A highly divergent cryptic SARS-CoV-2 lineage exhibits strong receptor binding and immune evasion

SARS-CoV-2 genomic surveillance in wastewater enables the identification of cryptic lineages, often with numerous mutations not observed in circulating variants. Here, we discovered a unique cryptic SARS-CoV-2 lineage (designated NJ) from New Jersey wastewater that carries many rare mutations and exhibits the highest binding affinity to the hACE2 receptor among all tested SARS-CoV-2 variant RBDs, including the latest Omicron lineages. Moreover, NJ shows extensive evasion against all five major classes of neutralizing antibodies to SARS-CoV-2. Deep mutational scanning further demonstrates the involvement of epistasis in the evolution of the NJ-RBD. Crystal structures of NJ-RBD in complex with hACE2 and with a broadly neutralizing antibody CC25.4 reveal key amino acid substitutions that affect receptor binding, antibody evasion, and explain its unique molecular characteristics. Overall, these findings not only elucidate the structural and functional features of a cryptic SARS-CoV-2 lineage, but also provide insights into potential future evolution of SARS-CoV-2.