Genetic diversity of pangolin coronaviruses reveals a key immuno-evasive substitution at spike residue 519

Malayan pangolins are unprecedented hosts for several SARS-CoV-2-related coronaviruses, which have previously been known to only infect Rhinolophus bats. Much debate has hence surrounded their possible role as intermediate hosts in the emergence of SARS-CoV-2, but the virological phenotypes of most pangolin coronaviruses (pCoVs) remain unclear. Here, we comprehensively analyze all pCoVs to date identified from trafficked pangolins seized in the Guangdong province of China, which are remarkably similar to SARS-CoV-2 in the spike protein. We explore an unknown genetic diversity within these viruses and uncover how this diversity translates to different virological phenotypes. Strikingly, several Guangdong pCoVs harbor a lysine substitution at residue 519 of spike protein, which contributes to marked immune evasion potentially by modulating the conformational state of spike protein. Furthermore, we highlight that a similar immuno-evasive mutation at residue 519 of the spike protein was acquired by SARS-CoV-2. These findings support that pangolin- and human-infecting coronaviruses represent independent spillover events from natural bat reservoirs, and that immuno-evasive mutations at residue 519 may be a common vector of viral evolution in coronaviruses that infect non-bat hosts.