We then translated the aligned genome and found that these inserts are present
in all Wuhan 2019-nCoV viruses except the 2019-nCoV virus of Bat as a host
[Fig.S4]. Intrigued by the 4 highly conserved inserts unique to 2019-nCoV we
wanted to understand their origin. For this purpose, we used the 2019-nCoV
local alignment with each insert as query against all virus genomes and
considered hits with 100% sequence coverage.

Surprisingly, each of the four inserts aligned with short segments of the Human
Immunodeficiency Virus-1 (HIV-1) proteins. The amino acid positions of the
inserts in 2019-nCoV and the corresponding residues in HIV-1 gp120 and HIV-1
Gag are shown in Table 1. The first 3 inserts (insert 1,2 and 3) aligned to
short segments of amino acid residues in HIV-1 gp120. The insert 4 aligned to
HIV-1 Gag. The insert 1 (6 amino acid residues) and insert 2 (6 amino acid
residues) in the spike glycoprotein of 2019-nCoV are 100% identical to the
residues mapped to HIV-1 gp120. The insert 3 (12 amino acid residues) in 2019-
nCoV maps to HIV-1 gp120 with gaps [see Table 1]. The insert 4 (8 amino acid
residues) maps to HIV-1 Gag with gaps.

Although, the 4 inserts represent discontiguous short stretches of amino acids
in spike glycoprotein of 2019-nCoV, the fact that all three of them share amino
acid identity or similarity with HIV-1 gp120 and HIV-1 Gag (among all annotated
virus proteins) suggests that this is not a random fortuitous finding. In other
words, one may sporadically expect a fortuitous match for a stretch of 6-12
contiguous amino acid residues in an unrelated protein.  However, it is
unlikely that all 4 inserts in the 2019-nCoV spike glycoprotein fortuitously
match with 2 key structural proteins of an unrelated virus (HIV-1).

https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf
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