The fact that relatively small changes in genetic information can have enormous effects on virus properties is due to the secondary structure of the genome sequences. The genome sequences of coronaviruses consist of RNA (ribonucleic acid), i.e. single-stranded chains of nucleotides in a row. The individual nucleotides can interact with one another, even if they are not directly adjacent in the chain. This creates structural elements, such as hairpin-shaped paired strands or loops, which can be essential for the replication of the virus. »Changes in the nucleotide sequence can lead to changes in the secondary structure which, in turn, can affect its functionality«, explains Kevin Lamkiewicz.
The bioinformaticians at the University of Jena have created partial alignments for SARS-CoV-2 and all known coronaviruses (including HCoV-229E) for the genome segments that are important for the formation of RNA secondary structures. Their results have been added to the »Rfam« database. The partial alignments can now be accessed by experimental research teams around the world to see whether these structures can be used as starting points for treatments.
Complete virus genome is supplied by mini sequencing device
Needless to say, the genome sequences of viruses can only be studied if the viruses are known in the first place. And that’s exactly what the bioinformaticians are working on at the University of Jena. Since March, they have been working regularly with researchers from the University Hospital to sequence samples from COVID-19 patients as part of the national NFDI4Microbiota consortium. They’ve been using the MinION system, a small mobile sequencing device that is hardly bigger than a USB stick and can be connected to a laptop or PC (see photo above).
This is an established piece of sequencing technology at the University of Jena. The MinION system is not only conveniently small and easy to use; Sebastian Krautwurst, a doctoral researcher working on the project, explains some of its additional practical advantages over previous sequencing methods: »On the one hand, we can now sequence entire genomes at once, whereas previous methods usually only supplied partial sequences that subsequently had to be pieced together«. On the other hand, the mini sequencer enables the direct analysis of RNA – in the past, it first had to be transferred to DNA.
When sequencing with the MinION device, individual DNA or RNA strands are pulled through tiny tunnels known as »nanopores«. Changes in the flow of electric current are measured as the individual nucleobases (adenine, guanine, cytosine, thymine or uracil) pass through the pore. The changes are specific for each base, enabling the subsequent determination of their exact sequence.
Sebastian Krautwurst and his colleagues have already sequenced different strains of HCoV-229E and transmissible gastroenteritis virus (TGEV), and they are now turning their attention to the sequencing of SARS-CoV-2 samples.
By Ute Schönfelder