COVID-19 originated in Bats
COVID-19 is a zoonotic virus, meaning that the virus originated in animals.
Our current understanding is that the current SARS-2-CoV originated from bats. This is because the COVID-19 virus looks like the bat coronavirus on histology, infects cells using the same ACE2 receptor mechanism, and has a genome similarity of 96% to the bat coronavirus from Rhinolophus sinicus.
This is more thoroughly described in Zhou et al. 2020. https://www.nature.com/articles/s41586-020-2012-7.
Zhou et al. describes that the spike protein, the protein that is needed for the coronavirus to infect human ACE2 receptors in the lungs, is highly divergent between bats in humans. In my opinion, this means that this spike protein mutated somehow, which led to this virus having the ability to infect humans. This is why scientists believe there was an intermediate host that harbored these bat coronaviruses before passing the virus to humans.
There is a lot of precedent for intermediate hosts for the human susceptibility of coronaviruses. The intermediate hosts were civets in the 2003 SARS virus and camels in the 2012 MERS virus.
The mystery intermediate host
My personal opinion is that the pangolin is the intermediate host for the current COVID-19 pandemic. This is because the pangolin coronavirus receptor binding domain of the S protein is virtually identical to the COVID-19 virus S protein – only one amino acid difference. https://www.biorxiv.org/content/10.1101/2020.02.17.951335v1
So, the current COVID-19 virus originated in bats, resided in pangolins where the virus took on the pangolin S glycoprotein and developed the ability to infect humans.
Pangolins are scaly anteaters near extinction which are poached and used in Chinese traditional medicine. Pangolin scales are dried and roasted and sold under the claim to stimulate lactation, drain pus, and relieve skin diseases. We know that ACE2 receptors are found in small intestine, so I believe the current COVID-19 pandemic came from consumption of these black market products
COVID-19 virus is NOT an engineered bioweapon
There are many speculations in the public media that the COVID-19 virus is an engineered Chinese bioweapon. Based on our understanding of the COVID-19 genome, we know that the spike protein is responsible for the transmission and infection to humans via the ACE2 receptor on lung alveoli cells.
The COVID-19 virus has developed new mutations in the spike protein genome that is fundamentally different from our past knowledge of how coronaviruses infected humans, such as from the 2003 SARS or 2012 MERS pandemics. This COVID-19 virus also has developed new protein cleavage mechanisms totally different from past coronaviruses, has random mutations throughout its genome, and has no common backbone to viruses we see in laboratory coronavirus strains.
Thus, it would be almost impossible to deliberately engineer the current COVID-19 virus.