Office of Research

A: More tests are needed but in the best-case scenario, it would be months, hopefully. Most of these drugs are available.

A: This is a great question. These are the next maps that we are going to be creating. SARS-2. vs SARS-1, vs other coronaviruses to try to get the underlying biology behind why SARS-1 and SARS-2 are so much more deadly than other, more common coronaviruses.

A: No, they did not. These compounds are being tested in laboratories around the world on two different continents to see what effects they have on human cells and primate cells. Promising candidates would be tested using ferret and hamster models and then hopefully transitioned into humans. The best-case scenario would be to have these ready in several months.

A: Dr. Nevan Krogan has it. Email him at [email protected] for more information.

A: This is not well understood yet. See Science journal article on this topic. 

A:  SARS-CoV-2 sequencing work that we and others are doing will allow us to detect and study genetic mutations in the virus and how they change over time. This viral genomic data is available from multiple groups around the world on nextstrain.org.

A: They are randomly distributed throughout the entire genome.

A: Genomic surveillance can enable us to track origins of the different lineages of SARS-CoV-2 circulating in the community. Usually just a couple of mutations (single nucleotide variants) in the genome are enough to define a cluster.

A: Many types of respiratory specimens can be evaluated- endotracheal aspirate works particularly well.

A: PCR sensitivity varies based on specimen type. Limited data from studies of other coronaviruses suggest that a combined nasopharyngeal + oropharyngeal swab may have greater sensitivity (~85%) than nasopharyngeal swab (~75%) or oropharyngeal swab (65%) alone.  False negative results may result in an underestimation of true cases.

A: Several serologic assays have become commercially available in the past week that will aid in seroprevalence studies.  These assays have not yet been rigorously validated for sensitivity/specificity but those data should become available soon.

A: Per CDC: "The immune response to COVID-19 is not yet understood. Patients with MERS-CoV infection are unlikely to be re-infected shortly after they recover, but it is not yet known whether similar immune protection will be observed for patients with COVID-19, nor for how long such protection would be active."

A: We haven't had a chance to look at people yet that are convalescent and re-exposed - that's definitely in the works! We're getting studies together to do longitudinal tracking to profile this as well.

A: Much better would be identifying relevant antibody sequences from patients that have recovered and manufacturing those at scale. DARPA is funding this effort (project FIREWALL / funding opportunity) through various partners - in lieu of a vaccine it would confer temporary protection. Plasma transfer is possible but variable quality, expensive, not scalable.  

A: See recent paper. TMPRRS2 is definitely a candidate target that is currently being looked at among other targets. Experts would argue that combination therapy has the best chance to inhibit virus replication reducing toxicity and preventing virus reversion. Similar to therapies used against HCV and HIV. 

A: A collection of labs are assembling a rapid-translation pathway based on organoids and lung culture systems. Those include the Gordon, Roose, Ott, Krummel, and Looney Labs. For information about plugging in to the program/platform, please contact [email protected] and/or reply to the survey at: https://app.smartsheet.com/b/form/0b6a4950f68f45719833590d941137b8.

A: Such sample data will serve as a possible clue as to what might have predisposed them to ARDS. For this, we think it is better to get material as early as possible and collect longitudinally. This is a goal of the newly initiated COMET program. If you are interested in that, a survey for proposals and ideas to use the project and data is found here and a site for faculty and trainee volunteers/redeployments is here.

A: Yes. The COVID-19 Multi-phenotyping for Effective Therapies (COMET) Clinical Study and the ImmunoX COVID-19 rapid path to discovery work ([email protected]) will be able to explore differences relative to patient presentation and symptoms.

A: Any adult anywhere can participate.  Use the normal website: https://covid19.eurekaplatform.org or text “COVID” to 41411.They are collecting medication data now and definitely plan to analyze.

A:  The curious thing is that there is no vaccine for SARS that has been around for about 17 years. Is it because there is not enough effort or is it something else? We will find out eventually. Below are at least some of the vaccine efforts on-going:

• Univ Oxford, ICL and Advent (Italy) adenoviral ChAdOx1 nCoV-19 (trial starting now)
• Moderna (RNA-based) (trial starting at NIH now) - Safety and Immunogenicity Study of 2019-nCoV Vaccine (mRNA-1273) to Prevent SARS-CoV-2 Infection - https://clinicaltrials.gov/ct2/show/NCT04283461?term=mRNA-1273&draw=2&rank=1
• Inovio (DNA-based) (trial to start in April)
• Univ Queensland (viral protein)
• Clover Bio (China) Covid-19 S-trimer (with GSK adjuvant)
• Sanofi working with NIH Biomedical Advanced Research and Development Authority (BARDA)

A: All work with SARS-CoV-2 must be performed under Biosafety Level 3 (BSL3) containment. To work with the virus at UCSF you must have access to a BSL3 facility, and you must have an approved Biological User Authorization that describes all experimental procedures and biohazard mitigation. In a matter of days, appropriately approved researchers will be working with SARS-CoV-2 under aerosol Biosafety Level 3 containment at UCSF.

A: Active (part of pre-existing ARDS study); we believe at least 1 COVID-19 patient has been enrolled in the MSC study.

A: We are not aware of any studies of AAT in COVID-19, but some proteomics studies have been proposed and samples collected as part of multicenter trials may be available for testing specific hypotheses.

A: We are still learning about the impacts of this infection on the human body. This article speaks to an aspect of this.

A: At this time, we do not have information available about the impact of COVID-19 on newborns of infected women. In prior outbreaks of coronavirus such as SERS and MERS, pregnant women had more severe disease and adverse pregnancy outcomes. It is possible that there are long term psychiatric effects on offspring. There is epidemiologic evidence, after the 1918 influenza pandemic, for example, of increased risk for schizophrenia in children born to women exposed to influenza. There is similar evidence for exposure to other viral infections and animal models suggest that this may be causal. However, I am not aware of long-term follow-up for SARS or MERS specifically.

The PRIORITY study is a nationwide registry run by UCSF/UCLA investigators that aims to understand the impact of COVID-19 on pregnant and postpartum women and their newborns. (Priority.ucsf.edu)

A: Please see this news release from NIH: "The virus that causes coronavirus disease 2019 (COVID-19) is stable for several hours to days in aerosols and on surfaces, according to a new study from National Institutes of Health, CDC, UCLA and Princeton University scientists in The New England Journal of Medicine.”

A: Quite good. There obviously is a range but the median incubation period to symptoms is 5.2 days, and you’re PCR positive 24-48 hrs before. The range is because there’s a range of incubation periods with the 95% confidence limit out to 14 days.

A: Exactly.  Reported cases will increase as testing becomes more available. It’s hard to adjust for that, so we use hospitalizations as a number that’s less likely to be sensitive to testing availability.

A: Great questions, and one that should be in high school calculus books. It’s not the same area under the curve, there are actually fewer cases.

A: The New York Times article (https://nyti.ms/2QNTXzH) data reference is https://covidtracking.com/data/.

A: We’re never going to have much in the way of population-level immunity. After this wave, it should be around 0.5-1.5%. We’ll have to protect the population in other ways, like aggressive contact tracing and supervised isolation and quarantine.

A: No, not yet. Their data are not more contemporary than ours. We’re now using data from Italy.

A: Great question. It’s because unlike SARS and MERS, which attack the lower respiratory tract, SARS-CoV-2 attacks both the upper and lower respiratory tract. Because it’s replicating in the upper respiratory tract, it’s a lot easier to transmit. Of note, there are at least two other beta-coronaviruses that have been identified in bats that seem to be candidates for species cross-over.

A: If you might be such an investigator, please drop an email to rdoinfo.ucsf.edu.

A: There are a number of individuals who have expressed an interest in validating methods for PPE decontamination. Currently there are UCSF virologists who are beginning the process of culturing SARS-CoV-2. It will take a few days to establish viral culture protocols and the ability of individual research labs to participate in decontamination studies is limited, especially because all such experiments must be performed under Biosafety Level 3 (BSL3) containment. The initial step of efficacy testing would be to write a detailed protocol of the precise experiment that would be used to validate viral inactivation. Will virus be added to N95 respirators and viral culture be attempted from the respirator before and after decontamination? What are the exact details of the experiment(s)? The next step would be to identify a collaborator at UCSF with access to a BSL3 facility, but please keep in mind that researchers are just launching initial experiments with SARS-CoV-2 and may not have the necessary bandwidth to collaborate at this time.

A:  UCSF has a rich history of partnering with the Bio/pharma industry.  Over the last 5 years the IV office has developed 8-10 large programmatic partnerships between industry and UCSF supporting around 100 UCSF investigators; this includes preclinical basic research to translational research, and into to clinical trials.  Examples of large industry partners include: J&J, AbbVie, Pfizer, GSK, Genentech, Sanofi, Celgene, BSM, Amgen, Bayer, Daichi-Sankyo. Often these relationships are structured with win-win scenarios to create tangible assets with novel IP to progress into human clinical trials with shared rewards on a commercialized product. On occasion, these partnerships may be enhanced by partnering with other leading academic institutions with the industry partner.

In the fight against the COVID-19 pandemic there will be opportunities for UCSF investigators to partner with the Bio/pharma industry.  Investigators can visit the UCSF Innovation Ventures home page (https://innovation.ucsf.edu/) to learn about Bio/pharma partnering with the Office of Strategic Alliances, as well as other IV programs supporting UCSF PIs with ideas or discoveries that could lead to commercialization and patient benefit.

A: The Office of Research is working with the UCSF research community to develop a centralized process for collecting, reviewing and prioritizing research on COVID-19 research. Every effort will be made to facilitate meritorious research proposals.

A. The Office of Research is working with the UCSF research community to develop a centralized process for collecting, reviewing and prioritizing research on COVID-19 research to address these important issues. In particular, careful coordination of research activities with the clinical units that are caring for COVID-19 patients will be essential.

A: Research inquiries should be sent to the appropriate principal investigator or to [email protected].

A: The Open Proposal discussion forum (https://open-proposals.ucsf.edu/covid19) is meant to be an initial effort in this regard.  However, the Office of Research will be working to find effective avenues for collaboration and will communicate these on research.ucsf.edu.

STUDENTS

A: Graduate Division has created a Volunteer Page on the Student Success website with information and links for opportunities, and will keep it updated as volunteer needs change in the coming weeks.

Please note! Caring for yourself and your loved ones and focusing on your education must remain your top priorities, and there is no obligation to volunteer your time. If now does not feel like a good time for you to volunteer, wait. There will be other opportunities in the future.

Also: students who want to volunteer to help with personal services (such as child care) can sign up with SitterCity (https://campuslifeservices.ucsf.edu/familyservices/services/back_up_care). Jen Rosko, Director of Student Involvement & Programs in SAA’s Student Life unit can serve as a contact if students have questions about using the platform.

Clinical Research Coordinators (CRCs)

A: The Office of Research has been working with HR and Labor & Employee Relations to implement a central process for identifying available, qualified and willing CRCs to be redeployed to COVID-19 research activities.