Natural transmission of bat-like SARS-CoV-2(ΔPRRA) variants in COVID-19 patients

Wong, Yik Chun; Lau, Siu Ying; To, Kelvin Kai Wang; Mok, Bobo Wing Yee; Li, Xin; Wang, Pui; Deng, Shaofeng; Woo, Kin Fai; Du, Zhenglong; Li, Cun; Zhou, Jie; Chan, Jasper Fuk Woo; Yuen, Kwok Yung; Chen, Honglin; Chen, Zhiwei

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 (ΔPRRA) can establish natural infection in humans. METHODS: Here, we developed a duplex digital PCR assay to examine ΔPRRA 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, ΔPRRA variants and upstream variants that have mutations upstream the PRRA motif. Moreover, the ΔPRRA 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-2(Δ)(PRRA) 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.