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

概述由于某些治疗、药物或疾病，有些人的免疫系统会减弱。免疫系统的削弱会使对抗病毒引起的感染变得更加困难，这意味着感染可能会持续很长时间。我们发现，一些人可能会持续感染导致新冠肺炎(也称为SARS-CoV-2)的病毒数月。当病毒在我们的体内复制时，它会发生变异，这是病毒遗传密码发生变化的地方。这些突变会导致病毒的“变种”。该病毒的一些变种可能更容易传播，导致更严重的疾病，或者使治疗和疫苗接种效果降低。免疫系统减弱的人持续感染可能会导致体内出现变异，因为病毒继续繁殖，而且他们虚弱的免疫系统无法在新变异出现时杀死它们。随着病毒产生新的变异，我们可以研究每个顺序突变如何改变病毒的特性。具体地说，这项研究将调查突变如何改变病毒与我们免疫系统的某些部分相互作用的方式。基因组测序以识别持续感染期间出现的变异。我们将使用基因组测序来识别持续感染期间出现的变异，特别是寻找已知的使病毒更容易传播或更致命的变异。使用深度基因组测序，我们将研究持续感染个体中存在的不同变异，即使是那些仅存在于感染个体中低水平的变异。这将包括实验，以了解变异如何逃脱免疫系统的控制，从而更好地了解不同变异的属性，以及变异如何与我们的身体相互作用。我们将使用从持续感染的个人那里纵向收集的样本，看看每个新的突变如何改变变异的特性，让我们深入了解病毒如何与我们的细胞和免疫系统相互作用。首先，我们将调查在持续感染期间出现的突变是否会降低抗体灭活病毒的能力。这将使用来自持续感染者、从病毒中康复的其他人以及接种疫苗产生的抗体的抗体。其次，我们将观察随着时间的推移，在持续感染的个体中出现的变异是否会增加病毒对细胞中限制感染的免疫反应的抵抗力，这种免疫反应称为干扰素。通过使用来自相同个体但在不同时间点出现新突变的病毒，它将使我们能够调查哪些变异赋予了逃避这些免疫反应的能力。在接下来的几个月里，可能会有更多针对新冠肺炎的治疗方法，例如抗体疗法。我们将调查这些个体中产生了哪些变异，然后在实验室中培养这些变异，以研究突变如何影响免疫反应。

OverviewSome 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.SummaryWe 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.