BACKGROUND: SARS-CoV-2 contains the furin cleavage PRRA motif in the S1/S2 region, which enhances viral pathogenicity but is absent in closely related bat and pangolin coronaviruses. It remains unknown if bat-like coronaviral variants without PRRA (DeltaPRRA) can establish natural infection in humans. METHODS: Here, we developed a duplex digital PCR assay to examine DeltaPRRA variants in Vero-E6-propagated isolates, human organoids, experimentally infected hamsters and COVID-19 patients. RESULTS: We found that currently transmitting SARS-CoV-2 contained a quasispecies of wildtype, DeltaPRRA variants and upstream variants that have mutations upstream the PRRA motif. Moreover, the DeltaPRRA variants were readily detected despite at a low intra-host frequency in transmitted founder viruses in hamsters and in COVID-19 patients including acute cases and a family cluster with a prevalence rate of 52.9%. CONCLUSIONS: Our findings demonstrate that bat-like SARS-CoV-2DeltaPRRA not only naturally exists but remains transmissible in COVID-19 patients, which have significant implications to zoonotic origin and natural evolution of SARS-CoV-2.