Machine learning for the identification of respiratory viral attachment machinery from sequences data.

At the outset of an emergent viral respiratory pandemic, sequence data is among the first molecular information available. As viral attachment machinery is a key target for therapeutic and prophylactic interventions, rapid identification of viral "spike" proteins from sequence can significantly accelerate the development of medical countermeasures. For six families of respiratory viruses, covering the vast majority of airborne and droplet-transmitted diseases, host cell entry is mediated by the binding of viral surface glycoproteins that interact with a host cell receptor. In this report it is shown that sequence data for an unknown virus belonging to one of the six families above provides sufficient information to identify the protein(s) responsible for viral attachment. Random forest models that take as input a set of respiratory viral sequences can classify the protein as "spike" vs. non-spike based on predicted secondary structure elements alone (with 97.3% correctly classified) or in combination with N-glycosylation related features (with 97.0% correctly classified). Models were validated through 10-fold cross-validation, bootstrapping on a class-balanced set, and an out-of-sample extra-familial validation set. Surprisingly, we showed that secondary structural elements and N-glycosylation features were sufficient for model generation. The ability to rapidly identify viral attachment machinery directly from sequence data holds the potential to accelerate the design of medical countermeasures for future pandemics. Furthermore, this approach may be extendable for the identification of other potential viral targets and for viral sequence annotation in general in the future.

Challenges in managing, sustaining, and assessing closed point of dispensing sites: Findings from a qualitative study.

Most U.S. public health agencies rely upon closed points of dispensing (PODs) to aid in medical countermeasure (MCM) distribution. However, few studies have focused on how to assess closed POD preparedness and none have examined best practices for managing sites once they have been recruited. This study involved qualitative interviews with U.S. disaster planners to elucidate their approaches and challenges to managing, sustaining, and assessing existing closed POD sites. In all, 16 disaster planners participated. Common management practices included frequent communication with sites, providing formal and informal training, and assisting with POD exercises. Very few jurisdictions reported doing formal assessments of closed POD sites. The largest challenges identified were staff turnover and keeping sites engaged, sometimes leading to sites voluntarily withdrawing or needing to be removed from being a closed POD. Frequent communication and building partnerships with closed POD site personnel were recommended to maintain and sustain existing sites. Formal and informal assessments will provide assurance of deployment readiness. Closed POD management is a challenging, but essential process to ensure readiness to deploy. Practices outlined by this study can be implemented to enhance closed POD network management at other jurisdictions. This should increase the ability to distribute MCMs rapidly during a future event, contributing to stronger community resilience. Public health officials should continue expanding and improving closed POD networks to enable MCM delivery and minimize morbidity and mortality related to mass casualty events.

The development of broad-spectrum antiviral medical countermeasures to treat viral hemorrhagic fevers caused by natural or weaponized virus infections.

The Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense (JPEO-CBRND) began development of a broad-spectrum antiviral countermeasure against deliberate use of high-consequence viral hemorrhagic fevers (VHFs) in 2016. The effort featured comprehensive preclinical research, including laboratory testing and rapid advancement of lead molecules into nonhuman primate (NHP) models of Ebola virus disease (EVD). Remdesivir (GS-5734, Veklury, Gilead Sciences) was the first small molecule therapeutic to successfully emerge from this effort. Remdesivir is an inhibitor of RNA-dependent RNA polymerase, a viral enzyme that is essential for viral replication. Its robust potency and broad-spectrum antiviral activity against certain RNA viruses including Ebola virus and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) led to its clinical evaluation in randomized, controlled trials (RCTs) in human patients during the 2018 EVD outbreak in the Democratic Republic of the Congo (DRC) and the ongoing Coronavirus Disease 2019 (COVID-19) pandemic today. Remdesivir was recently approved by the US Food and Drug Administration (FDA) for the treatment of COVID-19 requiring hospitalization. Substantial gaps remain in improving the outcomes of acute viral infections for patients afflicted with both EVD and COVID-19, including how to increase therapeutic breadth and strategies for the prevention and treatment of severe disease. Combination therapy that joins therapeutics with complimentary mechanisms of action appear promising, both preclinically and in RCTs. Importantly, significant programmatic challenges endure pertaining to a clear drug and biological product development pathway for therapeutics targeting biodefense and emerging pathogens when human efficacy studies are not ethical or feasible. For example, remdesivir's clinical development was facilitated by outbreaks of Ebola and SARS-CoV-2; as such, the development pathway employed for remdesivir is likely to be the exception rather than the rule. The current regulatory licensure pathway for therapeutics targeting rare, weaponizable VHF agents is likely to require use of FDA's established Animal Rule (21 CFR 314.600-650 for drugs; 21 CFR 601.90-95 for biologics). The FDA may grant marketing approval based on adequate and well-controlled animal efficacy studies when the results of those studies establish that the drug is safe and likely to produce clinical benefit in humans. In practical terms, this is anticipated to include a series of rigorous, well-documented, animal challenge studies, to include aerosol challenge, combined with human safety data. While small clinical studies against naturally occurring, high-consequence pathogens are typically performed where possible, approval for the therapeutics currently under development against biodefense pathogens will likely require the Animal Rule pathway utilizing studies in NHPs. We review the development of remdesivir as illustrative of the effort that will be needed to field future therapeutics against highly lethal, infectious agents.

Medical countermeasures against henipaviruses: a review and public health perspective.

Henipaviruses, including Nipah virus, are regarded as pathogens of notable epidemic potential because of their high pathogenicity and the paucity of specific medical countermeasures to control infections in humans. We review the evidence of medical countermeasures against henipaviruses and project their cost in a post-COVID-19 era. Given the sporadic and unpredictable nature of henipavirus outbreaks, innovative strategies will be needed to circumvent the infeasibility of traditional phase 3 clinical trial regulatory pathways. Stronger partnerships with scientific institutions and regulatory authorities in low-income and middle-income countries can inform coordination of appropriate investments and development of strategies and normative guidelines for the deployment and equitable use of multiple medical countermeasures. Accessible measures should include global, regional, and endemic in-country stockpiles of reasonably priced small molecules, monoclonal antibodies, and vaccines as part of a combined collection of products that could help to control henipavirus outbreaks and prevent future pandemics.

County-Level Planning for Efficient Distribution of Emergency Medical Countermeasures with RealOpt Software.

Emergency preparedness systems plan for antibiotic distribution and vaccine administration to respond to public health threats. The arrival of a COVID-19 vaccine underscores the importance of organized logistics for rapid administration to populations. The US Centers for Disease Control and Prevention Cities Readiness Initiative encourages frontline responders from 72 US cities and metropolitan statistical areas to use planning software, such as RealOpt-POD-v8.0.2, to design dispensing operations and predict staffing needs. However, planning can be difficult for local jurisdictions given uncertainty about how long it may take to complete various processes during a dispensing operation, including assessment of countermeasure needs for each person (eg, based on age or pregnancy status) and the careful dispensing of countermeasures and accompanying education. The Union County Health Department in Ohio gathered data on the timing of typical processes for an anthrax medical countermeasures distribution site through a small-scale drill and used these data to parameterize a RealOpt model capable of serving the rural county's population of just over 50,000 people within 24 hours. Results help fill a gap in parameterizing RealOpt-based planning models by highlighting the use of a small-scale drill to inform time estimates, which can be applied to RealOpt as part of county-level planning in advance of larger-scale drills to evaluate dispensing capabilities and effectiveness. The findings provide a methodological basis of future resource typing for adaptable and scalable dispensing, particularly for rural areas. Both the approach and resulting antibiotics dispensing schematic presented here could be tailored to support planning for population-based countermeasure administration to combat emerging pandemics.

Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO's virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.

Current State of Mass Vaccination Preparedness and Operational Challenges in the United States, 2018-2019.

Mass vaccination is a crucial public health intervention during outbreaks or pandemics for which vaccines are available. The US government has sponsored the development of medical countermeasures, including vaccines, for public health emergencies; however, federally supported programs, including the Public Health and Emergency Preparedness program and Cities Readiness Initiative, have historically emphasized antibiotic pill dispensing over mass vaccination. While mass vaccination and pill dispensing programs share similarities, they also have fundamental differences that require dedicated preparedness efforts to address. To date, only a limited number of public assessments of local mass vaccination operational capabilities have been conducted. To fill this gap, we interviewed 37 public health and preparedness officials representing 33 jurisdictions across the United States. We aimed to characterize their existing mass vaccination operational capacities and identify challenges and lessons learned in order to support the efforts of other jurisdictions to improve mass vaccination preparedness. We found that most jurisdictions were not capable of or had not planned for rapidly vaccinating their populations within a short period of time (eg, 1 to 2 weeks). Many also noted that their focus on pill dispensing was driven largely by federal funding requirements and that preparedness efforts for mass vaccination were often self-motivated. Barriers to implementing rapid mass vaccination operations included insufficient personnel qualified to administer vaccinations, increased patient load compared to pill-dispensing modalities, logistical challenges to maintaining cold chain, and operational challenges addressing high-risk populations, including children, pregnant women, and non-English-speaking populations. Considering the expected availability of a severe acute respiratory syndrome coronavirus 2 vaccine for distribution and dispensing to the public, our findings highlight critical considerations for planning possible future mass vaccination events, including during the novel coronavirus disease 2019 pandemic.

The Strategic National Stockpile: identification, support, and acquisition of medical countermeasures for CBRN incidents.

The Strategic National Stockpile (SNS) serves as a repository of materiel, including medical countermeasures (MCMs), that would be used to support the national health security response to a chemical, biological, radiological, or nuclear (CBRN) incident, either natural or terrorism-related. To support and advance the SNS, the National Institutes of Health (NIH) manages targeted investigatory research portfolios, such as Countermeasures Against Chemical Terrorism (CounterACT) for chemical agents, that coordinate projects covering basic research, drug discovery, and preclinical studies. Project BioShield, managed by the Biomedical Advanced Research and Development Agency (BARDA), guides and supports academia and industry with potential MCMs through the Food & Drug Administration's approval process and ultimately supports the acquisition of successful products into the SNS. Public health emergencies such as the COVID-19 pandemic and the ever-increasing number of MCMs in the SNS present logistical and financial challenges to its maintenance. While MCMs for biological agents have been readily adopted, those for chemical agents have required sustained investments. This paper reviews the methods by which MCMs are identified and supported for inclusion in the SNS, the current status of MCMs for CBRN threats, and challenges with SNS maintenance as well as identifies persistent obstacles for MCM development and acquisition, particularly for ones focused on chemical weapons.

Countermeasures for Preventing and Treating Opioid Overdose.

The only medication available currently to prevent and treat opioid overdose (naloxone) was approved by the US Food and Drug Administration (FDA) nearly 50 years ago. Because of its pharmacokinetic and pharmacodynamic properties, naloxone has limited utility under some conditions and would not be effective to counteract mass casualties involving large-scale deployment of weaponized synthetic opioids. To address shortcomings of current medical countermeasures for opioid toxicity, a trans-agency scientific meeting was convened by the US National Institute of Allergy and Infectious Diseases/National Institutes of Health (NIAID/NIH) on August 6 and 7, 2019, to explore emerging alternative approaches for treating opioid overdose in the event of weaponization of synthetic opioids. The meeting was initiated by the Chemical Countermeasures Research Program (CCRP), was organized by NIAID, and was a collaboration with the National Institute on Drug Abuse/NIH (NIDA/NIH), the FDA, the Defense Threat Reduction Agency (DTRA), and the Biomedical Advanced Research and Development Authority (BARDA). This paper provides an overview of several presentations at that meeting that discussed emerging new approaches for treating opioid overdose, including the following: (1) intranasal nalmefene, a competitive, reversible opioid receptor antagonist with a longer duration of action than naloxone; (2) methocinnamox, a novel opioid receptor antagonist; (3) covalent naloxone nanoparticles; (4) serotonin (5-HT)1A receptor agonists; (5) fentanyl-binding cyclodextrin scaffolds; (6) detoxifying biomimetic "nanosponge" decoy receptors; and (7) antibody-based strategies. These approaches could also be applied to treat opioid use disorder.

SARS-CoV-2: Impact on, Risk Assessment and Countermeasures in German Eye Banks.

INTRODUCTION: Since the beginning of the COVID-19 pandemic there has been some debate regarding the risk of transmission through tissue transplantation and tissue banking processes. AIM OF THE STUDY: To analyze the changes that SARS-CoV-2 has caused regarding the harvesting of corneal donor tissue and eye bank activities in Germany. METHODS: A questionnaire was provided to 26 eye banks in Germany, consisting of questions about adaptations made in the screening of potential donors and the harvesting of corneal tissue following the pandemic spread of SARS-CoV-2. RESULTS: Eighteen eye banks actively reduced recruitment of donors and two banks ceased all activity. Additional diagnostic screening was performed in eight banks, using conjunctival swabs and/or nasopharyngeal swabs. In six eye banks, additional protective measures, such as FFP2 masks and/or facial shields, were implemented. Overall, a mean reduction in the number of obtained donor tissues of 17% was observed. DISCUSSION: Conjunctival and/or nasopharyngeal swabs of donors have been implemented by a minority. Reasons for not performing additional tests may be moderate sensitivity and lack of validation for postmortem use of RT-PCR testing. Also, the hazard of SARS-CoV-2 entering the corneal donor pool with subsequent transmission might be perceived as theoretical. Face shields provide a sufficient barrier against splash and splatter contamination but may be insufficient against aerosols. Additional face masks would provide support against aerosols, but it remains debatable if corneal harvesting can be considered an aerosol-producing procedure. In the future we expect to see changes in current guidelines because of a surge in scientific activities to improve our understanding of the risks involved with cornea donation in the COVID-19 pandemic, and because current practice may reduce the availability of donor corneas due to new exclusion criteria while the demand remains unchanged.

Disease X: accelerating the development of medical countermeasures for the next pandemic.

WHO has listed several priority diseases with epidemic potential for which there are no, or insufficient, medical countermeasures. In response, the Bill & Melinda Gates Foundation (with support from PricewaterhouseCoopers) coordinated subject matter experts to create a preparedness plan for Disease X. Disease X is caused by Pathogen X, an infectious agent that is not currently known to cause human disease, but an aetiologic agent of a future outbreak with epidemic or pandemic potential. We have identified crucial areas for acceleration in medical countermeasure product development and international coordination. We have also reviewed novel platforms and process improvements related to manufacturing, which could revolutionise the response to the next pandemic. Finally, we created several coordination and engagement guides. These guides range from the rational design of an intervention target product profile, to the key facets of vaccine and therapeutic development, to accelerated manufacturing and regulatory mechanisms. In this Personal View, we provide a high-level summary of the outcomes of the medical countermeasure development workstream, intended for a broad audience including academia, medical countermeasure developers, and multilateral coordinating bodies. We hope that they might find this piece useful in prioritising strategic investments and efforts to accelerate medical countermeasure development. We observed that in-depth analyses of clinical trial design, chemistry, manufacturing and control activities, and accelerated regulatory pathways are necessary for shortening the timelines for the product development of medical countermeasures. We intend to cover these topics in future publications.