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 106.13 million cases and 2.32 million deaths as of 11am EST on February 9. The global weekly incidence decreased for the fourth consecutive week, down to 3.12 million new cases last week, the lowest weekly total since mid-October. This is a 17.7% decrease from the previous week and a 38.2% decrease from the peak in reported incidence in early January. After holding relatively steady for the last 2 weeks of January, global weekly mortality decreased for the first time since mid-October*, a decline of 10% compared to the previous week. If this is indicative of a longer-term trend, it would correspond to approximately 3-4 weeks after the peak in global weekly incidence.
*With the exception of the weeks corresponding to the Christmas and New Year’s holidays.

Our World in Data reports that 134.65 million vaccine doses have been administered globally, a 31% increase compared to this time last week.

The Johns Hopkins Coronavirus Resource Center reported 27.11 million US cases and 465,648 deaths as of 12:30pm EST on February 9.

The US CDC reported 26.85 million total cases and 462,037 deaths. The US surpassed 450,000 cumulative deaths on February 4. Daily incidence in the US continues to decrease steadily, now down to 116,904 new cases per day. Since the peak on January 8 (248,607), the national average daily incidence is down by more than half; however, it is still nearly 75% higher than the previous peak (67,230 on July 22, 2020). The US is still #1 globally in terms of total daily incidence, and it is still reporting more than double the daily incidence in #2 Brazil (42,188).

The US reported 5,189 deaths on February 4. This is the second highest single day total reported by the US to date, following April 15, when New York City reported more than 3,700 previously unreported probable deaths from the onset of its epidemic. The February 4 spike was due to 1,507 deaths reported by Indiana, which caused the state’s cumulative total to jump 15.8%, from 10,091 to 11,637 deaths—and the per capita mortality to increase from 150 deaths per 100,000 to 173. These deaths caused the national daily average to jump from 3,056 to 3,227 deaths per day. The CDC is working with health officials from Indiana to determine the time frame corresponding to these deaths.

As the US daily incidence continues to decline, we want to take a closer look at US testing data to determine whether the decreasing daily incidence is a result of a true decrease in community transmission or a function of testing or reporting. To start, we will look at testing volume. US testing volume scaled up steadily from the onset of the pandemic through mid-July, around the peak of the summer 2020 surge, before declining in late summer. Testing increased again during the autumn 2020 surge and reached its highest peak in November. Testing volume has declined consistently since that time, with the exception of reporting fluctuations due to the Thanksgiving, Christmas, and New Year’s holiday weekends.

As we have covered previously, test positivity is one of the better measures of effective testing programs and sufficient volume. Test positivity in the US has varied widely over the course of the US epidemic. The peak national test positivity was more than 20% during the initial surge in the spring of 2020, when the supply of test kits was limited and testing was largely limited to symptomatic patients and/or those with relevant travel history. Test positivity fell as the initial surge receded and testing capacity scaled up, and it then climbed with the summer 2020 surge, up to approximately 10%. The minimum test positivity was approximately 5%, reported in mid-to-late September*, before it increased again in conjunction with the autumn 2020 surge. Test positivity peaked at 15.4% during the last week of December 2020, and it has decreased steadily over the past 4 weeks. The current test positivity is 9.7%, down from 11.2% the previous week. For reference, the cumulative national test positivity over the course of the US COVID-19 epidemic is 9.19%, and the current national average is quickly approaching this benchmark.
*The lowest preliminary values reported were 4.8% in 2020 Week 38 and Week 39; however, these were updated in the following weeks’ reports to 5.0% and 5.2%, respectively. The first reported weekly increase was from 5.3% to 5.4% during 2020 Week 41.

The combination of steadily declining daily incidence, testing volume, and test positivity provides a good indication that the overall declining trend in the US not an artifact of reporting or testing issues.

At the state level, the US CDC is currently reporting elevated test positivity (6% or higher) in 34 states, including 12 with 11% or higher, based on the average over the past 7 days. While this is still a concerning number of states above the 5% recommended threshold, many states are trending in the right direction. For comparison, the 30-day average test positivity is 6% or more for 41 states, including 23 reporting 11% or higher. The difference between the 30-day and 7-day averages indicates that numerous states are reporting decreasing test positivity over the past several weeks. In fact, 17 states have a lower 7-day average than 30-day average, and no states have a higher 7-day average. The COVID Exit Strategy website reports 15 states with test positivity greater than 15%, including 6 greater than 30%, and only 2 states with test positivity below 5% (Vermont and Hawai’i); however, 26 states are reporting decreasing test positivity over the past 2 weeks, including 8 of the 15 states currently reporting test positivity greater than 15%.

US Vaccination
The US CDC reported 59.31 million vaccine doses distributed and 42.42 million doses administered nationwide. The US has administered 71.5% of the distributed doses, an increase of more than 10 percentage points since Friday (61.2%). In total, 32.34 million people (nearly 10% of the entire US population) have received at least 1 dose of the vaccine, and 9.52 million (2.9%) have received both doses. The average daily doses administered is once again increasing, now up to a record high of 1.46 million doses per day.

A total of 4.95 million doses have been administered at long-term care facilities (LTCFs) through the Federal Pharmacy Partnership for Long-term Care (LTC) Program*, including residents and staff. This covers 3.78 million individuals with at least 1 dose and 1.15 million with 2 doses. Approximately 60% of the doses have gone to residents, and 40% to staff.
*The dashboard only includes data for doses administered through the federal program. It does not report data from West Virginia, which opted out of the program.

VACCINATION & VIRAL LOAD As vaccines continue to progress through clinical trials and vaccination efforts scale up in countries around the world, many questions remain about the efficacy of vaccines and vaccine candidates, particularly with respect to their ability to mitigate transmission risk. Researchers in Israel published (preprint) findings from a study on the viral load due to SARS-CoV-2 infection in vaccinated individuals. The researchers evaluated quantitative PCR results from individuals vaccinated with the Pfizer-BioNTech vaccine who subsequently tested positive for SARS-CoV-2 infection to determine any effect of vaccination on viral load. The study included specimens from nearly 3,000 patients in Israel collected December 23, 2020-January 5, 2021.

The researchers identified a significant decrease in the viral load in specimens collected 12 or more days after vaccination, corresponding to the expected “onset of early vaccine protection.” The researchers also compared the viral loads between vaccinated and unvaccinated individuals and identified a significant decrease in viral loads among the vaccinated individuals—12 days or longer after vaccination. In order to slow community transmission, a vaccine must be able to decrease the risk of infection in vaccinated individuals or decrease the transmissibility of vaccinated individuals. The viral loads in vaccinated patients indicates that they are still capable of being infected with SARS-CoV-2, but the risk of infection remains unclear. While this study does not assess transmissibility directly, it provides further evidence that the Pfizer-BioNTech vaccine can reduce the viral load, which could potentially contribute to reduced transmissibility.

VACCINATION EQUITY Inequity in vaccine access remains a major challenge in the US, and state and local health officials are working to mitigate equity issues as eligibility requirements expand. In many jurisdictions, efforts to administer vaccinations as quickly as possible have focused on populations that are more easily accessible, which in some instances, has resulted in lower vaccination coverage for high-risk groups, including racial and ethnic minorities, older adults, and lower-income communities. The location of vaccination sites and online scheduling systems can be barriers for many individuals, and health officials are combatting vaccine hesitancy in many communities. While some of these disparities may have been driven early on by the demographic characteristics of the earliest priority groups (eg, LCTF residents and staff, frontline healthcare workers), they have persisted as eligibility expands.

In New York City, the population is approximately 29% Latinx and 24% Black; however, these communities represent only 15% and 11% of the vaccinated population, respectively. The disparities increase with age as well, with Black individuals accounting for only 9% of vaccinees aged 65 years and older. New York City officials have identified major racial and ethnic disparities at some vaccination sites, which appear to be driven, in part, by individuals who live outside the community (eg, those who commute into the city for work). In order to mitigate these disparities, some vaccination sites will actively prioritize local residents for vaccination, and city health officials will begin reporting demographic data for vaccinations by ZIP code.

Researchers from The Working Group on Equity in COVID-19 Vaccination, CommuniVax, led by Dr. Monica Schoch-Spana at the Johns Hopkins Center for Health Security and Dr. Emily Brunson at the Department of Anthropology at Texas State University released their first report, part of an ongoing effort to promote equity in SARS-CoV-2 vaccination. The report focuses on state and local plans to engage Black, Indigenous, and People of Color (BIPOC) communities to support ongoing and future vaccination efforts, based on findings from a series of key informant interviews. The report outlines 5 key principles to facilitate effective engagement with racial and ethnic minority communities: Iteration, Involvement, Information, Investment, and Integration. Additionally, the researchers provide detailed descriptions of short- and long-term recommendations and tools to support state and local officials in their efforts to mitigate the disproportionate effects of the COVID-19 pandemic on these vulnerable communities.

SOUTH AFRICA VACCINATION In response to clinical trial data that indicate that the AstraZeneca-Oxford University SARS-CoV-2 vaccine exhibits low efficacy against the B.1.351 variant, South Africa announced that it is suspending vaccination efforts for that vaccine. The B.1.351 variant was first identified in South Africa in November 2020. Researchers from the Wits University Vaccines and Infectious Diseases Analytics (VIDA) Research Unit, which is conducting clinical trials for the vaccine in South Africa, found that the vaccine “provides minimal protection against mild-moderate COVID-19.” Notably, the researchers estimated the vaccine’s efficacy against the B.1.351 variant to be only 22%, based on a small study of approximately 2,000 participants. The study did not evaluate efficacy in preventing severe disease or death. South Africa will implement a new vaccination plan, which will aim, in part, to provide data needed to better characterize the vaccine’s efficacy against the B.1.351 variant. The data from this study have not yet been subjected to peer review, and further investigation is required.

EMERGING VARIANTS A study (preprint) by researchers in California (US) found that the prevalence of the B.1.1.7 variant of SARS-CoV-2 is rapidly increasing in the US. The researchers analyzed rates of S gene target failures (SGTFs) for PCR-based diagnostic tests and genomic sequencing to analyze the growth dynamics of the emerging and highly transmissible variant. SGTFs in specimens collected in the UK led to the initial detection of the B.1.1.7 variant, and they can serve as a proxy for the presence of the variant in clinical specimens.

Based on data from approximately 500,000 specimens collected from July 2020-January 2021, the researchers observed a slow but steady increase in the prevalence of SGTFs starting in October 2020, with a more rapid increase in January 2021—up from 0.8% in early January to 4.2% in late January. Based on the proportion of specimens with SGTFs, the researchers estimate the doubling time for the B.1.1.7 variant in the US to be approximately 10 days, which indicates increased transmissibility compared to the predominant strain. The genomic analysis of specimens collected in December 2020-January 2021 suggests that the variant was introduced to the US numerous times; however, most of the domestic transmission likely stems from “independent introductions into California...and Florida.” The researchers expect that the variant has been circulating in the US since November 2020.

US VACCINE PRODUCTION & DISTRIBUTION Shortly after taking office, US President Joe Biden indicated that he would utilize the Defense Production Act (DPA) to scale up production of critical supplies, including SARS-CoV-2 vaccines. In the February 5 White House COVID-19 response briefing, Tim Manning, the US government’s COVID-19 Supply Coordinator, announced that efforts are underway to give Pfizer “priority access” to critical supplies and equipment under the DPA in an effort to rapidly scale up production capacity. Some experts argue that the DPA is not sufficient to rapidly or meaningfully increase vaccine production capacity, because vaccine production processes are complex and require time to scale up. A senior official from Pfizer recently indicated that the company expects to shorten vaccine production time by half, which will significantly increase the overall production capacity. The improvements appear to stem from internal efforts to optimize the manufacturing process; however, improved availability of critical equipment and supplies could support further improvements to capacity.

Even as production capacity is scaling up, US states continue to struggle to implement vaccine administration operations at the local level. One of the principal challenges is uncertainty regarding the timing and quantity of vaccine deliveries. Without a clear idea of how many doses will arrive and when to expect them, hospitals, health departments, and other vaccinators are finding it difficult to schedule appointments, which is slowing vaccination progress. Reliable, longer-term delivery scheduling and tracking could provide state and local jurisdictions the confidence needed to schedule more appointments in advance or expand capacity at mass vaccination clinics; however, the existing process remains “opaque.” Eligibility is expanding in many states, and the demand for vaccination is easily exceeding the current supply. But even as efforts are ongoing to expand production capacity, it is likely that the supply will continue to fall short of demand for months to come.

ISRAEL VACCINATION Israel is conducting one of the most effective SARS-CoV-2 vaccination campaigns in the world. On a per capita basis, it currently ranks #2 in terms of daily doses administered (behind the UAE) and #1 in terms of cumulative doses—it is also #5 globally in terms of total cumulative doses, despite having a population of only 8.7 million. Israel has administered nearly 66 doses per 100 population, which corresponds to single-dose coverage for 66 percent of the population or full, 2-dose coverage for 33%. 

It is unclear exactly how many individuals have received 1 or 2 doses of the vaccine, but of all countries, Israel is likely the closest to achieving coverage sufficient to make an impact on its COVID-19 epidemic. Israel’s daily incidence has decreased somewhat from its highest peak in mid-January; however, at more than 6,000 new cases per day, it remains equal to or higher than its previous peak in late September. While Israel may not yet be at the point of making an impact on the national scale, the effects of high coverage among the earliest priority groups are starting to become evident. A report published in Nature indicates that COVID-19 incidence among adults aged 60 years and older decreased 41% from January to February, including a 31% decrease in hospitalizations. For comparison, incidence and hospitalizations fell by only 12% and 5%, respectively, among younger adults over that time.

Israel’s COVID-19 response, including its vaccination efforts, has not been without challenges. Despite notable national progress toward vaccination coverage, a report published in New York magazine indicates that “until last week, [Israel] did not distribute vaccines to the Palestinian Authority, the semi-autonomous government of the West Bank,” illustrating disparities in vaccine access for the vulnerable minority population. Some human rights organizations argue that Israel is responsible for vaccinations in the Israeli-occupied territory and the “blockaded Gaza Strip,” but the Israeli government argues that Israeli citizens are its top priority.

WHO SARS-CoV-2 ORIGIN INVESTIGATION A WHO team of international experts visited China to further investigate the origins of the SARS-CoV-2 virus. The joint China-WHO investigation began on January 14, 2021, including investigations and site visits at several critical locations in Wuhan and other parts of China. At a press conference on February 9, the team presented their initial assessment. Perhaps most notably, the team concluded that a laboratory release of the virus was “extremely unlikely.” Rather, the investigation suggests that zoonotic transmission from an existing animal reservoir is much more likely. It will be very difficult, however, to determine the exact nature of the original spillover event.

Team leader Dr. Peter Ben Embarek stated that, while the understanding of the pandemic scenario did not change dramatically as a result of the investigations, the team’s research added important details to the story. The investigation was not able to identify a specific animal reservoir, but bats and pangolins remain the principal focus for future investigations. Dr. Marion Koopmans suggested that future investigations should include surrounding farmlands and farmers where human-bat or other human-animal interactions could facilitate the spillover of SARS-CoV-2 into humans. Another working theory is that the virus could have been introduced into humans via frozen food, such as the types of products sold at the Huanan seafood market, where one of the first clusters of cases was identified. This investigation alone was unlikely to pinpoint the exact origin of the COVID-19 pandemic, and further efforts over the coming years will continue to investigate potential sources and factors associated with the pandemic’s origin. 

MASK MANDATES Although mask mandates and mask use have been sources of contention throughout the pandemic, including in the US, a study by the US CDC COVID-19 Response Team found that mask mandates are associated with decreased COVID-19 hospitalizations. This study analyzed COVID-19 data from 10 US states that instituted statewide mask mandates, implemented approximately from March through October 2020. The study included data collected by hospitals in the COVID-19–Associated Hospitalization Surveillance Network (COVID-NET) in California, Colorado, Connecticut, Maryland, Michigan, Minnesota, New Mexico, New York, Ohio, and Oregon.

The researchers found that states that implemented statewide mask mandates reported a significant decrease in COVID-19 hospitalization growth rates among adults aged 18-64 years. Within 2 weeks of implementing the mask mandate, hospitalization growth rates among adults aged 40-64 years decreased by nearly 3% compared to before the mandate. At 3 weeks or longer, the hospitalization growth rates decreased by 5.5% for adults aged 18-39 and 40-64 years. Hospitalization rates did not fall significantly for adults aged 65 years or older, but this group does face higher risk of severe COVID-19 disease. COVID-19 risk, including hospitalization, is the result of numerous factors, and it is not necessarily possible to determine causative associations; however, the correlation between statewide mask mandates and decreased COVID-19 hospitalizations provides further evidence of mask efficacy. Currently, 36 states, plus Puerto Rico, have statewide mask mandates in place, and states that do not have statewide mandates may have local requirements, such as at the city or country level.

VACCINE CERTIFICATES International vaccination certificates are already used to document travelers’ protection against some endemic diseases, such the “Yellow Card” for yellow fever vaccination. Some countries are beginning to investigate the possibility of a similar system for SARS-CoV-2 vaccination, which would allow travelers to enter a country without being subjected to testing or quarantine. The EU is reportedly evaluating a universal system for Member States, but individual countries are also creating their own certificates in the interim. Iceland was among the first to create its own certification system in January, and Poland is utilizing a digital QR code to document vaccination status. Denmark and Sweden reportedly plan to unveil vaccination certificates in June, and the UK is considering its own “vaccine passport,” which could be implemented this summer. Other countries, such as the US, have indicated interest in vaccine certificates but have not yet announced an anticipated timeline. The WHO has also been working with Estonia to create a universal digital vaccination certificate.