The central theme of this article is that this virus is very similar to something else, so it's man-made. Then this virus is very different than other coronaviruses, so it's man-made. It's very confusing as to what their logic is...
I have some expertise on the so-called "rare codons", discussed in their article. Firstly, a bit of background. We all know that proteins are the work horses of biological systems. Protein amino acid sequences are encoded by DNA/RNA. Within a genome, a 3-base pair DNA sequence is called a codon and encodes an amino acid. However, this correlation is not unique. Many times, multiple kinds of 3-base pair DNA sequences can encode the same amino acid. Hypothetically, a DNA codon of "ABC" encodes an amino acid of alanine. Another DNA sequence of "XYZ" can also encode alanine. Then "DHK" combination can also encode alanine. So the amino acid alanine has 3 codes: ABC, XYZ and DHK. In the natural biological world, the chances of these 3 codes are not equal. Again hypothetically, in 60% of living species, you will find the combination of ABC coding alanine. In 39% of living species, you will find XYZ coding alanine. Only in 1% of living beings, you will see DHK coding alanine. This "DHK" is then considered as a "rare codon".
"rare codons" are usually used by cells to suppress/limit the production of certain proteins. DNA is translated to RNA, then to proteins, by a complex machinery. This process of called transcription/translation. When you have "common codons", commonly found machines can be used to finish this process. When you have "rare codons", cells typically have very limited machinery that can recognize these weird DNA sequences, thus making the DNA-RNA-protein process more difficult. It's like someone writes a book using Hebrew. How many people can read Hebrew? How do you expect your book to be popular when no one knows what you are saying? This is what "rare codons" are. We hate "rare codons" in research because these weird sequences make every step of any experiment slow and difficult. Like every other profession, time is money. We need things to move along fast to produce data fast, so that we can publish and get funding. This is why there is a whole industry out there that aims to help researchers to convert all their natural "rare codons" to common codons. This is called codon optimization.
Now, this article actually says that they found a lot of "rare codons" coding the spike protein of SARS-CoV-2. Normally, this is actually a sign that no one has messed with it. As I mentioned above, researchers hate "rare codons". Whenever we want to work on a genome, we actually want to change them to common codons, as in "codon optimization". Companies charge us money to do that. But now, the authors of this article actually claim that these "rare codons" are evidence of human involvement??? This makes no sense whatsoever. Why would anyone use these weird DNA sequences on purpose, when they can easily use the common ones to achieve the same results (making the exact same proteins), but faster and cheaper? This article has no real evidence at all. Just speculations after speculations after speculations. No wonder they couldn't get it published anywhere. I would reject it outright if I were asked to review the manuscript.