Free COVID-19 testing for everyone who lives or works in Davis, and their households, is a primary strategy in Healthy Davis Together’s (HDT) approach to prevent the spread. With the recent global spread of the B.1.1.7 variant (which originally emerged and spread in the UK) the UC Davis Genome Center added genotyping of positive samples to the Healthy Davis Together testing protocol to detect the presence of any variants of concern – and in February identified and confirmed the first known case of the B.1.1.7 variant in the Sacramento region.
Routine, rapid turn-around testing provides critical data.
At the outset of HDT planning in Spring 2020, we knew mass testing at scale was needed to identify individuals who were infected and quickly mobilize quarantine support and contact tracing efforts. The gold standard testing approach, PCR clinical tests, was highly effective but its high cost prohibited rolling it out at scale. Instead, UC Davis Genome Center implemented the IntelliQube PCR System from LGC Biosearch Technologies to develop a relatively inexpensive, rapid turnaround, high throughput saliva direct COVID-19 test.
This instrument, designed for the high throughput genotyping used in genetic mapping studies, was adapted for SARS CoV-2 PCR testing. Instead of the uncomfortable nasal swab, this “spit test” uses saliva samples and is quick and painless. In the lab, we adapted our processing system using robotics and the IntelliQube tape array to process the samples more quickly and safely than traditional methods. This approach has allowed us to process over 200,000 tests citywide to date, identify and assist over 1,000 asymptomatic infected individuals, and build capacity to process 8,000 tests a day.
HDT encourages testing once to twice a week, and while signing up and getting the test is fast and easy (about 5 minutes once you are at a testing location), it’s still a significant commitment. We’re grateful to our neighbors and colleagues and we’re learning a lot about what motivates regular visits (more in a future post). It’s this system of routine data collection that makes monitoring for new variants possible.
How we built rapid genotyping and DNA sequencing into our process.
In recent weeks, much attention has been focused around the world on the evolution of new variants of SARS CoV-2 bearing mutations that are in some cases of clinical relevance to the spread and severity of COVID-19. It has become increasingly important to follow the spread of these variants around the world, including the variant B.1.1.7, which researchers have found is more contagious and predict will spread rapidly in the U.S., doubling in relative frequency approximately every 10 days.
The B.1.1.7 variant has a mutation in the receptor binding domain (RBD) of the spike protein at position 501, where the amino acid asparagine (N) has been replaced due to a single nucleotide change by the amino acid tyrosine (Y). The shorthand for this mutation is N501Y. This variant also has several other mutations, including the 69/70 deletion, which has occurred spontaneously multiple times and likely leads to a conformational change in the spike protein.
Because the IntelliQube PCR System HDT uses for routine testing was originally designed as a genotyping instrument, scientists at UC Davis Genome Center were quickly able to add rapid genotyping of all positive samples to our protocol. In our first week, whole genome sequencing of a sample identified through genotyping became the first known case of the B.1.1.7 variant of the SARS-CoV-2 virus in the Sacramento region. The virus sample contained the N501Y substitution and 69/70 deletion, two of the mutations associated with B.1.1.7.
Moving forward, all positive samples identified by the testing lab will be genotyped immediately for all currently known variants of concern. Samples of interest will also be sequenced.