Edgeworth, J. | bioRxiv Science

bioRxiv2025

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.

microbiology↗

bioRxiv2021

ADNKA overcomes SARS-CoV2-mediated NK cell inhibition through non-spike antibodies

The outcome of infection is dependent on the ability of viruses to manipulate the infected cell to evade immunity, and the ability of the immune response to overcome this evasion. Understanding this process is key to understanding pathogenesis, genetic risk factors, and both natural and vaccine-induced immunity. SARS-CoV-2 antagonises the innate interferon response, but whether it manipulates innate cellular immunity is unclear. An unbiased proteomic analysis determined how cell surface protein expression is altered on SARS-CoV-2-infected lung epithelial cells, showing downregulation of activating NK ligands B7-H6, MICA, ULBP2, and Nectin1, with minimal effects on MHC-I. This correlated with a reduction in NK cell activation, identifying a novel mechanism by which SARS-CoV2 antagonises innate immunity. Later in the disease process, strong antibody-dependent NK cell activation (ADNKA) developed. These responses were sustained for at least 6 months in most patients, and led to high levels of pro-inflammatory cytokine production. Depletion of spike-specific antibodies confirmed their dominant role in neutralisation, but these antibodies played only a minor role in ADNKA compared to antibodies to other proteins, including ORF3a, Membrane, and Nucleocapsid. In contrast, ADNKA induced following vaccination was focussed solely on spike, was weaker than ADNKA following natural infection, and was not boosted by the second dose. These insights have important implications for understanding disease progression, vaccine efficacy, and vaccine design.

immunology↗