Introduction
Middle East respiratory syndrome (MERS) was first reported in Saudi Arabia in 2012 (1). By the end of November 2019, a total of 2494 laboratory-confirmed cases of MERS were reported globally, which include 858 associated deaths (case–fatality rate is 34.4%) (2). 84.2% of these cases were from Saudi Arabia (2102 cases, including 780 related deaths). 27 countries have been affected by MERS (2). The causative pathogen of MERS is MERS-related coronavirus (MERS-CoV) that infect humans and camels (3). Like Severe acute respiratory syndrome coronavirus-1 and -2 (SARS-CoV-1 and SARS-CoV-2) that caused outbreak of SARS in April 2003 and ongoing pandemic of coronavirus disease 2019 (COVID-19) in 2020, respectively, MERS-CoV is also a member of the genus β-coronavirus (4). MRES-CoV enters host cell by binding to cellular receptor dipeptidyl peptidase 4 (DPP4, also known as CD26) (5). The genome of MERS-CoV is a positive-sense, single-stranded RNA with the length of over 30,000 nucleotides (nt), which contains 10 predicted open reading frames (ORFs) flanked by untranslated regions at 5’- and 3’-ends of viral genome (named 5’-UTR and 3’-UTR, respectively). MERS-CoV encodes 2 replicase polyproteins (pp1a and pp1b), 4 structural proteins including envelope (E), membrane (M), nucleocapsid (N), and spike glycoprotein (S), and 4 non-structural proteins (6). Coding sequences of MERS-CoV, in particular those for RNA polymerase, N and S proteins have been well analyzed in phylogenetic analysis (7, 8) and used as targets in molecular diagnostic assay (9, 10). Non-coding sequence in the 5’- and 3’-UTR was less studied. Herein, the secondary structure and sequence conservation of 5’-UTR were focused in this report. We found two conserved pyrimidine nucleotides in the loop region of 5’-UTR stem loop 2 and explored its potential implication as a novel genetic signature in epidemiology.