The impact of clade B lineage 5 MERS coronaviruses spike mutations from 2015 to 2023 on virus entry and replication competence

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging coronavirus that can cause zoonotic disease in humans with lethal severe viral pneumonia. Dromedary camels are the source of zoonotic infection. As of June 2025, MERS-CoV has resulted in a total of 2626 reported cases, 36% of these being fatal. The number of reported human cases has been on a decreasing trend since 2016 and reached a minimum level during the COVID-19 pandemic. The reason for the reduction of cases is unclear and may be multifactorial. We hypothesized that mutations accumulating in the virus spike protein may have reduced zoonotic potential. Here, we investigate the impact of recently emerged virus spike-protein mutations on virus replication competence using pseudoviruses and replication-competent recombinant viruses. We found that two spike variants detected in 2019 show a reduced cell entry and lower viral replication in human cells. However, spike variants detected in 2023 sequences, did not show significant changes in cell entry and viral replication. All the MERS-CoV spikes tested showed a cell-entry pathway preference via the cell-surface TMPRSS2 route. Our data suggests that spike protein mutations are not a major determinant of the fewer MERS-CoV human cases observed. Author SummaryMERS-CoV is identified by the World Health Organization (WHO) as a potential pandemic candidate. The ability of coronaviruses to mutate and adapt in new hosts raises concerns about the impact of virus genetic changes on human zoonotic potential. There has been a notable decline in human MERS cases reported to the WHO since 2018, but the underlying reasons remain unclear. Here, we focus on investigating whether the recently emerged virus spike mutations may contribute to this observation. We found that while some spike mutations detected in 2019 reduce cell entry and viral replication, more recent viruses do not share this phenotype. This study highlighted a need for comprehensive genomic surveillance and phenotyping of recent MERS-CoV isolates to understand the potential role, if any, of other non-spike virus mutations on viral zoonotic competence and to explore alternate hypothesis, such as cross-reactive immunity from COVID-19 contributing to reduced human MERS-CoV disease.