High Throughput Testing for SARS-CoV-2 and SNP Analysis for Variants of Concern

As part of Healthy Davis Together, we have implemented rapid, inexpensive, high throughput testing for SARS-Cov-2 using technology repurposed from the agricultural biotechnology sector.  This is providing at least weekly testing for the campus and the City of Davis.   This may have contributed to the consistently low prevalence of Covid-19 in the community. The workflow involves testing saliva samples from asymptomatic individuals without RNA extraction; more than 4,000 samples are routinely processed per day with over 90% of results reported within the day after sample collection.  This throughput required the deployment of a superplex assay for N1 and N2.  One key step is treating the saliva with papain protease to reduce viscosity.  This has a sensitivity comparable to EUA approved tests of nasal swabs.  To date, we have processed over 400,000 tests and identified more than 1,700 positive individuals.  The IntelliQube qPCR machine is not the rate limiting step, which provides the opportunity for high throughput genotyping of all positive samples for variants of SARS-CoV-2.  Genotyping using SNPs that discriminate between known variants of concern is more efficient, less expensive, technically less demanding, and importantly much more rapid than sequencing.  It will not, however, discover new variants and is therefore complementary to sequencing.  In collaboration with LGC, we have developed and deployed SNP assays that can distinguish all the current variants of concern and interest.  All positive samples are assayed and genotypes assigned within a few days of sample collection.  Non-wildtype genotypes are validated by sequencing.  This provides rapid resulting to the county health authorities. Robust genotyping technology is available for monitoring large numbers of positive samples on a global scale; this will be particularly important in geographical areas where sequencing is not feasible.  The regulatory framework for this is more challenging than the technical aspects.

Learning Objectives:

1. What were the key elements to the development of high throughput testing for Sars-CoV-2?

2. How can SNP genotyping be used for rapid monitoring of variants of SARS-CoV-2?