So I had this thought and would like to hear other people's opinion.
I am usually working on plant genomics, so I know very little about virology or diagnostics. Also I'm not deeply familiar with the molecular aspect of lab work.
So, as far as I understand, one of the main efforts in current COVID19 outbreak is to do massive testing to detect cases. The main method used right now is (again AFAIK) RT-PCR, and health authorities have been making huge efforts to perform as many tests as possible. The method is fairly simple and quick, but the throughput isn't great - basically you have to test samples one by one (although I did hear suggestions that pooling could work).
What if we apply NGS for testing multiple samples at once? We could use some multiplexing method (e.g. as offered by iGenomX - can multiplex up to 960 samples) for pooling many samples together. The procedure could be something like:
- Collect samples
- Library prep - including creating cDNA, multiplexing and optionally PCR using some virus-specific primers
- Sequencing using short reads
- Alignment of reads to the virus reference genome to determine if it's present, per sample
Of course this would take much longer than RT-PCR, but I'm wandering if the higher throughput could be worth it. Additionally this method has the bonus that while we do testing we can also collect sequence information that can tell us about virus evolution and strain divergence.
I tried googling for such ideas, but only found this commercial option. Maybe it wasn't done yet because there are difficulties that I didn't think of...
What do you think? Can it work?