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.
WASTEWATER SURVEILLANCE The US CDC has added wastewater surveillance of SARS-CoV-2 RNA to its COVID Data Tracker, as virus levels in sewage water may be capable of providing an early warning signal for transmission surges. The tool comprises data from more than 400 testing sites in 37 states, with more than 34,000 samples representing 53 million US residents collected so far. Hundreds of additional testing sites are expected to begin submitting data to the system in coming weeks. The CDC initiated the National Wastewater Surveillance System (NEWS) in September 2020, and it has become a critical tool for public health officials since it can show where viral loads are changing, which communities are at risk of a surge in cases, and where medical supplies should be deployed. 

An additional benefit of the COVID wastewater tracking system is the identification of novel and “cryptic” variants of SARS-CoV-2. Cryptic variants are lineages of SARS-CoV-2 that contain mutations never before observed in humans. A number of cryptic lineages have been detected in the New York City sewer system. The origin of these out-of-the-ordinary lineages, which also have been detected in Missouri and California, has not yet been determined, but the most popular hypothesis is the mutations arose simultaneously in similar animal hosts, such as rodents that live in the sewer systems. Whatever the source, the new surveillance system could be critical in identifying and tracking the next major variant of concern.

US CDC ACIP MEETING The US CDC's Advisory Committee on Immunization Practices (ACIP) met on February 4 to provide updates to clinical considerations for utilization of COVID-19 vaccines. Topics of discussion included the FDA-approved Spikevax SARS-CoV-2 vaccine from Moderna, vaccination recommendations specific to immunocompromised individuals, and lengthening the gap between the first two doses of mRNA COVID-19 vaccines. 

ACIP voted unanimously to recommend the use of a 2-dose primary series of Spikevax among US adults aged 18 years and older, and CDC Director Dr. Rochelle Walensky endorsed the recommendation later that day. ACIP members also discussed concerns regarding the risk of myocarditis following vaccination. Results of investigations into 13 deaths from myocarditis following mRNA vaccination found that the myocarditis was not caused by vaccination, and most other myocarditis cases among mRNA vaccine recipients were resolved within 90 days with no reported impact on quality of life. Additional discussions centered on potentially widening the time interval between initial mRNA vaccine doses from the current 21-28 days to 8 weeks apart. The change might reduce the risk of myocarditis among some recipients and increase vaccine effectiveness. However, no official vote was taken on the suggestion.

Officials also presented anticipated changes to vaccine guidance for certain immunocompromised individuals. The proposed revised guidance notes that people who are moderately or severely immunocompromised should receive a booster dose at least 3 months—instead of the current 5 months—after the last dose of a 3-dose primary series of mRNA SARS-CoV-2 vaccine. For immunocompromised individuals who received the single-dose J&J-Janssen vaccine, the guidance likely will change from the current recommendation—a primary dose followed by a booster 2 months later—to a 3-dose schedule of an additional mRNA dose at least 28 days after the initial dose and then an mRNA booster dose 2 months after the second dose. The guidance was expected to be updated on February 7 but the new recommendations are not yet published on the CDC’s website. 

OMICRON-ONLY VACCINES As noted in previous briefings, both Moderna and Pfizer are pursuing the development and testing of Omicron variant-specific vaccines. Some health officials, such as those from the European Medicines Agency, support the efforts. However, research from the US National Institutes of Allergy and Infectious Diseases' (NIAID) Vaccine Research Center posted on February 3 to the preprint server bioRxiv suggests that an Omicron variant-specific booster developed by Moderna might not provide additional or greater protection beyond the company’s already authorized mRNA vaccine booster dose. The research, which is not yet peer-reviewed, tested the boosters in primates. These findings mirror the results of other small animal studies testing vaccines targeting other individual variants. But predicting the future emergence or dominance of SARS-CoV-2 variants is difficult, with scientists uncertain if a new dominant variant might evolve from Omicron, a past variant, or have mutations very different from either Omicron or other past variants. This concern has led some scientists and health officials to advocate publicly for broad protection in future vaccines—to multiple variants, all betacoronaviruses, or even all coronaviruses. Several NIAID researchers recently published a commentary in the New England Journal of Medicine (NEJM) calling for a universal coronavirus vaccine to help mitigate the impacts of any future coronavirus pandemic.

LONG COVID/PASC Long COVID, or post-acute sequelae of COVID-19 (PASC), are both terms that represent a broad range of symptoms that individuals with SARS-CoV-2 infection can develop days to months after initial infection. Some public health experts are warning that the most recent surge in Omicron cases could lead to a different type of public health crisis, with extended burdens on patients and the healthcare system long after the pandemic ends. Some studies suggest that convalescent COVID-19 patients, especially those who had more severe disease or certain symptoms during acute infection, could be at higher risk of long-term cardiovascular complications or abnormal brain changes. Many patients experiencing long COVID already are waiting months for care, as physicians and clinics try to determine the best way to treat the huge constellation of symptoms that characterize the condition. Research continuously suggests that vaccination could blunt the development of long-term symptoms

A new cohort study published February 4 in JAMA Network Open sought to better understand certain new symptoms and their prevalence among individuals who test positive and negative for SARS-CoV-2 infection, stratified by age and disease severity. New-onset shortness of breath, heart rhythm abnormalities, and type 2 diabetes were more common 31 to 150 days after testing positive than among those with negative results. Among positive individuals over 20 years old, fatigue, shortness of breath, and sleep disorders were the most common new symptoms, whereas change in bowel habits, fatigue, and shortness of breath were the most common new symptoms for positive individuals under 20. The researchers also found that new symptoms—such as anxiety, depression, neuromuscular disorders, peripheral nerve disorders, and uncoordinated movements—were more common among hospitalized and ventilated patients. They called for healthcare providers to be aware of symptoms that might develop among patients after SARS-CoV-2 infection, particularly those who required hospitalization.

ANTIBODY DURABILITY Researchers are continuing to gain insight into SARS-CoV-2 immune responses—and the durability of antibody production—following infection. A study published February 3 in JAMA Network Open suggests that antibodies targeting the receptor-binding domain (RBD) of the spike protein can persist for up to 20 months in unvaccinated individuals who reported test-confirmed COVID-19. While the data are encouraging, it remains unclear how the antibody levels correlate to protection against future infections, especially with new variants. Another study, published February 7 in Nature Microbiology, had similar results, with researchers finding the magnitude of persistent antibody responses were correlated with COVID-19 severity in unvaccinated individuals. They note that while the neutralizing antibody (nAb) response seen in most individuals in the study would be sufficient to provide protection against reinfection and severe infection at 480 days from disease onset, people who had asymptomatic or mild infections likely would need to be vaccinated to maintain antibody-mediated protection against future SARS-CoV-2 infection. With more people becoming infected with SARS-CoV-2 and recovering from COVID-19, the future of the pandemic may see surges of infections due to new variants, but hopefully those cases will result in fewer hospitalizations and deaths. Vaccination remains the most reliable way to help prevent infection, severe disease, and death.

NOVAVAX Novavax on January 7 said it has received expanded US government funding to support late-stage clinical trials for its 2-dose SARS-CoV-2 vaccine among adolescents aged 12 to 17, including a booster component. The company has filed with the US FDA for Emergency Use Authorization (EUA) of its vaccine among adults, and the vaccine has received clearances for use in adults in Great Britain and Germany, as well as endorsement in New Zealand. Israel recently signed a deal to purchase 5 million doses of the protein-based vaccine, and Australia this week received its first shipment of a total order of 51 million doses. Some experts hope that Novavax’s use of protein-based technology will help win over individuals who are reluctant to be vaccinated with shots using newer mRNA technology.

SOUTH AFRICAN VACCINE REPLICATION Scientists at South Africa’s Afrigen Biologics and Vaccines announced last week that they have used publicly available information to produce a close copy of Moderna’s SARS-CoV-2 mRNA vaccine, without the company’s support. The effort—which is backed by the WHO-supported mRNA technology transfer hub launched in June 2021—represents the first mRNA vaccine designed, developed, and produced in an African lab. Scientists are using Moderna-patented technology because the company has vowed to not enforce its COVID-19-related patents against those making vaccines intended to combat the pandemic. However, without the involvement of an mRNA vaccine producer, the process to bring the new vaccine to market could take up to 3 years, instead of about 1 year with support from an outside company, according to the WHO’s Initiative for Vaccine Research. Human clinical trials using the Moderna mimic are expected to begin in the fourth quarter of this year after production is scaled up. Though the long timeline for vaccine production and testing does not address Africa’s urgent need for vaccines, many scientists are enthusiastic that the effort will lay the groundwork for the future development and production of mRNA vaccines on the continent.

OTTAWA STATE OF EMERGENCY The mayor of Canada’s capital declared a state of emergency this week to help police and city staff obtain the resources they need to address a 12 day-long demonstration involving a convoy of truck drivers and other protestors who are blocking the streets of Ottawa, running their large vehicle engines, honking horns, and bringing the city to a standstill. The initial purpose of the “Freedom Convoy,” which arrived in the city on January 29, was to protest vaccine mandates for cross-border truckers, but it has since evolved into a broader demonstration against general COVID-19-related public health measures and now involves others with ties to far-right groups. Over the weekend, police began ticketing and arresting people who were caught bringing fuel, food, or other “material aid” to protestors and cautioned that demonstrators “exhibited extremely disruptive and unlawful behavior” that presents risks to public safety. Some residents reported being harassed for wearing masks. 

Additionally, the crowdfunding platform GoFundMe is facing allegations of fraud from the Florida Governor and Texas State Attorney General after the fundraising platform froze nearly US$10 million in donations to the Freedom Convoy’s fundraiser and said it would redistribute the money to a different charity. After threats of investigations, GoFundMe said it instead will automatically issue refunds to donors, based on police determinations that what began as a peaceful protest has became an occupation. Donors are now using a Christian crowdfunding site called GiveSendGo, which has raised more than US$6 million as of today. The Ottawa demonstrations have become a rallying cry for far-right and anti-vaccine groups worldwide. In Australia today, hundreds of anti-vaccine demonstrators blocked the streets of the capital Canberra, as politicians and their staff return to the city for a week of parliamentary proceedings. 

WHITE-TAILED DEER White-tailed deer infected with SARS-CoV-2 have been identified in at least 15 US states—Arkansas, Illinois, Iowa, Kansas, Maine, Massachusetts, Minnesota, New Jersey, New York, North Carolina, Ohio, Oklahoma, Pennsylvania, Tennessee, and Virginia—adding to concerns that the wild animals could become a potential source of new variants. Researchers looking at deer in Iowa found 1,200 of 2,000 lymph node samples collected from deer that were killed by hunters or car strikes tested positive for the virus. Additionally, white-tailed deer on Staten Island, New York, have been found to be carrying the Omicron variant, the first time the variant has been detected in wild animals. Researchers say it is likely deer are being infected through human contact, then spreading the virus to other deer, and so far there is no evidence that the animals have transmitted the virus back to humans. But more widespread infection among the estimated 30 million deer in the US raises the risk that the animals could become a viral reservoir, which could lead to spillover into humans or other animal species.