Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis Mechanisms of SARS-Related Coronaviruses

Yongjun Tan; Theresa Schneider; Matthew Leong; L Aravind; Dapeng Zhang

One possible mechanism is that, like the adenoviral CR1 proteins, it interferes with MHC molecules to 249 attenuate antigen presentation, resulting in ineffective detection of the virus by the host immune 250 system. Consistent with this, the SARS-CoV ortholog translocates to the ER (48) and its higher variability 251 indicates probable selection due to its interaction with a rapidly evolving host molecule. Notably information about the genomes that were used in this study, refer to Table S1 . 285 286 . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.977736 doi: bioRxiv preprint Similarity Plot of SARS-related CoVs against human SARS-CoV-2 Wuhan-Hu-1 genome (NC_045512.2) based on a multiple sequence alignment of the whole genomes. Each point represents a different slicing window size from the alignment with a different step size between each point. For each plot, the window size and step size are shown in the top left. Horizontal bars above the top plot correspond to the different open reading frames of the SARS-CoV-2 genome (NC_045512.2). Each different colored line corresponds to the nucleotide similarity between the human SARS-CoV-2 genome (NC_045512.2) and the respective SARS-related CoV genome. The red arrows and solid lines surround regions which display recombination within the SARS-related CoV genomes. The single red arrows point to specific regions of recombination.