January 6, 2022 Johns Hopkins COVID Report

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.

EPI UPDATE The WHO COVID-19 Dashboard reports 294 million cumulative cases and 5.45 million deaths worldwide as of January 5. Global weekly incidence increased substantially last week, up 72% over the previous week. This is the 11th consecutive week of increasing weekly incidence, setting a new record with 9.73 million new cases. The increase is largely due to surges in the Americas (+100%) and Europe (+66%), but all WHO regions reported increases last week. Notably, the WHO reported increases of 38.1% in the Western Pacific, 39.8% in the Eastern Mediterranean, and 77.6% in South-East Asia, but the magnitude of those surges are much smaller than those in the Americas and Europe. Global weekly mortality decreased for the fourth consecutive week, down 8.3% from the previous week. The weekly total of 41,990 deaths is the lowest since the week of October 19, 2020.

Several countries in Europe are setting new records in terms of per capita daily incidence. To our knowledge, the previous record per capita daily incidence was 3,385 daily cases per million population in Seychelles (May 2021). Over the past several days, Greece (3,418), Ireland (3,927), San Marino (4,364), Andorra (4,554), and Cyprus (4,855) all surpassed that record. A number of other countries in Europe, as well as the US, are exhibiting rapidly increasing trends and could surpass the previous record in the coming days or weeks.

Global Vaccination

The WHO reported 9.12 billion cumulative doses of SARS-CoV-2 vaccines administered globally as of January 5. A total of 4.57 billion individuals have received at least 1 dose, and 3.86 billion are fully vaccinated. Analysis from Our World in Data indicates that the overall trend in global daily vaccinations increased from mid-October (21.3 million doses per day) through mid-December (39.9 million). Daily vaccinations have decreased since December 15, down from 40.6 million doses per day to 30.4 million. The trend has persisted since before the holiday season, but some of the decline could be due to vaccination clinics being closed during that time.* Our World in Data estimates that there are 4.63 billion vaccinated individuals worldwide (1+ dose; 58.8% of the global population) and 3.91 billion who are fully vaccinated (49.7% of the global population).

*The average daily doses administered may exhibit a sharp decrease for the most recent data, particularly over the weekend, which indicates effects of reporting delays. In an effort to reflect the longer-term trends, the numbers reported here may not correspond to the most recent data.

UNITED STATES

The US CDC is currently reporting 57.2 million cumulative cases of COVID-19 and 827,879 deaths. The US is averaging 554,328 new cases and 1,238 deaths per day.*

*Changes in state-level reporting may affect the accuracy of recently reported data, particularly over weekends. In an effort to reflect the longer-term trends, the numbers reported here may not correspond to the most recent dates.

Since December 27, 2021, the US has continually set new records for both single-day incidence and average daily incidence. Notably, the US exceeded 300k, 400k, 500k, 600k, 700k, 800k, and 900k new cases reported in a single day for the first time since the onset of the pandemic. The United States’ average daily incidence also exceeded 300k, 400k, and 500k new cases per day for the first time. We expect that part of these massive reports are a result of delays in reporting over the Christmas and New Year’s holiday weekends; however, even reports from the holidays themselves, both of which fell on weekends, were considerably higher than the weekends leading up to the holiday season. The US reported more than 100,000 new cases on Christmas Day and another 200,000 on Sunday, December 26, which is more than 75% higher than the previous weekend total. Similarly, the average from January 1 and January 2 exceeded the previous single-day record from January 2021. On January 3, 2022, the US reported 956,893 new cases. For context, only 45 other countries have reported more cumulative cases than the new US single-day record. The new US record is also a global single-day record, surpassing India’s May 2021 peak of 414,188 new cases by more than double, despite India having nearly 4 times as many people.

Since the US Thanksgiving holiday weekend, daily incidence in the US has increased by a factor of nearly 6, and it has quadrupled since just December 19. The current average of 554,328 new cases per day is more than double the previous record—250,435 on January 11, 2021. The US has reported more than 6 million new cases since December 20.

COVID-19 hospitalizations in the US are rapidly approaching a record high as well. The record is 16,497 new hospitalizations per day (January 8, 2021), and the CDC reported 14,776 on January 2, 2022. The average has nearly doubled since December 18, 2021. The CDC is also reporting a surge in the number of current hospitalizations, up from an average of 61,574 hospitalized COVID-19 patients on December 20 to 85,423 on January 2, an increase of nearly 40% over that period. The current average is 31% below the record high—124,031 on January 11, 2021—but the trend is increasing rapidly. Daily mortality appears to have increased slightly over the past several weeks, but reporting fluctuations over the holidays make it difficult to determine whether this is the start of a longer-term trend. A surge in hospitalizations could place severe stress on health systems nationwide, particularly in the context of staffing shortages in many parts of the country, which could contribute to increased mortality for COVID-19 patients as well as those seeking care for other conditions.

Genomic sequencing data from the US CDC show a continued increase in the prevalence of the Omicron variant across the US. When we last looked at the genomic data, the estimated prevalence at the national level was 73.2% for the week of December 18, 2021; however, the CDC revised its estimate that week down to 37.9%. While that estimate fell substantially, the increasing trend continues, up to an estimated 95.4% for the week of January 1, 2022.** Omicron is estimated to be the dominant variant in all 10 HHS regions, including 8 regions with more than 90%. The lowest estimates are 82.4% in Region 1 (New England) and 77.4% in Region 7 (Central).

**US CDC Nowcast projection.

US Vaccination

The US has administered 514 million cumulative doses of SARS-CoV-2 vaccines. Daily vaccinations peaked on December 6, with 1.71 million doses administered per day. The trend in daily vaccinations continues to decline, down from a recent high of 1.74 million doses per day on December 6 to 971,000 on December 31, a 45% decrease over that period.* Some of this decline could be a result of vaccination clinics, pharmacies, and other vaccination sites being closed over the Christmas and New Year’s holiday weekends, but the trend was already decreasing prior to the holidays.

A total of 245 million individuals have received at least 1 vaccine dose, equivalent to 73.9% of the entire US population. Among adults, 85.9% have received at least 1 dose, as well as 23.3 million children under the age of 18. A total of 207 million individuals are fully vaccinated**, which corresponds to 62.3% of the total population. Approximately 73.0% of adults are fully vaccinated, as well as 18.2 million children under the age of 18. Since August 13, 72.3 million fully vaccinated individuals have received an additional or booster dose. An estimated 34.9% of fully vaccinated individuals have received a booster, including 59.4% of fully vaccinated adults aged 65 years or older.

*Due to delays in reporting, estimates for the average daily doses administered are less accurate for the most recent 5 days. The most current average provided here corresponds to 5 days ago.

**Full original course of the vaccine, not including additional or booster doses.

RAPID ANTIGEN TEST PERFORMANCE As the SARS-CoV-2 virus mutates over time, changes in its genetic makeup could impact the ability of certain tests to recognize and detect viral antigens. A preprint study posted to medRxiv this week raises questions about the reliability of at-home rapid antigen tests in the early days of infection with the highly mutated Omicron variant of concern (VOC). The small real-world study, which is not yet peer-reviewed, examined test results from 30 people who, because of their workplace rules, were undergoing both rapid antigen and polymerase chain reaction (PCR) tests on a daily basis. On days 0 and 1 following a positive PCR test, both of the at-home rapid antigen tests in use—Abbott BinaxNOW and Quidel QuickVue—produced false-negative results despite the presence of viral loads high enough for transmission. The researchers confirmed that 4 cases transmitted the virus between false-negative test results and noted there likely were more transmissions that were unconfirmed. On average, it took 3 days for people to test positive on a rapid antigen test after testing positive on a PCR test. The researchers shared their results with US CDC and US FDA officials and called for the real-world performance of rapid antigen tests to be reassessed for each new VOC.

The study’s results suggest that even if the supply and accessibility of at-home tests were sufficient, rapid antigen testing might not be reliable as an early warning, when people are most infectious and before symptoms begin. Although these findings warrant further study, scientists and public officials are urging the public to continue rapid testing but to use caution when interpreting the results. Some evidence suggests that Omicron might replicate more quickly and efficiently in the throat and mouth than in the nose. And while some individuals have reported swabbing their throats and noses in the hope of increasing the accuracy of test results, the FDA maintains the at-home tests should be used only as authorized. The agency recently updated its information on how SARS-CoV-2 variants could impact tests’ performance.

PFIZER-BIONTECH BOOSTER & ADDITIONAL DOSES This week, the US FDA and US CDC made several adjustments to the emergency use authorization (EUA) and recommendations for the Pfizer-BioNTech SARS-CoV-2 vaccine. On January 3, the FDA made 3 amendments to the EUA, including expanding the use of booster doses to include adolescents aged 12-15 years; shortening the time between primary series and booster to 5 months from 6 months for people who received the Pfizer-BioNTech vaccine; and allowing for a third primary series dose for certain immunocompromised children ages 5 to 11 years. The following day, the CDC updated its recommendation for booster dose timing to 5 months, noting the interval recommendations for other vaccines remains the same (2 months for J&J-Janssen; 6 months for Moderna). The agency also recommended that moderately or severely immunocompromised 5- to 11-year-olds receive an additional primary dose of vaccine 28 days after their second shot. The CDC’s Advisory Committee on Immunization Practices (ACIP) on January 5 voted 13-1 in favor of expanding eligibility of and strengthening the recommendation for Pfizer-BioNTech booster doses in adolescents aged 12-15 years, and the CDC later that day endorsed the recommendation. In a statement, CDC Director Dr. Rochelle Walensky said booster doses 5 months after a primary series “will provide optimized protection against COVID-19 and the Omicron variant” for adults and adolescents aged 12-17. Only the Pfizer-BioNTech vaccine is authorized for individuals under age 18.

During a White House press briefing, Dr. Walensky cited outcomes from several studies conducted in Israel that suggest booster doses decrease the risks of infection, severe disease, and death. Notably, the studies were conducted when the Delta variant of concern was predominant, but Dr. Walensky said “we expect to see a similar trend of increased protection” for the Omicron variant. Israel on January 2 became the first country to officially recommend a fourth dose of SARS-CoV-2 vaccine to people aged 60 and older and medical workers who had their last dose at least 4 months ago. Fourth doses already were available to people with weakened immune systems and residents and staff of nursing homes. The Israeli government said preliminary data show a fourth dose of the Pfizer-BioNTech vaccine spurred an average fivefold increase in antibodies 1 week post-shot. However, some experts question the move, saying too many booster rounds could further vaccine inequity and potentially dampen the immune response if too many doses of the same vaccine are administered. Israel is reporting a record number of new COVID-19 cases, with nearly 12,000 recorded on January 5. Little data on the safety and efficacy of additional doses is not stopping some in the US from seeking fourth, fifth, or even sixth shots, particularly those with compromised immune systems who fear infection. However, some researchers believe that certain immunocompromised people may never generate immune system responses to the vaccines, no matter how many doses they receive.

US CDC QUARANTINE & ISOLATION GUIDANCE In late December, the US CDC updated its guidance regarding isolation for individuals who test positive for SARS-CoV-2 infection. The CDC shortened the recommended isolation period to 5 days for individuals who are asymptomatic or whose symptoms have resolved. After that point, those individuals should wear masks in public to mitigate the risk of transmission to others. The shortened isolation period is based on data that indicate that “the majority of SARS-CoV-2 transmission occurs…in the 1-2 days prior to onset of symptoms and the 2-3 days after.”

Notably, the updated isolation guidance did not include a negative test as a condition to end the isolation period. In response to criticism regarding the absence of a testing requirement—particularly in the context of a shorter isolation period in the midst of the United States’ largest surge to date—the CDC issued a subsequent update on January 4. But rather than including a testing requirement, the CDC provides recommendations regarding how an individual should proceed if s/he “has access to a test and wants to test.” The American Medical Association on January 5 released a statement expressing concern over the guidelines’ exclusion of testing, saying the “recommendations put our patients at risk and could further overwhelm our healthcare system.”

The CDC also updated its guidance regarding quarantine following exposures to known COVID-19 cases. Individuals who are not fully vaccinated should quarantine for 5 days following the exposure, followed by strict mask use for an additional 5 days. If a 5-day quarantine is not practicable, then exposed individuals should wear a mask for 10 days. Individuals who are fully vaccinated do not need to quarantine following an exposure, as long as they remain asymptomatic; however, they should wear a mask in public for 10 days. In this context, the CDC defines fully vaccinated as having received a full original course of the vaccine—eg, 2 doses for the Moderna and Pfizer-BioNTech vaccines and 1 dose of the J&J-Janssen vaccine—as well as a booster dose as recommended—6 months after the second dose of the Moderna or Pfizer-BioNTech vaccines and 2 months after the J&J-Janssen vaccine for adults. Individuals who have tested positive for SARS-CoV-2 in the past 90 days are treated similarly to fully vaccinated individuals. The CDC also recommends testing for all exposed individuals at Day 5 or later after the exposure. As with the previous guidance, anyone who develops symptoms should self-isolate until they receive a negative test or an alternate diagnosis that explains the symptoms.

On December 23, the CDC updated guidance specifically for healthcare workers following exposures to SARS-CoV-2. The new recommendations include updates regarding the process and timeline for returning to work following an exposure as well as the definition of “higher-risk exposures.” The update includes specific testing requirements and timelines for healthcare workers to return to work following SARS-CoV-2 infection, depending on their vaccination status and the presence and severity of symptoms. Largely, fully vaccinated and boosted healthcare workers do not face any work restrictions following an exposure, as long as they remain asymptomatic and do not test positive for SARS-CoV-2 infection, even with a higher-risk exposure. Under the updated guidance, healthcare workers wearing a face mask are no longer considered to have a higher-risk exposure if the patient is also wearing a face mask. Previously, exposures were considered to be higher risk if the healthcare worker was not wearing a respirator. At least 4 nursing organizations have expressed concern over the guidance for healthcare workers, with the American Nurses Association saying the “guidance is premature given what is known about the Omicron variant and tips toward economic needs as opposed to the health needs of nurses and other healthcare workers.”

COVID-19 TREATMENTS As the number of new COVID-19 cases skyrockets in the US, hospitalizations too are beginning to rise. While some nations—including South Africa and the UK—have seen lower hospitalization rates due to the Omicron variant of concern (VOC) compared with previous variants, it remains unknown whether this will be the case in the US. Full vaccination with a booster dose remains the best way to prevent severe COVID-19, but keeping people with the disease from progressing to more severe disease requiring hospitalization is imperative, to both save lives and lessen the strain on the healthcare system. Two highly anticipated and recently authorized antivirals—Pfizer’s Paxlovid and Merck and Ridgeback Biotherapeutics’ molnupiravir—are administered to patients recovering at home to help prevent progression to more severe disease, but the medications are in limited supply, causing dismay among healthcare providers. US President Joe Biden on January 4 announced the government will double its order of Paxlovid to 20 million courses, but long manufacturing times means only 435,000 of those courses are expected to be delivered over the next 2 months. The US government also has purchased 3 million of molnupiravir, with about 300,000 courses already delivered to states based on population. With the limited supply, doctors must make choices about who might benefit the most from the antivirals, both of which are recommended to be administered within 5 days of symptom onset.

While both of the newly authorized antivirals are expected to work against Omicron, 2 of the 3 monoclonal antibody treatments available under FDA emergency use authorization (EUA) do not work against the VOC. After a short pause in distribution, the US government restarted shipments of both Eli Lilly’s bamlanivimab plus etesevimab and Regeneron’s casirivimab plus imdevimab (REGEN-COV) monoclonal antibody therapies, which should be used for patients in areas where the Delta VOC represents a significant portion of cases and other options are not available. The US Health and Human Services (HHS) in a statement warned that the treatments would be ineffective if given to patients with the Omicron VOC and noted other therapeutics—including oral and intravenous (IV) antivirals and GSK/Vir Biotechnology’s sotrovimab monoclonal antibody—are effective alternatives against Omicron. A study published December 22, 2021, in the New England Journal of Medicine (NEJM) examining the IV antiviral remdesivir (Veklury) in symptomatic, non-hospitalized patients with COVID-19 at high risk of disease progression showed a 3-day course of the drug was safe and resulted in an 87% lower risk of hospitalization or death than placebo. Notably, Gilead Sciences, the drug’s maker, funded the study and submitted the trial results to the US FDA to consider expanding the drug’s approval for use in earlier stages of COVID-19.

On December 28, the FDA both expanded and limited the EUA for convalescent plasma to treat COVID-19 by restricting the use of high-titer convalescent plasma to patients with immunosuppressive disease or receiving immunosuppressive treatment but allowing its use in either outpatient or inpatient settings. Previously, the therapy was allowed to be used among any hospitalized COVID-19 patients early in their disease course, but EUA revisions have narrowed the treatment’s use since it was first authorized in August 2020. Additionally, a group of physician-scientists led by Dr. David Boulware of the University of Minnesota filed an EUA application with the FDA for fluvoxamine—a generic selective serotonin reuptake inhibitor (SSRI) that is used to treat several mental health conditions such as depression—to treat COVID-19. Technically, physicians could prescribe the medication off-label for COVID-19 but some might be reluctant to or work in settings that prohibit the practice. The EUA application is based primarily on 2 randomized controlled clinical trials supporting fluvoxamine’s use to prevent disease progression, and Dr. Boulware noted several other studies are looking at whether the drug can help prevent hospitalizations or death among COVID-19 patients.

OMICRON SCHOOL DISRUPTIONS The Omicron variant of concern (VOC) is causing disruptions in nearly every country worldwide. While there is still uncertainty regarding the variant’s clinical presentation, evidence suggests it causes less serious disease, is more transmissible than its predecessors, and is able to at least partially evade preexisting immunity. But a rapid increase in the number of cases worldwide has led to interruptions and staffing shortages in the healthcare, travel, and other industries. Schools are no exception. Analysis from Burbio's School Tracker shows nearly 5,000 pandemic-related disruptions to K-12 US public schools in this week alone. In Chicago, Illinois, the third largest school district in the US closed schools again for a second day, sending more than 350,000 students home as the teachers union and city officials continue a standoff over COVID-19 safety protocols. School closures, delays in returning to in-person learning after the winter holidays, and returns to remote learning in other districts nationwide have parents scrambling for resources and clarity, with some desiring children return to schools and others relieved their children do not have to return to classrooms. According to US CDC data, a record high number of children are being hospitalized with confirmed COVID-19.

In Europe, countries are prioritizing the reopening of schools. France, Greece, and Ireland—which boasts 91% of ages 12 and older fully vaccinated—are returning to in-person schooling with strategies including increased testing and expanded inoculations to kids as young as 5 years old. In England, school leaders are witnessing high levels of staff absences at schools and daycare centers due to COVID-19. Some teachers and one union have expressed concern about government guidance that advises combining classes in the event of staff shortages, citing the possibility of increased transmission. Like the US, countries across the European region are loosening quarantine and isolation restrictions to ease staffing shortages and missed time in class.

PREGNANCY & BIRTH OUTCOMES Pregnant people with COVID-19 have an increased risk for severe illness and adverse birth outcomes. Still, many are reluctant to receive vaccination against COVID-19, with only about 40% of pregnant people in the US fully vaccinated as of mid-December. A retrospective cohort study involving more than 45,000 pregnant people published this week in the US CDC’s Morbidity and Mortality Weekly Report (MMWR) found that SARS-CoV-2 vaccination during pregnancy was not associated with increased risks of preterm delivery or underweight newborns. The data—drawn from 8 healthcare organizations in 6 US states—support the CDC’s recommendation of vaccination and booster doses for all people who are pregnant, recently pregnant, or who are trying to become pregnant. Notably, most of the people involved in the study became pregnant prior to the availability of vaccines and those who were vaccinated received the shots in the second or third trimester, so the study does not include information on first-trimester vaccinations. Experts continue to recommend vaccination for all pregnant people, as the risk of preterm birth is higher among those infected with SARS-CoV-2 and vaccination may help protect infants by passing along beneficial antibodies. A study published in Pediatrics this week suggests that vaccine-induced SARS-CoV-2 antibodies in human breast milk, including IgG and neutralizing activity, persist for up to 6 months.

Another study, published in JAMA Pediatrics, found that in utero exposure to maternal SARS-CoV-2 infection was not associated with differences in neurodevelopment at age 6 months. However, the researchers did find that birth during the pandemic, regardless of SARS-CoV-2 exposure, was associated with slightly lower scores on developmental screening tests of social and motor skills at 6 months compared to infants born right before the pandemic. The researchers said the results suggest that pandemic-related stresses among parents or caregivers, such as job loss or housing insecurity, could have contributed to the small differences between infants born before and during the pandemic. They noted the results of the small study do not necessarily mean infants born during the pandemic will have lasting neurodevelopmental impairment, and they plan to follow the 255 newborns involved in the study.

B.1.640.2 VARIANT Researchers late last year identified a new SARS-CoV-2 variant with 46 mutations and 37 deletions compared with the original novel coronavirus, but the WHO has said the variant is of little concern, for now. The B.1.640.2 variant was first recognized in October 2021 by researchers in France, who dubbed the variant “IHU” after the Méditerranée Infection University Hospital Institute (IHU) that helped to identify it. The isolate came from a vaccinated person who had recently traveled to Cameroon, where the variant is assumed to have originated. So far, fewer than 20 samples have been sequenced, and only 1 in December, compared to the more than 120,000 Omicron variant sequences that have been uploaded to the Gisaid database since its discovery in late November. Many SARS-CoV-2 variants have been identified since the beginning of the pandemic, but many of them never cause widespread infections. The B.1.640.2 variant is likely piquing interest due to the publication of a preprint article (not peer-reviewed) describing it posted on December 29, as well as the heightened anxiety surrounding the recently discovered, highly transmissible, and extensively disruptive Omicron variant of concern. Although experts are not worried about the B.1.640.2 variant at this time, new variants continue to be a threat until more of the world is vaccinated.