Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections

Evolution of SARS-CoV-2 in long-term persistent infections is hypothesized to be a major source of variants of concern (VOCs). However, linking intra-host variants into haplotypes that reflect viral subpopulations is limited by commonly used genomic sequencing techniques. We develop sequencing and analysis methods for identifying full-length spike haplotypes and analyze their diversification during persistent infections in individuals with inherited or acquired immunodeficiencies. This reveals accelerated evolutionary rates, with mutations frequently emerging at VOC-associated sites that confer escape from neutralizing antibodies, often undergoing strong positive selection. In a single infection lasting over 500 days from the first wave of the pandemic, we detail the evolution of spike as it acquires mechanisms to evade both autologous and heterologous neutralizing antibodies, redolent of Omicron variants. This evidence reinforces the argument for persistent infections being the source of immune-evasive variants, underscoring their impact on the evolutionary trajectory of SARS-CoV-2.