Machine learning methods accurately predict host specificity of coronaviruses based on spike sequences alone

Kuzmin, Kiril; Adeniyi, Ayotomiwa Ezekiel; DaSouza, Arthur Kevin; Lim, Deuk; Nguyen, Huyen; Molina, Nuria Ramirez; Xiong, Lanqiao; Weber, Irene T.; Harrison, Robert W.

Coronaviruses infect many animals, including humans, due to interspecies transmission. Three of the known human coronaviruses: MERS, SARS-CoV-1, and SARS-CoV-2, the pathogen for the COVID-19 pandemic, cause severe disease. Improved methods to predict host specificity of coronaviruses will be valuable for identifying and controlling future outbreaks. The coronavirus S protein plays a key role in host specificity by attaching the virus to receptors on the cell membrane. We analyzed 1238 spike sequences for their host specificity. Spike sequences readily segregate in t-SNE embeddings into clusters of similar hosts and/or virus species. Machine learning with SVM, Logistic Regression, Decision Tree, Random Forest gave high average accuracies, [Formula: see text] scores, sensitivities and specificities of 0.95–0.99. Importantly, sites identified by Decision Tree correspond to protein regions with known biological importance. These results demonstrate that spike sequences alone can be used to predict host specificity.