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

TL;DR

Long-term SARS-CoV-2 infections in immunocompromised individuals lead to rapid evolution of spike proteins that evade antibodies, resembling future variants like Omicron.

Contribution

New sequencing and analysis methods reveal full-length spike haplotypes in persistent infections, showing accelerated evolution and antibody escape.

Findings

Persistent infections show accelerated spike evolution with mutations at VOC-associated sites.

A 506-day infection acquired mutations resembling Omicron three months before BA.1 emergence.

Mutations confer escape from both autologous and heterologous neutralizing antibodies.

Abstract

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.

•Divergent intra-host spike haplotypes accumulate in persistent SARS-CoV-2 infections•Positively selected mutations accrue at sites associated with variants of concern•Spike evolves global neutralization escape over a 506-day wave 1 chronic infection•These mutations are redolent of Omicron, 3 months before the emergence of BA.1

Divergent intra-host spike haplotypes accumulate in persistent SARS-CoV-2 infections

Positively selected mutations accrue at sites associated with variants of concern

Spike evolves global neutralization escape over a 506-day wave 1 chronic infection

These mutations are redolent of Omicron, 3 months before the emergence of BA.1

Snell et al. develop sequencing methodology to identify full-length spike haplotypes and show that persistent SARS-CoV-2 infections drive divergent haplotype emergence, accelerating viral evolution and promoting immune escape. Their work highlights how long-term infections in immunocompromised individuals can generate variants with enhanced resistance to neutralizing antibodies, shaping SARS-CoV-2’s evolutionary trajectory.

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