saving millions of lives rather than padding the pockets of a few pharmaceutical companies. At the summit’s closing press conference, European Commission President Ursula von der Leyen committed to reaching a solution on the matter by spring.
Moderna has said it will not enforce existing patents on its SARS-CoV-2 vaccine during the pandemic. But the company recently applied for patents related to its vaccine in South Africa, raising concerns the company will move to prevent the technology transfer hub from making its own version of the shot once the pandemic phase is declared over. Moderna Chief Executive Officer Stéphane Bancel said the company has not yet decided whether it will enforce patents in LMICs when the pandemic ends. In an interview with STAT, WHO Chief Scientist Dr. Soumya Swaminathan said the global health agency would like Moderna to not enforce its patents on its SARS-CoV-2 vaccine during and beyond the pandemic. Without Moderna’s assistance, the Afrigen-developed mRNA vaccine must go through human clinical trials and could take another 2 years to come to market. But the effort is seen as building a foundation for the production of future mRNA vaccines on the continent. Additionally, BioNTech last week announced it is deploying modular vaccine production facilities—housed in shipping containers and dubbed BioNTainers—to several African nations to help increase production of the company's current and future mRNA vaccines for COVID-19, malaria, tuberculosis, and cancer. The increased manufacturing capacity could be a sign of improving global vaccine equity, but much more needs to be accomplished to reach that goal, including billions more dollars of investment and efforts to increase vaccine uptake.
Meanwhile, the US Agency for International Development (USAID) last week released case studies from Côte d'Ivoire, Uganda, and Zambia detailing successful efforts to increase vaccination uptake, including actions by its Global Vaccine Access, or Global VAX, initiative. US officials announced the government will intensify assistance to 11 African countries under the initiative, efforts worth more than US$250 million. The countries—Angola, Côte d'Ivoire, Eswatini, Ghana, Lesotho, Nigeria, Senegal, South Africa, Tanzania, Uganda, and Zambia—were selected based on their COVID-19 incidence, healthcare system capacity, readiness to administer the vaccines, and ability to deploy additional US investments. On February 18, the administration of US President Joe Biden requested an additional US$5 billion for overseas COVID-19 response efforts, far less than the approximately US$19 billion USAID originally recommended would be needed. Of that funding, US$2.55 billion would be used for vaccinations, US$1.7 billion for therapeutics and supplies, and $750 million for humanitarian aid.
US STATES’ PANDEMIC ESCAPE PLANS Two days after the White House COVID-19 Response Team signaled that the administration of US President Joe Biden is planning for the pandemic to cease being a crisis, President Biden on February 18 announced he is continuing the designation of COVID-19 as a national emergency. Meanwhile, most US states have announced the end of or plans to end statewide indoor mask mandates—leaving Hawaii as the lone holdout. Many states and cities also have lifted their proof-of-vaccination requirements and called state and municipal employees back into the office after 2 years of work-from-home rules. Governors and mayors cite plummeting numbers of new COVID-19 cases, with the 7-day national average down 87% since January 15. California Governor Gavin Newsom last week announced California will move into the “next phase” of managing the pandemic, with a focus on early detection of variants, keeping schools open, wastewater surveillance, and stockpiling masks and tests. Newsom’s SMARTER plan—which stands for Shots, Masks, Awareness, Readiness, Testing, Education, and Rx—is billed as a response plan for COVID-19 as well as future health emergencies. Some state legislatures are taking additional steps to roll back public health measures, introducing legislation to restrict mask mandates, ban vaccine requirements, and revise visitation policies for long-term care facilities and hospitals.
A model from the Institute of Health Metrics and Evaluation (IHME) estimates that about three quarters of the US population currently is immune to Omicron due to natural immunity, vaccine-mediated immunity, or a combination. However, many experts warn that the currently circulating Omicron BA.2 sublineage or future variants could escape current immunity, and most are confident that existing immunity will wane. While the number of deaths is beginning to decline nationwide, around 2,000 people continue to die of COVID-19 each day, with unvaccinated individuals making up the majority of those deaths. Even California Governor Newsom acknowledged that there is no end date to the crisis, “not a moment where we declare victory.” But he said California’s plan will allow residents to shift from a “crisis mentality” to one relying on prevention and adaptability, with health officials stepping up measures to quell outbreaks when they occur. Still, experts who encourage control measures such as vaccination and masking continue to experience backlash and warn that trust in public health is at an all-time low. Notably, some evidence suggests trust, between people or in government or scientists, is the most critical factor in addressing crises such as COVID-19.
US CDC DATA According to reporting by The New York Times, the US CDC is sharing only a small portion of the data it collects on COVID-19, 2 full years into the pandemic. The data could help state and local officials better understand how and when to use specific mitigation measures, what populations are most at risk, who needs booster doses, and where outbreaks might occur or new variants emerge. CDC representatives gave various reasons why the agency has been slow to release some information, including outdated systems incapable of handling large amounts of data, fear that the information might be misinterpreted, and concerns over some data representing only a sampling of the US population. A string of necessary bureaucratic approvals also adds to the delays. Several epidemiologists and scientists said gaps in data have the potential to erode trust in public health and science and countered that the release of detailed data analyses and effective communication of that information can help bolster public trust and provide a better understanding of the pandemic.
OTTAWA PROTESTS Police in Ottawa, Canada, regained control of most of the capital city over the weekend after a push to disperse the so-called “Freedom Convoy.” The demonstration, which began in late January with protestors and far-right organizations denouncing COVID-19 vaccination requirements and other pandemic restrictions, turned into a 3-week-long occupation. Police arrested nearly 200 people, having to use pepper spray, stun grenades, and other anti-riot tactics, and vowed a months-long investigation leading to financial sanctions and criminal charges. The Ottawa police chief resigned last week after receiving criticism about why it took so long to break up the convoy.
The demonstration led Canada Prime Minister Justin Trudeau to invoke the Emergencies Act for the first time ever, in order to help quell the protests by permitting authorities to freeze bank accounts associated with the convoy and seize protestors’ vehicles. Last night, the House of Commons approved the Emergencies Act, extending its use for an additional 30 days. Prime Minister Trudeau said there “continues to be real concerns” and that the government will evaluate daily whether to continue the state of emergency. Royal Canadian Mounted Police (RCMP) said they have frozen more than 200 bank and corporate accounts worth several million Canadian dollars in relation to the protests. Now that the convoy has ended, many Canadians—including Ottawa residents, politicians, policy experts, and the demonstrators themselves—are wondering how the organized and financially backed protests might affect the country’s future political landscape.
