SARS-CoV-2 orf1b Gene Sequence in the NTNG1 Gene on Human Chromosome 1

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense single-stranded RNA virus. It is contagious in humans and is the cause of the coronavirus disease 2019 (COVID-19) pandemic. In the current analysis, we searched for SARS-CoV-2 sequences within the human genome. To compare the SARS-CoV-2 genome to the human genome, we used the blast-like alignment tool (BLAT) of the University of California, Santa Cruz Genome Browser. BLAT can align a user sequence of 25 bases or more to the genome. BLAT search results revealed a 117-base pair SARS-CoV-2 sequence in the human genome with 94.6% identity. The sequence was in chromosome 1p within an intronic region of the netrin G1 (NTNG1) gene. The sequence matched a sequence in the SARS-CoV-2 orf1b (open reading frames) gene. The SARS-CoV-2 human sequence lies within non-structural proteins 14 and 15 (NSP14 and NSP15), and is quite close to the viral spike sequence, separated only by NSP16, a 904-base pair sequence. The mechanism for SARS-CoV-2 infection is the binding of the virus spike protein to the membrane-bound form of angiotensin-converting enzyme 2 and internalization of the complex by the host cell. It is probably no accident that a sequence from the SARS-CoV-2 orf1b gene is found in the human NTNG1 gene, implicated in schizophrenia, and that haloperidol, used to treat schizophrenia, may also be a treatment for COVID-19. We suggest, therefore, that it is important to investigate other haloperidol analogs. Among them are benperidol, bromperidol, bromperidol decanoate, droperidol, seperidol hydrochloride, and trifluperidol. These analogs might be valuable in the treatment of COVID-19 and other coronavirus infections.

Keywords: COVID-19; NTNG1 gene; haloperidol; orf1b gene; the UCSC Genome Browser.

Figure 1. The 117-bp orf1b (your seq) gene sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in an intronic region of the human netrin G1 (NTNG1) gene on chromosome 1p is shown in the University of California Santa Cruz genome browser.

Figure 2. Side by side alignment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (upper sequences) and human chromosome 1p (lower sequences).

Figure 3. Οrf1ab genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), showing the 16 non-structural proteins (NSPs) and the viral spike. The human sequence is within NSP 14 and NSP 15 (arrow). The human sequence is separated from the spike by NSP16, a small sequence of 904 bases. The mechanism for SARS-CoV-2 infection is the binding of the virus spike protein to the membranebound form of angiotensin-converting enzyme 2 and internalization of the complex by the host cell.