key: cord-319578-n1ee1688
authors: Kakhki, Reza Kamali; Kakhki, Mohammad Kamali; Neshani, Alireza
title: COVID-19 target: A specific target for novel coronavirus detection
date: 2020-05-30
journal: Gene Rep
DOI: 10.1016/j.genrep.2020.100740
sha: 
doc_id: 319578
cord_uid: n1ee1688

An ongoing outbreak of pneumonia associated with a novel coronavirus has been reported worldwide and become a global health problem; hence, the diagnosis and differentiation of this virus from other types of coronavirus is essential to control of the disease. To this end, the analysis of genomics data plays a vital role in introducing a stronger target and consequently provides better results in laboratory examinations. The modified comparative genomics approach helps us to find novel specific targets by comparing two or more sequences on the nucleotide collection database. We, for the first time, detected ORF8 gene as a potential target for the detection of the novel coronavirus. Unlike previous reported genes (RdRP, E and N genes), ORF8 is entirely specific to the novel coronavirus (COVID-19) and has no cross-reactivity with other kinds of coronavirus. Accordingly, ORF8 gene can be used as an additional confirmatory assay.

Coronaviruses are enveloped positive-sense RNA viruses belonging to the family Coronaviridae and the order Nidovirales spread among humans and animals (Richman, Whitley, & Hayden, 2016) . Although most of the coronavirus species (e.g., 229E, OC43, NL63, and HKU1) cause common cold in humans, some other species such as the Middle East respiratory syndrome coronavirus (MERS-CoV) and the severe acute respiratory syndrome coronavirus (SARS-CoV) cause severe respiratory diseases with mortality rates of 37% and 10%, respectively (MERS-CoV; Organization, 2003) . The World Health Organization (WHO) announced the outbreak of another coronavirus in China at the end of 2019 and named this novel coronavirus (COVID-19), which is currently a worldwide pandemic (Organization, 2020) . The increasing cumulative incidence of different coronavirus genotypes throughout many countries poses a challenge to the public health laboratories in terms of diagnostic. Although molecular methods such as RT-PCR and real-time PCR are among the most common procedures in detecting coronavirus, the use of specific targets still is the first critical step in the accurate diagnosis of the agent. Bioinformatics analysis can assist in the identification of specific targets based on genetic diversity. The present study aimed to introduce a novel specific target and evaluate the known target genes in order to analyze COVID-19 bioinformatically.

In this study, COVID-19 novel target was detected using the modified comparative genomic analysis (Kakhki, Najafzadeh, Kachuei, & Ghazvini, 2020; Kakhki et al., 2019; Neshani et al., 2018) . The genome of Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1 (NC_045512) was considered as reference strain and compared with the other types of coronavirus isolates. The gene exhibiting less cross-reaction with the other coronaviruses was considered as the conserved sequences of COVID-19. Then the primers and a probe were designed by Primer Premier Software version 5.0 (Premier Biosoft Intl., CA USA), and then the secondary structures and the predicted melting temperature were checked. Afterwards, the specificity of the primers was determined bioinformatically using BLAST software for all databases to check any cross-reactivity with other bacterial or human genomes. Furthermore, we analyzed the targets, primers, and probes, which were introduced previously (V.

M. Corman et al., 2020) for the detection of the novel coronavirus using the Basic Local Alignment Search Tool (BLAST) search.

Coronavirus, as published in 2019 and 2020 using Primer-BLAST (https://www.ncbi.nlm.nih.gov/tools/primer-blast/). We also designed a specific probe (K_COV-P1) for the novel Coronavirus to differentiate COVID-19 from all other human coronaviruses.

The location and characteristics of the designed primers and probe are illustrated in Figure 1 and 

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