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.

中东呼吸综合征冠状病毒 （MERS-CoV） 在阿拉伯半岛的单峰骆驼中传播，偶尔会引起人类溢出感染。由于 COVID-19 大流行期间缺乏采样，人们对 MERS-CoV 多样性知之甚少。我们在 2023 年 11 月至 2024 年 1 月期间从沙特阿拉伯的单峰骆驼收集了 558 份拭子样本。我们发现逆转录 PCR 显示 39% 的 MERS-CoV RNA 阳性。我们使用高通量测序从骆驼拭子样本中对 42 例 MERS-CoV 和 7 例人类 229E 相关冠状病毒进行了测序。来自两种病毒的序列在最近可用的基因组的顶端形成了单系分支。MERS-CoV 序列与 B5 谱系序列最相似，并具有独特的遗传特征，包括刺突蛋白中新的氨基酸多态性。需要进一步的表征来了解它们的影响。MERS-CoV 溢出到人类造成了相当大的公共卫生问题。我们的研究结果表明，需要监测和表型研究来识别和监测 MERS-CoV 大流行的潜力。