Divergence of delta and beta variants and SARS-CoV-2 evolved in prolonged infection into distinct serological phenotypes

SARS-CoV-2 continues to evolve variants of concern (VOC) which escape antibody neutralization and have enhanced transmission. One variant may escape immunity elicited by another, and the delta VOC has been reported to escape beta elicited immunity (1). Systematic mapping of the serological distance of current and emerging variants will likely guide the design of vaccines which can target all variants. Here we isolated and serologically characterized SARS-CoV-2 which evolved from an ancestral strain in a person with advanced HIV disease and delayed SARS-CoV-2 clearance. This virus showed evolving escape from self antibody neutralization immunity and decreased Pfizer BNT162b2 vaccine neutralization sensitivity. We mapped neutralization of evolved virus and ancestral, beta and delta variant viruses by antibodies elicited by each VOC in SARS-CoV-2 convalescent individuals. Beta virus showed moderate (7-fold) and delta slight escape from neutralizing immunity elicited by ancestral virus infection. In contrast, delta virus had stronger escape from beta elicited immunity (12-fold), and beta virus even stronger escape from delta immunity (34-fold). Evolved virus had 9-fold escape from ancestral immunity, 27-fold escape from delta immunity, but was effectively neutralized by beta immunity. We conclude that beta and delta are serologically distant, further than each is from ancestral, and that virus evolved in prolonged infection during advanced HIV disease is serologically close to beta and far from delta. These results suggest that SARS-CoV-2 is diverging into distinct serological phenotypes and that vaccines tailored to one variant may become vulnerable to infections with another.