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 hypothesised to be a major source of variants of concern (VOC). However, determination of viral subpopulations by linkage of intra-host variants into haplotypes has been limited by commonly used genomic sequencing techniques. We developed a sequencing and analysis methods for identifying full-length intra-host spike haplotypes and analysed their diversification over the course of persistent infections in individuals with inherited or acquired immunodeficiencies. Mutations frequently emerged in positions found in VOCs that confer escape from neutralising antibodies, while selection analyses showed strong evidence of positive selection and identified specific amino acid positions undergoing selection. In a single chronic infection lasting more than 500 days from the first wave of the pandemic, we detailed the evolution of spike as it gradually acquired mechanisms to evade both autologous and heterologous neutralising antibodies, redolent of Omicron variants. This provides one of the strongest pieces of evidence for persistent infections being the source of immune-evasive variants with accelerated evolution, underscoring their impact on the evolutionary trajectory of SARS-CoV-2.