MERS-CoV nucleic acid and antibody prevalence
The nasal swab of one sheep (1.8 %) repeatedly tested positive for
MERS-CoV nucleic acid by RT-qPCR (Ct values 32.5-34.8; Table 1), and the
nasal swab of one goat tested borderline positive (Ct values 38.1-39.4;
Table 1). The positive sheep was a two-year-old female, presumably
locally raised Nuaimi breed. It was kept in a pen at the market used for
sheep only, which was the second closest pen to the camel area
(approximately 25 m away; Fig. 1, Supplementary Table 1). The borderline
positive goat, a one-year-old locally raised male Omani goat, was kept
in one of the pens directly adjacent to the camel pens, with only
approximately 20 m between them (Fig. 1, Supplementary Table 1).
The RT-qPCR-positive sheep sample was confirmed by two different
RT-PCRs. The obtained sequences [lengths without primer sequences:N – 293 bp (GenBank acc. number: MZ558082), ORF1b –
341 bp (GenBank acc. number: MZ558083)] were >99 %
identical to many MERS-CoV sequences belonging to clade B, lineage 5
[according to the classification by , including human and camel
strains from the UAE, Saudi Arabia, South Korea, Jordan, Qatar, and the
United Kingdom. Unfortunately, we were not able to uncover the complete
MERS-CoV genomes using NGS; however we succeeded to establish the
complete N gene sequences of the virus-positive sheep and five
selected MERS-CoV-positive dromedaries (Figure 2). The sheep-derivedN gene sequences obtained by NGS and Sanger sequencing were
identical. By NGS, the average sequencing coverage of the N gene
from the sheep (S90_N) and five camel samples (C53_N, C5_N, C6_N,
C28_N, and C50_N) was >6X across all samples (Figure 2A).
The percentage of sequence identity of the N gene of the same
samples along with three reference MERS-CoV sequences (GenBank acc.
numbers KF192507, MG757604 and MK462253) revealed that the sheep sample
showed high nucleotide identity (>99 %) with all other
MERS-CoV sequences (Figure 2B). In detail, multiple sequence alignment
revealed five positions of nucleotide variations between the
sheep-derived MERS-CoV sequence and the camel-derived sequences and/or
reference sequences (representative positions 533 and 637 of theN gene are shown in Figure 2C). The GenBank accession numbers of
the complete MERS-CoV N gene sequences are: sheep-derived
(S90_N): MZ558076; dromedary-derived: C53_N - MZ558080; C5_N -
MZ558077; C6_N - MZ558078; C28_N - MZ558079; and C50_N - MZ558081.
Unfortunately, the borderline-positive result of the goat sample could
not be confirmed by either RT-PCR or NGS.
The serological survey revealed that, although in the initial screening
with 1:40 dilutions 15 serum samples (eight sheep, four goats, three
cattle) appeared questionable, the presence of antibodies could not be
confirmed in any sample by retesting using a dilution series of 1:10 –
1:320 (Supplementary Tables 1 and 2).