The rate of spread of a pandemic depends on two things: how many people each case infects, and how long it takes for the infection to spread between people. The former is the reproduction number, while the latter is the serial interval. Ebola, for example, has a serial interval of several weeks, while COVID-19 has a serial interval of only a few days. This short serial interval means emerging COVID-19 outbreaks will grow quickly and can be difficult to prevent from spreading.
By the end of March 2020, no country had tested more than ~3% of their population, and there continues to be massive variation regarding exactly how much testing has been done globally. This underscores the need for faster testing and results. The faster a test can be administered, the sooner results can be received, and the quicker measures can be put in place to mitigate further spread. But how can we test for COVID-19—and how do we make it faster?
Accelerating testing with automation
Technology—especially automation—can help. Automated systems are being used to speed up testing and minimize errors in sample handling by fast-tracking sample prep, an integral part of the workflow.
Researchers are using Agilent research equipment, such as the Bravo, for investigation of COVID-19 research, exploring the development of new technologies and data analysis tools, and generating new biological insights. Scientists have adapted the CDC protocol, which is designed to be performed manually at low throughput, so that it could be run on automated liquid handling machines. This has given some facilities the ability to process 2,000 samples a day, adding to the capacity of labs and reducing the time needed to turn results around from several days to several hours.
A Boston-based bioengineering company is synthesizing DNA to help detect coronavirus with the help of the Bravo, Agilent custom oligonucleotide libraries, and enzymes. They are also sharing the information freely with other researchers. Research groups in California are also using the Bravo to ramp up their COVID-19 efforts. The feedback so far is that the Bravo has become an integral part of the workflow by helping with automation. It continues to surpass their initial expectations of running 1,000 samples and is closing in on nearly 3,000 samples per day!
Bravo automates the process of transferring liquids from one container to another. While a person can only transfer one or a few liquid samples at a time, Bravo does 96 samples at once. This not only accelerates throughput, but also maintains precision and accuracy while helping employees avoid repetitive stress injuries.
Hand-in-hand with increased sampling comes the need for increased consumables. The Bravo instrument utilizes 96-well reservoir microplates designed and manufactured specifically by Agilent for automated liquid handlers. In fact, two major pharmaceutical companies in Europe are supporting government initiatives, and are relying on Agilent microplates for their automation protocols for COVID-19 efforts.
The role of qRT-qPCR technology
qRT-qPCR is a powerful and cost-effective detection method consisting of isolating the RNA and amplifying the cDNA (making millions to billions of copies of the DNA), the use of labeling reagents, an integrated instrument for amplification and detection of the targeted DNA, and a data analysis workflow. Agilent supplies key reagents used across the qPCR workflow, including the Absolute RNA kit (for isolating viral RNA), AffinityScript reverse transcriptase (for converting isolated RNA into DNA), Brilliant Master Mixes for amplification and labeling, and the Aria Mx/Dx qPCR instrument. These reagents and instruments are supporting researchers striving to better understand COVID-19.
Supporting the front line
In January, a research and manufacturing group, PrimerDesign, reached out to discuss an order for a AffinityScript reverse transcriptase, which is used for cDNA synthesis. Recognizing the critical need for this reagent and the growing threat of coronavirus, we agreed to expedite their request. The group developed their own kit, which is now one of the FDA-approved Emergency Use Authorization (EUA) kits and was also one of the first CE-IVD marked kits used in Europe.
On the amplification and detection side, a number of Agilent Brilliant III qRT-PCR probe kits are being used to create detection kits. Additionally, a company in Italy has released a CE-IVD kit for the detection of COVID-19, which is compatible with commercially available Real Time PCR systems including the Agilent AriaDx Real-Time PCR System.
Going beyond qPCR: microarray analysis of COVID-19
While quick, cost-effective, and straightforward, qPCR is not the only way to assay for viral RNA.
Several weeks ago, when the situation with COVID-19 began to hit critical mass, researchers reached out to see if Agilent could expedite a request to add coronavirus sequences on a microarray. The answer was a resounding, "Yes."
The team was able to add sequences to the array for not only the novel coronavirus, but for two other coronaviruses (MERS and SARS) as well. The design optimization process, which can sometimes take many months, took less than two weeks. Within 48 hours the microarrays were printed, shipped, and in their hands.
Speed remains a need
While COVID-19 cases are predicted to peak in the next several weeks, testing is—and will remain—a pressing need in order to manage the current pandemic and prevent its resurgence. More testing, faster results, and faster action are all necessary to not only help prevent the spread of COVID-19, but further understand and combat it.