Here at the UCSC molecular diagnostic lab
We conduct PCR tests on swab
samples to determine whether
the sample contains SARS-CoV-2
coronavirus, which causes Covid-19.
The MDL is a nonprofit testing
lab dedicated to assisting in
in areas of need, including
the uninsured or essential
workers, and serving the UC
Santa Cruz population.
Our goal is to facilitate a
return to education, learning
and research, and to support
economic and community recovery
The idea for this lab was built
in March 2020.
By May 1st, we received
approval from the state to start testing.
We test samples that we receive
From our partner medical providers.
Our partnerships are aligned
with our mission and commitment
we have partnered with
federally qualified centers
such as Santa Cruz community
health, and Salud Para La Gente
which serve all populations
including agriculture workers
homeless and low-income families
and with the county, to serve
emergency testing needs.
Through Santa Cruz County Public Health,
we are piloting testing with
several hospitals and organizations
essential for Santa Cruz's safety and recovery.
Our expectation is that we will
continue to provide such
emergency testing through the pandemic
Let's start with a few terms
A qPCR stands for quantitative
polymerase chain reaction and
is a technology used for making
copies of DNA and RNA.
By doing this, the quantity of DNA
or in this case, RNA, can be measured
testing on a qPCR device
is consistent with the Centers for Disease Control
or CDC approach.
In fact, our test is based on
the same principle as the CDC test
but uses different probes to detect the virus.
This assay builds on a qPCR
assay developed by Columbia University
and modifies it to use reagents
that are not used widely,
therefore, avoiding reagent supply problems.
The assay also uses automation
at every key step.
From RNA extraction, reagent dispensing, and qPCR.
An assay is a test of a
substance to determine its components,
and is frequently used to test
for the presence or concentration
of infectious patients.
Reagents are substances added
to a system to cause a chemical
reaction, or to test if a reaction occurred.
Through rapid innovations, the
MDL has been able to move
from the manual process shown,
to scale testing and return results
within 24-48 hours without
sacrificing sample integrity and quality.
Before entering the lab,
All personnel must wear
personal protective equipment
otherwise known as PPE.
and must be trained on
biosafety and protected health information.
The PPE required includes
N95 mask, lab coat, goggles, and gloves.
This is to protect the lab
staff and to ensure that there
is no contamination in the lab.
Any small amount of DNA from
from personnel can compromise
results and change effectiveness
of the testing.
The protected health information
training is directed to
ensuring patient privacy, and
is part of regulatory rules.
We use the robot to dispense
RNA shield, which is a reagent
that inactivates the virus
so that it is no longer a
threat to the labs, staff, or
anyone touching the sample.
RNA shield is able to provide
this protection while maintaining
the virus's genome.
That way, we can safely test
for the presence of the virus.
RNA shield is dispensed into
1.4 ml 2D pre-barcoded tubes.
Etched barcodes allow us to
process samples in a high-
throughput manner to instantly
know which samples are coming
back to us.
The test kits are built in
house, in our lab. The kits
can be assembled in minutes
using our Agilent Bravo, which
is a 96-well liquid handling
robot. Which can very
accurately dispense liquid.
The kits include tubes, filled
with RNA shield, racks, and swabs.
Once kits are assembled,
they are sent to providers to
collect patient samples.
The providers take one of these
tubes and scan the tube's
barcode to register the patient
The swab will then be conducted
And they return the kits to us by courier.
Once the kits arrive back at our campus,
they are brought to the lab and
Sterilized in an oven at 70
degrees Celcius.
This is a safety measure
designed to ensure that the
virus is deactivated and the
genomic material is maintained
Once the kits are sterilized,
they are inserted into a barcoded rack
which is placed on a scanner
Then up to 96 tubes can be scanned all at once.
The scanner automatically
registers and uploads their data
into our laboratory information management system
Also known as the L.I.M.S
The L.I.M.S tracks all samples
scanned all at once
checking for personal health
information to be sure it matches
Because of this automation, we
have been able to scale up in
order to process many patient
samples all at once.
Once samples are registered,
we can begin our automated workflow
to extract the samples RNA material.
This is when we begin the
process of the qPCR assay
PCR is able to exponentially
amplify the virus, so that it
Can be detected even if present in low quantities.
Our assay can detect less than
a single viral genome per microliter
of swab material.
To build this assay, we took
primer and probe sequences that
recognize SARS-CoV-2
developed by Columbia University
We then modified the RNA
extraction method and reagents
to avoid reagents that are in limited supply.
Finally, we implemented the
assay in a 96-well plate format
so that 93 samples and 3 controls
can be processed simultaneously using our robots
Once those samples are run on a
thermocycler, the data is outputted.
We load a positive control to
ensure that the reagents are
working as planned, and we can detect the virus.
Whether a sample reaches that
threshold or is below that threshold
determines whether the patient is positive.
In this image showing data output,
there are 3 wells highlighted
depicting one particular sample
In this case, RP is the internal control
that tells us that we collected enough material.
N1 and N2, which are the purple
and fuchsia colors, measure the presence of the virus
N1 and N2 are amplified in this
sample, indicating that the patient has covid.
A clinical laboratory scientist
will review the data output,
and assign a result to every sample.
In addition to detected and
not detected results,
The sample can be of poor quality
and the result will be reported
as quality unsatisfactory
Another type of result is inconclusive
when we cannot tell when the virus is present or not.
This could happen if the virus
is present at a minuscule level
or the patient has another virus
that is very similar to SARS-CoV-2
usually if samples come back positive,
the patient is notified within 24 hours
All results are returned to the provider
within a 24-48 hour time frame
Our expanded testing capacity
has been made possible in part
through funding from the Coronavirus Aid
Relief and Economic Security act,
support from Santa Cruz County
Citris, and philanthropic individuals.