June 14, 2022: Johns Hopkins COVID 19 Situation Report

COVID-19 Situation Report

Editor: Alyson Browett, MPH

Contributors: Clint Haines, MS; Noelle Huhn, MSPH; Natasha Kaushal, MSPH; Amanda Kobokovich, MPH; Christina Potter, MSPH; Matthew Shearer, MPH; Marc Trotochaud, MSPH; and, Rachel A. Vahey, MHS.

MONKEYPOX OUTBREAKS UPDATE Read our latest update from June 1 on the monkeypox outbreaks and visit our monkeypox resource page. We will continue to analyze the situation and provide updates, as needed. If you would like to receive these updates, please sign up here.

SARS-CoV-2 ORIGINS On June 9, the WHO Scientific Advisory Group for the Origins of Novel Pathogens (SAGO) published the first preliminary report from its efforts to determine key analyses necessary to identify the origin of SARS-CoV-2 and future emerging and re-emerging pathogens. While SAGO was not explicitly tasked with identifying the original source of SARS-CoV-2, the report indicates that the available evidence remains insufficient to fully characterize the circumstances around the emergence of the virus. The experts indicate that the available evidence suggests that the closest ancestor of the virus likely circulated in wild bat populations before the spillover event into humans. The report indicates that it is not possible to rule out that the virus escaped from a research laboratory, but additional investigation is required to more fully characterize that scenario. Several SAGO members included a note in the report, however, to emphasize that they identified “no new scientific evidence” to support this theory and did not support continuing this line of investigation.

The report includes a series of recommendations regarding data and analyses that would further support efforts to identify the original source of the COVID-19 pandemic. SAGO recommends further analysis of environmental specimens from the Hunan seafood market and of potential animal and environmental sources to identify the route of SARS-CoV-2 introduction to the market. Additionally, analysis of human respiratory pathogen specimens (eg, influenza, enteroviruses) collected prior to the emergence of COVID-19 could help identify previously undetected SARS-CoV-2 infections. Genetic analysis of infections in wild and livestock animal populations could similarly help identify related coronaviruses or intermediate hosts that may have facilitated spillover into human populations. The SAGO report also highlights the need for these types of analyses regarding the emergence of new SARS-CoV-2 variants. Some independent experts continue to call attention to the lack of transparency by the Chinese government, including restrictions on access to specimens, facilities, and personnel necessary to conduct these investigations.

SAGO also outlines key components of a global framework to guide response activities and investigations into the emergence or re-emergence of future pathogens. This framework largely mirrors SAGO’s calls for additional data related to SARS-CoV-2. Specifically, the group notes the importance of investigating human and animal specimens; interactions between humans, animals, and the environment; genomics and phylogenetics; biosafety and biosecurity systems and processes; and research activities or other human interaction with related pathogens.

ACUTE HEPATITIS & LONG COVID Researchers from Israel published findings from their study on instances of long-term COVID-19 liver manifestation among children. The study, published in the Journal of Pediatric Gastroenterology and Nutrition, involved a retrospective investigation of 5 patients hospitalized in an Israeli children’s hospital. Each of the patients had a confirmed SARS-CoV-2 infection and presented with long-term liver injury stemming from their infection. Two of the patients in the study, both under 6 months of age, presented with acute liver failure, the other 3 patients, ranging between ages 8 and 13 years, presented with acute hepatitis and cholestasis.

This review adds to the growing list of evidence tying post-acute sequelae of COVID-19 (PASC/Long COVID) to cases of acute hepatitis of unknown origin. Last month, multiple technical and news media publications documented an international cohort of children with severe hepatitis. Many experts have suggested that COVID-19 could be a potential source for this unexplained manifestation, considering the lack of apparent epidemiological explanations. The US CDC is examining a series of US cases of acute hepatitis as well, and a recent update indicates that adenovirus type 41 could be a possible causative agent as well. While much has been written about Long COVID, many questions remain, and advocates continue to call for expanded research efforts into explanations and treatments.

US PEDIATRIC VACCINATION Last week, the Biden Administration outlined its SARS-CoV-2 vaccination plans for children under 5 years of age. The current estimates suggest that up to 18 million children may become eligible for SARS-CoV-2 vaccination once the US FDA authorize existing vaccines for emergency use in younger children. The White House has allocated 10 million doses for states to distribute to dispensing sites. Notably, the White House estimates that 85% of the newly eligible pediatric population lives within 5 miles of one of these sites. The allotment of vaccines is approximately even between the Pfizer-BioNTech and Moderna vaccines. Despite a ready supply of vaccines and a plan to make them accessible to a large number of children in this age group, questions remain regarding the willingness of parents and caretakers to get the children vaccinated. In the age group of children from 5-11 years, only one-third of eligible children have received the vaccine.

US TRAVEL RESTRICTIONS On June 12, the US CDC lifted its testing requirement for travelers arriving in the US on flights originating in other countries. In the CDC’s announcement rescinding the policy, CDC Director Dr. Rochelle Walensky noted that the availability of vaccines, therapeutics, and alternative testing options (eg, rapid at-home test kits)—as well as the current prevalence of vaccination coverage in the US—largely render the testing restrictions obsolete, and she emphasized that the CDC continues to recommend full vaccination against SARS-CoV-2, including with the appropriate booster dose/s.

Previously, international air travelers with destinations in the US were required to obtain a negative PCR-based or antigen test within 1 day of departure—or provide documentation of recent recovery from SARS-CoV-2 infection—regardless of vaccination status. The policy was instituted in the final days of the Trump Administration and continued under President Joe Biden. Notably, the restrictions only applied to international air travel and did not cover individuals entering the US via land borders nor domestic air travel. The travel industry, particularly airlines, has long called for the testing requirement to be eliminated, arguing that it was originally instituted at a time when the vast majority of the US was unvaccinated. Additionally, some health officials and other experts have argued that the testing mandate provided little protection for travelers or benefit in terms of slowing domestic transmission or the introduction of new SARS-CoV-2 variants into the US.

US SEROPREVALENCE The US CDC COVID-19 Response Team published updated analysis of infection- and vaccine-induced SARS-CoV-2 seroprevalence in the US. The findings, published in JAMA, are based on more than 2.4 million blood donations collected from individuals aged 16 years and older across all 50 states; Washington, DC; and Puerto Rico from July 2020-December 2021. The research does not include individuals with active SARS-CoV-2 infection or who were suspected COVID-19 cases, and results were weighted by demographic factors, including age, sex, race, and ethnicity.

The researchers observed increases in both infection-induced seroprevalence and combined seroprevalence between May 2021 and December 2021, increasing from 20.2% to 28.8% and 83.3% to 94.7%, respectively. At the end of the timeframe for the study, researchers observed the highest level of infection-induced seroprevalence in multiple demographic groups—including individuals aged 16-29 years (40.0%), non-Hispanic Black individuals (32.5%), and Hispanic individuals (32.5%)—as well as the Midwest (31.7%) and South (33.5%) regions.

Notably, regions with higher vaccine coverage seroprevalence exhibited a significantly smaller increase in infection-induced seroprevalence. In regions with vaccine-induced seroprevalence less than 60%, infection-induced seroprevalence increased by 19.8% over the course of 2021, compared to only 10.6% in regions with vaccine seroprevalence greater than 80%. Despite widespread combined seroprevalence at the end of 2021, the Omicron variant was still able to drive a major surge in early 2022, and the researchers note that this illustrates the transmissibility and immune escape potential of new variants.

BA.4 & BA.5 SUBVARIANTS IN EUROPE The European CDC published an epidemiological update on the emergence and prevalence of the BA.4 and BA.5 sublineages of the SARS-CoV-2 Omicron variant of concern (VOC). The subvariants were first detected in Europe in March, and in May, Portugal was the first European country to report a COVID-19 surge associated with one of the subvariants (BA.5). Notably, Portugal’s daily incidence appeared to peak in late May/early June. While most European countries have reported relatively low prevalence of these subvariants, they represent an increasing proportion of new sequenced specimens in multiple countries over the past several weeks, including Austria, Belgium, Denmark, France, Germany, Ireland, Italy, Netherlands, Spain and Sweden. In particular, the BA.4 and BA.5 subvariants represent more than 25% of sequenced specimens in Belgium over the second half of May, and more than 10% in some communities in Spain. The increasing prevalence of BA.4/BA.5 corresponds to increasing COVID-19 daily incidence in most of those countries as well.

The ECDC projects that BA.4 and BA.5 will become the dominant variants across Europe “in the coming weeks” and that the continent can expect an associated COVID-19 surge like those in the countries noted above. The daily incidence in Europe has increased nearly 30% since June 6, with even larger increases in the UK. While there is “no evidence” these subvariants pose higher risk of severe disease, the ECDC notes that an overall increase in transmission can be associated with subsequent increases in hospitalizations and mortality.

WASTEWATER SURVEILLANCE Researchers from the University of Illinois and University of Florida published (preprint) findings from a study on the implementation of neighborhood-scale SARS-CoV-2 wastewater surveillance systems. The COVID-19 pandemic has popularized wastewater surveillance as a tool to provide early warning of impending outbreaks; however, most of these efforts have focused on large-scale sewer systems. Neighborhood-scale systems can provide more targeted early warning capacity, but as the catchment population decreases, the volume of fecal matter is less consistent, which can make it more difficult to analyze the concentration of SARS-CoV-2 and accurately detect emerging outbreaks.

This study covered 7 neighborhood-scale wastewater surveillance systems in Champaign County, Illinois, from January-November 2021, with catchment populations ranging from 853 to 2,402 individuals. In an effort to improve the system’s accuracy, the researchers developed a methodology to normalize the concentration of SARS-CoV-2 N gene fragments by the concentration of pepper mild mottle virus (PMMOV) detected in the system. The presence and concentration of PMMOV served as an analogue for the presence of fecal matter in the sample, which enabled the researchers to establish more accurate baseline metrics and better analyze the relative concentration of SARS-CoV-2. Based on the concentration of SARS-CoV-2 N gene fragments to PMMOV, the system output a binary risk assessment (ie, Low or High).

Over the 11 months of the study, the 7 neighborhoods experienced 26 total local COVID-19 outbreaks, and the surveillance system identified High COVID-19 risk corresponding to 19 of those time periods (73% sensitivity). The system identified 17 total High-risk time periods, and 12 of those corresponded to local COVID-19 outbreaks (71% specificity). The researchers also indicated that the surveillance system was capable of providing sufficiently accurate risk assessment for specific variants of SARS-CoV-2, which could provide early warning of the geographic spread of variants of concern. This study provides evidence that smaller-scale wastewater surveillance systems can provide indication of increased transmission risk among specific communities, particularly during periods of relatively low local incidence.