Sequencing COVID19 Virus Genome By Johns Hopkins APL Biologists
From the Johns Hopkins Applied Physics Laboratory, biologists work to track the mutation of the virus that causes COVID-19, SARS-CoV-2.
The biologists from Johns Hopkins Applied Physics Laboratory, Peter Thielen and Tom Mehoke are now working on understanding the virus that causes COVID-19 as this new strain of coronavirus spreads across the globe.
These biologists, the members of the Johns Hopkins Center of Excellence in Influenza Research and Surveillance and of APL’s Research and Exploratory Development Department are now waiting to learn more about the rapidly spreading virus by studying more positive cases.
To conduct immediate on-site genome sequencing of SARS-CoV-2—the virus that causes COVID-19, Thielen and Mehoke are using handheld DNA sequencers, with the software and molecular biology approaches developed in part at APL.
Thielen said, “The evolution of the virus can be tracked using this information. It helps us to gain insights into how long transmission may have occurred undetected and a sense of where the new cases could have originated. We can get the information on how quickly the virus mutates, developing an effective vaccine and also integral information for mapping its spread.”
Thielen said it does not appear that
the virus that causes COVID-19 is mutating as fast.Thielen explained, “To start the process of developing a vaccine for the virus, the information from when the virus was first sequenced in China was helpful. Information on if the virus is mutating away from that original sequence or not and if it is, then how quick is it, can be gained from our research. Early data based on the mutation rate of the virus, it indicates that this would likely be a single vaccine.”
The mutations will inform how the virus is spreading, in the near-term.
The public health department can have another tool for evaluation by having the ability to understand how outbreaks are linked. Advice on what measures must be put in place in order to contain the virus can be obtained by understanding mutations as it can explain how long the virus may have gone undetected and the supposition that there are likely far more cases than diagnosed.
As scientists work to trace the source of the regional outbreaks of the virus, the sequencing of the virus’ genome is being performed all over the globe. For instance, the Bay Area outbreak in northern California has been linked to the Grand Princess cruise ship, which linked back to the virus found in Washington State, which likely came from China, and this information could be obtained by genome sequencing.
Thielen and Mehoke have completed the analysis of the first four COVID-19 samples’ from the Baltimore and Washington, D.C., regions, they will gain more virus genomes to sequence as in the coming weeks, they expect many more cases.
Before the results could be transferred, Thielen and Mehoke’s process required a several-day wait as they were operating remotely with handheld sequencers and laptop computers. However, they now have validated a new process that can be done by the hospital staff members already administering the diagnostic tests that enable same-day sequencing and faster results.
To help train scientists from low- and middle-income countries on how to use the handheld sequencers to do this work, Thielen and Mehoke held two workshops with the National Institutes of Health Fogarty International Center in the last nine months. Last week, stateside researchers were trained to do the same type of on-site sequencing in their own laboratories through a workshop held virtually.
Thielen said, “In the event that there would be a future pandemic, we were doing that to prepare as many researchers as we can. It is now, here.”
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Sequencing COVID19 virus genome
