Updates on the COVID-19 pandemic from the Johns Hopkins Center for Health Security.
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FIRST, A THANK YOU The COVID Tracking Project is ending its long-term monitoring and analysis of the US COVID-19 epidemic. From early on in our own COVID-19 efforts, we have come to rely on their data, analysis, and figures in our briefings. Thank you to the COVID Tracking Project team for their hard work over the past year in helping provide data to track the pandemic.
EPI UPDATE The WHO COVID-19 Dashboard reports 115.29 million cases and 2.56 million deaths as of 10:00am EST on March 5.
As global attention on emerging variants continues to increase, this week we will look at global data on several of the prominent variants of concern (VOCs): B.1.1.7, B.1.351, and P.1. In many (if not most) countries, surveillance systems are not fully capturing the spread of emerging variants, but epidemiological data are increasing in many parts of the world. Unlike general COVID-19 incidence and mortality, which are tracked via countless official and unofficial databases and dashboards, obtaining quality data on emerging variants is more difficult. Efforts to track the geographic and community spread of these variants are growing, however.
While traditional diagnostic and serological testing are designed to generally identify current or past infection, genomic sequence data are often required to identify the specific variant causing the infection. Some traditional diagnostic tests do target specific sections of the viral genome that can vary between variants—such as the S-gene target failure (SGTF) in specimens infected with the B.1.1.7 for certain PCR-based tests—which can enable them to serve as a “proxy” for sequencing. The values reported below are certainly underestimates of the prevalence of these variants, and sequencing capacity varies considerably between and within countries.
The B.1.1.7 variant is the most geographically widespread of the 3 primary VOCs. In total, more than 121,000 sequences of the B.1.1.7 variant have been reported worldwide, and infections have been reported in at least 94 countries (84 with sequence data). The variant was first reported in the UK, and it was then detected throughout Western Europe and Australia. Canada, India, and the US were among the next countries to report the variant. More recently, several countries in South America, across Eastern Europe and the Eastern Mediterranean region, Southeast Asia, and Russia have reported cases. Several countries in Africa have also reported the variant. The UK still leads all countries in terms of the number of reported sequences, with more than 100,000 (nearly 90% of the global total). Notably, the proportion of sequenced specimens containing the B.1.1.7 variant is increasing on nearly every continent.
The B.1.351 variant appears to be much less pervasive than the B.1.1.7 variant, with only 2,515 total sequences globally across 48 countries (41 with sequence data). The variant first emerged in South Africa, followed by several other countries in Southern Africa and Australia. These countries were followed by Western Europe and then Canada, the US, Japan, and South Korea. While the relative proportion of B.1.1.7 in sequenced specimens is increasing, the B.1.351 appears to be remaining more consistent across most continents.
In total, 429 infections with the P.1 variant have been reported across 25 countries (19 with sequence data). The variant was first reported in Brazil, which has reported more than 60% of the global sequences to date. The variant has been reported in several other South American countries, Western Europe, Canada, the Faroe Islands, Japan, South Korea, Turkey, and the US. The relative proportion of the P.1 variant among sequenced specimens is relatively low outside of South America (approximately 20-40%); however, it appears to be increasing slowly in Europe.
In the US, the CDC is utilizing multiple surveillance systems and networks to gather genomic data from positive SARS-CoV-2 tests, including the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance (SPHERES) consortium and the National SARS-CoV-2 Strain Surveillance (NS3) system. The US has reported 2,672 infections of the B.1.1.7 variant across 46 states; Washington, DC; and Puerto Rico. Most of the cases involving the B.1.1.7 variant have been identified in Florida (642), Michigan (421), and California (250). Independent analysis by a private sector laboratory company, Helix, shows the highest incidence of the B.1.1.7 variant in Florida, California, Georgia, and Pennsylvania.
The US CDC has reported considerably fewer cases involving other VOCs, including 68 infections of the B.1.351 variant across 16 states and Washington, DC, and 13 infections with the P.1 variant across 7 states. These totals are certainly an underestimate of the total impact of these variants, as only a small portion of specimens undergo genomic sequencing or other genetic analysis. In fact, even the best-performing state, Wyoming, has only sequenced 3.5% of its positive specimens, and more than half of all US states have sequenced fewer than 0.5%. As discussed below, researchers and health officials in the US are identifying newly emerging variants as well, including the B.1.526 variant, first reported in New York, and the B.1.427/429 variants, first reported in California, but the US CDC is not yet reporting data on those variants.
In mid- February, Center experts published a report on policy recommendations to identify and manage variants of concern.
Our World in Data reports that 283.6 million vaccine doses have been administered globally, a 24% increase compared to this time last week. The daily average increased to 7.78 million doses, 64% higher than this time last week (up from 4.73 million doses). Vaccination efforts have been reported in at least 119 countries and territories.
The US CDC reported 28.58 million total cases and 517,224 deaths. The decline in daily incidence and mortality that persisted for the past several weeks appears to have leveled off to some degree. Daily incidence has remained between approximately 63-67,000 new cases per day since February 20, and daily mortality has hovered between approximately 1,900 and 2,100 deaths per day since February 19. Some of this trend could be the result of states catching up on reporting after recovering from severe winter weather, but it could be an early sign that the steep decline is coming to an end. Notably, both the daily incidence and mortality remain elevated, on par with or higher than the first 2 peaks.
The US CDC surpassed 100 million vaccine doses distributed (109.9 million) and 80 million million doses administered (82.6 million) nationwide. In total, 54.0 million people (16.3% of the entire US population; 21.2% of the adult population) have received at least 1 dose of the vaccine, and 27.8 million (8.4%; 10.9%) have received both doses. The US set a new record high for daily doses administered, with 1.8 million doses per day*. The breakdown of doses by manufacturer remains relatively steady, with slightly more Pfizer-BioNTech doses (42.2 million) than Moderna (40.3) doses administered nationwide. No doses of the J&J-Janssen vaccine have been reported yet.
*The US CDC does not provide a 7-day average for the most recent 5 days due to anticipated reporting delays for vaccine administration. This estimate is the most current value provided.
A total of 7.3 million doses have been administered at long-term care facilities (LTCFs)**, including residents and staff. This covers 4.7 million individuals with at least 1 dose and 2.5 million with 2 doses.
**The dashboard only includes data for doses administered through the Federal Pharmacy Partnership for Long-Term Care (LTC) Program. It does not report data from West Virginia, which opted out of the program.
EMERGING VARIANTS Novel SARS-CoV-2 variants, and associated surveillance data, continue to emerge around the world. Several high-profile variants—including B.1.1.7, B.1.351, and P.1—have gained attention due to concerns about their ability to transmit more efficiently, evade immune responses from therapeutics and vaccines, and increase disease severity. While the world focused on these variants, others continue to emerge, including in the US. Recently, researchers identified the B.1.526 variant in New York and the B.1.427 and B.1.429 variants in California.
The B.1.526 variant emerged in New York in November 2020, and 2 recent studies by researchers at the California Institute of Technology (Caltech) and Columbia University (New York)—both preprints—provide preliminary analysis of the variants’ characteristics relative to existing strains. The B.1.526 variant currently includes 2 versions of the virus, with one exhibiting the E484K mutation—found in the P.1 and B.1.351 variants—that helps the virus evade vaccine-induced immune response and the other exhibiting the S477N mutation that is believed to “affect how tightly the virus binds to human cells.”
The B.1.427 and B.1.429 variants were recently identified in California by researchers at the University of California, San Francisco (UCSF) and Cedars-Sinai Medical Center in Los Angeles. Early research on these variants* suggests that their transmissibility could be on par with the B.1.1.7 variant, which is quickly becoming the dominant variant in multiple countries. Reportedly, one study found that the variants were “40 percent more effective at infecting human cells than earlier variants.” Researchers also identified elevated viral loads in patients infected with the new variants, and they found evidence that the variants are better able to evade immune responses.
*To our knowledge, two studies on these emerging variants have not yet been published publicly.
Further study is needed to more fully characterize these new variants, but their emergence in the US illustrates the importance of containing transmission as vaccination efforts scale up. Vaccination is an important tool in bringing the pandemic under control, but it cannot be an excuse to prematurely relax risk mitigation measures or vigilance in adhering to existing guidance. Scaling up sequencing volume for SARS-CoV-2 specimens and facilitating collaboration and data sharing across disparate institutions will be key to generating a more comprehensive picture of genetic variations and evolution of SARS-CoV-2 in the US and around the world. Additionally, increasing the pace of global vaccination efforts, including through expanding international production of US- and European-developed vaccines, is critical to limiting transmission in countries around the world and mitigating the risk of future novel variants emerging.
GERMANY AUTHORIZES AZ-OXFORD VACCINE FOR ADULTS 65+ Germany’s national vaccine committee on Thursday formally recommended the AstraZeneca-Oxford SARS-CoV-2 vaccine for use in all adults, including those age 65 years and older. Germany initially withheld endorsement for older adults, citing a lack of data; however, recent real-world data from the UK and clinical studies show the vaccine is highly effective among older adults. While Health Minister Jens Spahn called the committee’s move “good news,” many Germans remain skeptical of the vaccine’s effectiveness. Germany’s decision to expand eligibility for the AstraZeneca-Oxford vaccine comes alongside similar announcements by Belgium, Denmark, France, and Sweden.
INDIAN VACCINE Bharat Biotech, developer of India’s SARS-CoV-2 vaccine, announced preliminary Phase 3 clinical trial results. The vaccine is already authorized for emergency use in India—issued on January 3, 2021, more than 2 months prior to release of the Phase 3 trial data. The trials included 25,800 participants (including more than 2,400 over the age of 60), half of whom received the vaccine. The vaccine demonstrated an overall efficacy of 81% in preventing COVID-19 disease (mild, moderate, or severe). The researchers have identified 130 total cases of COVID-19 among the participants, but the interim analysis is based on data from only the first 43 cases (36 among the control group and 7 among vaccinated participants). Like many of the existing SARS-CoV-2 vaccines, the results were announced via press release, and the full trial data have not yet been published publicly or been subjected to peer review. Bharat committed to publishing both the second interim analysis and final analysis via preprint servers and in peer-reviewed journals. Reportedly, many Indians have been hesitant to get vaccinated with the Bharat product until Phase 3 trial data were published.
Like many other SARS-CoV-2 vaccines, the Bharat vaccine requires 2 doses, but it does offer several advantages. The vaccine is stable at normal refrigerator temperatures (36-46°F; 2-8°C), and it can remain viable for 28 days after vials are opened, both of which can ease logistical and operational challenges for mass vaccination efforts. One notable difference from existing vaccines is that the Bharat vaccine utilizes an inactivated version of the SARS-CoV-2 virus, as opposed to mRNA or other viral platform to stimulate the immune response, similar to the vaccines developed by Sinopharm and Sinovac in China.
LONG-TERM EFFECTS IN CHILDREN A report from Kaiser Health News (KHN) discusses increases in pediatric cases of post-acute sequelae of SARS-CoV-2 infection (PASC)—commonly referred to as “long COVID-19.” Perhaps the most serious of these conditions is multisystem inflammatory syndrome in children (MIS-C), which has been reported in at least 2,060 children across the US, including 33 deaths (through March 1, 2021). Black and Hispanic/Latino children are disproportionately affected, representing 66% of the reported cases.
Children’s hospitals across the country are struggling to treat pediatric PASC patients, because so much remains unknown about the condition, particularly in children. Several facilities—including the University Hospitals Rainbow Babies & Children’s Hospital in Cleveland, Ohio—are establishing dedicated clinics to treat these patients and gather data to better characterize the long-term effects of SARS-CoV-2 in pediatric patients. KHN notes that disparities in US health coverage could potentially lead to large out-of-pocket costs specialize care, particularly because uncertainty surrounding the condition could necessitate a large number of tests and treatments.
With no available vaccine for children under age 16, and many school systems resuming in-person classes, in the US and around the world, it will be important to study the lasting effects of SARS-CoV-2 infection among children, including those with mild or asymptomatic infection in children.
US VACCINATION US President Joe Biden announced this week that the US has secured enough vaccine supply to vaccinate every US adult by the end of May, accelerating the previous timeline, which aimed to achieve that milestone by July. He also highlighted the ongoing efforts by FEMA to support vaccine distribution and collaborate with state governments to establish mass vaccination sites. Notably, President Biden urged all states to prioritize teachers, school staff, and childcare providers for vaccination as essential workers. He emphasized that existing CDC guidance can help schools mitigate COVID-19 risk and enable them to resume in-person classes even if teachers are not yet vaccinated, but he acknowledged that many educators have concerns. Currently, at least 30 states already prioritize teachers for vaccines, but President Biden aims to make that consistent across the country. He challenged states to administer at least 1 dose of the vaccine to every educator, school employee, and childcare provider by the end of March, and the US government intends to utilize federal vaccine distributions to pharmacies to further this effort.
GLOBAL VACCINE DISTRIBUTION Italy denied a request by AstraZeneca to export more than 250,000 doses of its SARS-CoV-2 vaccine, developed in collaboration with the University of Oxford, to Australia. According to a statement issued by the Italian Ministry of Foreign Affairs, Italy previously permitted the export of small quantities of the vaccine for research purposes; however, due to the quantity of vaccine in the recent request, Italy submitted a request to the European Commission (EC) to deny the export, which was approved by EC leadership. As part of its justification, Italy noted that Australia “is considered ‘non-vulnerable’” and that the large export would exacerbate ongoing shortages in Italy and the rest of the EU. This is the first time an EU country has blocked the export of a SARS-CoV-2 vaccine. Reportedly, Australia requested that the EC review its decision, but Australian officials emphasized that the blocked shipment would not have a major impact on its vaccination or COVID-19 control efforts. This incident highlights challenges in terms of ensuring equitable global access to SARS-CoV-2 vaccines, particularly for countries without domestic production capacity.
US VACCINE EQUITY & ACCESS State-level decisions regarding local distribution of SARS-CoV-2 vaccine doses have called attention to disparities in access between urban and rural areas. In some states, lawmakers and public health officials have raised concerns that too many vaccine doses are being distributed to urban centers and too few to rural areas. The vaccine supply in some urban areas is not sufficient to cover the large populations of healthcare workers who live there, which in turn, limits availability for other high-priority populations, such as older adults. In some instances, rural areas have already expanded eligibility to younger portions of the population, and older adults from urban areas who are unable to obtain a vaccination appointment locally are traveling to rural areas to get vaccinated.
According to a report from STAT News, a recent vaccination event in a rural, low-income area of Florida, where 60% of the population are Black and 25% Hispanic, most of the available doses were administered to individuals who lived elsewhere, including wealthier communities in West Palm Beach and Miami, many of whom were White. Even in wealthier communities, there are noticeable racial and ethnic disparities in terms of vaccination. For example, Black and Hispanic individuals make up nearly 40% of the population in Palm Beach County, but they have received less than 10% of the doses administered there.
Some experts and public health officials have expressed concern that the Johnson & Johnson (J&J)-Janssen vaccine could face challenges in terms of equitable distribution. Unlike the Moderna and Pfizer-BioNTech vaccines, the J&J-Janssen vaccine requires only one shot and can be stored for up to 3 months under normal refrigeration temperatures. Some experts have raised concerns that earmarking the J&J-Janssen vaccine for lower-income or rural communities could raise equity issues due to its lower reported efficacy relative to the other vaccines.
Dr. Marcella Nunez-Smith, head of the White House's COVID-19 Health Equity Task Force, acknowledged the vaccine’s advantages, but added its distribution "should be even across communities." Dr. Ruth Faden, Director of the Johns Hopkins Berman Institute of Bioethics, and Dr. Ruth Karron, Director of the Johns Hopkins Center for Immunization Research, emphasize that perceptions that certain communities are receiving an inferior vaccine could exacerbate existing vaccine hesitancy, particularly among lower-income and racial and ethnic communities. While the J&J-Janssen vaccine offers some logistical and operational advantages over other vaccines, it is essential to continue even distribution of all 3 vaccines.
BRAZIL Brazil is reporting its highest daily incidence and mortality to date, and health systems across the country are straining to handle the ongoing surge. Brazil is averaging more than 57,000 new cases and 1,300 deaths per day, an increase of 27% and 31%, respectively, over the past 2 weeks. On March 3, Brazil reported 1,910 deaths, its highest single-day total since the onset of the pandemic. According to a report by Fundação Oswaldo Cruz (FioCruz), the ICUs in 18 of 26 states are operating at over 80% capacity, and 9 of those are above 90% capacity, the most severe situation since the beginning of Brazil’s COVID-19 epidemic. Among the worst affected states are Rondônia and Rio Grande do Sul, where ICUs are operating at 97.5% and 97.2%, respectively. Additionally, the Federal District—home to Brazil’s capital city, Brasilia—is reporting ICUs at 96.45%. Vaccine rollout has been incredibly slow, with only 3% of the population receiving at least 1 dose of the vaccine and only 1% receiving both doses.
The combination of emerging variants, including the P.1 variant first identified in Brazil, and recent large-scale events such at Carnival are raising concerns about the potential for the emergence of new variants. Ongoing widespread community transmission will continue to provide the virus with an opportunity to mutate. Dr. Miguel Nicolelis, a epidemiologist and neuroscientist from Duke University (North Carolina, US) described the situation as “the largest open laboratory in the world for the virus to mutate.” Over the course of its epidemic, the Brazilian government has often been reluctant to impose risk mitigation measures, and the country is on track to surpass the US as the #1 country globally in terms of daily incidence in the coming days.
HUNGARY The Hungarian government announced tighter COVID-19 restrictions following in response to its ongoing COVID-19 surge. From March 8 to 22, non-essential businesses and services are suspended, restaurants will close for in-person dining, and in-person learning for kindergarten and primary school will be suspended until after spring break (April 7). Sporting events will continue, but no spectators will be permitted. These measures will be implemented in addition to existing restrictions, including an 8pm-5am curfew, mask mandate, and remote learning for high schools and universities. All measures will be enforced with fines or the closure of violating places. The new measures aim to curb transmission in time for the Easter holiday.
In an effort to expand vaccination coverage, Hungary decided to alter its vaccination plan to focus on ensuring as many people as possible receive the first dose of vaccine. Hungary will delay the interval between the first and second dose for both the Pfizer-BioNTech and AstraZeneca-Oxford vaccine. The second dose of the Pfizer-BioNTech vaccine will be administered at 35 days instead of 21, and the second dose for the AstraZeneca-Oxford vaccine will now be administered at 12 weeks.
COMMUNIVAX WEBINAR The Johns Hopkins Center for Health Security is hosting a webinar as part of the CommuniVax initiative to discuss recommendations from its first report on engaging communities of color to promote equity in SARS-CoV-2 vaccination. The combination of longstanding disparities and mistrust in government and the healthcare system among racial and ethnic minority communities and a disproportionate impact of COVID-19 pose significant challenges to ensuring equitable access to SARS-CoV-2 vaccination for those at elevated risk for infection and severe COVID-19 disease and death.
The webinar will include presentations by Dr. Monica Schoch-Spana from the Johns Hopkins Center for Health Security, Lois Privor-Dumm from the Johns Hopkins International Vaccine Access Center, Dr. Stephen B. Thomas from the Maryland Center for Health Equity, and Ysabel Duron from The Latino Cancer Institute, with Dr. Emily Brunson from Texas State University as moderator. The webinar will be held on Thursday, March 18 at 2pm EDT. Advance registration is required.
HEALTH SECURITY SPECIAL FEATURE: GENE DRIVES The Johns Hopkins Center for Health Security’s peer-reviewed journal, Health Security, is publishing a Special Feature devoted to regulation for gene drives and similar biotechnology in the US. Existing biotechnology frameworks may not adequately address emerging capabilities like gene drives. This Special Feature will focus on methods, programs, research, and policies that promote an optimal balance between developing and leveraging gene drive capabilities and effective oversight to mitigate the risk of misuse. Articles can be submitted for consideration though May 31, 2021.