Ongoing Evolution of Middle East Respiratory Syndrome Coronavirus, Saudi Arabia, 2023-2024

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) circulates in dromedary camels in the Arabian Peninsula and occasionally causes spillover infections in humans. MERS-CoV diversity is poorly understood because of the lack of sampling during the COVID-19 pandemic. We collected 558 swab samples from dromedary camels in Saudi Arabia during November 2023-January 2024. We found 39% were positive for MERS-CoV RNA by reverse transcription PCR. We sequenced 42 MERS-CoVs and 7 human 229E-related coronaviruses from camel swab samples by using high-throughput sequencing. Sequences from both viruses formed monophyletic clades apical to recently available genomes. MERS-CoV sequences were most similar to B5 lineage sequences and harbored unique genetic features, including novel amino acid polymorphisms in the spike protein. Further characterization will be required to understand their effects. MERS-CoV spillover into humans poses considerable public health concerns. Our findings indicate surveillance and phenotypic studies are needed to identify and monitor MERS-CoV pandemic potential.

Keywords: MERS-CoV; Middle East respiratory syndrome coronavirus; Saudi Arabia; coronavirus; coronavirus disease; emerging viruses; respiratory infections; virology; viruses; zoonoses.

Figure 1

Phylogenetic analysis of Middle East respiratory syndrome coronavirus (MERS-CoV) clades and sample distribution in study of ongoing evolution of virus, Saudi Arabia, 2023–2024. Tree was constructed by using the maximum-likelihood method. Black circles indicate 620 complete MERS-CoV genomes sampled until 2019; colored circles indicate 41 MERS-CoV genomes sequenced in this study. Blue circles indicate B5-2023.1, orange circles B5-2023.2, green circles B5-2023.3, yellow circles B5-2023.4, and magenta B5-2023.5 sublineages. Black triangles indicate collapsed clades A, C, B1–B4, and B7. Scale bar indicates nucleotide substitutions per site.

Figure 2

Phylogenetic analyses of Middle East respiratory syndrome coronavirus (MERS-CoV) clade B5-2023 sequences from Saudi Arabia, 2023–2024. Trees were constructed using the maximum-likelihood method. Each tree is rooted with MERS-CoV B5 lineage sequence from 2019 (GenBank accession no. OL622036.1); numbers on nodes indicate bootstrap support. Colored circles indicate B5-2023.1–5 subclades. A) Phylogenetic tree of complete MERS-CoV B5-2023 genomes. B) Phylogenetic tree of spike sequences of MERS-CoV B5-2023 genomes. Amino acid substitutions in the spike protein relative to those of OL622036.1 are indicated on the branches except for substitutions T387P and I743S, which are unique to OL622036.1. The reversion of the R1179–I1180 deletion and V1181I substitution in Al Duwadimi/P6–25 is most likely caused by a recombination event (Appendix 1 Figure 2, panel G). Scale bars indicate nucleotide substitutions per site.

Figure 3

Spatial distribution of B5-2023.1–5 subclades in study of ongoing evolution of Middle East respiratory syndrome coronavirus, Saudi Arabia, 2023–2024. Pie charts show the number of sequences from each subclade found at each of the 6 sampling sites (indicated by black circles on the map) in Saudi Arabia; size of the pie chart corresponds to the number of sequences. Thin black lines indicate administrative regions; gray lines indicate roads. Map was generated by using QGIS v3.28 (https://www.qgis.org).

Figure 4

Phylogenetic analysis of 26 human coronavirus 229E-related coronavirus sequences in study of ongoing evolution of Middle East respiratory syndrome coronavirus, Saudi Arabia, 2023–2024. Tree was constructed by using the maximum-likelihood method. Red text indicates sequences from this study, 5 from Jeddah and 2 from Sajir. Numbers on nodes indicate bootstrap support. Tree was rooted with the bat sequence KT253269/Bat/GHA/KW2E-F151 (GenBank accession no. KT253269). Scale bar indicates nucleotide substitutions per site. GER, Germany; GHA, Ghana; KEN, Kenya; KSA, Kingdom of Saudi Arabia; USA, United States of America.