No Species-level Losses of the Horizontally Transferred Genetic Element s2m Within the SARS-related Coronaviruses

Horizontal transfer of genetic elements is a common phenomenon in nature. Both prokaryotes, eukaryotes and viruses have been shown to contain genetic elements acquired through horizontal transfer. Some of these elements may be retained over long periods of time after being integrated into the recipient genome because they offer a selective advantage. The genetic element s2m has been acquired through horizontal transfer by many distantly related viruses, including the SARS-related coronaviruses. Here we show that s2m is evolutionarily conserved within this cluster of viruses and that while several short-lived SARS-CoV-2 lineages devoid of the element have been sequenced, there do not appear to be any species-level losses. This pattern strongly suggests that s2m is essential to virus replication in SARS-CoV-2 and related viruses, and that further experiments are needed to characterize its function.