The coronavirus is still a mystery for scientists. Lots of research has been done and still is, but so far, neither of the theories is exhaustive. At this point, the World Health Organization considers bats to be the source of SARS-CoV-2. Still, given the differences between it and the bat coronaviruses, they say that an intermediate host is to blame for the mutations and transmission.
Researchers say that SARS-CoV-2 is a combination of two SARS-like bat coronaviruses that originated in Rhinolophus sinicus and Rhinolophus affinis. The two species of bats belonging to the genus Rhinolophus of the family Rhinolophidae are commonly known as the horseshoe bat. They are the same origins of the 2002–2004 SARS outbreak.
Two of the viral nucleic acid sequences come from the Rhinolophus sinicus and have a resemblance of 80% to SARS-CoV-2, which is too small percentage to make it responsible for it.
A third viral nucleic acid sequence originated in Rhinolophus affinis was found to have a 96% resemblance to SARS-CoV-2. But the virus named RaTG13 isolated from bat R. affinis proved to be incapable of penetrating the human cell.
Researchers found out that the new coronavirus is the result of the combination of two viruses
Previously research linked SARS-CoV-2 to the pangolin, a mammal with ample keratin scales that Chinese and Vietnamese people use for medicinal purposes as well as for their edible meat, considered to be a delicatessen.
A virus with 99 % of genomic concordance with the SARS-CoV-2 virus was found in the pangolin. Unlike RaTG13, it can penetrate the walls of the human cell. Thus the pangolin can be considered the origin. But, a more recent study proved that the concordance between pangolin’s virus and SARS-CoV-2 is of only 90%, which is not enough to make it the origin.
So, neither of the viruses is the direct origin, but rather recombination between two of them. For that to be possible, the animal-host from which humans contacted it must have had them at the same time.
Which organism hosted the recombination, and under what circumstances did it pass it to humans is still unanswered.