COVID-19 Situation Report
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Starting next week, we will shift to 1 detailed epidemiological analysis each week. We will continue to publish 2 situation reports per week, including the high-level epi data, but the in-depth epi analysis will only be included on Fridays.

EPI UPDATE The WHO COVID-19 Dashboard reports 180 million cumulative cases and 3.9 million deaths worldwide as of 4:30am EDT on June 25.

While African countries have largely contained their respective COVID-19 epidemics, the continent as a whole has exhibited a substantial increase in daily incidence since mid-May. Africa’s daily incidence has more than tripled since its most recent low on May 17, increasing from 7,849 new cases per day to 26,250. If it continues on this trajectory, Africa could soon surpass its highest peak (32,750). On a per capita basis, the only continent reporting fewer daily cases is Oceania, but if it continues on this trajectory, Africa’s per capita daily incidence could potentially reach the same range as Asia, Europe, and North America. Previously, Africa has briefly exhibited higher per capita daily incidence than Asia, but it has not really been close to Europe or North America until now. In terms of total daily incidence, Africa surpassed North America on June 22. The last time Africa reported higher total daily incidence than any continent other than Oceania was July 2020, when the peak of Africa’s first wave briefly exceeded Europe’s low between its first and second waves.

Many countries in sub-Saharan Africa are reporting substantial increases in daily incidence. In fact, at least 14 countries are reporting relative biweekly changes of +100% or higher, mostly in Central, Eastern, and Southern Africa. Notably, the biweekly change is +1,363% in Lesotho; +791% in South Sudan; +694% in Rwanda; and +649% in Zimbabwe. In West Africa, Gambia, Liberia, and Sierra Leone are reporting biweekly increases of more than 300%. Namibia and South Africa are exhibiting the longest surges, starting in early May (or possibly mid-April for South Africa), with daily incidence increasing by a factor of 13 and 10, respectively, since that time. Zambia’s surge began closer to mid-May, and its daily incidence is now more than 50 times higher than it was at that time—up from fewer than 50 new cases per day to more than 2,500. The remaining countries’ surges began around early June. Fortunately, most of these countries are still reporting fewer than 100 new cases per day, and the large relative changes are principally a factor of very low daily incidence at the start of the surge—in some instances, fewer than 10 new cases per day. But Zambia’s surge illustrates the risk that even epidemics that were once largely contained can accelerate rapidly to substantial levels of community transmission.

South Africa, the most severely affected country in Africa, is combating its third wave and quickly approaching its highest peak. Namibia and Zambia have already set new records for daily incidence. Analysis from Reuters indicates that Sierra Leone, Rwanda, and Zambia are all reporting record-high daily incidence, and the Democratic Republic of the Congo and Namibia are currently reporting at least 90% of their highest peak.

Looking globally, Africa continues to stand out as having among the lowest vaccination coverage, illustrating the critical importance of providing international support and increasing access to vaccine doses. Only 10 countries in Africa are reporting 1+ dose coverage greater than 5%, and only Mauritius and Seychelles are reporting greater than 30%. In terms of full vaccination, only 13 countries are reporting greater than 1% coverage, but data are not available for many countries. As a whole, Africa’s 1+ dose vaccination coverage is 2.6%, 14 percentage points below Oceania and approximately one-tenth the global average (22.6%). Similar trends are evident with respect to full vaccination.

Most countries in Africa have limited genomic sequencing data available, which limits the ability to understand changes in prevalence for emerging SARS-CoV-2 variants. South Africa is one of the few countries with enough sequence data available to provide some indication of these changes. There, the Beta variant (B.1.351) became the dominant strain over the course of 2020 and has remained dominant through the first half 2021. The Delta variant began to emerge in late April, and its prevalence appears to be increasing rapidly. Alpha variant (B.1.1.7) prevalence began to increase around the same time, but the Gamma variant (P.1) does not represent a meaningful proportion of new cases. The extent to which the Delta variant is driving the ongoing surges in Africa remains uncertain, but similar associations have been observed in other parts of the world.

Global Vaccination
The WHO reported 2.6 billion doses of SARS-CoV-2 vaccines administered globally as of June 24, and 1.03 billion individuals have received at least 1 dose. After a period of steady increase, the global daily doses administered decreased slightly from the record high of 41.6 million doses per day on June 23 to 41.2 million yesterday. Our World in Data estimates there are 806 million people worldwide who are fully vaccinated, corresponding to 10.3% of the global population, although reporting is less complete than for other data.

The US CDC reported 33.4 million cumulative COVID-19 cases and 600,442 deaths. The US surpassed 600,000 cumulative deaths on June 22, the first country to do so:
1 death to 100k*- 84 days
100k to 200k- 113 days
200k to 300k- 86 days
300k to 400k- 33 days
400k to 500k- 33 days
500k to 600k- 130 days
*From February 29, 2020, the date of the first reported COVID-19 death in the US. Since then, health officials have identified more than 200 COVID-19 deaths that occurred prior to that date.

The CDC updated its SARS-CoV-2 genomic surveillance data, adding official data for May 23-June 5 and projections for June 6-19. Including the new projection period, the Delta variant (B.1.617.2) prevalence has increased from less than 1% to 20.6% over a period of 8 weeks, more than doubling in every 2-week period. Based on the current projection, the Delta variant is now the #2 variant nationwide. Gamma variant (P.1) prevalence also continues to increase steadily, now up to 16.4% of new cases. While still technically dominant based on the estimated prevalence, Alpha variant (B.1.1.7) prevalence has noticeably decreased over the past 2 reporting periods, down from a high of 70% to 52.2% in the June 6-19 projection. Combined, the Alpha, Gamma, and Delta variants account for more than 90% of all new cases in the US. These genomic data provide further evidence that the Delta variant is poised to become the dominant variant in the US over the coming weeks. In fact, the projection indicates that Delta is already the dominant variant in HHS Regions 7 (Central; 47.5%) and 8 (Mountain; 46.4%).

US Vaccination
The US has distributed 379 million doses of SARS-CoV-2 vaccines and administered 321 million. A total of 178 million individuals in the US have received at least 1 dose of SARS-CoV-2 vaccine, equivalent to 53.7% of the entire US population. Among adults, 65.7% have received at least 1 dose, and 8.5 million adolescents aged 12-17 years have received at least 1 dose. A total of 151 million individuals are fully vaccinated, which corresponds to 45.6% of the total population. Among adults, 56.2% are fully vaccinated, and 6.0 million adolescents aged 12-17 years are fully vaccinated.

mRNA VACCINES & MYOCARDITIS/PERICARDITIS The US CDC’s Advisory Committee on Immunization Practices (ACIP) is meeting this week as part of ongoing evaluation of SARS-CoV-2 vaccine safety and efficacy data. A major portion of this week’s meeting addressed emerging data regarding the risk of myocarditis and pericarditis—inflammation of the heart muscle and lining around the heart, respectively—following vaccination. Researchers presented data collected from several systems the CDC uses to monitor for adverse events after vaccination.

The data indicate there is a “likely association” between the mRNA-based SARS-CoV-2 vaccines, from Pfizer-BioNTech and Moderna, and elevated risk of myocarditis and pericarditis in adolescents and younger adults, although the risk appears to be very low. The rates of myocarditis/pericarditis are higher in males than females, and the conditions are more common after the second dose of the vaccine. The analysis estimates the overall rate of myocarditis/pericarditis to be 12.6 cases per million second doses of the vaccines in individuals aged 12-39 years old. The conditions tend to present within approximately 5 days, and while most of the affected individuals were hospitalized, symptoms were generally mild and most recovered quickly. To our knowledge, neither condition has resulted in death among recently vaccinated individuals.

Importantly, the available data indicate that the benefits of vaccination still far outweigh the risks of myocarditis/pericarditis. Even for males aged 12-17 years—the group with the lowest COVID-19 risk and highest myocarditis/pericarditis risk—risk and benefit calculations* estimate that 1 million second doses of the mRNA vaccines would prevent 5,700 COVID-19 cases, 215 hospitalizations, and 2 deaths, compared to 56-69 cases of myocarditis/pericarditis. A group of prominent public health and healthcare organizations—including HHS, CDC, and the American Academy of Pediatrics—issued a statement emphasizing the rarity of myocarditis/pericarditis following vaccination and encouraging all eligible individuals to get vaccinated. The US FDA is expected to update associated information for the mRNA vaccines, and the CDC continues to recommend SARS-CoV-2 vaccination to all eligible age groups.
*Calculated over a 120-day period.

US VACCINATION COVERAGE White House Coronavirus Response Coordinator Jeff Zients said the US will not reach US President Joe Biden’s goal of 70% of adults receiving at least 1 dose of SARS-CoV-2 vaccine by July 4. With the expectation now being that the US will fall slightly short of that benchmark, the White House issued a new goal of at least 1 dose of vaccine to 70% of adults aged 27 years and older by July 4. Currently, 150 million people are fully vaccinated, and Mr. Zients said that the US is expected to reach 160 million by mid-July.

As we have discussed previously, there are some regional disparities in terms of vaccination coverage in the US. In particular, several states in the South and West regions are lagging behind in their vaccination campaigns. Fewer than 40% of adults in Alabama, Mississippi, Louisiana, Idaho, and Wyoming have received at least 1 dose. Though Missouri is reporting 44% of adults receiving at least one dose, health officials are concerned about several counties in the south and north of the state reporting well below that rate, with one county reporting only 13% vaccination coverage. There is concern that lagging interest in vaccination among younger adults could provide a large enough unprotected population to continue fueling COVID-19 surges. At one hospital in Springfield, Missouri, nearly two-thirds of COVID-19 patients in the ICU last weekend were under 40 years old. In Missouri, Arkansas, and Utah, COVID-19 hospital admissions have increased more than 30% since the beginning of June. The Mayo Clinic’s ”hot spot” map shows Missouri as one of only 2 states reporting more than 10 daily cases per 100,000 population—the other being Nevada. The states reporting between 5 and 10 are largely located in the Southeast and Western portions of the country.

As the prevalence of variants of concern (VOCs) increases, including the Delta variant, vaccination remains a critical tool for containing community transmission and protecting against severe disease and death. Analysis from the Associated Press found that “breakthrough” infections accounted for only 0.1% of US COVID-19 cases in May, and only 0.8% of the 18,000 COVID-19 deaths were among fully vaccinated individuals. Previously, Dr. Andy Slavitt—former White House COVID-19 advisor—estimated that 98-99% of COVID-19 deaths are among unvaccinated individuals.

DELTA VARIANT The Delta variant (B.1.617.2) currently accounts for an estimated 20% of new COVID-19 cases in the US and likely will become the dominant strain in a matter of weeks, according to White House Chief Medical Advisor Dr. Anthony Fauci, who also noted the variant as the United States’ greatest threat in dealing with COVID-19. The European CDC (ECDC) Threat Assessment for the Delta variant projects that the variant will be responsible for 90% of cases by the end of August. Russia has already reached that threshold, where 90% of new cases in Moscow are being attributed to the Delta variant. This variant of concern (VOC) has been reported in 85 countries, is 40-60% more transmissible than Alpha (B.1.1.7), and may be associated with a higher risk of hospitalization. 

According to a Public Health England study, a single dose of either the Pfizer or AstraZeneca vaccines reduced a person’s risk of developing COVID-19 symptoms caused by the Delta variant by 33%, compared to 50% for the Alpha variant. A second dose of AstraZeneca brought protection to 60% (66% for Alpha), and a second dose of Pfizer increased protection to 88% (90% for Alpha). A Scottish study found an increased likelihood of hospitalization among patients infected with the Delta variant, nearly double the risk for the Alpha variant. Additionally, that study showed that among fully vaccinated individuals, Pfizer’s vaccine provided 79% protection against the Delta variant, while it offered 92% against the Alpha variant. Vaccination with the AstraZeneca vaccine showed substantial but reduced results among those fully vaccinated, with 60% efficacy against the Delta variant and 73% protection against the Alpha variant. These studies underline the importance of vaccination as a tool to reduce hospitalizations and disease severity among COVID-19 patients. 

CUBAN VACCINES Cuban health authorities on June 21 released new data on the nation’s home-grown Abdala SARS-CoV-2 vaccine, showing efficacy on par with several existing vaccines. As noted in previous updates, Cuba had foregone outside assistance when it came to vaccine imports, choosing to hold off and vaccinate its population with the 3-dose Abdala vaccine. The country began vaccinations in May, prior to the completion of studies examining the vaccine’s efficacy, in parts of the country where SARS-CoV-2 was spreading quickly. New results from the manufacturer’s Phase 3 trial suggest that this early vaccination initiative may have paid off. Abdala showed 92.28% efficacy among individuals who received all three doses. Following the announcement of these results, study organizers shared they would be opening the study codes of the Phase 3 clinical trial to vaccinate all participants who received the placebo.

Cuban health officials also announced that a second vaccine candidate, Sovereign 02, boasted 62% efficacy following its two-dose schedule. These are encouraging results, especially given the epidemiological backdrop of Cuba’s COVID-19 outbreak. Cuba is in the midst of a peak of COVID-19 cases, reporting a record-high 7-day average of new cases of about 1,625. The rate of people who have been vaccinated continues to increase alongside this change in the country’s epidemiological situation, with just over 20% of the population having received at least one dose of a COVID-19 vaccine. Hopefully, recent clinical trial results will spur vaccination rates to counter increased disease activity. 

CHINESE VACCINE EFFECTIVENESS Several countries that mostly relied on the Chinese Sinopharma and Sinovac Biotech vaccines are currently facing large outbreaks. Despite high vaccination coverage, Seychelles, Bahrain, Chile, and Mongolia have all reported their highest daily incidence since mid-May*, all after reaching 50% coverage with at least 1 dose. In March, Seychelles was one of the world’s most vaccinated countries, with approximately 57% of its vaccinations using the Sinopharm vaccine. Between 50-68% of the population has been fully vaccinated in these countries, compared to 45% in the US, raising some questions regarding the effectiveness of the vaccines.
*Chile’s peak on June 8 was within 30 new cases per day (0.04%) of its highest peak.

Breakthrough infections are certainly possible, as no vaccine is 100% effective, but lower efficacy for the 2 Chinese-made vaccines and the role of emerging variants could be driving the increases in daily incidence in these countries. The Sinopharm vaccine’s efficacy rate is estimated to be 78.1%, and the Sinovac vaccine’s is 51%. In comparison, the Pfizer-BioNTech and Moderna vaccines have over 90% efficacy, AstraZeneca-Oxford is at 63%, and J&J-Janssen has 85%. Bahrain has now begun offering booster shots of the Pfizer-BioNTech vaccine to those who originally received the Sinopharm vaccine, which accounts for about 60% of the doses administered there. More than 95 countries have received doses of the Chinese-produced vaccines.

AFRICA Africa is facing a rapidly increasing third surge, with the number of new COVID-19 cases rising for 5 consecutive weeks since the beginning of this wave on May 3. At the current rate of infection, the third surge will surpass the previous one by early July, with at least 12 nations experiencing case increases. Experts are citing the spread of the Delta variant (B.1.617.2) as one factor influencing this latest surge, with 14 nations across the continent reporting cases of the variant. In Kisumu, Kenya, health officials say Delta is driving an upswing in cases, particularly among young people, and have expressed fear that a wave of infections like that seen in India in April and May could be on the horizon. Weak adherence to public health measures, including an increase in social gatherings and movement, also is contributing to a rise in infections. Many hospitals are overwhelmed, and a shortage of oxygen on the continent is hindering patient care for those who do find beds.

Only about 1.1% of the continent’s population is fully vaccinated. According to WHO Regional Director for Africa Dr. Matshidiso Moeti, the continent needs an additional 215 million vaccine doses to fully vaccinate 10% of its population, and about 700 million doses to reach 30% of the population by the end of the year. Eighteen (18) countries have used 80% of their doses received through COVAX, with 8 of those having exhausted their supplies, and another 29 nations having used more than 50% of their doses. Just under 1.5% of the 2.7 billion vaccine doses administered globally have been administered in Africa. Many health experts were confused by how African countries initially kept COVID-19 at arm’s length, and if this surge proves as devastating as India’s latest, a collective failure of the international community to adequately support the continent could be to blame.

AUSTRALIA The Australian government has run a highly effective COVID-19 response, with efforts to close borders and enforce physical distancing rules limiting the cumulative number of COVID-19 cases to just over 30,300. The country has seen only two spikes of COVID-19 incidence, with the latter tapering off around the end of September 2020. Roughly 11% of Australia’s cumulative COVID-19 cases have come since the beginning of October 2020, representing a slow burn of new cases. These new cases have come in small outbreaks, forcing the Australian government to enact stricter public health measures intermittently. Notably, a recent outbreak in Queensland of nine cases is being attributed to the Delta SARS-CoV-2 variant. Health officials have expanded mandates on mask wearing, citing concerns of the Delta variant’s heightened transmissibility. A separate and larger COVID-19 outbreak of the Delta variant is ongoing in Sydney, leading the city to implement stricter public health measures to limit the spread of the virus. The Australian government has raised concerns over the longevity of its response measures in light of these recent clusters of new cases. Nearly 25% of the country’s adults have received one dose of vaccine, but less than 5% are fully vaccinated. The low vaccination rates have led some to question whether the nation is prioritizing contact tracing and testing over vaccination, while some experts blame shortfalls in expected vaccine shipments for lagging rates. 

ISRAEL Israel reinstated its indoor mask mandate today, less than 2 weeks since the mandate was dropped on June 15. Public Health Director Dr. Sharon Alroy-Preis said the Ministry of Health previously determined the mask mandate should be reintroduced if Israel records a daily average of 100 new COVID-19 cases over one week. As of June 24, the rolling 7-day average of confirmed cases was 99.57, with daily incidence rising, according to Our World In Data. Israel’s coronavirus czar Dr. Nachman Ash announced the country recorded 227 new cases on June 24, though he said he does not feel the nation is entering a fourth surge. Dr. Alroy-Preis blamed a lack of adherence to mandatory quarantine rules for travelers from high-risk countries for the introduction of the Delta variant into the country, one of the causes of the latest outbreak, and she called on the government to more strongly enforce the rules. Israel is one of the world’s most vaccinated countries, but the Delta variant is driving new cases among unvaccinated children and vaccinated individuals, who account for as much as 50% of new cases. However, there is not yet enough data to conclude the vaccines’ effectiveness against the Delta variant, according to Dr. Alroy-Preis. Prime Minister Naftali Bennett, who took office last week, announced the government will reestablish its coronavirus cabinet to assist in future decisions related to the pandemic.