Daily updates on the emerging novel coronavirus pandemic from the Johns Hopkins Center for Health Security.

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June 29, 2020

EPI UPDATE The WHO COVID-19 Situation Report for June 28 reports 9.84 million cases (189,077 new) and 495,760 deaths (4,612 new). This is the highest daily incidence reported to date, and the global totals could surpass 10 million cases and 500,000 deaths in today’s Situation Report. The pandemic continues its acceleration.

India reported 19,459 new cases, its second highest daily incidence to date. This slight decrease from its record high the previous day is consistent with India’s recent reporting trend, and we expect India to report increasing incidence as the week continues. India’s daily incidence has essentially doubled since June 11, and its epidemic continues to accelerate. India is currently #3 globally in terms of daily incidence . Pakistan reported 3,557 new cases. This is elevated compared to late last week, but it is still considerably lower than its June 13 peak (6,825 new cases). Pakistan is now #12 globally in terms of daily incidence and continues to fall down the list. Following several days of slightly lower daily incidence, Bangladesh reported 4,014 new cases, its highest daily incidence to date. Bangladesh has reported 4 of its 7 highest daily totals over the past 5 days. Bangladesh remains at #9 globally in terms of daily incidence.

Brazil reported 30,476 new cases. While this is fewer new daily cases than were reported over the weekend, it is considerably higher than early week reports in previous weeks. We expect Brazil to report increasing incidence in the coming days. Brazil is currently #2 globally in terms of daily incidence . Daily incidence in both Brazil and the United States are increasing, and both are reporting nearly double the daily incidence as India.

Mexico has reported decreasing daily incidence for 3 consecutive days; however, Mexico does not yet appear to have reached its peak. Based on recent trends, we expect Mexico to report increasing daily incidence over the coming days. Mexico is currently #6 globally in terms of daily incidence. Broadly, the Central and South American regions are still a major COVID-19 hotspot. Including Brazil and Mexico, the region represents 5 of the top 11 countries globally in terms of daily incidence—including Chile (#7), Colombia (#10), and Peru (#11). Additionally, several other countries in the region are reporting more than 1,000 new cases per day . Central and South America also represent 4 of the top 12 in terms of per capita daily incidence —Chile (#3), Panama (#6), Brazil (#7), and Peru (#12).

Overall, the Eastern Mediterranean Region remains a global hotspot as well, representing 5 of the top 10 countries in terms of per capita incidence : Bahrain (#1), Qatar (#2), Oman (#4), Kuwait (#8), and Saudi Arabia (#10). Additionally, nearby Armenia is #5. Notably, Bahrain overtook Qatar as #1 globally in terms of per capita daily incidence. Qatar’s per capita daily incidence has decreased by nearly 60% since May 31. The region also includes several notable countries in terms of total daily incidence . In addition to Pakistan, Saudi Arabia is #11, Iran is #13, and several other countries in the region are reporting more than 1,000 new cases per day .

South Africa is among the top countries globally in terms of both per capita (#11) and total daily incidence (#5). South Africa reported its 5 highest daily incidence over the past 5 days, and its daily incidence has nearly doubled since June 19.

The US CDC reported 2.50 million total cases (44,703 new) and 125,484 deaths (508 new). The CDC reported the United States’ 2 highest daily totals over the past 2 days, and 4 of the top 5 over the past 4 days. In total, 19 states (increase of 1) and New York City reported more than 40,000 total cases, including California and New York City with more than 200,000; New Jersey and New York state with more than 170,000; and Florida, Illinois, and Texas with more than 130,000. Following an overall decrease in daily incidence from mid-April through the end of May, the United States’ national COVID-19 incidence is clearly increasing. The United States’ daily incidence has nearly doubled since June 9, up from 20,338 new cases per day to 38,006 ( 7-day average ).

The Johns Hopkins CSSE dashboard reported 2.56 million US cases and 125,927 deaths as of 12:30pm on June 29.

US EPIDEMIC & RESPONSE Numerous US states have begun to slow reopening or reverse course by suspending efforts to progress through recovery plans or re-instituting previously lifted policies and strengthening statewide or local restrictions in order to mitigate community transmission risk and ensure sufficient health system capacity.

Following weeks of increasing COVID-19 incidence, hospitalizations, and test positivity , Florida Governor Ron DeSantis issued an executive order reversing some recent efforts to ease social distancing restrictions. Notably, the order, issued on Friday, prohibits on-site consumption of alcohol at bars statewide , which some state officials have blamed for statewide increases in transmission . Florida has reported its 6 highest daily case counts over the past 6 days, including its record of 9,557 on June 26. The Florida Department of Health only reports current COVID-19 hospitalizations (as opposed to providing a longer-term display); however, the Florida Agency for Health Care Administration indicates that 23.2% of the state’s adult intensive care unit (ICU) beds are available as of today, which would rank it #48, ahead of only Rhode Island and Arizona—according to analysis by COVID Exit Strategy . In terms of testing, Florida’s positivity increased from 2% for the week of May 17 to 11.7% last week, and it is currently 15.5%, according to the Johns Hopkins SARS-CoV-2 testing dashboard . Like Texas last week, reinstituting social distancing restrictions represents a major shift for Florida, which implemented restrictions later than many states and began lifting them earlier and more aggressively than many states. While Florida reported promising COVID-19 trends for several weeks, health officials and experts warned that increased social interaction could facilitate increased community transmission.

Florida continued to ease social distancing, even in the midst of increasing transmission. Florida’s daily incidence (7-day average) climbed from 584 new cases per day on May 11 to 876 on June 3 (50% increase), when Florida entered Phase 2 of its recovery plan. Notably, testing inherently lags behind infection, on the order of several weeks for COVID-19. From there, Florida’s daily incidence doubled by June 15 and again by June 24—and it is on pace to double again in the next day or so. It could potentially take several weeks before we begin to observe any effects of the newest order on Florida’s COVID-19 epidemic.

In addition to Florida, Texas and California also closed bars either statewide or in high-risk areas. Some believe that bars can be epicenters of community transmission, particularly among younger individuals. The United States continues to report decreasing COVID-19 deaths, but health experts warn that increasing COVID-19 mortality could be coming in the near future. As we covered previously, the age distribution of recent COVID-19 cases in the United States is shifting toward younger individuals, particularly in areas that are reporting surges in incidence. While younger individuals are at lower risk for severe disease and death, there is concern that increased transmission among younger, healthier portions of the community could drive increased transmission among higher-risk parts of the community .

Additionally, increased hospitalizations place additional burden on hospitals and health systems, which could affect the quality of care patients may receive. This was a major challenge in areas affected severely early in the pandemic, including New York, northern Italy, and Wuhan, China. Increased hospitalizations are stressing health system capacity in some affected areas in the United States, including Texas and Arizona , which could potentially limit care available to some patients and contribute to increased mortality as patient surge continues and worsens. Reported COVID-19 deaths also tend to lag several weeks behind trends in incidence, because it takes time for patients to progress through the various stages of disease. Dr. Anthony Fauci recently highlighted this issue, noting in his testimony to the US Congress that he expects to see increased COVID-19 deaths in the coming weeks commensurate with the increased incidence we are currently observing.

CHINA SARS-CoV-2 VACCINE The Chinese military reportedly received authorization to administer a SARS-CoV-2 vaccine candidate to service members. The vaccine, Ad5-nCoV, was developed as a collaboration between CanSino Biologics and the People’s Liberation Army , and it uses an adenovirus-based delivery mechanism. The vaccine has previously demonstrated safety and the ability to induce a protective immune response against SARS-CoV-2 in humans. Researchers previously published Phase 1 clinical trial data in The Lancet . The data also included preliminary efficacy data, which showed that the vaccine induced an immune response in some individuals. Approximately half of the study participants had pre-existing immunity to the adenovirus strain used in the vaccine, however, which may have “dampened” their immune response. Other vaccine development efforts have moved away from this particular strain of adenovirus due to high levels of exposure, potentially 70% or more in some populations. This new authorization is limited to Chinese military service members only, and it does not apply to the general public, healthcare workers, or others. Further study is necessary to better characterize the immune response associated with this vaccine.

POOLED TESTING As the United States and other countries look ahead to more fully relaxing social distancing measures, testing capacity is a critical barrier to proceeding with these plans. Pool testing , a method of testing patients for SARS-CoV-2 as a group instead of as individuals, is one potential option to dramatically increase testing capacity. Pool testing combines samples from multiple individuals in order to reduce the amount of testing materials needed to conduct tests (compared to multiple individual tests) and return results to individuals more quickly. If the pooled sample tests negative, then it can be assumed that nobody in that pool is infected, and no further testing is necessary. If a sample is positive, then each person in that pool can be tested individually to determine who among them is infected. In low prevalence settings, pooling the samples can reduce the overall tests performed.

Dr. Deborah Birx, the White House Coronavirus Response Coordinator, stated that the method could increase testing capacity by 900%, which would enable the United States to conduct 5 million tests per day. The US FDA is working to validate pooled sample techniques. A study published in The Journal of the American Medical Association: Network Open illustrates the potential benefits of pooled testing, particularly if disease prevalence in the test population is less than 30%. The authors warn that false negatives could increase due to pooled sampling techniques due to diluting positive samples with multiple negative samples, so test characteristics and processes could be closely selected and monitored. 

COVID-19 CLINICAL MANIFESTATIONS Clinicians and researchers continue to study the clinical manifestations of COVID-19. A study published in The Lancet: Psychiatry discusses the neurological and neuropsychiatric complications of 153 COVID-19 cases in the United Kingdom. A review of existing peer-reviewed literature regarding neurological or psychiatric manifestations of COVID-19 yielded only small case studies or studies utilizing vague descriptions of symptoms such as “dizziness” or “headache.” Surveillance of UK patients, collected retrospectively, provided more detailed data across a larger study population. The researchers identified a range of neurological presentations, including cerebrovascular events (e.g., ischaemic stroke, intracerebral hemorrhage); altered mental status, including patients with encephalopathy or encephalitis and patients with presentation of psychiatric conditions (e.g., dementia-like symptoms) after their COVID-19 diagnosis.

STAT News published an overview of efforts to better understand non-respiratory symptoms of COVID-19. SARS-CoV-2 binds to ACE2 receptors in order to enter human cells, which could potentially account for the virus’ effects throughout the body. ACE2 receptors are present on a variety of cell types, including blood vessels, kidneys, the gastrointestinal tract, and “even in the testes.” Effects on blood vessels could impact blood flow and clot formation, which could potentially explain a variety of complications, including “ COVID toe ,” painful swelling and redness in the toes of some COVID-19 patients.

ACT-ACCELERATOR The Access to COVID-19 Tools Accelerator (ACT-Accelerator) is a global effort—unveiled in April by the WHO, France, the European Commission, and the Bill and Melinda Gates Foundation—that aims to facilitate rapid development and global equitable access to new tools to combat COVID-19. On Friday, ACT-Accelerator published its “ investment case ,” which outlines timelines and priorities for investment. The plan calls for US$31.3 billion in investments, distributed across 3 primary pillars—vaccines (US$18.1 billion), therapeutics (US$7.2 billion), and diagnostics (US$6 billion)—over the next 12-18 months. So far, a total of US$3.4 billion has been donated, leaving US$27.9 billion remaining, US$13.7 billion “to cover immediate needs” over the next 6 months.This plan would aim to provide 500 million diagnostic tests, 245 treatment courses, and 2 billion vaccines by 2021, much of which will be allocated to low-and-middle-income countries. Notably, the plan to provide 2 billion doses of vaccine relies on donations of 950 million doses by upper middle- and high-income countries that are capable of purchasing their own vaccine, through the Gavi Advance Market Commitment for COVID-19 Vaccines facility. In addition to the 3 primary pillars, a fourth pillar is directed at strengthening health system capacity, including training and personal protective equipment management, but the proposed budget for these activities is still under development.