key: cord-1013434-pwi42oj7
authors: Zandi, Milad; Fani, Mona
title: Target genes used for biosensor development in COVID-19 diagnosis
date: 2022-03-15
journal: Biosens Bioelectron
DOI: 10.1016/j.bios.2021.113924
sha: 3adc05506280214f3b64c0108a9304c42eef7edb
doc_id: 1013434
cord_uid: pwi42oj7

In a published review entitled “COVID-19 diagnosis —A review of current methods”, the authors considered hemagglutinin esterase as one of the structural proteins of SARS-CoV-2 and also they did not represent ORF3b, ORF9b, and ORF9c in SARS-CoV-2 genome structure. However, according to the scientific evidence, among coronaviruses only some betacoronaviruses (Embecovirus subgenera) contain HE, and the genome of most of the coronaviruses such as SARS-CoV-2, SARS-CoV, and MERS-CoV lack the HE gene. In addition, the genome of SARS-CoV-2 contains several accessory proteins ORFs including ORF3a, ORF3b, ORF6, ORF7a, ORF7b, ORF8, ORF9b, ORF9c, and ORF10.

In a published review entitled "COVID-19 diagnosis -A review of current methods", the authors considered hemagglutinin esterase as one of the structural proteins of SARS-CoV-2 and also they did not represent ORF3b, ORF9b, and ORF9c in SARS-CoV-2 genome structure. However, according to the scientific evidence, among coronaviruses only some betacoronaviruses (Embecovirus subgenera) contain HE, and the genome of most of the coronaviruses such as SARS-CoV-2, SARS-CoV, and MERS-CoV lack the HE gene. In addition, the genome of SARS-CoV-2 contains several accessory proteins ORFs including ORF3a, ORF3b, ORF6, ORF7a, ORF7b, ORF8, ORF9b, ORF9c, and ORF10.

Severe acute syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus that contains a single-stranded, positive-sense RNA as genome (Pal et al., 2020) . SARS-CoV-2 belongs to Coronaviridae family, this viral family is classified into four genera α-, β-, γ-and δ-coronavirus(2). Human coronaviruses belong to β-coronavirus and α-coronavirus genera (2). β-coronavirus genus has five subgenera including Embecovirus (HCoV-OC43, HCoV-HKU1), Sarbecovirus (SARS-CoV, SARS-CoV-2), Merbecovirus (MERS-CoV), Nobecovirus, and Hibecovirus (Decaro and Lorusso, 2020; Zandi and Soltani, 2021) . The SARS-CoV-2 genome encodes four structural proteins (Spike (S), Envelope (E), Membrane (M), and Nucleocapsid (N), about 16 nonstructural proteins (nsp1-16), and several accessory protein ORFs (3a, 3b, 6, 7a, 7b, 8, 9b, 9c, and 10) (Michel et al., 2020; Gordon et al., 2020; Thomas, 2021; Pyke et al., 2021) . Accessory proteins of SARS-CoV-2 such as ORF3b, ORF9b and ORF9c are essential as virulence factors during SARS-CoV-2 infection, although some of the accessory proteins are not important for replication.

All members of betacoronavirus from the Embecovirus subgenus have an additional HE gene which is located upstream of that encoding the S protein. HE is an integral membrane protein with a single TM domain and a relatively large ectodomain, which has the esterase core domain and a lectin subdomain acting as the RBD (Zeng et al., 2008) . This gene is suspected to be transferred from the influenza C virus to the Embecovirus subgenus through heterologous recombination (Llanes et al., 2020) .

There are three categories of diagnostic tests on the throat swab, nasopharyngeal swab, saliva, and blood samples have been commonly utilized to detect SARS-CoV-2 according to (a) virus detection via hybridization between sequence complementary to the target RNA genome, (b) antigen protein detection by the interaction of monoclonal antigen-specific antibody and virus antigen protein and (c) antibody detection by the interaction of recombinant antigen and target neutralizing antibody (Lim et al., 2021) . However, the development of biosensors utilizes these approaches to target SARS-CoV-2. The RNA genome of SARS-CoV-2 (ORF1ab gene, RNA-dependent RNA polymerase gene, S gene, N gene), specific antigen protein (S protein (S1 subunit/RBD)), and also neutralizing antibody (IgM, IgG) are preferred to use in developing biosensors for COVID-19 diagnosis (Lim et al., 2021) . We read with great interest a review by Yuce et al., entitled COVID-19 diagnosis -A review of current methods (Yüce et al., 2020) . In, the authors represented hemagglutinin esterase (HE) as one of the structural proteins of SARS-CoV-2, and stated hemagglutinin-esterase dimer, which acts as a potent mediator of attachment and destruction of sialic acid receptors on the host cell surface (Yüce et al., 2020) . However, according to the scientific evidence, among β-coronavirus only (β-coronaviruses of Embecovirus subgenera) contain HE, and the genome of other β-coronaviruses such as SARS-CoV, MERS-CoV, and SARS-CoV-2 lack the HE gene and they have no hemagglutinin-esterase glycoprotein (Zandi and Soltani, 2021; Shi et al., 2019; Crawford et al., 2020; Kumar et al., 2020) .

In addition, the authors did not represent ORF3b, ORF9b, and ORF9c in the SARS-CoV-2 genome structure in (Yüce et al., 2020) . ORF3b protein with 22 aa in length as an interferon antagonist, can suppress the induction of type I interferon, studies have shown that SARS-CoV-2 ORF3b inhibits interferon more efficiently than its SARS-CoV ortholog (Konno et al., 2020) . ORF9b, an alternative open reading frame within the N gene can suppress interferon type 1 production as a result of targeting mitochondria (Jiang et al., 2020) , Kreimendahl et al. presented that ORF9b forms a complex with a mitochondrial import receptor (Tom70) which this complex may modulate the host immune response (Kreimendahl and Rassow, 2020) .

ORF9c another accessory protein of SARS-CoV-2 can interfere with interferon signaling, antigen presentation and other immune and stress pathways (Lu, 2020; Andres et al., 2020) . ORF9c also interacts with Sigma receptors that are implicated in lipid remodeling and ER stress response (Redondo et al., 2021) . Thus, accessory proteins cannot use in developing biosensors for COVID-19 diagnosis.

SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells

Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 spike protein for neutralization assays

Novel human coronavirus (SARS-CoV-2): a lesson from animal coronaviruses

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70

SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is increased by a naturally occurring elongation variant

The mitochondrial outer membrane protein Tom70-mediator in protein traffic, membrane contact sites and innate immunity

Morphology, genome organization, replication, and pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Emerging biosensors to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): a review

Betacoronavirus genomes: how genomic information has been used to deal with past outbreaks and the COVID-19 pandemic

SARS-CoV-2 ORF9c: a mysterious membrane-anchored protein that regulates immune evasion?

Characterization of accessory genes in coronavirus genomes

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): an update

Replication kinetics of B. 1.351 and B. 1.1. 7 SARS-CoV-2 variants of concern including assessment of a B. 1.1. 7 mutant carrying a defective ORF7a gene

Sars-cov-2 accessory proteins in viral pathogenesis: knowns and unknowns

SARS-Coronavirus Open Reading Frame-8b triggers intracellular stress pathways and activates NLRP3 inflammasomes

Mapping the nonstructural transmembrane proteins of severe acute respiratory syndrome coronavirus 2

COVID-19 diagnosis-a review of current methods

Hemagglutinin-esterase cannot be considered as a candidate for designing drug against COVID-19

Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.