Faculty Bibliography

In the past decade we have seen two major Ebola virus outbreaks in Africa, the Zika virus in Brazil and the Americas and the current pandemic of coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There is a strong sense of déjà vu because there are still no effective treatments. In the COVID-19 pandemic, despite being a new virus, there are already drugs suggested as active in in vitro assays that are being repurposed in clinical trials. Promising SARS-CoV-2 viral targets and computational approaches are described and discussed. Here, we propose, based on open antiviral drug discovery approaches for previous outbreaks, that there could still be gaps in our approach to drug discovery.

BACKGROUND:Despite evidence of socio-demographic disparities in outcomes of COVID-19, little is known about characteristics and clinical outcomes of patients admitted to public hospitals during the COVID-19 outbreak. OBJECTIVE:To assess demographics, comorbid conditions, and clinical factors associated with critical illness and mortality among patients diagnosed with COVID-19 at a public hospital in New York City (NYC) during the first month of the COVID-19 outbreak. DESIGN/METHODS:Retrospective chart review of patients diagnosed with COVID-19 admitted to NYC Health + Hospitals / Bellevue Hospital from March 9th to April 8th, 2020. RESULTS:A total of 337 patients were diagnosed with COVID-19 during the study period. Primary analyses were conducted among those requiring supplemental oxygen (n = 270); half of these patients (135) were admitted to the intensive care unit (ICU). A majority were male (67.4%) and the median age was 58 years. Approximately one-third (32.6%) of hypoxic patients managed outside the ICU required non-rebreather or non-invasive ventilation. Requirement of renal replacement therapy occurred in 42.3% of ICU patients without baseline end-stage renal disease. Overall, 30-day mortality among hypoxic patients was 28.9% (53.3% in the ICU, 4.4% outside the ICU). In adjusted analyses, risk factors associated with mortality included dementia (adjusted risk ratio (aRR) 2.11 95%CI 1.50-2.96), age 65 or older (aRR 1.97, 95%CI 1.31-2.95), obesity (aRR 1.37, 95%CI 1.07-1.74), and male sex (aRR 1.32, 95%CI 1.04-1.70). CONCLUSION/CONCLUSIONS:COVID-19 demonstrated severe morbidity and mortality in critically ill patients. Modifications in care delivery outside the ICU allowed the hospital to effectively care for a surge of critically ill and severely hypoxic patients.

We report the case of a 46-year-old man abattoir worker who developed myalgias, shortness of breath, and irritability 2 weeks after sustaining a laceration to the hand with a knife at work. During his hospital evaluation for septic shock he was noted to be febrile, hypotensive, profoundly jaundiced with aseptic meningitis, and renal failure, and was diagnosed with Leptospirosis interrogans infection confirmed by serum and urine polymerase chain reaction. After standard antibiotic therapy and recovery from severe clinical illness, he developed unilateral orchitis with pyuria secondary to leptospirosis, a well-established complication in the veterinary literature, but of which we offer the first report in humans in the English literature. The case presented was also the index case that uncovered a cluster outbreak of leptospirosis in New York City during the winter of 2016-2017, involving a total of three patients who lived or worked within a block of the abattoir. Two patients survived whereas the third died of pulmonary hemorrhage shortly after seeking medical care.

Background/UNASSIGNED:Starting in December 2013, the Ebola virus disease (EVD) epidemic spread in West Africa through five countries (Sierra Leone, Liberia, Guinea, Nigeria, and Mali), killing over 11,300 people. In partnership with Côte d'Ivoire's Ministry of Health, the International Rescue Committee instigated a community-led strategy aimed at promoting behavior change in order to prevent potential Ebola outbreaks in the country. The strategy was implemented in Western districts bordering Liberia, Guinea, and Mali. This study aims to analyze the community-led strategy, to document lessons learned from the experience, and to capitalize on the achievements. Methods/UNASSIGNED:A case study in four districts of Western Côte d'Ivoire, i.e. Biankouma, Danané, Odienné and Touba districts was carried out. Qualitative data in 12 villages (i.e., three villages per district) was collected from 62 healthcare workers, community leaders, and ordinary community members. Data was de-identified, coded and analyzed using a thematic approach. Results/UNASSIGNED:The community-led strategy was socially accepted in the villages. Even though some community leaders reported that sensitization had been, at times, constrained by a lack of equipment, the people interviewed demonstrated accurate understanding of information about prevention practices. Some practices were easily adopted, while others remained difficult to implement (e.g., ensuring safe and dignified dead body management). Conclusion/UNASSIGNED:This research demonstrates that sensitization efforts led by well-integrated and respected community leaders can be conducive of behavior change. Lessons learned from the community-led strategy could be applied to future disease outbreaks.

To determine whether 2 readily available indicators predicted survival among patients with Ebola virus disease in Sierra Leone, we evaluated information for 216 of the 227 patients in Bo District during a 4-month period. The indicators were time from symptom onset to healthcare facility admission and quantitative real-time reverse transcription PCR cycle threshold (Ct), a surrogate for viral load, in first Ebola virus-positive blood sample tested. Of these patients, 151 were alive when detected and had reported healthcare facility admission dates and Ct values available. Time from symptom onset to healthcare facility admission was not associated with survival, but viral load in the first Ebola virus-positive blood sample was inversely associated with survival: 52 (87%) of 60 patients with a Ct of >24 survived and 20 (22%) of 91 with a Ct of <24 survived. Ct values may be useful for clinicians making treatment decisions or managing patient or family expectations.

The Zika virus (ZIKV) is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barre syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.

The Zika virus (ZIKV) outbreak in the Americas has caused global concern that we may be on the brink of a healthcare crisis. The lack of research on ZIKV in the over 60 years that we have known about it has left us with little in the way of starting points for drug discovery. Our response can build on previous efforts with virus outbreaks and lean heavily on work done on other flaviviruses such as dengue virus. We provide some suggestions of what might be possible and propose an open drug discovery effort that mobilizes global science efforts and provides leadership, which thus far has been lacking. We also provide a listing of potential resources and molecules that could be prioritized for testing as in vitro assays for ZIKV are developed. We propose also that in order to incentivize drug discovery, a neglected disease priority review voucher should be available to those who successfully develop an FDA approved treatment. Learning from the response to the ZIKV, the approaches to drug discovery used and the success and failures will be critical for future infectious disease outbreaks.

In the search for treatments for the Ebola Virus, multiple screens of FDA drugs have led to the identification of several with promising in vitro activity. These compounds were not originally developed as antivirals and some have been further tested in mouse in vivo models. We put forward the opinion that some of these drugs could be evaluated further and move into the clinic as they are already FDA approved and in many cases readily available. This may be important if there is a further outbreak in future and no other therapeutic is available.

The current Ebola virus epidemic may provide some suggestions of how we can better prepare for the next pathogen outbreak. We propose several cost effective steps that could be taken that would impact the discovery and use of small molecule therapeutics including: 1. text mine the literature, 2. patent assignees and/or inventors should openly declare their relevant filings, 3. reagents and assays could be commoditized, 4. using manual curation to enhance database links, 5. engage database and curation teams, 6. consider open science approaches, 7. adapt the "box" model for shareable reference compounds, and 8. involve the physician's perspective.