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.