September 3: Johns Hopkins COVID 19 Report

COVID-19 Situation Report

The COVID-19 Situation Report will not be published on Tuesday, September 7, 2021, in recognition of the Labor Day holiday in the US. The report will resume publication on Friday, September 10.

EPI UPDATE The WHO COVID-19 Dashboard reports 218.6 million cumulative cases and 4.53 million deaths worldwide as of September 3.

Global Vaccination

The WHO reported 5.29 billion cumulative doses of SARS-CoV-2 vaccines administered globally as of September 1. A total of 2.01 billion individuals have received at least 1 dose, and 1.21 billion are fully vaccinated. Analysis from Our World in Data indicates that global daily vaccinations are holding relatively steady at approximately 41 million doses per day, which is the third highest peak to date*. The global trend continues to closely follow the trend in Asia. Our World in Data estimates that there are 3.16 billion vaccinated individuals worldwide (1+ dose; 40.1% of the global population) and 2.16 billion who are fully vaccinated (27.4% of the global population). *The average doses administered may exhibit a sharp decrease for the most recent data particularly over the weekend, which indicates effects of reporting delays. In an effort to reflect the longer-term trends, the numbers reported here may not correspond to the most recent data.

UNITED STATES

The US CDC reported 39.5 million cumulative COVID-19 cases and 641,725 deaths. Daily incidence continues to increase, but the trend is tapering off toward a peak or plateau. On August 27, the US surpassed 150,000 new cases per day, and the current average of 153,245 is the highest since January 28. Daily mortality also continues to increase, and the mortality trend may be starting to taper off as well, although Florida’s new reporting scheme is impacting how we interpret the current trend (see below). The US surpassed 1,000 deaths per day on August 24, and the current average of 1,046 deaths per day is the highest since March 11*.

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

The Florida Department of Health updated its COVID-19 mortality reporting process, which affects how the official state and CDC data are interpreted. Previously, like other states, Florida assigned dates to COVID-19 deaths corresponding to the date they were reported; however, Florida now assigns dates that correspond to the date of death. While reporting mortality by the date of death is technically the most accurate approach, it makes it difficult to monitor current trends. Deaths can take days or weeks to be identified, confirmed, and reported, which results in a sharp artificial decline in daily mortality over the most recent several days, even though the actual trend could be increasing. As deaths are confirmed, they will be added to the correct date of death, so the data from recent days will fill in over time. These delays mean that it will take extra time to identify changing trends, including the peak during a surge or the start of a new surge. Based on recent trends, we believe Florida is averaging more than 200 deaths per day; however its most recent report includes only 11 deaths for September 1, bringing its average down all the way down to 64. Because Florida represents approximately 20% of the average national daily mortality, its new reporting scheme is affecting how we interpret the national-level trend as well. The US average could easily be 100-150 deaths per day higher than the current reported value.

US Vaccination

The US has administered 372 million cumulative doses of SARS-CoV-2 vaccines, and daily vaccinations have leveled off over the past several days, hovering at slightly more than 800,000 doses per day since August 23*. We have not observed a marked increase in daily vaccinations since the US FDA issued full approval for the Pfizer-BioNTech vaccine. There are 205.9 million individuals who have received at least 1 dose, equivalent to 62.0% of the entire US population. Among adults, 74.5% have received at least 1 dose, as well as 13.5 million adolescents aged 12-17 years. A total of 175.0 million individuals are fully vaccinated, which corresponds to 52.7% of the total population. Approximately 63.7% of adults are fully vaccinated, as well as 10.4 million adolescents aged 12-17 years.

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

As we have covered previously, there are considerable disparities in terms of both vaccination coverage and the impact of the ongoing US surge at the state and regional levels. This week, we will look more closely at COVID-19 mortality since July 1 (ie, during the current surge) and any potential associations with state-level full vaccination coverage. It is well documented that full vaccination provides good protection against severe COVID-19 disease and death, including from the Delta variant. In this analysis, we will compare the raw increase in per capita cumulative mortality from July 1-September 1. Comparing the per capita values will allow us to more directly compare states to each other, and using the raw increase—ie, as opposed to the relative increase—we can mitigate the effects of the baseline cumulative incidence, which varies widely by state. By July 1, all states had removed eligibility restrictions and opened vaccination up to the general public. Daily vaccination progress slowed, so we can reasonably assume that coverage—or at least the relative differences in coverage—remained relatively consistent over that period.

The median state-level increase in per capita cumulative mortality over this period was 8 deaths per 100,000 population, and the mean was 11. This indicates that most states reported lower increases, while a small number of states reported much higher totals. In total, 32 states reported increases of 10 or fewer, and 12 states* reported increases of 15 or more, including 4 states with increases of more than 30: Louisiana (40), Florida (36), Arkansas (35), and Mississippi (34). Of the 12 states reporting increases of more than 15, 10 are in HHS Regions 4 (Southeast), 6 (South Central), and 7 (Central). Among the 16 states reporting increases of 5 deaths per 100k or fewer, the top 5 are all in Region 1 (Northeast)**, 4 states are in Region 3 (Midwest), and 3 are in Region 5 (Mid-Atlantic).

Among the 12 states reporting increases of 15 deaths per 100k or more, all but Florida (#21; 53.4%) are in the bottom half of states in terms of full vaccination coverage. Florida is also the only one of these states with full vaccination coverage greater than 50%. Eight (8) of these states are in the bottom 12 in terms of vaccination coverage, including #48 Wyoming (39.1%), #49 Alabama (38.6%), and #50 Mississippi (38.5%). Among the top 10 states in terms of full vaccination coverage, 6 are also in the top 10 in terms of the increased per capita mortality. Only 1 of the top 28 states in terms of vaccination coverage reported an increase in mortality greater than 10 deaths per 100k: Florida (+49).

Several states reported notably lower or higher increases in per capita mortality than would be expected based solely on their vaccination coverage. As noted above, Florida reported the second-largest increase in mortality, but it ranks #21 in terms of full vaccination coverage. While vaccination is a key tool in terms of mitigating the impact of COVID-19, it needs to be combined with non-pharmaceutical interventions (NPIs), such as physical distancing and mask use, to slow transmission, and Florida officials have exhibited an unwillingness to implement those types of measures during the current surge. Increased transmission and incidence will inevitably lead to increased mortality. New Jersey, Oregon, and Washington also rank considerably lower in terms of increased mortality than they do for vaccination coverage—18, 19, and 20 positions lower, respectively—but it is not immediately clear why these states, in particular, faced elevated COVID-19 mortality compared to their vaccination coverage.

Conversely, North and South Dakota rank much better in terms of increased COVID-19 mortality than their vaccination coverage would suggest. North Dakota is #44 in terms of vaccination coverage (41.8%), but it is #4 in terms of the increase in mortality (4 deaths/100k), a difference of 40 positions. South Dakota also ranks #4 in terms of increased mortality**, but it ranks #26 in terms of vaccination coverage (49.4%), a difference of 22 positions. Similarly, Nebraska and Ohio each rank 18 positions higher in terms of increased mortality than they do for vaccination coverage. Notably, these and other similar states—including Idaho, Michigan, Minnesota, and West Virginia—appear to still be in the early stages of their respective surges, so it is possible that we could observe larger increases in mortality as they move closer to their respective peaks. In contrast, most of the Region 1 states appear to already be peaking in terms of COVID-19 mortality, and their lower mortality during this surge suggests that higher vaccination coverage provided protection against severe disease and death at the state level.

With some notable exceptions, there appears to be an association between higher vaccination coverage and lower COVID-19 mortality during the current surge. The surge first emerged in Missouri, before moving south and east, into Arkansas, Louisiana, Mississippi, Alabama, and Florida, so it has been present there longer than in other parts of the country. The lower vaccination coverage in these states, however, appears to be contributing to elevated hospitalizations and mortality—in some instances, equal to or worse than their previous records. The timing of the geographic spread of the surge could also potentially factor into the lower mortality reported in states that are still in the early stages of their respective surges, particularly those with lower vaccination coverage. Additional analysis, including after more states pass their peaks and on case-fatality ratios over this period, could provide further insight into the association between state-level vaccination coverage and COVID-19 mortality during this surge.

*Delaware reported an overall increase of 20 deaths/100k, but this included a jump of 13 on August 1 due to a bolus of 130 newly reported deaths, most of which were previously unreported. Without this reporting anomaly, Delaware would have had an estimated increase of 7.

**Including ties; 6 states reported increases of 4 deaths per 100k, all tying for the #4 rank.

VARIANT OF INTEREST: MU In its August 31 COVID-19 Epidemiological Update, the WHO announced the addition of another SARS-CoV-2 variant to its list of variants of interest (VOIs), B.1.621 or “Mu.” The Mu variant, which also includes the descendent Pango lineage B.1.621.1, includes several mutations that show the potential for immune escape in both people previously infected with SARS-CoV-2 and those who are vaccinated; however, more research is necessary to confirm the theory. As of August 29, more than 4,500 sequences of the lineage were recorded in 39 countries. The Mu variant was first identified in Colombia in January 2021. Since then, the variant has spread worldwide, with cases reported in the UK, US, Europe, and Hong Kong. While the global prevalence of the Mu variant among sequenced cases is below 0.1% globally and declining, the variant accounts for at least 39% of cases in Colombia and 11% in Ecuador, with prevalence in both countries continuing to increase. But WHO warned that reports on the variant’s prevalence should be “interpreted with due consideration” because of variations in countries’ sequencing capacities. Mu is the fifth variant of interest named by the WHO since March 2021. In August, Public Health England (PHE) released a risk assessment for the variant, which it calls VUI-21JUL-01, highlighting that laboratory findings show it is similar to the Beta variant first detected in South Africa and raising concerns over its potential for immune escape. The WHO said it will continue to monitor and study the variant’s epidemiological evolution.

MASK-USE TRIAL A group of researchers from Stanford Medicine and Yale University this week released findings from the first randomized controlled trial (RCT) in a real-world setting designed to evaluate the effects of mask use on SARS-CoV-2 transmission. The researchers found that mask use, even when worn inconsistently in the community, can lead to a reduction in symptomatic COVID-19 cases. Additionally, relatively low-cost, targeted interventions promoting mask wearing can significantly increase the use of face coverings in rural, low-income countries, according to the results. Although the study is not yet published, the researchers have submitted the paper to the journal Science, whose editors encouraged its public release given the current public health policy relevance, as the pandemic worsens in many parts of the world.

The study included more than 340,000 adults in 600 villages in Bangladesh. In 300 villages, researchers implemented a mask distribution and promotion initiative, now called the “NORM” model, which stands for “No-cost mask distribution, Offering information, Reinforcement to wear masks, and Modeling by local leaders.” The researchers saw a 29 percentage-point increase in mask-wearing in the intervention villages (42%) versus the comparison villages (13%). Overall, the increased mask usage led to a 9% reduction in serologically confirmed symptomatic SARS-CoV-2 infection. Notably, 100 of the villages received cloth masks, resulting in a 5% reduction in symptoms, while 200 villages that received surgical masks saw a 12% reduction in symptoms. The use of surgical masks was especially effective for people aged 60 years or older, leading to a 35% reduction in symptomatic SARS-CoV-2 infections in that age group. The team plans to conduct further research evaluating how masks limit symptomatic cases, whether by reducing exposure to viral load or by preventing infections entirely. For now, the study provides a “gold standard” showing mask wearing is an effective way to limit symptomatic COVID-19, and the interventions are being rolled out in other parts of Bangladesh and in Pakistan, India, Nepal, and areas of Latin America.

LONG-TERM HEALTH EFFECTS The scientific community continues to investigate the long-term impacts of COVID-19 on individual health. Researchers from the University College of London announced earlier this week that their survey of children with positive COVID-19 diagnoses provided reassurance that post-acute sequelae of COVID-19 (PASC), or so-called “long COVID,” does not impact large numbers of adolescents. The research team conducted a survey of 11- to 17-year-olds in England who had positive SARS-CoV-2 tests between September 2020 and March 2021. The study, which is not yet peer-reviewed, suggests that 2-14% of children with a positive test reported having symptoms 15 weeks after their initial diagnosis. While the reported prevalence still presents a public health concern for children with COVID-19, it suggests that these issues may not be as prevalent among younger people as previously thought.

Research also continues into the scope of COVID-19's long-term impacts among adults. A recent article published in The Lancet describes 1-year outcomes of individuals who survived hospitalization due to COVID-19. The study included 1,276 survivors discharged from the Jin Yin-tan Hospital in Wuhan, China, between January 7 and May 29, 2020. The cohort was followed for 12 months, with follow-up visits at 6 and 12 months. The research team found that the proportion of patients with at least 1 residual symptom decreased from 68% to 49% between the 6-month and 12-month follow-up appointments. However, researchers noted a slight increase in the proportion of patients experiencing anxiety and depression symptoms between the 6-month check-in (23%) and the 12-month follow-up (26%). The findings show that while most individuals returned to good health 1 year following their hospitalization, the overall health status of the COVID-19 survivors remained lower than for those in a non-hospitalized control group.

Another study published in The Lancet Infectious Diseases analyzed the risk of PASC among vaccinated adults. The research team conducted a community-based, case-control study among UK-based adults who used the COVID Symptom Study mobile phone app. The study matched individuals who contracted SARS-CoV-2 after vaccination with individuals who contracted the virus before vaccination in an attempt to parse out differences in disease presentation. The research team found that the odds of COVID-19 symptoms persisting for 28 days or more among those who were fully vaccinated was approximately halved (OR 0.51) compared with unvaccinated controls. While this risk reduction provides additional reasons to support COVID-19 vaccination, there is still a low but present risk that vaccinated adults could develop long COVID.

There already are reports of individuals suffering long-term COVID symptoms who feel that the scientific community is leaving them behind. Understanding and minimizing the long-term impacts of COVID-19 disease is an essential part of response and recovery, and research endeavors such as the ones described above can help characterize what could be a long tail on the end of the pandemic.

US SCHOOLS As the school year begins for many in the US, COVID-19 cases among children are rising, with nearly 204,000 new cases added the week ending August 26, representing 22.4% of the total weekly reported cases. This marks the second week with child cases at the level of the winter surge of 2020-21 and a 5-fold increase from July 22 to August 26, according to the American Academy of Pediatrics (AAP). US CDC data show the number of COVID-19 cases and related emergency room visits and hospitalizations among children were 4 times higher in states with low vaccination rates than those with higher vaccination rates during the month of August. CDC Director Dr. Rochelle Walensky said last week that recently opened schools with COVID-19 outbreaks generally are not following federal guidelines for vaccination and universal masking among staff and students. In one Iowa school district where masking is optional, parents are being given the option to quarantine their children if they have a known exposure, as long as they remain symptom-free, increasing the risk of transmission among asymptomatic children. In schools already operating, some outbreaks have caused districts to return to virtual learning, including one Texas school district where 2 junior high teachers died of COVID-19 complications the same week.

The US Department of Education announced this week it has begun investigations into 5 states—Iowa, Oklahoma, South Carolina, Tennessee, and Utah—whose bans on mask mandates in schools might violate civil rights laws meant to protect students with disabilities. The department has not opened investigations in Florida, Texas, Arkansas, or Arizona because all of the bans in those states are not being enforced due to ongoing legal or other actions. On August 27, a Florida judge ruled that Governor Ron DeSantis and the Florida Department of Education had overstepped their authority when they banned mask mandates in the state’s school districts because the policy does not provide a parental opt out. Governor DeSantis’s lawyers on September 2 filed an appeal with the 1st District Court of Appeal in Tallahassee.

A new survey from the National Parent Teacher Association, conducted with support from the CDC Foundation, shows fewer parents want their children attending in-person classes. Prior to July 27, when the CDC updated its health guidance for schools in light of the highly contagious Delta variant, 58% of 1,448 parents and guardians surveyed said they wanted their children back in classrooms, but that figure dropped to 43% by August 8. The proportions were lower for Black (41%) and Hispanic (37%) parents, who expressed a preference for online learning. These results likely reflect the fact that Black and Hispanic children, as well as adults, are disproportionately impacted by COVID-19. On August 31, the CDC released updated FAQs for parents with school-aged children. 

US PRISONS & JAILS Reducing the number of people detained in US prisons and jails could have prevented millions of COVID-19 cases and hundreds of thousands of related deaths, as the overcrowded, tight quarters fuel a constant risk of outbreaks among inmates and staff, according to a study published September 2 in JAMA Network Open. Researchers from Northwestern Medicine, the Toulouse School of Economics, and the French National Centre for Scientific Research analyzed data collected in 1,605 US counties from January to November 2020 and found that an 80% reduction in the U.S. jail population—a level achievable simply by finding alternatives to jail detention for people accused of non-violent offenses—was associated with a 2% drop in the growth rate of daily COVID-19 cases. The reduction was greater in counties with large urban areas and when jail turnover was taken into account. The US jail population has a 55% weekly turnover rate, the study notes. This turnover, in addition to staff returning home to their communities daily, has contributed immensely to the overall number of COVID-19 cases in the US, according to the researchers. For comparison, the study also looked at other anticontagion policies, finding that nursing home visitation bans were associated with a 7.3% reduction in COVID-19 case growth rates, followed by school closures (4.3%), mask mandates (2.5%), prison visitation bans (1.2%), and stay-at-home orders (0.8%). Besides mass decarceration efforts, some experts are calling for mandatory SARS-CoV-2 vaccinations for staff and detainees in jails and prisons to help reduce the risk of outbreaks.

US HOSPITAL BURDEN Across the US, hospitals are straining under the volume of COVID-19 patients, and several states are nearly out of ICU beds. Alabama, Arkansas, Florida, Georgia, and Texas have less than 10% of their ICU beds available. Georgia hospitals have topped their January highs on some days, and adult ventilator use has far outpaced the previous high. A US Department of Health and Human Services (HHS) dashboard paints a grim picture, where 42 states are reporting 70% or greater use of inpatient beds, and 7 of the remaining 8 are in the 60-69% use category. In several states, including Montana and Oregon, the National Guard is assisting to help ease staffing shortages. Children’s hospitals are no exception, with many at or near capacity. The CEO of the Children’s Hospital Association wrote a letter to US President Joe Biden requesting federal help to handle the surge. Adding to the stress, about US$44 billion in federal aid from the US$178 billion Provider Relief Fund created last year and $8.5 billion allotted by the US Congress for rural medical care has not been distributed. Healthcare institutions, advocates, and lawmakers are urging the Biden administration to quickly decide how the funds will be divided and when they will be released. HHS has said a plan is being developed.

VACCINE EFFECTIVENESS AMONG HEALTHCARE WORKERS Coincident with the end of California’s (US) mask mandates in June 2021 and the rise of the SARS-CoV-2 Delta variant, the University of San Diego Health (UCSDH) workforce experienced an increase in SARS-CoV-2 infections, despite high vaccination rates. According to correspondence published in the New England Journal of Medicine (NEJM), between March 1 and July 31, 2021, 227 UCSDH healthcare workers tested positive for SARS-CoV-2 by rt-PCR, of whom 57.3% were fully vaccinated. Researchers calculated vaccine effectiveness by month, saying effectiveness exceeded 90% March through June, but fell to 65.5% in July (95% confidence interval [CI], 48.9 to 76.9). Additionally, the July attack rate among vaccinated individuals increased as time from vaccination grew, with those who were fully vaccinated later in the year (March through May; 3.7 per 1,000 persons [95% CI, 2.5 to 5.7]) showing an attack rate nearly half that of those vaccinated earlier in the year (January or February; 6.7 per 1,000 persons [95% CI, 5.9 to 7.8]). For unvaccinated workers, the attack rate was much higher (16.4 per 1,000 persons [95% CI, 11.8 to 22.9]). The authors attribute the change in vaccine effectiveness to the rise of the Delta variant and waning immunity, in addition to the end of masking requirements that likely resulted in increased community exposure.

But some experts have questioned the study’s conclusions, saying the reduction in vaccine effectiveness could be due to several additional or separate factors, including a small sample size for the July data; a single, large outbreak of 70 cases among workers in July; and an increase in close contacts due to loosened preventive measures. As more studies are published showing a possible decrease in vaccine effectiveness over time, it is important to consider behavior changes that could contribute to outcomes, even if the data are not captured in studies.

LATIN AMERICA & CARIBBEAN The Pan-American Health Organization (PAHO) has called on countries with surplus SARS-CoV-2 vaccines to urgently donate them to Latin American and Caribbean nations, where only 1 in 4 people have been fully vaccinated. While vaccination coverage in some countries such as Uruguay and Chile have exceeded 60%, rates are much lower in other countries, including Guatemala and Nicaragua. At a news conference, PAHO Director Dr. Carissa F. Etienne said that while every country in the region has begun administering vaccines, “immunizations are following the fault lines of inequality” in the region. She also announced the launch of the Regional Platform to Advance the Manufacturing of COVID-19 Vaccines and other Health Technologies in the Americas, which hopes to ease vaccine shortages within the region. During a recent virtual meeting, Dr. Etienne invited public and private manufacturers to submit proposals for transferring technologies or producing raw materials for mRNA vaccines, some of which PAHO already is in the process of reviewing.

In a related development, Pfizer and BioNTech announced a deal in late August with Brazilian pharmaceutical company Eurofarma to manufacture at least 100 million doses of the companies’ vaccine annually for distribution within the region, beginning next year. An additional 540 million doses are needed to ensure every country in the region can vaccinate 60% of the population.

INDIA Since mid-July, India has dramatically increased its SARS-CoV-2 vaccination rates in rural areas, where the majority of the population lives, with 70% of the nearly 120 million shots delivered in the past 3 weeks going to individuals in villages. That is up from about half in the beginning of May, when the country opened up vaccine eligibility to all adults. About 11% of the country’s population is fully vaccinated, and 37% have received at least one dose as of September 1, according to Our World In Data. While a boost in acceptance of vaccines in rural areas is promising news, India reported the largest single-day increase in new COVID-19 cases in 2 months on September 2, recording 47,092 cases. The densely populated Kerala state, which recently ended its biggest festival involving family and social gatherings, accounted for 70% of the new cases. The Kerala health ministry warned the public to take “adequate steps” to prevent the virus’s spread into surrounding states, and the federal government has warned that, like Kerala, the rest of India could see an increase in COVID-19 incidence as festival season gets underway this month and runs through early November.

Some parents and health experts are concerned the reopening of schools for the first time in 18 months amid an uptick in new cases could increase the risk of COVID-19 outbreaks. However, others say that without the ability to provide online schooling for poorer children, in-person learning is essential to keep kids on track. In Delhi, only older children will return to schools and strict measures are in place to help limit transmission, including vaccinated staff, limited classroom capacity, mandatory temperature checks, staggered lunch breaks, and physical distancing within classrooms. Several large Indian medical organizations are backing the resumption of in-person classes, urging governments to take a “calculated risk.” A recent serological survey conducted in 70 districts across 21 states showed 57% of 6- to 9-year-olds had antibodies to SARS-CoV-2, and 62% of 10- to 17-year-olds had antibodies, possibly boosting confidence in reopening schools. Still, some parents will be keeping their children at home for fear that a third wave could be looming.

NORTH KOREA North Korea has refused a shipment of nearly 3 million doses of China’s Sinovac SARS-CoV-2 vaccine from the COVAX facility, saying the vaccines should instead be provided to more seriously affected countries due to a limited global supply. Although the country has applied for assistance through COVAX, the government has yet to receive any doses, after the most recent development and a delay in a planned shipment of about 2 million AstraZeneca-Oxford vaccines earlier this year. Reportedly, the government rejected the AstraZeneca-Oxford vaccine over concerns of side effects. North Korea’s state media have reported incidents of breakthrough infections among vaccinated individuals and expressed overall doubt in the vaccines’ effectiveness. North Korea has reported zero confirmed COVID-19 cases to the WHO, but many health experts doubt those claims and worry that a large outbreak could overwhelm the country’s outdated healthcare infrastructure. In June, Supreme Leader Kim Jong-Un said the country’s COVID-19 situation was grave, without specifying details, and publicly chastised several high-ranking officials for failing to implement long-term preventive measures. Both the US and South Korea have discussed possibly offering humanitarian assistance to the impoverished nation, and Russia earlier this year offered to provide its Sputnik V vaccine, although it is unclear whether North Korea accepted.