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

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EPI UPDATE The WHO COVID-19 Dashboard reports 52.49 million cases and 1.29 million deaths as of 10:00am EST on November 13. The WHO has reported more than 628,000 new cases so far today, which is already a new single-day record.

As we have covered over the past several weeks and months, COVID-19 incidence and mortality are increasing across the US and Europe, surpassing previous waves or peaks and setting new records. Globally, much of the Northern Hemisphere is reporting increasing incidence and mortality over the past 2 weeks, while the Southern Hemisphere is generally reporting decreasing trends.

The pandemic emerged globally as the Northern Hemisphere transitioned from spring to summer (and the Southern Hemisphere from autumn to winter), but it was difficult to discern any seasonal trends on the global scale. Now, 6-9 months later, many countries across the Northern Hemisphere (incidence and mortality), including Canada and much of Europe, were able to bring COVID-19 under control over the warmer summer months, potentially due to a combination of social distancing and the ability to conduct activities outdoors, where transmission risk is lower. Around the same time, South America (incidence and mortality) experienced its first wave, serving as the major global hotspot during its winter season, and peaking in mid-August.

Now, as countries in Europe and North America enter their colder months, activities are moving indoors and incidence and mortality are surging. Looking at the current global maps representing biweekly changes in incidence and mortality, most of the Northern Hemisphere is displayed in red (increasing trends), and most of the Southern Hemisphere is displayed in blue (decreasing trends). Conversely, the same maps from June and July* generally show the opposite. Notable exceptions include the US, which never really brought its epidemic under control, and Africa and Oceania, which have largely managed to contain COVID-19 thus far.
*Unfortunately, the URLs above will not take you directly to a specific date, but you can move the slider at the bottom to view historical data.

The pandemic trends are driven by a number of diverse factors, and additional research is needed to better characterize any potential seasonality for COVID-19. The combination of “lockdown fatigue,” a shift toward indoor activities during the cooler months, and possibly even anticipation of a forthcoming vaccine poses severe challenges for European and North American countries. These challenges could be compounded over the holiday season when individuals and families typically travel and attend a variety of different gatherings. Many of these countries are in much worse shape than during their initial surges, and they are entering what could be the most dangerous time of the year.

The US CDC reported 10.31 million total cases and 241,069 deaths. The US reported a new single-day incidence record for the second consecutive day, with 143,408 new cases, and the average daily incidence surpassed 120,000 new cases per day. The US reported more than 3,300 deaths in the past 2 days, and the average daily mortality increased to 1,134 deaths per day, the highest average since the very peak of the summer resurgence on August 1 (1,145). The US could surpass 250,000 cumulative deaths by the end of next week, and if this trend continues, the US is poised to report the highest daily mortality since the first COVID-19 surge in March-May.

From September 28 to October 19, the US daily incidence increased by 32% (43,373 new cases per day to 57,291). Shifting the mortality data by 3 weeks to account for the lag between incidence and mortality, the US COVID-19 mortality increased by 35% over the same length of time, from 721 deaths per day on October 19 to 976 on November 9. If a similar trend continues over the next several weeks (ie, that mortality continues to lag behind incidence by approximately 3 weeks), the US could soon face a major surge in mortality. From October 20 through November 9, US COVID-19 incidence increased by 91% (57,291 new cases per day to 109,663), which would correspond to an increase in mortality from 976 deaths per day to more than 1,850 over the next 3 weeks.

Mortality does not necessarily increase proportionately with incidence, but even half of that increase would correspond to more than 1,400 daily deaths. For reference, the peak daily mortality was 2,856 deaths per day on April 21, at a time when the epidemic was surging in New York City, Boston, and a small number of other cities, and we knew very little about the disease or effective clinical care. Hospitals did not have adequate bed space, ventilators, PPE, and other critical supplies, and field hospitals were established—and humanitarian hospital ships deployed—because even large urban hospitals were unable to handle the patient surge. Notably, the US CDC ensemble model forecasts that weekly mortality could reach more than 8,600 deaths by the first week of December, which would equate to approximately 1,230 daily deaths (50% prediction range: 1,052 to 1,536 deaths per day).

Half of all US states have reported more than 150,000 cumulative cases, and more than one-third have reported more than 200,000 cases:
>900,000: California, Texas
>800,000: Florida
>500,000: Illinois, New York

California’s COVID-19 website is reporting 991,609 cumulative cases, and Texas’ is reporting 993,841. We expect both states to surpass 1 million cases in the coming days. We also expect Virginia to surpass 200,000 cases in the near future.

The Johns Hopkins CSSE dashboard reported 10.59 million US cases and 242,811 deaths as of 12:30pm EST on November 13.

CHINA Shanghai, China, reported a locally acquired case of COVID-19 on November 10. While many countries around the world are battling a surge in COVID-19 incidence, this marks the first locally acquired infection in Shanghai in several months. According to local officials in China, the individual worked at Shanghai Pudong International Airport, and at least 25 close contacts have been quarantined. While SARS-CoV-2 emerged in China, China has largely contained its epidemic. In fact, the vast majority of cases over the past several months have been among arriving travelers. In an effort to maintain this level of epidemic control, the Chinese government is reportedly taking new steps to limit the possibility of importing COVID-19. One aspect of these efforts involves disinfecting packaging and transport vehicles carrying imported frozen food, after China identified contaminated food products as the source of several SARS-CoV-2 infections among cargo handlers and port workers.

PERU The Congress of the Republic of Peru voted earlier this week to remove President Martín Vizcarra Cornejo from office due to “permanent moral incapacity.” The vote passed by a count of 105 to 19, with a minimum of 87 votes required. The decision was driven by a myriad of factors, including the government’s response to the ongoing COVID-19 epidemic. Now-former President Vizcarra announced that he would not contest the outcome of the vote, and former President of the Congress, Manuel Merino De Lama, was sworn in as President of Peru on Tuesday. While the transition is undoubtedly causing political turmoil, which is particularly concerning in the midst of a pandemic, the peaceful and uncontested process could be a positive indication that the transition will not hinder Peru’s COVID-19 response. Peru has reported the highest cumulative per capita COVID-19 mortality in South America, and it ranks #2 in terms of cumulative per capita incidence, just behind Argentina.

KENYA Kenya, like many other sub-Saharan African countries, has reported much lower COVID-19 disease burden than initially anticipated by many experts. Researchers in Kenya conducted a study of SARS-CoV-2 seroprevalence in blood donors in order to provide insight into the scale of transmission in Kenya. The study, published in Science, assessed the presence of IgG antibodies against SARS-CoV-2 among Kenyan blood donors from April-June. The researchers analyze more than 3,000 blood samples collected at 4 Kenya National Blood Transfusion Service centers. Among these samples, 174 (5.6%) tested positive for SARS-CoV-2 antibodies. Seropositivity in individuals under the age of 55 ranged from 3.4% for individuals 45-54 years old to 7.0% for individuals 35-44 years old. None of the 71 donors aged 55-64 years were seropositive. Seroprevalence also varied significantly by geographic region. Seropositivity was highest among individuals in the Western region of the country (10.0%) and lowest in the Rift Valley region (1.9%), with most regions falling in the 4-7% range. Seropositivity was elevated in major urban areas, including Mombasa (9.3%) and Nairobi (8.9%).

The authors concluded that seroprevalence observed in their study was comparable to that observed in other countries, including China, Switzerland, and the US after their initial peaks in incidence, which is elevated compared to what would be expected based on Kenya’s reported incidence. While the relatively high seroprevalence could indicate that existing surveillance systems are not adequately capturing COVID-19 incidence in Kenya, the researchers believe this is not the predominant factor. The researchers argue that the sample population—which skewed heavily toward males, younger adults (eg, 25-34 years), and coastal regions of the country—more likely overestimates the national seroprevalence. If existing surveillance systems under-ascertained COVID-19 cases to the degree indicated by the seroprevalence results, it is likely that COVID-19 hospitalizations and mortality would be much higher than what has been reported thus far.

UKRANIAN PRESIDENT HOSPITALIZED Another head of state has been hospitalized because of COVID-19. Ukrainian President Volodymyr Zelenskiy announced on Monday that he was diagnosed with COVID-19 and admitted to the hospital for treatment. Reportedly, President Zelenskiy is experiencing relatively mild symptoms, and he was hospitalized as a precaution and to better facilitate his isolation. In a public statement, President Zelenskiy emphasized that his infection illustrates that nobody is safe from COVID-19, even with the highest levels of protection. Like the rest of Europe, Ukraine is facing a major surge in transmission, although, in contrast to some other European countries that were severely affected early in the pandemic, Ukraine’s first “wave” was much smaller and later. Ukraine is currently setting new records in terms of daily incidence and mortality, reporting more than 10,000 new cases and nearly 175 deaths per day.

SOUTH AFRICA INTERNATIONAL TRAVEL South African President Cyril Ramaphosa announced that the country is lifting restrictions on international travelers. South Africa previously resumed international travel in early October, but it restricted entry for travelers arriving from countries with high levels of transmission. While country-specific restrictions have been lifted, travelers must still provide evidence of a recent negative SARS-CoV-2 test before entering South Africa. South Africa’s tourism website and Department of Home Affairs website both still include a list of high-risk countries. The policy change aims to boost South Africa’s tourism sector; however, the decision comes amid a global rise in SARS-CoV-2 transmission, which has raised concern by some public health professionals. President Ramaphosa also indicated that the South African government will monitor COVID-19 trends closely to determine if the policy change has any adverse effects on COVID-19 incidence. South Africa has reported nearly 750,000 cases and more than 20,000 deaths, leading all African countries in both categories. South Africa’s daily incidence is well below its peak in late July, but it has increased nearly 20% over the past week.

MINK The WHO published a Disease Outbreak News covering the emerging information on COVID-19 in mink. Since June, Danish health officials have reported at least 214 human COVID-19 cases in humans that involve strains associated with mink. More recently, 12 of these cases have been infected with a new variant, now referred to as the “cluster 5” variant. This variant includes several mutations not previously documented, which appear to have evolved during transmission among mink. Based on preliminary information from these human cases, the variant does not appear to result in increased disease severity; however, there is some evidence that it could be slightly more resistant to neutralizing antibodies.

Denmark recently announced plans to cull all farmed mink nationwide, but its parliament did not pass a bill to implement the program. The plan was met with resistance both from animal rights groups and economists, causing Danish officials to change course. Despite the current hold, there are reports of “mass graves” at some mink farms that have already begun the process, and the Danish Veterinary and Food Administration reportedly indicated that at least 116 farms have culled their entire mink population. Mink farming is an economic driver in Denmark, and large culls could have significant economic effects, particularly for mink famers. Danish Prime Minister Mette Frederiksen apologized publicly for the plan and noted that the government did not have the authority to implement such an effort.

In the US, mink farmers have nearly 400,000 mink used for breeding and produced approximately 2.7 million pelts last year. To date, more than 15,000 mink have died from COVID-19 in the US, but there is no current plan for widespread culling at mink farms. Approximately 12 farms are currently under quarantine due to detected SARS-CoV-2 among mink. There have been no reported instances of transmission from mink to humans in the US, but the US CDC and US Department of Agriculture, in collaboration with state officials, are investigating outbreaks at mink farms.

CRUISE SHIPS Even among the broader travel and tourism sector, which has been severely affected by COVID-19, the pandemic’s effect on cruise lines has been particularly devastating. High-profile outbreaks early in the pandemic, including the Diamond Princess, led most cruise lines to suspend activity earlier this year. After months of essentially zero cruise ship activity worldwide, cruise lines are beginning to resume operations and attempting to demonstrate that new safety measures can provide protection for passengers and crew. This week, the SeaDream 1, the first cruise ship to resume sailing in the Caribbean, reported a case of COVID-19 onboard. Several days into the cruise, one passenger tested positive for SARS-CoV-2, and the ship returned to Barbados to test everyone onboard. The passengers were instructed to quarantine in their cabins until the ship returned to port. Several media reports indicate that at least 5 passengers have tested positive so far, representing approximately 10% of the 53 passengers onboard. The SeaDream 1 tested passengers before the start of the trip, immediately prior to boarding, and 4 days after boarding. The ship made several port calls prior to the positive test, but the passengers reportedly did not interact with anyone outside the ship, including taking private shuttles to empty beaches.

The US CDC recently lifted its “no sail” order for cruise ships and published new requirements for a phased process to resume cruise ship activity. Under the new order, cruise ship operators cannot begin any operations in US waters without a COVID-19 Conditional Sailing Certificate issued by CDC. In order to obtain the certificate, ships must complete a simulated voyage to test their new protocols, including quarantine and isolation for passengers and crew, among other requirements. Most cruise lines have suspended activities until 2021, but some are beginning to make arrangements for the test voyages. Royal Caribbean cruise line, for example, is looking for volunteers to take free test cruises in the coming months, and thousands of people have reportedly already expressed interest.

D614G MUTATION As SARS-CoV-2 spread globally, the virus’ genetic sequence has mutated and evolved, like any other virus. One mutation in particular, the D614G mutation, has garnered significant attention over the past several months as it quickly became a dominating feature in the pandemic. Early in the pandemic, the mutation was identified in relatively few of the specimens sequenced globally, but by June, it was identified in nearly every specimen sequenced globally. Several early studies found evidence that the mutation could enable the virus to transmit more efficiently, which could explain its rapid global spread relative to other variants. Many of these initial studies evaluated the mutation in vitro, but in vivo studies (eg, in live animals) can provide more detailed insight into the mutation’s effects. Now that the mutation is ubiquitous globally, further research is being conducted into the associated phenotypic characteristics.

A study published this week in Science, found evidence that the mutation could potentially make the virus more susceptible to vaccines. The study, conducted by researchers at the Universities of North Carolina and Wisconsin (US), utilized an animal model (hamsters) to evaluate various characteristics of the mutation. They found that the virus did transmit more readily among the hamsters, but the disease severity was not noticeably different than a strain isolated from early patients in China. The D614G variant replicated more rapidly in primary nasal epithelial cells, which are “potentially [an] important site for person-to-person transmission.” Perhaps most notably, they found evidence that the D614G mutation could make the virus more susceptible to antivirals and vaccines. The same mechanism that allows the mutation to spread more efficiently could also potentially provide an opening through which antivirals and vaccines can neutralize the virus.

Another study, published in late October in Nature, came to similar conclusions. The study, conducted by researchers at the University of Texas Medical Branch (US), used a similar hamster model and found that the D614G variant replicated more efficiently in the upper respiratory tract, but not the lungs. This provides further evidence that the variant could make the virus more transmissible. Additionally, the researchers also noted that “all of the [SARS-CoV-2] vaccines currently in clinical trials are based on the original D614 spike sequence,” but their research did not indicate that the D614G mutation would be any less susceptible to neutralization.