Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies
The National Academies of Sciences, Engineering, and Medicine (NASEM) released a framework to “define and describe the data needs for a system to track and correlate viral genome sequences with clinical and epidemiological data.” The report, Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies, also provides a set of question that this framework could answer and explores regulatory and governance factors. Genomic data play an important role in vaccine development and monitoring, because a protein mutation has the potential to alter vaccine safety and efficacy. Such data provide insight into the causes of new cases – local spread or virus importation. Further, integrated analysis of genomic, clinical, and epidemiological data provides a distinct, real-time picture of the outbreak. The report is an output of the Committee on Data Needs to Monitor the Evolution of SARS-CoV-2 and Dr. Saskia Popescu, an alumna of the Biodefense PhD Program, is a member.
The Folly of Circumventing the CDC
Recently, the administration decided to circumvent the Centers for Disease Control in Prevention (CDC) in the collection of data regarding COVID-19 infections in hospitalized patients. Prior to this poor decision, these data were sent to the CDC’s public National Healthcare Safety Network (NHSN), but it is now sent a new system run by TeleTracking Technologies. NHSN is a 15-year old database that receives data from health care facilities about anything that impacts the occurrence of infection once a patient is admitted. The change was sudden as hospitalization data vanished from the CDC website, sparking immediate outrage. The American Public Health Association (APHA), the Johns Hopkins Center, and Resolve to Save Lives, a nonprofit led by former CDC director Tom Frieden, released a comprehensive report on COVID-19 data collection, characterizing it as an “information catastrophe.” The circumvention creates further worries that data will be lost or duplicated. A remedy to the catastrophe is not to sideline the CDC, but to untangle the data collection mess by creating comprehensive and standardized network for the US coronavirus response. NHSN collected institutional data, but was not collecting infection data outside of a healthcare setting; however, the network could be expanded to better capture all infection-related data. NPR conducted its own investigation into the new system for COVID-19 data collection, and some of its key findings include that the process by which the Department of Health and Human Services (HHS) awarded the multi-million dollar contract is normally used for innovative scientific research and that the contract may have been awarded as a no-bid contract. Such irregularities in the contract process are raising questions about the ethics behind the decision. Suspicious circumstances aside, bypassing the CDC – US authority on infectious diseases – in the collection and use of COVID-19 infection data harms the US response to the pandemic.
How Do We Know If a Virus Is Bioengineered?
Since the onset of the pandemic, theories and accusations that it was intentionally engineered have ricocheted through the public, despite the consensus that the virus’s genetics indicate that it is most likely a zoonotic pathogen. In fact, on 30 April, the US Office of the Director of National Intelligence (ODNI) announced that the virus was neither human-made not genetically modified. The intelligence community came to this conclusion based, in part, on a Finding Engineering-Linked Indicators (FELIX) analysis, which found that the virus had not been engineered using foreign genetic sequences. That said, the detection of bioengineering is a “fraught task” given that there are many methods to identify engineering in a virus and there are many methods to engineer a virus. Tools such as FELIX are being deployed to “test the veracity of online stories claiming that SARS-CoV-2 was engineered in a laboratory.” Though the result of the FELIX analysis provides evidence against the possibility that SARS-CoV-2 was the result of engineering, Dr. Filippa Lentzos clarifies that this finding only rules out certain types of bioengineering. While other methods for testing and detecting intentional adjustments to a virus exist, they share a critical limitation: reliance on the records of known organisms and known “signatures of engineering.” These tools aim to increase biosecurity, but they bear the potential for dual-use purposes – offense and defense. Further, Dr. Gregory Koblentz, Director of the Biodefense Graduate Program, asserts that these detection tools send a message to the world the such research is “driven by this perception that the diffusion of increasingly sophisticated biotechnology is creating new potential threats that we are not prepared to detect.” Put simply, the US is signaling that it considers biothreats as clear and present dangers.
New Course Announcement: Building Health System Resilience
Dr. Saskia Popescu, alumna of the Biodefense PhD Program, is offering a new course this fall: Building Health System Resilience! This course will provide students with a foundation in how healthcare systems prepare and respond to pandemics, disasters, and biological events. The ability of healthcare systems to respond to biological threats will have impacts at the community, national, and international levels. Health resilience in the United States is a particular challenge given multiple stakeholders, economic factors, and regulatory fragmentation. Students will review case studies, such as Ebola, Hurricane Katrina, 9/11, and COVID-19, to examine the unique challenges of building and sustaining the resilience of the American healthcare and its role in global health security. Dr. Popescu is an epidemiologist and infection preventionist who is currently working on the frontlines of the pandemic.
The Scramble for Vaccines and the COVAX Facility
The Commission on Strengthening America’s Health Security at the Center for Strategic and International Studies (CSIS) is offering an online event, The Scramble for Vaccines and the COVAX Facility. The COVAX Facility is an international initiative to develop and equitably distribute vaccines against SARS-CoV-2 in order to benefit all nations. The discussion panel includes Nikolaj Gilbert, President and CEO at PATH, Kendall Hoyt, Assistant Professor of Medicine at Dartmouth University’s Geisel School of Medicine, and Nicole Lurie, Strategic Advisor to the CEO at the Coalition for Epidemic Preparedness Innovations (CEPI). The event will be livestreamed here on 11 August at 9am EST.
The Center for Health Security in the Bloomberg School of Public Health at Johns Hopkins University released a report detailing federal, state, and local level policy actions that needed to rein in the COVID-19 pandemic. The report, Resetting Our Response: Changes Needed in the US Response to COVID-19, provides 10 recommendations to “reset” the largely bungled response. These recommendations include reinstituting stay-at-home orders in localities were healthcare systems are overloaded and scaling up contact tracing. Read the full report here.
Desperate Times Do NOT Call for Desperate Countermeasures
The mad scramble for a COVID-19 vaccine may be falling short in terms of safety and effectiveness. A vaccine trial is now underway that possesses a minute chance of supplying a vaccine before Election Day this November. Unfortunately, such a condensed timeline worries many public health experts, because political pressure on the Food and Drug Administration (FDA) to grant emergency approval of a vaccine could undermine efforts if the final product is unsafe or fails to impart protection against SARS-CoV-2. Prior to the pandemic, the anti-vaccination movement was gaining support from individuals across the spectrum of political ideologies; a poorly designed and disseminated COVID-19 vaccine could provide the movement with leverage to gain even more support. Dr. Joshua Sharfstein, a former FDA deputy commissioner and a professor at Johns Hopkins University, emphasizes the importance of avoiding politicization of public health issues. The landmark phase 3 trial for the Moderna vaccine plans on enrolling 30,000 subjects, and another significant phase 3 trial for a vaccine by Pfizer and BioNTech commenced this week. The fear with these phase 3 trials is that a rushed decision could be made to progress a candidate through the approval process before adequate data are collected and analyzed to ensure that it imparts protection against the novel coronavirus without causing severe adverse events. Though it is quite unlikely that the FDA would fail to require clear evidence in support of a vaccine before approving it for the masses, the possibility that political pressure could sway the approval of a vaccine that imbues only partial protection could, in the long-run, undermine testing and uptake for future vaccines. If so, what further restraints and risks will the next pandemic hold?
The reliance and hope to end the current pandemic are concentrated in a still-hypothetical vaccine, but the reality is that a vaccine only allays part of the crisis and the realization of it is likely still months away. Despite the rose-colored outlook of the administration, a vaccine will likely not offer complete protection nor will it be readily accessible to all once one is approved. Though Operation Warp Speed is spurring investment in manufacturing facilities, producing hundreds of millions of doses of a new vaccine designed using nascent technologies remains quite a challenge. The FDA experienced such a challenge in 2009 when H1N1 (“swine flu”) threatened the world: when millions of doses of a vaccine were in production, there were not sufficient facilities to package them into individual vials. If this experience is repeated with a COVID-19 vaccine, the response would suffer another horrendous failure that could erode trust in vaccines and public health in general for many years to come. The development and quick dissemination of a robust vaccine are certainly critical milestones in the battle against the pandemic; however, the virus is likely here to stay as it is too prevalent. So, a more realistic goal is to design a vaccine that mitigates severe cases of disease and render COVID-19 “easier to live with.”
Update: Mystery Seed from China
The packages of mystery seeds sent via the mail to individuals across the country are continuing to pop up. Unsolicited packages from China have also been reported in Canada, the European Union, and Australia. Officials from the US Department of Agriculture (USDA) have identified 14 species of seeds found in the packets received on our soil as a medley of ornamental, fruit, vegetable, herb, and weed species. Specifically, cabbage, hibiscus, lavender, mint, morning glory, mustard, rose, rosemary and sage have been identified by the USDA’s Animal and Plant Health Inspection Service (APHIS). More species are awaiting identification. All 50 states have issued warnings against planting the unsolicited seeds.
Dicey DIY COVID-19 Vaccine
Nearly two dozen scientists, including a renowned geneticist, are serving as lab rats for a DIY COVID-19 vaccine developed by Preston Estep. This vaccine undergoing an informal human trial is the product of a biologist who possessed no animal data nor ethics board approval. Estep formulated the vaccine in a borrowed laboratory located in Boston with merely its ingredients and a single willing subject. Estep and his posse of researchers established the Rapid Deployment Vaccine Collaborative, nicknamed Radvac, which published a white paper detailing their nasal vaccine. The group asserts that the risks of trying the DIY vaccine exceed the risks associated with the COVID-19 disease; however, the legality of their endeavor is unclear. The US Food and Drug Administration (FDA) requires authorization to test novel drugs through an investigational new drug approval, but Radvac does not have permission, nor did it get a seal of approval from any ethics board. The FDA released a statement ruling that self-administered gene therapy, such as Radvac’s DIY vaccine, violates drug safety laws since it lacks approval.
25% in US See At Least Some Truth in Conspiracy Theory that COVID-19 Was Planned
About 70% of Americans have heard a conspiracy theory alleging that the novel coronavirus pandemic was planned by “powerful people.” A June survey conducted by the Pew Research Center found that 5% of US adults believe that this conspiracy theory is definitely true and another 20% believe that it is probably true. The poll also asked demographic questions to respondents, showing that those with lower levels of educational attainment tended to believe the COVID-19 origin stories fueled by disinformation. Beyond the unsubstantiated notion that the virus was some sort of evil plot, absurd false claims, including some that have already been studied and repudiated, regarding the pandemic are going viral on social media. In particular, physician and minister Stella Immanuel – who has previously asserted that gynecological issues like endometriosis are caused by demon sperm – is spreading the falsity that the antimalarial hydroxychloroquine is a cure for COVID-19. Adding further fuel to this disinformation fire, Trump praised Immanuel as “spectacular” and supported her inaccurate advice to use the antimalarial against the coronavirus disease. Trump’s praising tweets have been deleted, and the videos that shared Immanuel’s untruths have removed from social media as it violates COVID-19 misinformation policies. Russia, an unsurprising purveyor of disinformation, has been accused of spreading spurious information about the pandemic. Specifically, Russian intelligence services are amplifying false arguments from China that the coronavirus was engineered by the US military. Russia seems to be pushing false propaganda in order to influence the upcoming US election. Though the disinformation spurring from Russia is quite concerning, the litany of disinformation stemming from within our own borders is, perhaps, more terrifying.
Possible Long-Term Symptoms in COVID-19 Patients
As we continue await medical countermeasures to fight COVID-19, doctors are worried about the long-term effects of the disease. A recent Morbidity and Mortality Weekly Report (MMWR) from the Centers for Disease Control and Prevention (CDC) adds information about symptom duration and risk factors for delayed recovery. Although relatively little is known about the clinical course of COVID-19 and a patient’s return to baseline health, a new telephone survey of symptomatic adults who tested positive for SARS-CoV-2 infection sheds a little light on the topic. Thirty-give percent of respondents who had a positive outpatient test result indicated that they had not returned to their usual state of health when interviewed 2-3 weeks after testing. Also, among adults aged 18-34 years who did not report prior chronic medical conditions, 1 in 5 had yet to return to their usual state of health. These initial survey results spur concern that COVID-19 can result in prolonged illness in those with relatively mild cases of COVID-19.