ELLIS against Covid-19

A Rapid, International COVID-19 and Microbial Monitoring Network

ellis Chris Mason 01 April 2020 - 01 April 2020
01 April 2020 • 14:30 - 14:45

Chris Mason (Weill Cornell Medicine)

Chris Mason talks about his group's efforts studying the COVID-19 outbreak in New York City and the research they are conducting to better understand the spread of the virus. He presents the global MetaSUB consortium, which collects DNA and RNA samples all over the world and sequences them to compare the urban microbiomes and microviromes in different cities. He also describes their novel LAMP test, which can detect the SARS-CoV-2 virus in about 30 minutes at room temperature in a single test tube. They are planning to use this test in 'pop-up labs' in different US cities to test people in real time.


Question & Answers

Link to the recording of the live Questions & Discussion session for this talk. 

  • Q: Is it possible to observe a correlation between the prevalence of old coronaviruses in a population/area and the severity of the SARS-COV-2 outbreak? If so, might it help answer the question if having been infected by those common cold viruses improves the immune response?

    • A: Good question - we don't know yet but we are looking at this now.

  • Q: Why is the direct RNA sequencing with the minION so slow (1-3 days)?

    • A: It should be 0-2 days, but you normally run it for 48h and this includes analysis time.

  • Q: In Germany, a "Corona App" is in preparation (Robert Koch Institut) to identify infection chains. Data are anonymously collected. Is it foreseen/planned to use this data also as input for your project (predictive analysis)?

    • A: Yes, please!

  • Q: Is there a prevalent bacteria strain that is responsible for the pneumonia-related to COVID-19? Can one see that?

    • A: We will look for it, but don't know yet.

  • Q: Has someone worked on correlating altered host response using RNASeq to microbial profiling of lower respiratory tract mucosal layer. Does this infection affect the microbial niche?

    • A: We will look! Don't know yet.

  • Q: Do we have genome sequencing data of COVID-19 patients? Is it open source?

    • A: Pending - will be in dbGAP.

  • Q: Is there any difference in the diversity of RNA viruses in the different regions collected based on temperature, humidity etc and could that have a possible effect on why certain viruses spread in few areas than the rest? Would this be the same in case of SARS-CoV-2 as well? Also, have you looked at the RNA virus diversity between COVID patients of different severity? If yes, is the RNA virus diversity have any effect?

    • A: Just started to look - good questions!