Normally "inserts" used in the manuscript are "indels" in protein alignments, short for insertions and deletions.
What I think has happened is a group investigating indels in HIV env noticed indels in 2019-nCov. Essentially I think the correlation is spurious - but I haven't test it, but the area of research in understanding indels is certainly valid and important.
What is certain is that indels induce a large structural change to a protein structure and any Gibbs free-energy style calculation will identify this.
The spike protein will be the primary candidate to make a 2019-nCov vaccine and that is a very important reason why the sequence was rapidly released. So it is an important protein and the structural changes indels induce mean that a SARS vaccine will probably not provide much protection against 2019-Cov, even apart from the amino acid divergence (below).
Differences 2019-nCov vs HIV
In summary, alot. HIV env and particularly HIV gag are very different from coronaviruses, both in the mechanism of genome replication, coronavirus never leaves the cytoplasm, clinical outcomes, tissue tropism and duration of infection.
HIV env and the glycoprotein spike of coronaviruses are the receptor binding protein to gain entry into a cell. They are called structural proteins. Entry to a cell can be blocked by antibodies and these antibodies are called "neutralizing antibodies". Neutralizing antibodies are catastrophic for a virus. Other antibody responses can be effective, such as IgM, but to clear an infection just using antibodies, you need neutralising antibodies. Both HIV env and the coronavirus spike protein are subject to neutralising antibodies. HIV gag has nothing to do with HIV env, in terms of function or antibody exposure. This is why the spike protein will be the primary vaccine candidate for a subunit vaccine.
Coincidence, law of chance
There is large variation of indels in HIV env within HIV and what the authors are inferring is there is a resemblence to that between SARS and 2019-nCov. In my opinion this is a coincidence, because they are comparing a large repertoire of HIV varients against a single indel pattern in the coronaviruses.
Why coronavirus indels?
That is a very good question. Generically indels in viral surface antigen genes are common, much more common in other proteins - such as those involved in virus replication (non-structural proteins). The amino acid identity between SARS and 2019-nCov is 80%, and in any virus, such as flaviviruses 80% identity means indels will be present in surface antigens between the viruses. The answer is it is not unusual in any RNA virus to see indels at a comparatively large amino acid divergence.
What function could they serve
I've briefly looked at indel bioinformatics between flaviviruses (Zika virus, yellow fever virus etc..) notably using envelope (E) protein sequences, and they also occur between African Zika viruses in the E-protein. E-protein being the equivalent of coronavirus spike protein, the receptor-binding protein. No-one has ascribed a function to them and that is the problem with this manuscript.
- One theory is that a structural change in the protein will occur to stop antibody binding.
- Another theory is they have functional differences, such as cell tropism
Bioinformatically separating the two theories is extremely hard without wetlab experimentation.