ABSTRACT
A severe respiratory pneumonia COVID-19 has raged all over the world, and a coronavirus named SARS-CoV-2 is blamed for this global pandemic. Despite intensive research into the origins of the COVID-19 pandemic, the evolutionary history of its agent SARS-CoV-2 remains unclear, which is vital to control the pandemic and prevent another round of outbreak. Coronaviruses are highly recombinogenic, which are not well handled with alignment-based method. In addition, deletions have been found in the genomes of several SARS-CoV-2, which cannot be resolved with current phylogenetic methods. Therefore, the k-mer natural vector is proposed to explore hosts and transmission traits for SARS-CoV-2 using strict phylogenetic reconstruction. SARS-CoV-2 clustering with bat-origin coronaviruses strongly suggests bats to be the natural reservoir of SARS-CoV-2. By building bat-to-human transmission route, pangolin is identified as an intermediate host, and civet is predicted as a possible candidate. We speculate that SARS-CoV-2 undergoes cross-species recombination between bat and pangolin coronaviruses. This study also demonstrates transmission mode and features of SARS-CoV-2 in the COVID-19 pandemic when it broke out early around the world.