May 28; Johns Hopkins COVID 19 Report

COVID-19 Situation Report

The Center also produces US Travel Industry and Retail Supply Chain Updates. You can access them here.

Editor’s Note: Our COVID-19 Situation Report team is taking a break next week. We will be back on Tuesday, June 8, with our curated analysis of the latest COVID-19 news and research.

Thanks to our wonderful team who pulls these together: Alyson Browett, Natasha Kaushal, Amanda Kobokovich, Margaret Miller, Christina Potter, Dr. Caitlin Rivers, Matthew Shearer, Marc Trotochaud, and Rachel Vahey.

SCHOOL VENTILATION Many K-12 schools in the US do not have good ventilation, a longstanding problem with negative effects far beyond COVID-19. The Johns Hopkins Center for Health Security published a new report, School Ventilation: A Vital Tool to Reduce COVID-19 Spread, to present findings and recommendations regarding school ventilation in the context of COVID-19. The analysis is based on interviews with more than 30 subject matter experts and current scientific evidence and guidance. Ventilation improvements may be perceived as a complicated and expensive investment, but these upgrades can actually be cost-effective compared to enhanced cleaning and disinfection. As new and potentially more transmissible SARS-CoV-2 variants continue to emerge, improvements in indoor air quality are important for reducing transmission risk, and federal COVID-19 funding could provide the resources to make necessary improvements in K-12 schools, particularly as many schools plan to resume in-person classes before the next school year starts in the fall.

EPI UPDATE The WHO COVID-19 Dashboard reports 169 million cumulative cases and 3.5 million deaths worldwide as of 8:00am EDT on May 28.

While much of the world’s attention has been on the surging COVID-19 epidemics in India and nearby countries, the ongoing surges in South America have remained comparatively under the radar. In terms of per capita daily incidence, South America represents 5 of the top 10 countries globally—Uruguay (#4), Argentina (#5), Paraguay (#7), Colombia (#8), and Suriname (#10)—as well as Chile at #11, Brazil at #12, and Bolivia at #16. Additionally, nearby Costa Rica (#6) and Trinidad and Tobago (#9) also are in the top 10. Most of these countries are setting new national records or are near their highest peak. The daily incidence in some countries—including Bolivia, Paraguay, and Suriname—has increased steadily since at least early April. Others—such as Argentina, Brazil, Chile, and Colombia—reported peaks or plateaus in mid-to-late April before increasing again in early-to-mid May. All 8 of the South American countries listed above are reporting increasing trends in daily incidence over the past 2 weeks, including Bolivia (+59.4%) and Suriname (+89.7%) with biweekly increases greater than 50%.

In terms of per capita daily mortality, South America represents 7 of the top 10 countries globally, including the top 3: Paraguay (#1), Uruguay (#2), and Argentina (#3). Additionally, Bolivia is #11, Guyana is #18, and Chile is #19. Nearby Trinidad and Tobago (#5) and Costa Rica (#16) also are among the top countries globally. Notably, Bolivia (+128%) and Suriname (+170%) are reporting biweekly increases in daily mortality greater than 100%.

Of the 8 South American countries reporting test positivity data, only Chile (11.0%) and Peru (15.4%*) are reporting less than 20%. Paraguay (36.9%), Argentina (32.6%), Colombia (29.2%), and Ecuador (29.2%) are all reporting higher than 25%, well above the 5% target. Notably, South America accounts for 6 of the top 12 countries globally: #2 Paraguay, #4 Argentina, #7 Colombia, #9 Ecuador, #11 Uruguay, and #12 Bolivia.

*Peru’s most recent data are from April 26, 2021.

Following a report of 8.6 million doses of SARS-CoV-2 vaccine administered on May 25, South America’s average jumped up similar to Asia and North America, at approximately 0.45 daily doses per 100 population—up from 0.23 on May 24—although it will likely decrease once May 25 moves out of the 7-day average window. At the national level, Uruguay is the highest-ranked South American country in terms of per capita daily doses administered, ranking #18 with 0.88 daily doses per 100 population. In terms of total daily doses administered, Brazil is #1 in South America and #4 globally with 1.33 million doses per day. Concerningly, Venezuela is reporting fewer than 2,000 doses per day, which equates to fewer than 0.01 daily doses per 100 population—or fewer than 1 dose per 10,000 population. Venezuela reportedly did not officially join the COVAX effort in April 2021, and it has received a limited number of vaccine doses from China and Russia.

On a cumulative basis, South America ranks #3 globally, with approximately 8.9% of the total population fully vaccinated and 17.7% with at least 1 dose. At the national level, Chile (53%) is #11 globally in terms of coverage with at least 1 dose, and Uruguay (49%) is #17, right behind the US (50%). In terms of full vaccination coverage, Chile (41%) ranks #6 globally, just ahead of the US (40%), and Uruguay (29%) ranks #16.

Global Vaccination

The WHO reported 1.55 billion doses of SARS-CoV-2 vaccines administered globally as of May 26, and 736 million individuals have received at least 1 dose. Our World in Data reported 1.81 billion cumulative doses administered globally, and the global cumulative total continues to increase at 13% per week. Daily doses administered continue to increase, up to a new record of 31.0 million doses per day on May 26 before falling slightly to 30.4 million. Our World in Data estimates there are 413 million people worldwide who are fully vaccinated, corresponding to approximately 5.3% of the global population, although reporting is less complete than for other data.

UNITED STATES

The US CDC reported 33.0 million cumulative cases and 589,547 deaths. Daily incidence continues to decline, to the lowest levels since early in the pandemic. The current average daily incidence—21,627 new cases per day—is the lowest since June 4, 2020. The lowest daily incidence between the United States’ first and second surge was 20,733 on June 1, 2020, and the US could fall below that average in the coming days, if it continues on this trajectory. Daily mortality continues to decline as well, down to 437 deaths per day, the lowest average since March 31, 2020, early in the United States’ initial surge.

US Vaccination

The US has distributed 361 million doses of SARS-CoV-2 vaccines and administered 291 million. After a brief increase, the daily doses administered* is once again decreasing, down to 1.5 million doses per day, the lowest average since February 23. Approximately 843,000 people are achieving fully vaccinated status per day, down from a high of 1.8 million per day on April 12.

A total of 166 million individuals in the US have received at least 1 dose of  SARS-CoV-2 vaccine, equivalent to 50% of the entire US population. Among adults, 62% have received at least 1 dose, and 5.8 million adolescents aged 12-17 years have received at least 1 dose. A total of 133 million people are fully vaccinated, which corresponds to 40% of the total population. Among adults, 51% are fully vaccinated, and 2.1 million adolescents aged 12-17 years are fully vaccinated. Progress has largely stalled among adults aged 65 years and older: 86% with at least 1 dose and 74% fully vaccinated. In terms of full vaccination, 68 million individuals have received the Pfizer-BioNTech vaccine, 54 million have received the Moderna vaccine, and 10.4 million have received the J&J-Janssen vaccine.

*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.

The Johns Hopkins Coronavirus Resource Center is reporting 33.2 million cumulative cases and 593,314 deaths in the US as of 10:15am EDT on May 28.

SINOPHARM VACCINE PHASE 3 CLINICAL TRIALS Researchers from China and several Eastern Mediterranean countries published Phase 3 clinical trial efficacy data for 2 SARS-CoV-2 vaccines developed by Sinopharm (China). While the WHO issued an Emergency Use Listing (EUL) to one of the Sinopharm vaccines several weeks ago and the vaccines are in use in multiple countries, to our knowledge, this is the first time that the Phase 3 trial data have been published publicly. Additionally, this is the first efficacy data available for an inactivated virus vaccine—to date, the others have utilized mRNA or viral vector platforms. The data, published in JAMA, presented interim analysis from clinical trials conducted in Bahrain and the UAE involving more than 40,000 adult participants with no known history of COVID-19. Nearly 27,000 participants received one of 2 vaccines (2 doses each, 21 days apart).

The vaccine authorized by the WHO (designated HB02) demonstrated 78.1% efficacy against laboratory-confirmed, symptomatic COVID-19 at least 14 days following the second dose, and the other vaccine (designated WIV04) demonstrated 72.8% efficacy. In December, Sinopharm announced a preliminary efficacy estimate of 79% via press release and an updated estimate of 72.5% in February 2021. The study did not evaluate efficacy against asymptomatic infection, and there were only 2 severe cases (both in the placebo group), which was not sufficient to support efficacy analysis against severe disease. Additionally, efficacy was not assessed against specific variants of concern (VOCs; eg, B.1.1.7, B.1.351, P.1), as their prevalence was not high enough in the trial locations to provide sufficient data. The trials included only 612 participants aged 60 years and older, so additional data is required to allow efficacy analysis in older adults—or other high-risk groups. Both vaccines demonstrated an acceptable safety profile. Additional data from clinical trials in Jordan and Egypt will be included in the final analysis.

SARS-COV-2 ORIGIN INVESTIGATION US President Joe Biden announced on May 26 that he has asked the US Intelligence Community to redouble its efforts to investigate the origins of SARS-CoV-2 and report back to him in 90 days. As we covered previously this week, the Wall Street Journal reported on an “undisclosed US intelligence report” that there is some evidence to support a theory that the virus originated at the Wuhan Institute of Virology (WIV; China) in November 2019. According to intelligence officials, there remains a bulk of information needing additional computer analysis, and the US government’s announcement of a reinvigorated investigation could bring allies to mine their own intelligence data for new information to determine whether an accidental laboratory leak led to the COVID-19 pandemic. A previous investigation led by the WHO determined that the likelihood of the pandemic originating from a laboratory release to be “extremely low,” but in the absence of definitive evidence of another source, it is nearly impossible to rule it out. A source familiar with the call for a revived investigation said the US government was prompted in part because China refused to fully cooperate with the original WHO-led query. US officials cautioned there is no proof the virus originated in a Chinese lab.

The US announcement brought counter accusations from the Chinese government, with one official reigniting an unsubstantiated theory blaming the US for releasing the virus from an Army research facility. Perhaps more notably, researchers around the world raised concern over the volatility of the debate, warning the tone could harm efforts to investigate the virus’s origin but also hinder cooperation during upcoming high-level discussions about pandemic preparedness. Others worry the rhetoric is fueling online bullying of scientists and anti-Asian harassment in the US. While knowing the origin of SARS-CoV-2 could help prevent future disease outbreaks, it is feared that political posturing will continue to impede investigations and transparency.

BREAKTHROUGH INFECTIONS The US CDC COVID-19 Vaccine Breakthrough Case Investigations Team published analysis of breakthrough infections reported through April 30. The study, published in the US CDC’s MMWR, includes 10,262 breakthrough infections from 46 states. From preliminary data, 27% of breakthrough cases were asymptomatic, 10% were hospitalized, and 2% died. Of the hospitalized cases, 29% were asymptomatic or hospitalized for a reason other than COVID-19. Sequence data were available for only 5% (555 cases) of cases, 64% of which identified variants of concern: B.1.1.7 (56%), B.1.429 (25%), B.1.427 (8%), P.1 (8%), and B.1.351 (4%). The University of Washington Virology Lab (UWVL) also found variants of concern to be responsible for breakthrough infections. They sequenced 20 vaccination breakthrough infections from UW Medicine and found that all 20 cases were classified as variants of concern. Of the variants, B.1.1.7 represented 40%, B.1.429 40%, B.1.427 10%, B.1.351 5%, and P.1 5%. Compared to the control group, the frequency of VOC breakthroughs increased 1.47 fold. During that same time interval, 68% of Washington state cases sequenced at UWVL consisted of variants of concern.

As of May 1, the CDC is no longer investigating all vaccine breakthrough infections, instead focusing only on hospitalized and fatal cases. Vaccine effectiveness studies will continue, but only in limited populations.

IMMUNITY DURATION Two new studies shed light on questions surrounding the longevity of SARS-CoV-2 immunity following infection or vaccination. In one study, published May 24 as an unedited manuscript in Nature, researchers from the University of Washington Medical School (Missouri; US) examined COVID-19-convalescent individuals for evidence of long-lived bone marrow plasma cells (BMPCs), a persistent and essential source of protective antibodies. Among 77 individuals who had recovered from mild COVID-19, the researchers found that serum anti-SARS-CoV-2-spike antibodies decayed significantly 4 months after infection with a continued, more gradual delay for at least 7 more months. Among 18 patients from whom bone marrow aspirates were obtained, spike-specific BMPCs persisted 7-8 months post infection, suggesting that they were part of a dormant, long-lived compartment. The research team concluded that previous SARS-CoV-2 infection resulting in mild symptoms led to a robust antibody response, showing potential for these immune factors to persist months after infection.

In another study, published in bioRxiv (preprint), researchers from Rockefeller University (New York; US) report on a cohort of 63 COVID-19-convalescent individuals assessed at 1.3, 6.2, and 12 months after infection, 41% of whom also received mRNA vaccines. In individuals who were not vaccinated, neutralizing activity and a specific type of memory B cells remained relatively stable from 6 to 12 months. Notably, vaccination increased all components of the humoral response and resulted in serum neutralizing activities against variants of concern that are comparable to or greater than neutralizing activity against the original SARS-CoV-2 strain achieved by vaccination of naïve individuals. The data suggest that immunity among recovered COVID-19 patients likely will be very long lasting, and those who receive mRNA vaccines should produce enough antibodies and memory B cells to provide protection against circulating SARS-CoV-2 variants. The researchers speculate this is evidence to consider boosters for non-convalescent but vaccinated individuals as new variants of concern emerge.

VACCINE EFFICACY IN RECOVERED CASES A group of researchers from Italy, the UK, and the US have called for updating vaccination guidance to recommend a single dose of mRNA-based SARS-CoV-2 vaccines for individuals who have recovered from SARS-CoV-2 infection. The commentary, published in The Lancet, cites several recent studies that provide evidence that a single dose of these vaccines in individuals who were previously infected with SARS-CoV-2 stimulates a similar or better protective immune response than in naïve individuals after their second dose. Essentially, the first dose would act like the booster dose in individuals who have recovered from SARS-CoV-2 infection. The authors acknowledge that these were small studies; however, they argue that eliminating the second dose for these individuals would allow additional doses to be distributed to areas of need and expand the reach of the existing limited vaccine supply. This could increase the number of vaccinated individuals without sacrificing protection for recovered individuals. If this strategy were applied globally, it potentially could save nearly 170 million doses (ie, at 1 dose per reported case), which would be sufficient to fully vaccinate an additional 85 million people.

UK INCREASE IN VARIANT CASES A software error in the UK government’s test and trace system might have contributed to the spread of the B.1.617.2 variant in the country, with reported cases of that variant rising more than 160% over the week ending May 19. Case numbers of the variant, first detected in India, rose from 1,313 to 3,424, according to data from Public Health England. The agency has designated another variant, known as VUI-21MAY-01 or AV.1, as a “variant under investigation,” with 49 cases detected across the country. Several localities that experienced an increase in B.1.617.2 cases did not have access to full data on positive test results in their areas between April 17 and May 17, meaning 734 positive tests went unreported to local authorities, who in turn could not conduct contact tracing. Officials say the issue has been resolved, and they are working to contain the outbreaks.

INDIA This week, India became the third country to record more than 300,000 COVID-19 deaths, although the true death toll is likely much higher. In the coastal areas of West Bengal and Odisha states, officials evacuated about 1.5 million people to cyclone shelters ahead of Cyclone Yaas, which made landfall May 26, complicating efforts to contain SARS-CoV-2 amid the country’s devastating second wave. Although officials appealed for evacuees to double-mask and maintain physical distance, experts worry evacuation efforts never took the pandemic into account, instead focusing on rescuing as many people as possible in a short time span.

Meanwhile, Indian officials have recorded nearly 9,000 cases of mucormycosis, the so-called black fungus, primarily among people with COVID-19 or those who have recovered. The increase in cases of the usually rare fungal infection is raising fears that it could impact COVID-19 patients more severely than others, as it spreads through the respiratory tract and is especially harmful to those with weakened immune systems and underlying conditions. Health officials say the disease is more prevalent in rural areas and smaller cities, where unqualified doctors are improperly treating COVID-19 patients with steroids, which increasingly is associated with contracting mucormycosis. Some experts speculate unsanitary conditions, including the use of improperly or non-sanitized oxygen cylinders or ventilators, could be contributing to the outbreak, although others argue unsanitary conditions in many hospitals existed prior to the pandemic.

OXYGEN SHORTAGES As India continues to struggle amid a surge in COVID-19 cases, experts warn other nations are reporting record increases over the last few weeks. Countries from Argentina to Nepal are experiencing record surges, while inequity in vaccine distribution continues. Like India, these countries face oxygen shortages amid increasing demand, according to an analysis by the Bureau of Investigative Journalism. The report—based on data provided by Every Breath Counts Coalition, PATH, and the Clinton Health Access Initiative (CHAI), as well as global vaccination data—determined 19 countries are most at risk of elevated death rates from oxygen shortages. Those countries—including Argentina, Colombia, Iran, Nepal, the Philippines, Malaysia, Thailand, Pakistan, Costa Rica, and South Africa—need more than 50,000 cubic meters a day for COVID-19 patients. The report notes that in nearly all of the countries, less than 1% of the population has received one dose of vaccine, underscoring the need to quickly distribute and administer vaccines in low- and middle-income countries (LMICs).

AUSTRALIA In response to an ongoing COVID-19 outbreak, Victoria, Australia is entering its fourth “lockdown.” The state government is implementing COVIDSafe “circuit breaker” restrictions for a period of 7 days due to concerns that contact tracing efforts are not able to keep up with community transmission. Like previous lockdown periods, individuals are directed to remain at home, except for essential activities, including grocery shopping, health care (including SARS-CoV-2 vaccination), authorized work or study, and exercise. Additionally, several other Australian states have implemented travel restrictions, including mandatory quarantine, for travelers from Victoria. Reportedly, case investigations of 26 recent infections have identified approximately 10,000 contacts who may be at risk of exposure at more than 150 locations across the state.

PROPOSED LIMITS ON PUBLIC HEALTH AUTHORITY The Network for Public Health Law and the National Association of County and City Health Officials (NACCHO) published a report on the risks posed by new and pending legislation to limit public health authority in US localities, including during public health emergencies. In response to executive and public health orders issued at the state and local levels during the US COVID-19 response, a number of state legislatures have passed or are actively considering bills to “limit severely the legal authority of public health agencies to protect the public from serious illness, injury, and death.” The report provides an overview of the history of public authority in the US and outlines current efforts to “undermine the authority of public health agencies.” Current efforts to limit local public health authority attempt to shift power away from local public health agencies and toward either other local entities or to the state level.

Additional efforts are targeting executive authority of governors in favor of state legislatures, and others aim to eliminate the authority to implement specific public health interventions, including mask mandates, business closures, and quarantine. While these efforts are arising from the COVID-19 experience, they could have far-reaching impacts on other public health threats. In addition to impacting routine disease control efforts or non-emergency outbreak responses, they could remove decision-making authority from public health and medical experts and place it in the hands of elected officials, who may not possess the necessary expertise. The report also concludes that some of these efforts could exacerbate racial and ethnic disparities during the ongoing pandemic response.

RURAL HOSPITAL CLOSURES For decades, a variety of issues have put US rural hospitals in a fragile position, challenges amplified by the COVID-19 pandemic. According to research by the University of North Carolina at Chapel Hill, a record 19 rural hospitals shuttered in 2020 amid the pandemic, more than in any other year. For people with COVID-19, or those with suspected SARS-CoV-2 infection, these closures and crowding at other rural facilities are creating obstacles and delays for people seeking care and testing. A new STAT analysis shows that communities containing hospitals that closed experienced disproportionate COVID-19 deaths, 37% higher in counties where hospitals shut than in their states overall. In most rural counties—those with fewer than 50,000 residents and at least 50 miles from a major city—death rates were two-thirds higher than in their states. The closures are clustered across the South and Southeast, erecting another barrier to care for largely Black communities. Although several rural hospital closures were avoided last year due to US government support, experts fear more are on the horizon once short-term funding dries up. These closures are impacting care for primarily lower-income populations with declining health and forcing those who lose healthcare jobs to leave the areas. Experts fear the worst is yet to come, with rural hospital closures having impacts far beyond COVID-19 patients.

PARENTAL CONSENT FOR TEENS Young people across the US have taken to social media sites to promote SARS-CoV-2 vaccination among their peers. While many parents have lept at the opportunity to vaccinate their teenagers, there are some who are resisting the idea, with parents’ willingness to vaccinate their children usually aligning with their own intentions. According to data collected in April through the KFF COVID-19 Vaccine Monitor, 3 in 10 parents of children ages 12-15 say they will get their child vaccinated, 25% say they will wait a while to see how the vaccine is working, 18% plan to get their child vaccinated if their school requires it, and nearly 25% say they will definitely not get their child vaccinated. Parental consent is needed in most states, except for in North Carolina, where all teenagers can receive vaccinations without parental permission; in Tennessee and Alabama, where those 14 and older do not need consent; and in Oregon, where parental approval is not required for teens 15 and older. Public health experts maintain that vaccinating the US teen population is critically important for completely returning to in-person schooling and for the economy.

SOTROVIMAB EUA The US FDA issued an Emergency Use Authorization (EUA) for a new monoclonal antibody treatment for COVID-19. The drug, sotrovimab, was developed by Vir Biotechnology and GlaxoSmithKline (GSK) to target the SARS-CoV-2 spike protein. The FDA authorized the use of sotrovimab in COVID-19 patients aged 12 years and older who are at high risk for progressing to severe disease, including adults aged 65 years and older and those with underlying medical conditions. The treatment is currently undergoing rolling review by the European Medicines Agency (EMA). On May 21, the EMA’s Committee for Medicinal Products for Human Use (CHMP) recommended issuing a Conditional Marketing Authorization, but to our knowledge, the European Commission has not yet issued the authorization.

VACCINE EFFICACY AGAINST EMERGING VARIANTS In a study published in the New England Journal of Medicine, US pharmaceutical company Novavax reported its SARS-CoV-2 vaccine had an acceptable safety profile and exhibited strong neutralizing antibody responses in a Phase 2a-b clinical trial in South Africa. The study included 2,682 baseline seronegative participants, of which 94% were HIV-negative. Symptomatic COVID-19 was observed in 15 participants in the vaccine group and 29 in the placebo group, most of which were categorized as mild to moderate cases with the exception of one severe case in the placebo group. Vaccine efficacy in the HIV-negative group was 60.1% and 49.4% regardless of HIV status, which meets the efficacy criteria for primary Phase 2b evaluation. Researchers sequenced 41 isolates from the symptomatic cases, of which 38 (92.7%) were the B.1.351 variant. In a post hoc analysis, the vaccine’s efficacy against the B.1.351 variant was 51.0% in the HIV-negative group and 43.0% in the combined HIV-negative and HIV-positive population.