Science magazine has a news article out that summarizes the situation nicely, they even address conspiracy theories. https://www.sciencemag.org/news/2020/01/mining-coronavirus-genomes-clues-outbreak-s-origins
According to Bedford’s analysis, the bat coronavirus sequence that Shi Zheng-Li’s team highlighted, dubbed RaTG13, differs from 2019-nCoV by nearly 1100 nucleotides. On nextstrain.org, a site he co-founded, Bedford has created coronavirus family trees (example below) that include bat, civet, SARS, and 2019-nCoV sequences. (The trees are interactive—by dragging a computer mouse over them, it’s easy to see the differences and similarities between the sequences.) Bedford’s analyses of RaTG13 and 2019-nCoV suggest that the two viruses shared a common ancestor 25 to 65 years ago, an estimate he arrived at by combining the difference in nucleotides between the viruses with the presumed rates of mutation in other coronaviruses. So it likely took decades for RaTG13-like viruses to mutate into 2019-nCoV.
So, right now we know that this coronavirus is very similar to bat viruses, but it remains unclear how it jumped to humans. Scientists suspect that the virus may have jumped to another animal first and identifying that intermediary species remains a big priority and challenge.In the absence of clear conclusions about the outbreak’s origin, theories thrive, and some have been scientifically shaky. A sequence analysis led by Wei Ji of Peking University and published online by the Journal of Medical Virology received substantial press coverage when it suggested that “snake is the most probable wildlife animal reservoir for the 2019‐nCoV.” Sequence specialists, however, pilloried it.