Environmental Sampling Working Group

Environmental sampling for SARS-CoV-2 is important because it allows us to better understand where and for how long the virus persists in the environment. This information will improve our understanding about transmission dynamics and risk mitigation. It also can help direct community testing, since resources are limiting and it's not possible to test every person every day.

These efforts are being organized by Drs. Jonathan Eisen and David Coil at the UCD Genome Center. Please contact us if you’re interested in chatting about these projects, becoming involved, etc. (jaeisen@ucdavis.edu, dcoil@ucdavis.edu)

Right now we are focused on three different topic areas. UCDMC Sampling, Wastewater and air filter sampling at UCD, and Viability detection of SARS-CoV-2. We are also involved in discussions regarding the scale-up of community testing before Fall quarter 2020 begins.

UCDMC sampling

female scientist sampling Two different projects in this space, the first was a pilot project (initiated by Dr. Angela Haczku) in collaboration with Drs. Stu Cohen, Tim Albertson, and Christian Sandrock. The actual sampling was done by Maya Juarez, Brandt Robinson, and Dan Tompkins. They collected 60 swab samples, (5 each from a hospitalist room, 5 from each of 2 resident rooms, and the remaining 45 from two patient rooms). Those samples were processed by Dr. Tracey Goldstein’s lab where they performed RNA extractions and qRT-PCR (work done by Alex Tremeau-Bravard). Some of those (positive) RNA extractions then went to Dr. Sam Diaz-Munoz at UCD for whole genome sequencing, which we hope to compare to the sequenced clinical isolate data. In addition, a few “duplicate” swabs went to Dr. Qizhi Gong at UCD to test a “quick” RNA isolation procedure and help get their lab up and running to do the qRT-PCR test for environmental sampling. 6 of the swabs (10%) were positive which is in line with published studies. All of the staff areas were negative, the positive samples were all found in the COVID19 patient rooms. The Illumina sequencing didn't produce sufficient viral sequence, so we plan to try a different protocol moving forward. The Nanopore sequencing was more successful, but still needs to be optimized for such low input RNA (compared to clinical samples). We obtained one almost-complete genome and are currently working to get the patient isolate genomes for comparison. Funding for this project was from a UCD CRAFT award to Drs. Jonathan Eisen and David Coil.

With the pilot data in hand we then undertook a much larger sampling project at the Medical Center, this time to include viability testing by cell culture in the BSL3 lab run by Dr. Satya Dandekar and Dr. Stefan Rothenburg (work done by Dr. Greg Brennan). We collected about 170 pairs of swabs through the Medical Center, including more outpatient areas this time. We collected again in the ICU and out on the floor... but collected from a non-COVID-19 patient room adjacent to a COVID-19 patient room. In addition we tried to collect more swabs from staff areas and from the floor/hallways which are a potential transmission risk between spaces. The 170 swabs are being processed for qRT-PCR as above, and any positive samples will be genome sequenced as well. Then the paired swabs from any positive will be cultured by the BSL3 lab which will give us information about how much infectious virus is actually present in these locations. Updates will be posted here. Funding is being provided by Dr. Angela Haczku and the UCD Medical Center.

A recent addendum (July 2020) to this work was the addition of air filter sampling at the Medical Center. Dr. David Coil collected air filter samples from the HVAC system of both a floor containing COVID-19 patients, and a floor without. These samples are currently being processed.

Wastewater sampling

wastewater This multi-faceted work is being led by Drs. Karen Shapiro, Heather Bischel, and David Coil. Dr. Bischel has started a pilot study in collaboration with the municipal wastewater treatment facility in Sacramento. The focus of this effort is wastewater surveillance for SARS-CoV-2 in the Sacramento area. In addition Drs Shapiro, Bischel, and Coil have received money from UCD to begin a surveillance program on campus, using both wastewater and air filter sampling. Wastewater sampling is going on around the country and the world and appears to be a great way to get community level data (in the absence of mass community testing, or perhaps as a way to direct community testing). Air filter sampling is similar in concept but is getting directly at the amount of virus present in the air within a building. Assuming we detect the virus, we would again do genome sequencing with Dr. Sam Diaz-Munoz. Wastewater sampling began at the start of August 2020 and air filter sampling began at the start of September. The plan is to have adequate baseline samples before students return to campus and then continue collecting through the entirety of Fall quarter to observe any changes and potentially use that information to direct individual testing. The wastewater sampling is being undertaken by Dr. Minji Kim and the air filter sampling by Dr. David Coil with help of the Facilities Department.

Viability detection of SARS-CoV-2

samples Drs Jonathan Eisen, David Coil, and Satya Dandekar received a CITRIS award to work on this topic. The idea is to use Propidium Monoazide (PMA) to detect viable SARS-CoV-2 virions under BSL2 conditions instead of the BSL3 required to do current viability assays. BSL3 work is much more complicated, risky, and should be conserved for clinical work. If PMA works, it would greatly expand the utility of other environmental sampling efforts (such as both above) since we would get information about viable virus, not just viral RNA. Validating this approach however, does need to take place under BSL3 conditions. The first round of these experiments was conducted in July 2020 and the results were difficult to interpret. Follow up control experiments are currently underway, including work with a non-pathogenic species of coronavirus. This is a collaboration with the University of Oregon (Dr. Kevin Van Den Wymelenberg, Patrick Horve, Leslie Dietz)