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 are currently undertaking a much larger sampling project at the Medical Center, this time including 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 are collecting 200 pairs of swabs through the Medical Center, including more outpatient areas this time. We will collect before and after cleaning, possibly through a time series in a patient room, and a larger number of non-ICU locations. The 200 swabs will be 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.