CoViT: Real-time phylogenetics for the SARS-CoV-2 pandemic using Vision Transformers

Real-time viral genome detection, taxonomic classification and phylogenetic analysis are critical for efficient tracking and control of viral pandemics such as Covid-19. However, the unprecedented and still growing amounts of viral genome data create a computational bottleneck, which effectively prevents the real-time pandemic tracking. We are attempting to alleviate this bottleneck by modifying and applying Vision Transformer, a recently developed neural network model for image recognition, to taxonomic classification and placement of viral genomes, such as SARS-CoV-2. Our solution, CoViT, places newly acquired samples onto the tree of SARS-CoV-2 lineages. One of the two potential placements returned by CoVit is the true one with the probability of 99.0%. The probability of the correct placement to be found among five potential placements generated by CoViT is 99.8%. The placement time is 1.45ms per individual genome running on NVIDIAs GeForce RTX 2080 Ti GPU. We make CoViT available to research community through GitHub: https://github.com/zuherJahshan/covit.