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

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The Johns Hopkins Center for Health Security 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.
CORRECTION: On Monday, we mistakenly reported that UK Prime Minister Boris Johnson announced new social distancing restrictions for the UK. The new restrictions, scheduled to start November 5, apply only to England. Northern Ireland, Scotland, and Wales are implementing their own COVID-19 response measures.

EPI UPDATE The WHO COVID-19 Dashboard reports 47.36 million cases and 1.21 million deaths as of 10:00am EST on November 4.

The US CDC reported 9.27 million total cases and 230,893 deaths, including 86,190 new cases reported yesterday, the fourth highest daily total to date. The daily COVID-19 incidence continues to increase and set new records. With an average of 84,029 new cases per day, the US is now exceeding the previous peak in late July by more than 20%, and it is more than 2.5 times the first peak in mid-April. The daily incidence has more than doubled since the low on September 12, and it is rapidly approaching India’s record of 93,199 new cases per day, set in mid-September. Since October 18, the US COVID-19 mortality has increased from approximately 700 deaths per day to 829, an 18% increase and the highest average since September 16.

More than half of all US states have reported more than 100,000 cumulative cases, including 14 with more than 200,000 cases:
>900,000: California, Texas
>800,000: Florida
>500,000: New York
>400,000: Illinois
>300,000: Georgia

In order to better account for the level of transmission in many states across the Midwest and Mountain regions, the COVID Exit Strategy website added a new category. The new classification, greater than 500 cases per million population (purple), covers 11 states. Notably, North and South Dakota are reporting 1,510 and 1,312 daily cases per million population. To put those figures in context, that corresponds to more than 1 out of every 1,000 people in those states testing positive for SARS-CoV-2 every day.

In addition to COVID-19 incidence, the US is reporting increasing impact on hospitals and increasing COVID-19 mortality. Nationally, emergency department (ED) visits for COVID-19 have increased steadily over the past several weeks. The percentage of ED visits for COVID-19 coronavirus-like illness increased from approximately 2% in early September to nearly 3.5% in early November, a 65% increase. This trend is even more pronounced in some states, including Alaska (up from 2.5% to more than 6%), Connecticut (1% to nearly 4%), Idaho (2.5% to more than 7%), Illinois (2.5% to 6.5%), Montana (2% to 8%), Nebraska (1.5% to more than 6%), New Mexico (1.5% to 5%), North Dakota (3% to 11%), Utah (2.5% to 8%), and Wisconsin (1.5% to more than 5%). On a regional basis, Region 5 (Illinois, Indiana, Michigan, Ohio, Wisconsin) increased from 1.7% to 5% and Region 8 (Colorado, Montana, North and South Dakota, Utah, Wyoming) increased from 2% to more than 6%.*
*ED data not presented for South Dakota; all values are approximate.

Over the past week, 9 states have reported per capita COVID-19 mortality greater than 0.5 deaths per 100,000 population, including 3 states with 1 or greater. Indiana, Missouri, Mississippi, and Tennessee all reported 0.5 deaths per 100,000, and Arkansas and Wisconsin both reported 0.7. South Dakota reported 1 COVID-19 death per 100,000; Montana reported 1.1; and North Dakota reported 1.5. With the exception of Mississippi, all of these states are reporting increasing COVID-19 mortality over the past several weeks. In some cases, like Arkansas and Tennessee, the trend has persisted for months, whereas most began approximately 3-4 weeks after the most recent surge in incidence. For example North and South Dakota’s incidence began to surge in mid-to-late August, followed by mortality in mid-September. Montana’s most pronounced surge in mortality started in mid-October, following a surge in incidence that began in mid-to-late September.

The Johns Hopkins CSSE dashboard reported 9.39 million US cases and 232,742 deaths as of 11:30am EST on November 4.

US ELECTION After many months of US presidential campaigns defined, in large part, by the COVID-19 pandemic, the US general election was held yesterday. Even in a typical election year, many polling sites can face long lines and wait times of several hours or longer, and 2020 was no exception. While a record number of Americans cast their votes before election day, either by mail or in person, many millions voted in person yesterday. In addition to record-setting voter turnout in this year’s presidential election, social distancing and enhanced hygiene procedures at polling sites posed additional challenges and, to some degree, slowed the voting process. Tallying of the votes is still underway. At this time, no victor has been declared in the presidential election, and some states anticipate counting votes over the next several days.

In addition to the direct impact on the voting process, the outcome of the presidential election promises to have major implications for the US COVID-19 response. As the campaigns came to a close, COVID-19 remained a major talking point for both US President Donald Trump and former Vice President Joe Biden. President Trump continually argued that the US epidemic had turned a corner, despite record daily incidence, and focused on the economic damage associated with social distancing policies recommended by experts. Former Vice President Biden emphasized the absence of a national COVID-19 response strategy and repeatedly stated that he would follow the guidance of the nation’s scientific experts. Regardless of the final official result, it may be unlikely that a COVID-19 stimulus package is finalized during the Congressional “lame duck” session between now and Inauguration Day in January.

COVID-19 IN CHILDREN According to data published by the American Academy of Pediatrics (AAP), more than 61,000 pediatric cases of COVID-19 were reported in the US in the last week of October, the highest weekly total to date. Through October 29, more than 850,000 pediatric cases have been reported nationally since the onset of the pandemic, representing 11% of all US cases. The data continue to indicate that severe illness is relatively rare among children; however, a number of states—including Missouri and North Dakota—recently reported deaths in teenagers, their youngest COVID-19 deaths to date. Beyond severe acute disease and mortality, the AAP calls for expanded efforts to evaluate the risk of longer-term health effects due to SARS-CoV-2 infection, including physical and mental health issues. This is particularly important for Black and Hispanic children, who are disproportionately affected by COVID-19. The AAP also notes that the pediatric data likely underestimates the true COVID-19 incidence in children. While many pediatric infections result in mild illness or asymptomatic infection, they can still lead to longer-term health effects or allow transmission of the infection to higher-risk individuals.

IMMIGRATION DETENTION FACILITIES A study published in JAMA analyzed SARS-CoV-2 testing and COVID-19 incidence among detainees at US Immigration and Customs Enforcement (ICE) facilities from April-August, based on data published on the ICE COVID-19 website. Compared to the pre-pandemic totals in February, ICE’s average daily detained population decreased by 45% through August, likely due to efforts to reduce the detained population during the pandemic. By the end of August, ICE had reported 5,379 cumulative cases of COVID-19 among ICE detainees, including 6 deaths. Notably, 20 of the 135 facilities accounted for more than 70% of the COVID-19 cases, indicating major outbreaks in these facilities.

ICE’s test positivity decreased from 47% in April to 11% in July, as testing capacity increased (from 3,224 tests per 100,000 detainees to 46,874); however, test positivity subsequently increased in August to 18%. In August, per capita testing volume decreased 23% compared to July, but incidence increased by 26%. The per capita incidence in ICE facilities was more than 13 times that of the broader US population, despite the per capita testing in ICE facilities only being 4.6 times the US public. At the peak in June, ICE facilities were reporting COVID-19 incidence nearly 22 times the per capita incidence in the US while performing fewer than 7 times the number of tests per capita. Consistent with previous studies, these data indicate that COVID-19 is spreading more rapidly among ICE detention facilities.

The researchers cite potential difficulties implementing ICE’s COVID-19 response plan—which includes guidelines for social distancing, enhanced hygiene and disinfection, testing protocols, and expedited detainee release—as a potential barrier to combating COVID-19 within ICE facilities, and they call for an independent assessment of the COVID-19 measures implemented in ICE facilities. They also advocate for expanded testing, including for asymptomatic individuals, in order to mitigate transmission risk. 

ANTI-ASIAN RACISM Racism against Asian Americans continues to be an issue across the US. A report to the UN Office of the High Commissioner for Human Rights (UN Human Rights) noted that “racially motivated violence and other incidents against Asian-Americans have reached an alarming level across the United States since the outbreak of COVID-19,” affecting Chinese Americans as well as individuals descending from other Asian nations. The documented incidents spanned a wide range, from verbal harassment to vandalism, to physical violence. Additionally, Asian Americans have been denied service at restaurants and retail stores, residences, and public transportation or ride-sharing services. Notably, the incidents disproportionately affected women of Asian descent. These incidents and trends are not exclusive to the US. study by researchers at Australian National University found that 84.5% of Asian Australians reported at least one instance of discrimination between January and October 2020. The study also found that Asian Australians were more likely to hold jobs that have been affected by the pandemic and social distancing policies, and Asian Australians reported feeling “more anxious about the pandemic” than those of other races or ethnicities. 

TESTING OVERSIGHT Early in the US COVID-19 epidemic, the country struggled to rapidly scale up testing capacity. One component of the effort to increase the volume of available tests was permitting laboratories—including at health departments, hospitals, universities, and private sector companies—to develop their own diagnostic tests. Laboratory developed tests (LDTs) were initially overseen by the US FDA, under Emergency Use Authorizations (EUAs), but the FDA stopped requiring EUAs for LDTs in August, at the direction of senior leadership at the US Department of Health and Human Services. This decision enabled increased access to the tests, due to reduced regulatory requirements; however, it reduced oversight of test quality and reliability. An investigation by STAT News discovered that HHS leadership and its general counsel were aware of “major concerns” about the quality and accuracy for “many of the LDTs” in August, when the department directed the FDA to stop requiring the EUAs. Notably, tests that were issued EUAs prior to the policy change are required to report problems with the tests to the FDA, including false positive/negative test results, but the STAT News report indicates that the “vast majority of false Covid-19 results...are simply never reported.”

Grocery Stores
Researchers from Harvard and Boston Universities (Massachusetts, US) analyzed exposure and infection risks among 104 employees at a Boston-area grocery store. The study, published in BMJ, also evaluated the employees’ mental health, specifically evaluating for signs of anxiety and depression. As part of a testing program mandated by the local government, all employees underwent PCR-based diagnostic testing, and 21 tested positive for SARS-CoV-2. Notably, 76% of the positive employees were not symptomatic at the time of testing. Employees whose jobs involved direct interaction with customers were 5 times more likely to test positive for SARS-CoV-2 than those without direct customer contact. Among 99 participants who completed the mental health assessments, 24 reported “at least mild anxiety” and 8 “screened positive for at least mild depression.” Individuals who were able to practice effective social distancing at work were less likely to experience both anxiety and depression. Additionally, those who were able to commute to work without using public transportation (e.g., walk, bicycle, private vehicle) exhibited a 90% reduction in the risk depression. 

Construction Sites
A study published in JAMA: Network Open developed a stochastic model to analyze exposure risk among construction site workers in Austin, Texas (US). Using local demographic data and reported COVID-19 hospitalization rates, the researchers modeled 15 scenarios representing various worksite area sizes and degrees of transmission between workers, corresponding to the implementation of various COVID-19 control measures. Notably, at the time of the study, the researchers estimated that the per capita COVID-19 hospitalization rate among construction workers was 4.5 times the rate among the entire Austin population. The model illustrated that close contact in high-risk worksites with large construction crews not only corresponded to elevated workplace transmission and construction worker hospitalizations, but also increased community transmission. Based on the results of the study led local authorities in Austin to impose more restrictive worksite safety requirements, including increased cleaning of shared equipment, daily symptom monitoring, and enhanced documentation to support contact tracing.

INFECTION RISK FACTORS A study published in Clinical Infectious Diseases examined the risk factors associated with SARS-CoV-2 infection in the US Veterans Affairs (VA) healthcare system. The study population included more than 88,000 VA patients across the country who underwent PCR-based diagnostic testing for SARS-CoV-2 between March and May. Among these individuals, 11.5% tested positive for SARS-CoV-2 infection. The researchers found that male sex, older age, and non-White race/ethnicity were associated with increased odds of testing positive for SARS-CoV-2. It is well documented that individuals with underlying medical conditions, including overweight/obesity and diabetes, are at elevated risk of severe COVID-19 disease and death, but this study also found that having overweight/obesity or diabetes were also associated with increased risk of testing positive for SARS-CoV-2. Individuals who smoked were also more likely to test positive. While these findings are not unique to this study, the study setting of the VA national health system provides a more streamlined comparison between regions due to similar protocols and patient populations. Understanding infection risk can “help public health and health system initiatives to target testing, education, and preventive efforts.”

AGE-SPECIFIC MORTALITY A study published in Nature evaluated age-specific COVID-19 mortality and seroprevalence based on data from 45 countries, representing a combined population of approximately 3.4 billion people, and 22 serological studies. The researchers developed a model that merges seroprevalence study data with time-series mortality data to estimate the corresponding infection fatality ratio (IFR) for the 45 countries. The study found that COVID-19 mortality trends for individuals under the age of 65 were relatively consistent across countries and that mortality for individuals aged 65 and older was more heterogeneous.

Consistent with the current understanding of COVID-19 risk, children generally exhibited lower IFR than adults. The estimated IFR ranged from 0.002% among children aged 5-9 years to 8.29% among individuals aged 80 years and older. Starting at age 10, the IFR increased approximately 0.6% with an increase of 5 years in age. Considering challenges and limitations in testing and reporting, particularly for mild cases and asymptomatic infections, COVID-19 mortality can be among the most reliable data available. With that in mind, the researchers identified considerable variation in mortality data for individuals aged 65 and older. Notably, “many countries in South America had significantly fewer reported deaths in individuals ≥65 years than expected,” corresponding to as many as several thousand “missing deaths” in some countries. Conversely, European countries tended to report elevated mortality among older individuals than would be expected based on the model. The mortality model was highly sensitive to mortality estimates among nursing home populations, and the researchers note that the discrepancies in IFR among older individuals highlight the challenge of comparing mortality data between countries, particularly those that experienced “very different levels of transmission [among] hyper-vulnerable communities.”

IMMUNITY Despite tens of millions of cases worldwide and nearly a year’s worth of data on COVID-19, many questions remain regarding the body’s lasting antibody response to SARS-CoV-2 infection. A study of more than 30,000 infected individuals in New York City, published in Science, analyzed the neutralizing antibody response. From March to October, Mount Sinai Health System screened more than 72,000 individuals using an in-house serological assay. The researchers found that the “vast majority” of patients who were seropositive, indicating prior infection with SARS-CoV-2, had moderate-to-high titers for antibodies against the SARS-CoV-2 spike protein. The researchers acknowledge that the screening effort could have failed to identify individuals who were previously infected but did not produce lasting antibodies; however, prior research indicates that this is likely to be a small fraction of infected individuals.

Additional analysis using 120 specimens, including specimens ranging from seronegative to high antibody titers, determined that the neutralization capacity of the specimens correlated strongly with the spike protein antibody titer. The researchers also analyzed the duration of neutralizing antibody activity using additional specimens collected from 121 patients—representing “a variety of titer levels”—at approximately 82 and 148 days after symptom onset. Generally, the specimens exhibited a steady decline in antibody titer over time, but the specimens exhibited similar trends in neutralizing capacity as the initial specimens (ie, higher titers corresponds to increased neutralization), indicating that the antibodies against the spike protein could provide some measure of durable protection against subsequent infection. The researchers also observed an initial increase in titer among some individuals with initially low antibody levels, but several individuals with very low titers in the initial specimen had undetectable antibody levels in the subsequent specimens. This illustrates that some individuals with milder immune response can take time to build up antibody levels following infection; however, those with very low immune response can be at risk for losing antibody protection over a relatively soon after infection. The researchers intend to continue following this patient cohort over time to gather additional data.