Controlling the spread of the 2019 novel coronavirus SARS-CoV-2 and ensuring a return to 'normal' activities in a post-COVID world requires two complementary efforts: 1) Widespread availability of reliable and accurate testing at massive scale to identify and isolate those infected, and 2) Continued identification and monitoring of emerging variants of concern to identify and avoid spread of resistant or vaccine-bypassing strains.
During the height of the coronavirus pandemic, a group of leading experts came together to launch the Pandemic Response Lab (PRL) which was announced by NYC’s Mayor De Blasio in August 2020. The lab is a collaboration between Brooklyn-based Opentrons, a laboratory automation company, and scientists from NYU, Harvard, and beyond. PRL developed a novel platform for performing gold standard RT-qPCR COVID testing for upwards of 30,000 samples per day for the city of New York, with 24-hour turnaround time. We are now growing our footprint to new labs across the country to bring increased testing capacity where it’s needed most, as well as expanding our test capabilities to widespread surveillance of school children and businesses to allow safe reopening.
Most recently, we have further leveraged our scientific talent to rapidly develop a from-scratch high-throughput platform for COVID genome sequencing. The pipeline is low-cost and designed to be directly integrated into our PCR testing platform, such that we are capable of rapid turnaround of sequences within days of a positive test result. This platform is currently delivering over 1,000 COVID genomes per week within NYC, and we are scaling to an anticipated capacity of 10s of thousands per week very soon.
In this talk, I will discuss the origins and continued development of the PRL test and sequencing platforms, as well as some of the future vision for PRL in a post-COVID world.
1. What can the Ct value of a PCR-based test tell you about the collected specimen?
2. Explain the (current) primary goal of covid genome sequencing.
3. What are the pros and cons of using a PCR-based variant detection method vs. sequencing?