Characterization of SARS-CoV-2 minor variants and mutational signatures in immunocompromised patients

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) emerged nearly 3 years ago and caused the largest global health, social, and economic crisis of modern times. Although knowledge of the biology, epidemiology, immunology, evolution, and disease impact of the virus has grown tremendously, many questions remain unanswered. One of these are the clinical features and outcomes of COVID-19 in immunocompromised populations, particularly in patients with malignancies and solid organ transplants who may be at increased risk for severe disease development. Due to impaired immune defences from both underlying diseases and their treatment, immunocompromised patients with respiratory viral infections are generally at higher risk for a severe infection and have higher rates of bacterial and fungal superinfection. Additionally, assessing the infectivity of COVID-19 patients and monitoring the emergence of new SARS-CoV-2 viral variants has been a major issue worldwide as it requires high-containment facilities and is a tedious and slow process. Of particular concern are again immunocompromised patients who tend to remain SARS-CoV-2 RNA positive for a prolonged time. Not only, because of their immune status, as they can be a constant source of infectious viruses and serve as vessels for the emergence of new genetic variants, but also because managing the SARS-CoV-2 infection highly impacts the treatment of their underlying disease and the quality of their life. Management of such a chronically infected immunocompromised patient therefore imposes a dilemma either to follow precautionary guidelines and isolate the patient for an extended period or to abandon precautions and potentially expose other vulnerable individuals to infection. The goal of this project is to gain a better understanding of the underlying mechanism and potential consequences of persistent SARS-CoV-2 infection in immunocompromised patients. To the best of our knowledge, no study to date has comprehensively investigated the normalized viral load of genomic and subgenomic SARS-CoV-2 RNA in terms of managing the risk of shedding infectious virus. This would allow for a better management of immunocompromised patients in the future by avoiding prolonged quarantine and social isolation. Data from the proposed project would provide the most detailed analysis to date of the intra-host evolution of SARS-CoV-2 in these individuals. Identification of viral evolution in longitudinal samples with well-defined metadata and treatment information will allow us to assess changes in viral proteins targeted by antiviral agents and predict future evolution of SARS-CoV-2. Minor variant and mutational signature analysis is important because these can influence viral load, disease outcome, antigenic diversity, and vaccine efficacy in a patient. Understanding the characteristics of a large, clinically and microbiologically well-characterized cohort of immunocompromised patients, along with potential coinfections detected through an unbiased metagenomics approach, will lead to better patient management strategies, fewer secondary infections, and a reduced burden on the economic system. Furthermore, SARS-CoV-2 is not the only virus that causes persistent infection in immunocompromised patients, as this has been described for influenza and respiratory syncytial virus. Because of the high number of SARS-CoV-2 infections in the population, a larger number of immunocompromised patients are also affected. This allows us to investigate the mechanism of this persistent positivity and possible infectivity and to determine prognostic markers and relevant virus-host interactions that would give us the experience and flexibility to respond to new or emerging infectious diseases in the future as well.