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 108.82 million cases and 2.40 million deaths as of 10:30am EST on February 16.

Both the global weekly incidence and mortality continue to decrease steadily. Weekly mortality has decreased by nearly half since the peak reported the week of January 4, 2020. The current weekly incidence is the lowest since mid-October 2020. Weekly mortality decreased for the second consecutive week, down nearly 25% from the high reported the week of January 25, 2021. At the regional level, only the Eastern Mediterranean Region is currently reporting increasing weekly incidence—up 7.5% compared to the previous week, following 3 consecutive weeks of decreasing incidence. Weekly mortality is decreasing in all WHO regions.

Our World in Data reports that 177.94 million vaccine doses have been administered globally, a 20% increase compared to this time last week. Vaccination efforts have been reported in at least 86 countries and territories.

NOTE: The US CDC did not update COVID-19 epidemiological or vaccination data yesterday due to the President’s Day holiday. The data below correspond to the most recent update on February 14.

The US CDC reported 27.42 million total cases and 482,536 deaths. Daily incidence in the US continues its steady decline, falling below 100,000 new cases per day for the first time since November 3, 2020.

On February 12, the US reported 5,520 new deaths. This is the second highest single-day total to date; however, the 3 highest single-day totals are the result of previously unreported deaths from a single state—New York (April 15, 2020), Indiana (February 4), and Ohio (February 12). As we covered previously, Ohio announced last week that it identified more than 4,000 previously unreported deaths, and it reported 721 deaths on February 11; 2,259 on February 12; and 1,204 on February 13.

The recent spikes in reported mortality make it difficult to get an accurate picture of the longer-term national trend. The mortality reported on February 11, however, could provide some insight. February 11 was the first day after the 7-day average window following February 4, and it was also the day prior to the largest report from Ohio. The average national daily mortality of 2,784 deaths per day on February 11 did include the first elevated report from Ohio, but it provides some indication that the true daily mortality is much lower than the current average of 3,136 deaths per day. This is the lowest daily mortality since January 6, prior to the estimated peak mortality in mid-to-late January, and it provides further evidence that daily mortality continues to decrease nationally.

US Vaccination
The US CDC reported 70.06 million vaccine doses distributed and 52.88 million doses administered nationwide (75.5%).

In total, 38.29 million people (approximately 11.6% of the entire US population) have received at least 1 dose of the vaccine, and 14.08 million (4.3%) have received both doses. The average daily doses administered continues to increase, now up to a record high of 1.50 million doses per day*. The number of people receiving their second dose is increasing at nearly 600,000 per day*. The breakdown of doses by manufacturer continues to shift toward the Moderna vaccine. The CDC is still reporting slightly more Pfizer-BioNTech doses administered (27.27 million; 52%) than Moderna (25.51 million; 48%), but the gap is closing.
*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 5.82 million doses have been administered at long-term care facilities (LTCFs)*, including residents and staff. This covers 4.16 million individuals with at least 1 dose and 1.64 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 Pharmacy Partnership for Long-term Care (LTC) Program. It does not report data from West Virginia, which opted out of the program.

As the US SARS-CoV-2 vaccination effort continues, there remain substantial differences in terms of how efficiently states are administering their allotted doses. On a per capita basis, nationwide distribution remains relatively even. All by 9 states have received within 10%(+/-) of the median per capita doses distributed. Only Alaska has received more than 25% above the median, and no states have received less than 75% of the median. States vary widely, however, in terms of administration. By percent of doses administered, states range from 61.74% (Rhode Island) to 97.72% (West Virginia), with a median of 76.47%. In total, 36 states are within 10%(+/-) of the median in terms of percent of doses administered, a moderate decrease compared to the national distribution. Eight (8) states are reporting 60-70% of doses administered, 27 are reporting 70-80%, and 18 are reporting 80-90%. Three (3) states—New Mexico, North Dakota, and West Virginia—are reporting greater than 90%, which is more than 25% higher than the median. No states report less than 75% of the median.

States also vary widely in terms of how they are allocating doses between first and second vaccinations. In terms of the proportion of doses allocated for second vaccinations, states range from Delaware, with slightly more than one-fifth (21.35%), to West Virginia, the only state reporting more than one-third (35.92%). The median value is 27.33%. Approximately half of the states (26) are within 10%(+/-) of the median value. In total, 13 states are reporting 20-25%, 24 states are reporting 25-30%, and 12 states are reporting 30-35%. West Virginia is the only state reporting more than 35% and the only state reporting more than 25% higher than the median. No states are less than 75% of the median.

The Johns Hopkins Coronavirus Resource Center reported 27.71 million US cases and 486,572 deaths as of 12:30pm EST on February 16.

WHO VACCINE EMERGENCY USE LISTING The WHO issued Emergency Use Listings (EULs) for two versions of the AstraZeneca-Oxford University SARS-CoV-2 vaccine. The two versions are those produced directly by AstraZeneca-SKBio and those manufactured under the license to the Serum Institute in India. With the EUL in place, the AstraZeneca-Oxford vaccine can begin distribution through the COVAX facility, which will provide doses to low- and middle-income countries (LMICs) around the world, including nearly 340 million doses of the AstraZeneca-Oxford vaccine. The first COVAX distributions are expected later this month. Additionally, an EUL from the WHO can facilitate expedited regulatory authorization for the vaccine in many countries. This is the second EUL issued for a SARS-CoV-2 vaccine, following the Pfizer-BioNTech vaccine on December 31, 2020.

US SCHOOL GUIDANCE On February 12, the US CDC published updated guidance to support schools’ efforts to mitigate COVID-19 risk for in-person classes. The biggest update is a new “phased mitigation” strategy, which couples risk mitigation measures with the level of community transmission. The guidance emphasizes 5 key mitigation mechanisms—mask use, physical distancing, hand hygiene and respiratory etiquette, cleaning and sanitization, and surveillance and contact tracing—that are applicable across all levels of COVID-19 risk, but it also provides actionable information regarding how to implement those and other strategies at various levels of COVID-19 risk. The guidance also breaks down specific recommendations for elementary, middle, and high schools, and it includes guidance for extracurricular activities, including sports.

The updated guidance emphasizes that closing schools for in-person learning should be among the last measures taken to control local transmission. With that in mind, the guidance highlights some areas of flexibility in terms of the local community COVID-19 risk and what schools are capable of implementing. The guidance provides schools with recommendations regarding the minimum standards for conducting in-person classes for various levels of COVID-19 risk. For example, 6-foot physical distancing is recommended “to the greatest extent possible” for communities with low and moderate transmission; however, the CDC recommends mandatory 6-foot distancing for schools in substantial or high transmission areas. Schools that are unable to ensure the recommended physical distancing may need to reduce attendance and/or transition to hybrid or remote learning models, if community transmission is elevated. In addition to physical distancing, the guidance includes information on improving ventilation and implementing screening or testing programs for students and staff as well as additional risk mitigation measures if these programs cannot be implemented. Some view the guidance as a positive step toward supporting schools’ efforts to resume in-person learning, particularly the emphasis on closing schools as a last resort, whereas others argue that criteria for community transmission and testing are unrealistic and overly restrictive and that the guidance will ultimately keep schools closed longer.

Some aspects of the CDC’s previous school guidance remain in place, including the COVID-19 Mitigation Toolkit, Get Ready for In-Person Learning, Setting Up Your Classroom, and Teacher and Staff Checklists—all of which were published or updated in December 2020. The CDC also updated its Operating Schools During COVID-19 guidance on February 11, but there are no changes listed since December 31, 2020.

EMERGING VARIANTS Researchers from Switzerland and the US published (preprint) findings from a study of the emergence of new SARS-CoV-2 variants that include a specific mutation in the spike protein. Mutations at amino acid 677 affect the virus’ spike protein, which could potentially factor into the virus’ transmissibility or its susceptibility (or resistance) to antibodies, including those generated through vaccination. The researchers identified at least 7 distinct sub-lineages in the US that contain this mutation, all of which appear to have emerged in the US (ie, as opposed to imported from another country). These sub-lineages first appear in specimens sequenced at least as far back as August 2020, but it is unclear exactly when they first emerged. These sub-lineages already account for a substantial proportion of the documented SARS-CoV-2 genomes nationwide, but further research is needed to better characterize the effects of these mutations on transmissibility. Increased sequencing capacity is needed to improve surveillance for these and other emerging variants.

Researchers from the Johns Hopkins Center for Health Security—led by Dr. Caitlin Rivers and Lane Warmbrod and in collaboration with Dr. Matthew Frieman (University of Maryland) and Dr. Dylan George (In-Q-Tel)—published a report outlining recommendations to improve the United States’ ability to identify, monitor, and characterize emerging SARS-CoV-2 variants. Their principal recommendations address various aspects of containing and monitoring these variants. First, implementing policies to slow transmission can mitigate the risk of new variants emerging in the first place. In order to effectively monitor for the emergence of new variants, the US needs a national strategy for genomic surveillance, including resources necessary to implement it. At the local level, infections identified with variants of concern should be prioritized for contact tracing and other follow-up in order to effectively gather data regarding the variants’ performance compared to existing strains. And finally, coordination and resources are necessary to implement effective and efficient efforts to characterize the effects of specific mutations and the capabilities of emerging variants, including with respect to transmissibility, disease severity, and susceptibility to vaccines and therapeutics.

US TESTING CAPACITY A survey conducted by STAT News and The Harris Poll (February 5-7) indicates that SARS-CoV-2 testing capacity in the US is still not meeting demand. Among those who sought testing, 44% reported being unable to get tested*. Common complaints from the respondents who were unable to get tested included long wait times, distance to a testing site or lack of transportation, and uncertainty regarding where to get tested. Among those who had been tested at least once, the majority of testing (56%) occurred at drive-through or hospital-based testing sites, and most (69%) used nasopharyngeal swabs. The Biden Administration has acknowledged the ongoing nationwide shortage of test kits, and it is negotiating with the Congress to secure funding to purchase additional tests. Current plans include purchasing 8.5 million at-home rapid tests and scaling up production of the at-home kits to more than 60 million by this summer. At-home testing could potentially alleviate barriers due to test site location, transportation, and wait times by eliminating the need to find and travel to a testing site.
*31% sought testing and were able to be tested, 24% sought testing and could not get tested, and 45% did not seek testing.

An investigation conducted by The Wall Street Journal found that “at least 32 million of 142 million” rapid antigen tests distributed by the federal government to states remain unused. These tests were intended to support larger-scale screening efforts, including at schools and long-term care facilities, but logistical challenges for facilities implementing testing programs and reporting results has limited demand. The rapid tests were viewed by some as an important tool to ongoing screening programs that could be used to resume some activities (eg, in-person learning) and respond to outbreaks, but the low use is problematic. Many of the tests have a shelf life of 6 months, and millions of test kits delivered in autumn 2020 are approaching their expiration date.

US VACCINATION As US states continue to expand vaccination eligibility to larger portions of their populations and scale up vaccination capacity, some are limited by the available supply. As we noted in the Epi Update section above, at least half of all US states have administered more than 75% of the vaccine doses they have received from the federal government. Much of the remaining inventory at the state level is reserved for second doses. Some states have been forced to shut down various aspects of their vaccination programs, including large mass vaccination sites like Dodger Stadium in Los Angeles, California. Numerous local jurisdictions in the Atlanta, Georgia, area have also stopped scheduling new vaccination appointments due to insufficient supply. US President Joe Biden announced plans to bolster vaccine supply on February 2, but the increase to 10.5 million doses per week does not provide an increase over the current average of 1.5 million doses administered per day.

In addition to supply limitations, a massive winter storm that swept across much of the US is hindering vaccination efforts in many states. Shipments of doses to some areas have been delayed, and clinics and mass vaccination sites have closed in multiple states. In Texas, large-scale electrical outages have caused vaccine freezers to lose power, and health officials scrambling to administer doses of the vaccine before they go bad.

US TRIBAL VACCINATION Tribal nations in the US have been among the hardest hit by COVID-19 due to a variety of factors, including underlying health conditions, poverty, and limited access to healthcare services. Despite these challenges, evidence is emerging that many tribal nations are vaccinating their populations more efficiently than many other US communities. Among these success stories are the Cherokee and Navajo Nations, which are both reporting high rates of vaccination and high levels of interest in getting vaccinated. Notably, Navajo Nation reported that 47.7% of the population residing on tribal lands has received at least one dose of the vaccine. Both Nations credit culturally appropriate outreach and education efforts in the community as critical to the success of their vaccination efforts.

The ability of tribal nations to decide their own vaccination priorities also contributed to building greater confidence in the vaccine. For example, the Cherokee Nation chose to include their highly revered Cherokee language speakers and Cherokee National Treasures among its first priority groups. The decision signaled that tribal leaders were prioritizing Cherokee culture, and vaccinating respected tribal elders demonstrated to others that the vaccine is safe. The Navajo Nation is engaging in community outreach through a variety of fora, including radio broadcasts and frequent town halls, conducted both in English and the Navajo language. The apparent success of these efforts, exhibited by the high vaccine uptake and willingness to be vaccinated, underscore the importance of culturally relevant messaging and education in promoting SARS-CoV-2 vaccination.

MODERNA VACCINE DOSES The US FDA is reportedly considering allowing Moderna to increase the number of doses included in each vial of its SARS-CoV-2 vaccine. Moderna has been consulting with FDA officials to determine if it can increase the doses in each vial from 10 to 14 or 15. Moderna still needs to provide data to the FDA demonstrating that the increase in doses per vial would not compromise vaccine quality; however, increasing vial capacity by 40-50% could potentially increase the country’s overall COVID-19 vaccine supply by 20%. The associated modifications to Moderna’s production lines could be completed as early April. Filling and labeling the individual vials remains a major bottleneck in the vaccine manufacturing process, so increasing the volume of vaccine in each vial would substantially increase supply without adding time to the overall time to finish each vial. A substantial increase to the vaccine supply could have a major impact on vaccination operations, both in the US and around the world.

MASK EFFICACY A commentary published in JAMA by Dr. John T. Brooks and Dr. Jay C. Butler, two experts at the US CDC, provides an overview of the evidence supporting the use of facemasks during the COVID-19 pandemic. The researchers evaluate the existing body of evidence in support of universal masking, including results from contact tracing investigations, large surveys, and ecological studies that evaluate the effect of masking policies on COVID-19 incidence, including several that compare COVID-19 incidence before and after implementing a mask mandate. The authors draw a parallel between universal mask use and herd immunity, noting that increased mask use in a given community can increase the level of protection against SARS-CoV-2 transmission. Additionally, they argue that the specific type of mask used could be less important than the act of wearing the mask.

ISRAEL Israel continues to lead the world in terms of SARS-CoV-2 vaccination. Israeli Minister of Health Yuli Edelstein announced that 2.61 million individuals have received both doses of the vaccine, approximately 30% of Israel’s total population. With such a substantial portion of its population already vaccinated, Israel is among the first countries to begin evaluating the effect of vaccination on its COVID-19 epidemic. Israel’s largest healthcare provider—Health Maintenance Organization (HMO) Clalit, which covers more than half of Israel’s population—reported a 94% decrease in symptomatic COVID-19 cases among 600,000 individuals who received 2 doses of the Pfizer-BioNTech vaccine, compared to those who have not yet been vaccinated.

Despite its success, Israel still faces many challenges in terms of vaccine hesitancy. Like many countries, misinformation remains a major challenges during Israel’s COVID-19 epidemic, particularly with respect to SARS-CoV-2 vaccination. To combat misinformation, Israel’s Ministry of Health established a taskforce to find and remove misinformation on a wide range of social media sources, including in multiple languages. In further efforts to promote vaccination, Israel is reportedly considering measures to prohibit unvaccinated individuals from some public spaces, including museums or concerts. Israel is also implementing more creative measures to incentivize vaccination. At some mass vaccination centers, DJs play music in order to attract attention and draw in younger adults. Social media influencers have also been approached by the government to promote vaccination and disseminate information on the ongoing vaccination campaign.

NEW ZEALAND LOCKDOWN A cluster of COVID-19 cases in Auckland, New Zealand, has prompted new national “lockdown” measures. On February 14, the New Zealand Ministry of Health reported 3 cases in the same household. Case investigation efforts determined that several of the newly identified cases traveled to a nearby tourist attraction during the period when they could have been infectious, but it is not clear whether any of them were infectious at that time. All members of the household have been placed into isolation/quarantine. Genomic analysis from the cases indicates that the 3 individuals are infected with the B.1.1.7 variant of concern, but the analysis was unable to link the cases to any other known chains of transmission. To date, 109 close contacts have been identified and tested, and no additional cases have been linked to the cluster. The investigation is ongoing to identify the source of exposure.

Following the announcement, New Zealand implemented a Level 3 lockdown in Auckland and moved the rest of the country to Level 2 for a period of 72 hours to allow health officials time to investigate the cluster and assess the risk. The lockdown is currently scheduled to end at midnight on February 17. New Zealand health officials determined that several major events, including the America’s Cup (sailing) and the Big Gay Out festival could continue as scheduled, as long as event organizers implemented appropriate protective measures. The Big Gay Out festival reportedly did proceed as planned, but the America’s Cup postponed races scheduled for February 17 as a precaution.