Conserved pyrimidine nucleotides indicate a genetic drift of human MERS-CoV from 2012 to 2019
The conservation of both sequence and secondary structure of 5’-UTR from 252 human MERS-CoV reported from 2012-2019 was evaluated by using LocARNA program (11, 12). 5’-UTR contains 287 nucleotides in length (according to NCBI Reference Sequence: NC_019843.3) and forms 5 conserved stem loop regions (SL1-5). We found 2 conserved pyrimidine nucleotides in the longest stem loop region-2 (SL2) of MERS-CoV 5’-UTR (Figure 1). These two conserved pyrimidine nucleotides flank 4 consecutive nucleotides UAAU in the loop of SL2 (Figure 1). According to the conserved pyrimidine nucleotides, human MERS-CoV can be re-genotyped into 3 types, i.e. UUAAUU, CUAAUU, and CUAAUC (referred to as U—-U, C—-U, and C—-C types, respectively). In human population, MERS-CoV displays a U to C genetic drift over 8 years period from 2012 to 2019 in Saudi Arabia (Figure 2A) and in a global scale (Figure 2B). The first detected MERS-CoV is U—-U type virus that persisted from April 2012 until June 2015. C—-U type virus then emerged in 2013 and persisted until 2016. C—-C type virus emerged in April 2015 and then soon became dominant in Saudi Arabia until 2019. Only this type virus was detected after October 2016.