A longitudinal study of SARS-CoV-2 evolution and molecular characterisation of variants in immunocompromised individuals with persistent infection

Lead Research Organisation: King's College London
Department Name: Immunology Infection and Inflam Diseases


Some people have a weakened immune system due to certain treatments, medicines or illnesses. A weakened immune system can make it more difficult to fight infections caused by viruses, meaning infections can persist for a long time. We have found some individuals can become persistently infected for many months with the virus that causes COVID-19 (also known as SARS-CoV-2).

As the virus reproduces in our bodies it can mutate, which is where changes occur in the genetic code of the virus. These mutations cause 'variants' of the virus. Some variants of the virus may spread more easily, cause more severe disease, or make treatments and vaccination less effective. Persistent infection in individuals with a weakened immune system may allow variants to arise in their body, as the virus continues to reproduce and because their weakened immune system cannot kill new variants as they arise. As the virus develops new variants we can investigate how each sequential mutation changes the properties of the virus. Specifically this research will investigate how mutations change how the virus interacts with parts of our immune system.

Genome sequencing to identify variants arising during persistent infection.
We will use genome sequencing to identify the mutations that arise during persistent infection, especially looking for variants that are known to make the virus spread more easily or more deadly. Using deep genome sequencing we will look at the different variants that exist in persistently infected individuals, even those variants that exist only at low levels in the infected individual. This technique will allow us to see which variants arise over time and in response to different treatments for COVID-19 or medicines for other conditions affecting their immune system.

Laboratory experiments with variants of the virus.
From the patients' samples we can grow the virus in the laboratory to investigate how different variants behave in experiments. This will include experiments to see how variants escape control of the immune system, allowing a better understanding of the properties of different variants and how the variants interact with our bodies. We will use samples collected longitudinally from persistently infected individuals to see how each new mutation changes the properties of the variants, giving us insight into how the virus interacts with our cells and immune system. First we will investigate if mutations that arise during persistent infection decrease the ability of antibodies to inactivate the virus. This will use antibodies from the persistently infected individual, from others who recover from the virus, and from antibodies produced by vaccination. Second, we will see if variants that occur over time in persistently infected individuals increase resistance of the virus to immune responses in cells that limit infection, called interferon. By using virus from the same individuals but at different timepoints when there are new mutations it will allow us to investigate which variants confer the ability to escape these immune responses.

More treatments for COVID-19 may become available in the coming months, such as antibody therapies. By following individuals over time we will be able to see if these treatments lead to new variants being produced.

Scientists and clinicians carrying out this research.
The research will be conducted by clinicians and scientists working at King's College London, Guy's and St. Thomas NHS Foundation Trust, and University College London.

We aim to understand how variants of the virus that causes COVID-19 develop by investigating the virus in individuals persistently infected. We will investigate which variants develop in these individuals, and then grow these variants in the laboratory to study how mutations affect immune responses.

Technical Summary

Immunocompromised individuals can develop persistent infection with SARS-CoV-2. Mutations accrue due to ongoing replication, creating new 'variants' of the virus. These mutations have the potential to alter host-pathogen interaction, potentially affecting pathogenesis, transmissibility, severity of disease and susceptibility to vaccines or treatment. This longitudinal study will characterise viral evolution and the variants that arise during persistent infection with SARS-CoV-2, followed by molecular characterisation of these variants in vitro. By studying longitudinal viral isolates and sera from the same individual, sequential mutations can be studied to judge their effect on host-pathogen interaction.

The aims of this proposal include to 1) describe the patterns of SARS-CoV-2 intrahost evolution longitudinally during persistent infection, 2) correlate the emergence of SARS-CoV-2 variants with clinical course, immunosuppression and antiviral treatment, 3) characterise emergent variants in vitro, including experiments to judge neutralisation by antibodies and resistance to interferon.

Genomic sequencing of viral isolates using a deep sequencing protocol on Illumina technology will allow determination of the consensus genome and intrahost single nucleotide variants (iSNVs). The presence and frequency of iSNVs over time will be monitored, and in response to treatments for SARS-CoV-2 and other immunomodulating therapies for pre-existing conditions.

Viral isolates will be cultured for in vitro molecular characterisation experiments. Successive genomic mutations will be judged for their effect on neutralisation by antibodies and changes in susceptibility of the virus to interferon. Longitudinal serum samples from persistently infected individuals will be used in autologous neutralisation studies on the cultured virus.

Initial research utilises existing ethical approval to analyse already stored, residual samples from GSTT in collaboration with KCL and UCL.


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Snell LB (2023) Real-Time Whole Genome Sequencing to Guide Patient-Tailored Therapy of Severe Acute Respiratory Syndrome Coronavirus 2 Infection. in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America