"In 2020, Corman et al. (2020b) reported RdRP, E and N genes for the detection of the novel coronavirus (Table 2). The bioinformatic analysis of the probes designed to identify the novel coronavirus was evaluated by BLAST search. The designed probe located in N gene (N_Sarbeco_P1) illustrated a lot of cross-reactions with Coronavirus BtRs-BetaCoV (MK211374- MK211378), SARS coronavirus Urbani (MK062179-MK062184), Bat coronavirus (KY770858-KY770859), SARS coronavirus (AH013708-AH013709), and others. The designed probe located in E gene (E_Sarbeco_P1) also indicated some cross-reactions with Coronavirus BtRs-BetaCoV (MK211374- MK211378), SARS Coronavirus Urbani (MK062179-MK062184), Bat SARS-Like Coronavirus (KY417142-KY417152), Bat Coronavirus (KY938558), and many others. Two designed probes located in RdRP gene were also appraised. The first one (RdRP_SARSr-P1) covers many coronavirus isolates, including Bat SARS-like Coronavirus (MG772904-MG772932), Rhinolophus pusillus Coronavirus (KY775091), Bat SARS-like Coronavirus (MG772903) and many others; because degenerate bases like W, R, and M nucleotide codes were used to design probes. The second probe (RdRP_SARSr-P2) was more specific for COVID-19 and could not detect the other human coronaviruses, with the exception of Rhinolophus Bat Coronavirus BtCoV (KP876546.1), as reported in 2016. All these cross-reactions are associated with the sequences, as mentioned in papers published in 2018 and before."
COVID-19 target: A specific target for novel coronavirus detection