KRATEK POVZETEK PROJEKTA
Pandemija COVID-19, ki jo je povzročil novi koronavirus SARS-CoV-2, je v treh letih od prvega pojava v Wuhanu, na Kitajskem, povzročila največjo zdravstveno, ekonomsko in socialno krizo v modernem času. Čeprav se je znanje o biologiji, epidemiologiji, imunologiji in evoluciji virusa izjemno povečalo, ostaja nekaj vprašanj še neodgovorjenih. Ena izmed teh so klinične značilnosti in izid COVID-19 pri imunsko oslabljenih osebah, zlasti pri bolnikih z malignimi obolenji in presajenimi trdnimi organi, pri katerih je lahko povečano tveganje za hud potek bolezni. Zaradi oslabljene imunske obrambe, zaradi osnovne bolezni in/ali zdravljenja, so imunsko oslabljeni bolniki na splošno izpostavljeni večjemu tveganju za hud potek bolezni in imajo pogosteje, poleg SARS-CoV-2 okužbe, tudi bakterijske in glivične super okužbe. Pravilna ocena tveganja kužnosti bolnikov s COVID-19 in sprotno spremljanje bioloških značilnosti novih genetskih različic virusa SARS-CoV-2 sta se pokazali kot glavni prepreki v boju proti epidemiji, saj so postopki dolgotrajni in zahtevajo specializirano opremo in infrastrukturo. Pri imunsko oslabljenih bolnikih, ki ostanejo dolgo časa pozitivni na SARS-CoV-2, se lahko, zaradi zmanjšanega imunskega pritiska razvijejo nove virusne genomske različice in njihove podvrste. Dolgotrajno izločanje virusne RNA pri teh bolnikih ni problematično samo iz stališča obvladovanja okužbe s SARS-CoV-2, ampak predvsem, zato ker močno vpliva bolnikovo zdravljenje imunske boleznih in njihovo integracijo nazaj v socialno okolje. Pri obravnavi dolgotrajno pozitivnega imunsko oslabljenega COVID-19 bolnika je potrebno skrbno pretehtati ali upoštevati previdnostne smernice in takega bolnika osamiti za pogosto zelo dolgo obdobje ali pa, kljub previdnostim ukrepom, pristopati bolj življenjsko in prekiniti izolacijo preden bolnik popolnoma izniči okužbo in s tem morebiti izpostaviti druge ranljive posameznike okužbi. Cilj predlaganega projekta je pridobiti boljše razumevanje biološkega mehanizma, ki omogoča virusu SARS-CoV-2 dolgotrajno okužbo in podrobno razumevanje posledic dolgotrajne okužbe za bolnika in družbo. V predlaganem projektu bomo združili različne mikrobiološke metode: kvantifikacijo virusne RNK, normalizacijo virusnega bremena, izolacijo kužnega virusa, določanje različice SARS-CoV-2, analizo virusnih podvrst in mutacijskega podpisa virusa SARS-CoV-2 z globokim sekvenciranjem, skupaj s podrobnimi kliničnimi podatki o bolnikovi osnovni bolezni in poteku zdravljenja ter protivirusnim zdravljenjem bolezni COVID-19. Celovita analiza evolucije virusa znotraj gostitelja, kvantifikacija virusnih podvrst ter razumevanje dinamike izločanja kužnega virusa pri bolnikih z oslabljenim imunskim sistemom bo vodila do boljšega razumevanja tveganja za pojav novih virusnih različic, ter predvsem do boljšega kliničnega vodenja in zdravljenja teh bolnikov v prihodnosti. Dolgotrajne virusne okužbe pri bolnikih z oslabljenim imunskim sistemom so bile opisane tudi pri drugih respiratornih virusih, kot sta virusom gripe in respiratorni sincicijski virus, vendar prognostični označevalci niso bili prepoznani. Podatki pridobljeni v projektu bomo omogočili boljše razumevanje interakcije med virusom in gostiteljem, s čimer bi lahko pridobili vpogled v dejavnike, ki vplivajo na razvoj virusa in virusnih podvrst, zaradi česar bi bili v prihodnje bolje pripravljeni hiter odziv na nove porajajoče se nalezljive bolezni.
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SUMMARY
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.