The article mentions the state department had Steven Quay present an analysis of the origin of the virus: https://zenodo.org/record/4642956#.YIa66ehKhPY

The “engineered” component is about the Furin cleavage site on the sars-cov-2 spike protein.

The virus shares 92% genetic similarity to bat coronaviruses, except the spike protein, which is nearly identical to a pangolin coronavirus(which is otherwise only ~38% similar) with one key exception: The Furin cleavage site using “lab standard” sequences.

  The gene sequence for the amino acids in the furin site in CoV-2 uses a very rare set of two codons, three letter words so six letters in a row, that are rarely  used individually and have never been seen together in tandem in any coronaviruses in nature. But these same ‘rare in nature’ codons turn out to be the very ones that are always used by scientists in the laboratory when researchers want to add the amino acid arginine, the ones that are found in the furin site. When scientists add a dimer of arginine codons to a coronavirus, they invariably use the word, CGG-CGG, but coronaviruses in nature rarely (<1%) use this codon pair.  For example, in the 580,000 codons of 58 Sarbecoviruses the only CGG pair is CoV-2; none of the other 57 sarbecoviruses have such a pair.