Updates on the COVID-19 pandemic from the Johns Hopkins Center for Health Security.

Additional resources are available on our website.

The Center also produces US Travel Industry and Retail Supply Chain Updates that provide a summary of major issues and events impacting the US travel industry and retail supply chain. You can access them here.
EPI UPDATE The WHO COVID-19 Dashboard reports 107.42 million cases and 2.36 million deaths as of 9am EST on February 12. 

Approximately two-thirds of countries and territories worldwide are reporting decreasing trends in COVID-19 incidence. In total, 123 countries and territories (62.8%) are reporting a negative weekly growth rate—relative change in 1-week incidence compared to the previous week—compared to 73 with a positive growth rate over that time. 131 countries are reporting decreased incidence over the past 2 weeks (67.2%), compared to 64 with an increasing biweekly trend. Notably, 34 countries/territories are reporting decreases by half or more compared to 2 weeks ago, including 9 with decreases of 100% over the past 2 weeks (ie, currently averaging zero new cases per day). The largest biweekly increases are in Guinea-Bissau (+485%), Somalia (+473%), and Antigua and Barbuda (+436%), all of which exceed +400% over the past 2 weeks. In total, 28 countries are reporting biweekly increases of 50% or more, and only 11 with increases of 100% or more over that time. The overall global trend is a decrease of 24% over the past 2 weeks.

Countries and territories with decreasing daily incidence are spread across the globe, with several small pockets of increasing incidence. The areas with the highest concentration of countries/territories reporting positive biweekly growth rates are the northern part of Sub-Saharan Africa, including along the coast of West Africa and across Central Africa to Somalia; Southeast Europe; the Eastern Mediterranean region, including much of the Arabian Peninsula; and Southeast Asia, including Papua New Guinea.

Our World in Data reports that 160.07 million vaccine doses have been administered globally, a 28% increase compared to this time last week.

The US CDC reported 27.13 million total cases and 470,110 deaths. Daily incidence in the US continues its steady decline, now just slightly more than 100,000 new cases per day. Daily mortality continues to decrease as well, back down to slightly more than 3,000 deaths per day. We expect that to fall further in this afternoon’s update, as February 5 moves out of the 7-day window*. That being said, multiple reports indicate that Ohio may have inadvertently underreported COVID-19 deaths in November and December 2020. Ohio Governor Mike DeWine stated that Ohio underreported COVID-19 mortality by approximately 4,000 deaths over the past several months. An investigation into the mortality reporting is underway, and the deaths are expected to be included in official reports over the next several days. This would bring Ohio’s cumulative mortality from approximately 12,000 to 16,000, an increase of approximately one-third. This would also bring the cumulative national total to nearly 475,000 deaths, and depending on how the deaths are reported, it could artificially inflate the current daily average.
*On February 5, Indiana reported 1,507 new deaths, many of which were previously unreported deaths from earlier in its epidemic.

US Vaccination
The US CDC reported 68.29 million vaccine doses distributed and 46.39 million doses administered nationwide (67.9%). The CDC has added new data to its vaccination dashboard, including demographic data.

In total, 34.72 million people (10.5% of the entire US population) have received at least 1 dose of the vaccine, and 11.19 million (3.4%) have received both doses. The average daily doses administered is once again increasing, now up to a record high of 1.46 million doses per day*. The number of people receiving their second dose is increasing at nearly 550,000 per day*. The CDC is reporting slightly more Pfizer-BioNTech doses administered (24.25 million; 52%) than Moderna (22.04 million; 48%).
*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 5.35 million doses have been administered at long-term care facilities (LTCFs) through the Federal Pharmacy Partnership for Long-term Care (LTC) Program*, including residents and staff. This covers 3.96 million individuals with at least 1 dose and 1.36 million with 2 doses. Approximately 59% of the doses have gone to residents, and 41% to staff.
*The dashboard only includes data for doses administered through the federal program. It does not report data from West Virginia, which opted out of the program.

The Johns Hopkins Coronavirus Resource Center reported 27.41 million US cases and 476,183 deaths as of 12:30pm EST on February 12.

US SCHOOLS Last week, US CDC Director Dr. Rochelle Walensky stated that agency officials are finalizing recommendations regarding school reopening and that official guidance should be published soon. The guidance is expected to play a major role as state and local governments and school systems across the country continue to debate how to safely return students and teachers to the classroom. The issue has been fiercely debated, extending to courtrooms and picket lines. US President Joe Biden has indicated that he aims for most K-12 schools to reopen within his first 100 days in office. One of the biggest issues is how to prioritize teachers for vaccination and if or how to resume in-person classes before they can be vaccinated. Dr. Walensky recently stated that vaccinating teachers is not a prerequisite for resuming in-person classes. The CDC’s Advisory Committee on Immunization Practices (ACIP) includes teachers in its Tier 1b priority group, but Dr. Walensky indicated that schools can implement measures to mitigate transmission risk in the classroom until teachers can be vaccinated. In addition to teachers, there is also ongoing debate regarding the risk to students, most of whom are too young to be vaccinated against SARS-CoV-2.

Following protests in opposition to in-person learning in January, the Chicago Teachers Union approved an agreement with the nation’s third largest school district to resume in-person classes. With the agreement in place, Chicago avoids the risk of a teacher strike or lockout. While the agreement was approved by the union by a 2-1 margin, some are criticizing the terms as insufficient to protect teachers. Pre-kindergarten and special education classes will be among the first to return to in-person classes, followed by kindergarten through 8th grade returning for 2 days a week later this month or possibly in March. While in-person classes will resume, parents still have the option to continue remote/online learning for their students.

BRAZIL VACCINE PRODUCTION Brazil reportedly received its first shipment of the active pharmaceutical ingredients (APIs) necessary to manufacture the AstraZeneca-Oxford University SARS-CoV-2 vaccine. Vaccine production in Brazil will be conducted by the Oswaldo Cruz Foundation, commonly referred to as Fiocruz. Brazil expects to receive enough of the APIs in February to manufacture 15 million doses, and the government has purchased enough for 100 million total doses. While the vaccine was developed in the UK, a substantial portion of the APIs for the vaccine are produced by WuXi Biologics in China. According to a previous report by Reuters, Brazil struggled to navigate export procedures in China, which delayed the shipment of the APIs. While Brazil awaits domestic production capacity, it is utilizing the Chinese Sinovac vaccine in the early stages of its vaccination campaign. In addition to the Sinovac and AstraZeneca-Oxford vaccines, Pfizer submitted an application to regulatory authorities for the vaccine it developed in collaboration with BioNTech.

INDONESIA VACCINE AUTHORIZATION & PRIORITY GROUPS When Indonesia’s National Agency for Drug and Food Control (Badan POM) issued the Emergency Use Authorization (EUA) for China’s Sinovac vaccine, it only authorized the vaccine for use in adults aged 18-59 years. At the time, the clinical trial data available to Indonesian regulatory officials were not sufficient to determine the efficacy in adults aged 60 years and older. The age restriction drove Indonesia’s decisions regarding priority groups for vaccination, and eligibility was initially limited to healthcare workers, followed by other essential workers, aged 18-59. Without an EUA for adults aged 60 and older, Indonesia could not administer the vaccinations to older adults who are at elevated risk of severe disease and death.

Badan POM continued to monitor ongoing Phase 2 and 3 clinical trials in Brazil and China, and after evaluation of preliminary data from those trials, Indonesia determined that the vaccine demonstrated sufficient efficacy in older adults to warrant eliminating the upper age restriction. On February 5, Badan POM issued a new EUA that authorizes the vaccine for use in all adults aged 60 years and older. Following the announcement, the Indonesian MOH announced that eligibility would expand immediately to include all adults aged 60 and older. Indonesia began administering vaccinations to older adults on February 8, including doctors who were not previously eligible for vaccination due to their age. 

RWANDA TRAVEL RESTRICTIONS RwandAir, Rwanda's national airline, announced a temporary restriction on flights to and from South Africa, Zambia, and Zimbabwe, beginning February 8. Restricted locations include Johannesburg and Cape Town, the 2 most populous cities in South Africa, as well as Lusaka and Harare, the capitals of Zambia and Zimbabwe, respectively. The Rwanda Biomedical Centre also published guidance and requirements for passengers, including a negative SARS-CoV-2 test within 72 hours of departure and additional testing upon arrival, conducted at the traveler’s expense (US$60). Travelers will be required to remain at a designated transit hotel until results of their arrival test are available. Travelers will be required to undergo a 7-day self-quarantine period, even with a negative test, and a final test will be available after the quarantine (free of charge). 

UPDATED MASK USAGE RECOMMENDATIONS On February 10, the US CDC published updated guidance regarding ways to improve the efficacy of facemasks, which supplements existing mask guidance. The recommendations focus on 2 principal factors in how masks provide protection: fit and filtering ability. The CDC continues to recommend wearing a “mask [that] fits snugly against your face” and selecting masks that have multiple layers to filter respiratory droplets. The new guidance includes several additional recommendations and tips for improving both aspects of mask use.

Under the new guidance, the CDC now recommends selecting a mask with a “nose wire” that can be bent to mold the shape of your nose, which reduces the air that can escape around the top edge of the mask. The CDC also recommends using a “mask fitter or brace” on the outside of the mask to hold it more snugly to your face and provide a better seal around the edges. And finally, the CDC recommends adding layers of filtering material to your mask, including selecting a mask constructed of multiple layers of fabric or “double masking.” In the new guidance, double masking specifically refers to wearing a reusable cloth mask on top of a disposable mask (eg, medical, surgical mask). The CDC explicitly recommends against wearing multiple disposable masks or combining any kind of disposable or reusable mask with a respirator (eg, N95, KN95). The guidance also provides tips for determining whether your mask fits properly. The new guidance follows recent attention on double masking as a potential technique to reduce transmission risk in the face of emerging highly transmissible SARS-CoV-2 variants.

The updated guidance is based on findings from a study by the US CDC COVID-19 Response Team on improving the fit of facemasks. The researchers tested “double masking” and “knotting and tucking” to evaluate the extent to which they affected mask efficacy. Knotting and tucking refers to tying the straps/ear loops in a knot to bring the corners of the mask together and then tucking in the extra material “to minimize the side gaps.” One simulation compared the efficacy of double masking by comparing the combination of a cloth mask worn over a medical mask to each mask worn alone, and a second simulation compared various mask configurations, including double masking, to evaluate the effect of knotting and tucking. The simulations tested breathing and coughing and tested the effect for both exhalation and inhalation (ie, source and receiver, respectively). In the first experiment, the double masking configuration (unknotted) “blocked 92.5%” of cough particles, compared to 42% for the medical mask alone and 44.3% for the cloth mask alone. In the second experiment, when either the source (exhaling) or receiver (inhaling) utilized the double masking or knotted configuration (ie, only one of the two), the exposure to the receiver was reduced by approximately 82% and 63%, respectively. When either configuration was used on both the source and receiver, the receiver’s exposure was reduced by approximately 96%. A number of variables factor into the efficacy of these configurations, but this study provides evidence that these techniques can increase the level of protection for mask wearers. Notably, the new CDC mask guidance does not explicitly address knotting and tucking. See a quick tip from Sr. Scholar Caitlin Rivers to make your mask fit better.

UPDATED US VACCINATION GUIDANCE The US CDC published an update to its SARS-CoV-2 vaccination guidance. Most of the updates are relatively minor changes, including efforts to improve the reporting process for vaccine administration errors, clarifications on various contraindications, updated descriptions of injection-site reactions, and testing requirements for tuberculosis. The most notable update addresses quarantine requirements for vaccinated individuals after exposure to known COVID-19 cases. The new guidance largely eliminates quarantine recommendations for fully vaccinated individuals. Individuals who meet all of the following requirements do not need to quarantine after a known exposure:
Received all required doses of the vaccine (ie, 2 doses for a 2-dose vaccine; 1 dose for a single-dose vaccine)
Received their final doses 2 weeks or longer before the exposure
Are within 3 months of their final dose
Remain asymptomatic following the exposure

The guidance indicates that the timing associated with these requirements will be updated as additional information becomes available. Presumably, this will include extending the 3-month limit as new data are reported from clinical trials regarding the duration of immunity conferred by the vaccines. Notably, the CDC continues to emphasize that vaccination is not recommended as post-exposure prophylaxis and that eligible individuals with known exposure should wait until after the completion of their quarantine period to schedule their vaccination.

US VACCINE PRODUCTION Yesterday, US President Joe Biden announced that the US government finalized agreements to secure an additional 200 million doses of the Pfizer-BioNTech and Moderna vaccines, to be delivered by the end of July. He indicated that the total US procurement is now sufficient to fully vaccinate all Americans. At 300 million total doses, this should be enough to provide 2 doses to all US adults*. Dr. Anthony Fauci indicated that it could be “open season” for SARS-CoV-2 vaccination in America by April, with eligibility expanded beyond the initial high-priority groups.
*Currently, no SARS-CoV-2 vaccines are authorized for use in children.

While the federal government has procured enough doses, many barriers remain in terms of conducting nationwide mass vaccination operations. Distribution and logistics challenges continue to pose problems for state and local jurisdictions in terms of planning and scheduling, and many jurisdictions will likely face a shortage of the trained and qualified vaccinators that are critical to rapidly administering vaccinations to local populations. Additionally, it will be important to expand vaccination operations beyond those who will “readily seek” vaccination to ensure protection among those who may be hesitant or face barriers to accessing the vaccine. In addition to challenges to distributing and administering vaccinations domestically, many other countries have yet to access any doses, leaving most of the world vulnerable to COVID-19 as wealthier countries, principally in North America and Europe, scale up nationwide vaccination efforts. Without global protection through vaccination, COVID-19 will remain a threat everywhere.

COVID-19 DISPARITIES & EQUITY Research continues into the pandemic’s effects in exacerbating underlying and systemic disparities. The US national SARS-CoV-2 vaccination campaign is still in its early stages, but an investigation by STAT News already found that states with the largest gaps in wealth between counties are exhibiting similar gaps in vaccine coverage. For example, Connecticut has the largest disparity in median income at the country level of all US states. Early data indicate that vaccination coverage is 65% higher in the wealthiest counties than poorest.

COVID-19 has called attention to a broad scope of existing inequities in health and other sectors. One emerging issue that directly impacts COVID-19 patient care is the potential for pulse oximeters to be less accurate for patients of color. Pulse oximeters have emerged as an important tool in monitoring disease severity in COVID-19 patients, particularly those at risk of progressing from mild and moderate to severe disease. An editorial authored by several doctors at the University of Michigan, published in NEJM, presented a preliminary overview of data that shows significant disparities in the accuracy of pulse oximeters between Black and White patients. Based on data from nearly 50,000 blood oxygen saturation measurements, Black patients with pulse oximeter results in the normal range (92-96% oxygen saturation) were significantly more likely than White patients to have low oxygen saturation (<88%) when measured by arterial blood gas analysis. The study raised the attention of federal lawmakers, including several Senators who urged the US FDA to investigate racial and ethnic disparities in the accuracy of pulse oximeters and the requirements for testing their accuracy across a diverse set of study participants.

In an effort to combat inequities and disparities stemming from the pandemic, including in the vaccination plan, the White House announced the formation of a COVID-19 Health Equity Task Force. The task force will develop recommendations for addressing existing COVID-19 inequities and pathways to prevent such disproportionate impacts in the future. In addition to the task force’s 12 core members, leadership from 6 relevant federal government agencies will participate in and support the efforts: the Departments of Agriculture, Education, Health and Human Services, Housing and Urban Development, Justice, and Labor.

NORTHERN HEMISPHERE INFLUENZA SEASON Amid the COVID-19 pandemic, seasonal influenza rates are unusually low compared to historical data. Of the approximately 800,000 laboratory samples tested and reported to the US CDC since late September 2020, fewer than 1,500 were positive for seasonal influenza (0.2%). For comparison, that total was typically 25-30% at this point in the 2019-2020 influenza season. At this point in the season, there were nearly 100 times more cases last year than this year, even with approximately the same number of tests. Similar trends are also present for other respiratory viruses. Protective measures implemented for COVID-19, such as mask usage and social and physical distancing, may also be mitigating transmission risk for seasonal influenza. As we covered previously, the Southern Hemisphere also had a mild 2020 influenza season, which many believe was a direct result of COVID-19 risk mitigation measures.

GENOMIC SEQUENCING SURVEILLANCE The emergence of SARS-CoV-2 variants with the potential for increased transmissibility has provided the motivation necessary to rapidly scale up genomic sequencing capacity, in the US and elsewhere. Some members of the scientific community argue that existing capacity is available, at least in terms of having adequate hardware, technicians, and infrastructure; however, there is a lack of funding available to conduct this type of research, particularly on a scale needed to monitor the evolution of a national epidemic. In the global context, the US ranks #36 in terms of the proportion of specimens sequenced (0.36% of confirmed cases), compared to #1 Denmark, which has sequenced more than half.

In an article published in Science, the US CDC program officer responsible for the genomic surveillance efforts for emerging SARS-CoV-2 variants highlighted additional gaps in the system. Notably, linking samples and data from public health efforts to the sequencing technology is not necessarily a straightforward or direct process, and logistical solutions are necessary to enable the system to scale up the volume needed for COVID-19. The Biden Administration has called on the US Congress to authorize US$340 million dollars to support efforts to sequence 5% of all positive specimens. This number seems to be a middle ground, with some experts suggesting a loftier goal of 20%. Despite these efforts, there is still a sense that progress is moving too slowly. Mutation situation reports show that there are a number of notable SARS-CoV-2 variants of concern already circulating in the US, and public health and elected officials have a poor picture of the current prevalence of each of these variants. It is essential that the US and other countries develop better situational awareness of emerging variants, including the ability to rapidly detect those that emerge in the future.

MONOCLONAL ANTIBODY EUA On February 9, the US FDA issued an Emergency Use Authorization (EUA) for Eli Lilly’s monoclonal antibody cocktail of bamlanivimab and etesevimab as a treatment for COVID-19. The EUA specifically authorizes the treatment for “mild to moderate” COVID-19 in adults and pediatric patients aged 12 years and older who are “at high risk for progressing to severe” disease. Bamlaminivab was previously authorized for use under its own EUA. Under the new EUA, the two monoclonal antibodies are administered together in a single infusion, and the new EUA allows for infusion times as short as 16 minutes, which is less than a third of the time required for previous infusions. Like bamlanivimab by itself, the combination therapy can be administered as long as 10 days after symptom onset, but it is recommended to start treatment as soon as possible. The new EUA gives clinicians another outpatient option for treating individuals who are not ill enough to require hospitalization, which can reduce the burden on hospitals and health systems. According to a report from The New York Times, the FDA updated the EUA for bamlanivimab by itself to shorten its infusion time as well. The shortened infusion times are a result of feedback from clinicians, and the shorter time is expected to improve access and use of the treatments.

CARNIVAL & LUNAR NEW YEAR Major holidays and festivals around the world continue to face impacts from COVID-19 and associated protective measures. Carnival is an annual celebration that culminates with Fat Tuesday—the last day before Lent, observed by many Christian and Catholic denominations. It is a major festival in many locations around the world, perhaps most notably with the Carnival in Rio de Janeiro, Brazil, and Mardi Gras in New Orleans, Louisiana (US). This year, Fat Tuesday falls on February 16, but carnival celebrations have been scaled back considerably, including prohibitions on parades and mass gatherings in both Rio and New Orleans. In fact, the Sambadrome stadium in Rio is being utilized for mass vaccination operations this year instead of hosting some of Rio’s largest Carnival celebrations.

Today is the Lunar New Year, perhaps the most important holiday in China and celebrated in many other Asian nations. Last year’s Lunar New Year coincided with the earliest COVID-19 surge, which may have been driven, to some extent, by a high volume of international and regional travel associated with the holiday. Notably, many individuals who did travel last year found it difficult or impossible to return due to COVID-19 quarantines, “lockdowns,” and travel restrictions. This year, the Chinese government is encouraging individuals not to travel, reportedly including through “incentives” in the form of “gift baskets, activities and shopping discounts” to remain at home for the holiday. Despite the warnings, Chinese officials expect that hundreds of millions of people will travel over the course of the Lunar New Year season, which stretches to March. Those who do travel in China are required to provide documentation of a recent negative SARS-CoV-2 test, and some may face mandatory quarantine upon their arrival or return, depending on the destination.

TESTING TOOLKIT Researchers at the Johns Hopkins Center for Health Security, led by Dr. Gigi Gronvall, created the COVID-19 Testing Toolkit to provide information about SARS-CoV-2 test types, specific tests, and testing services, including how they work and what is known about their accuracy. SARS-CoV-2 testing has evolved rapidly over the course of the COVID-19 pandemic, as our understanding of SARS-CoV-2 improves and more tests enter the market. Testing is critical to identifying and monitoring the communities in which the virus is spreading as well as treating patients and informing good public health policies and operations during the pandemic. As more tests and test types become available, it is important to understand the purpose, capabilities, and limitations of these tests in order to select appropriate test types and test kits and accurately interpret the results. This toolkit provides a broad scope of information to support public health and healthcare decision-makers as well as the general public as they navigate an increasingly complex SARS-CoV-2 testing landscape.