Title: Long range sequencing of the human immunoglobulin loci to direct early diagnostics and functional gene-antibody correlations in COVID-19 disease.
Funder: The Academy of Medical Sciences

Abstract: The immunoglobulin (Ig) gene products are critical components of the adaptive response to infection and are instrumental in the diagnosis, prevention and treatment of multiple infectious diseases. Using whole-blood RNA-sequencing in COVID-19 patients I have found that immunoglobulin genes may represent a specific marker of SARS-CoV-2 infection. However, the complex gene structure and organisation of Ig genes across the human genome impedes our ability to accurately map Ig sequence reads within individuals and perform downstream correlation with repertoire expansion and functional neutralisation responses that may correlate with protection against severe disease. In this project I aim to use methods that I helped to develop in my PhD to comprehensively characterise the Ig heavy and light chain loci in 100 individuals with a diagnosis of COVID-19 using long-range sequencing to achieve the following aims: i) accurately determine germline DNA sequence diversity at Ig loci for affected individuals ii) map and quantify at high resolution specific Ig gene expression in all individuals, iii) demonstrate the specificity of select Ig genes to COVID-19 diagnoses that may alter likelihood of diease severity, iv) correlate specific genes with neutralisation antibody responses and B-cell repertoire and somatic hypermutation, v) assess the impact of germline variants on Ig gene expression. Together, these results could facilitate the use of Ig gene expression in early detection and prognostication of infectious disease using COVID-19 as an exemplar whilst simultaneously increasing our understanding of human germline variation impacting Ig gene expression and protection from disease.

Lay abstract: Antibody responses are vital components of our response and protection against many infections including SARS-CoV-2, the virus driving a worldwide pandemic of the devastating disease COVID-19. However, it remains unclear why some people fail to generate antibody against SARS-CoV-2, and why some people develop antibodies that can kill (or neutralise) the virus better than others. I have recently found that we can detect specific antibody (or immunoglobulin; Ig) genes in the whole blood of all patients with COVID-19 that is an effect not seen in other infections. This observation could facilitate an early, specific prediction method of diagnosis and possibly protection against SARS-CoV-2. However, the Ig region is one of the most poorly characterised areas of the human genome owing to substantial structural complexity. Here I propose to use methods that I developed in my PhD to understand the Ig region in detail in 100 COVID-19 individuals to accurately quantify Ig gene expression in whole blood and understand how genetic variation can affect specific Ig gene usage and subsequent ability to produce total antibody against parts of the virus and how this may help kill the virus. This will be undertaken using cutting-edge genetic sequencing methods and tailored algorithms and then application to independent datasets of several thousand individuals. If we can confirm specific Ig gene usage correlating with COVID and with differential protection I will aim to then take these findings forwards to improve diagnostic and prognostic approaches to COVID-19 management.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION