Clinical features, immune response, and virological factors associated with SARS-CoV-2 infection outcomes

Abstract

The severity of the COVID-19 pandemic has unleashed an unprecedented scientific activity focused, firstly, on the search for effective treatments to alleviate the effects of the disease and block the replication of the virus, to develop preventive vaccines, and on better understanding the pathogenesis and epidemiology of COVID-19, as well as in identifying prognostic factors that allow classifying those patients with a higher risk of ICU admission or death. Current information on risk factors for unfavourable COVID-19 outcomes in hospitalized patients are focused on patients’ demographics, comorbidities, severity of the symptoms and laboratory findings. While there is abundant information regarding risk factors associated with unfavorable outcome in the general population, these are scarce for the immunosuppressed patients. There is a lack of robust studies to define the SARS-CoV-2 infection behavior in the very variable population of immunosuppressed patients, regarding the kinetics of viral infection and immune clearance, the degree and time of viral shedding, the disease severity risk factors, and clinical manifestations and outcomes. Moreover, recommendations for a better management of the disease in these patients are urgently needed. Recent data suggest that patients with primary and secondary immunodeficiencies, including malignancies and SOT, may be at increased risk of severe COVID-19 disease and death, but new prospective and controlled studies are needed to determine the attributable risk of immunocompromising conditions and therapies on COVID-19 disease prognosis. Moreover, the relationship between COVID-19 disease outcomes, SARS-CoV-2 kinetics, and the innate and specific immune responses has not been fully elucidated. In addition, mutations of SARS-CoV-2 virus have emerged, with VOC disseminated in several world areas. Independently of the increased dissemination ability, some VOC have presumed higher severity or possible reduction of vaccine effectiveness, without data on its impact in immunosuppressed patients and on the neutralizing activity of antibodies after the infections by the Wuhan original lineage. A profound knowledge of the epidemiology, immune response, and clinical course of SARS-CoV-2 infection in this group of patients would allow for the establishment of proper diagnostic strategies, and accurate prophylactic and therapeutic approaches focused on possible complications, decrease of hospital admission and secondary mortality. In addition, clinical algorithms regarding the adjustment of immunosuppressive medication, antiviral treatment, need for hospital admission, and duration of isolation measures should also be addressed. The general objective of this thesis is to study the incidence of COVID-19 in patients with immunosuppression, to analyze the SARS-CoV-2 infection and immune response dynamics in these patients, and to determine the impact of COVID-19 on clinical outcomes, as well as the risk factors associated with the unfavorable outcomes. The first article Risk factors for unfavorable outcome and impact of early post-transplant infection in solid organ recipients with COVID-19: A prospective multicenter cohort study published in PLoS ONE (doi: 10.1371/journal.pone.0250796) analyzes the characteristics and predictors of unfavorable outcomes in SOTRs with COVID-19. This is a prospective observational cohort study of 210 consecutive SOTRs hospitalized with COVID-19 in 12 Spanish centers from 21 February to 6 May 2020. Data pertaining to demographics, chronic underlying diseases, transplantation features, clinical, therapeutics, and complications were collected. The primary endpoint was a composite of ICU admission and/or death, and logistic regression analyses were performed to identify the factors associated with these unfavorable outcomes. To gain insight in the innate immune response in SOTRs with COVID-19, compared with no SOT patients, we conducted a second article Serum IFN-γ and RNAemia temporal profiles as biomarkers of severe COVID-19 in solid organ transplant and immunocompetent patients published in Journal of Infection (doi: 10.1016/j.jinf.2023.01.019) addressing the IFN serum levels and RNAemia detection at hospital admission and by days from symptoms onset, as well as their association with unfavorable clinical outcomes (death and/or invasive mechanical ventilation [IMV]). This was a multicenter prospective observational cohort study, including 47 SOTRs and 408 non SOTRs consecutive adult inpatients with confirmed COVID-19 and available samples for IFN-α/IFN-γ serum levels and RNAemia determinations, from January 6th, 2020, to August 13th, 2021. Data were separately analyzed for SOTRs and non SOTRs. In addition, we performed a matched cohort analysis in which patients undergoing transplantation were paired with those from the non SOTRs cohort (1:2) according to their propensity score (PS) to control for residual confounders. IFN-α and IFN-γ levels were analyzed as discrete (undetectable and detectable) and continuous (pg/mL) variables. Multivariate Cox regression and logistic regression analyses were performed to identify factors independently associated with 30-day all-cause mortality and unfavorable clinical outcomes. For coping with the best clinical attention to COVID-19 patients it is crucial to perform prognosis estimations at the first clinical evaluation, offering personalized attention based on early and easily detectable predictors that support decision making, guide level of care, and optimize the allocation of health resources. In this regard, different studies have addressed the possible association between viral load in NP swabs and clinical outcomes. However, this issue remains controversial. In our third article SARS-CoV-2 viral load in nasopharyngeal swabs is not an independent predictor of unfavorable outcome published in Scientific Reports (doi: 10.1038/s41598-021-92400-y) we present a prospective cohort study including 321 adult patients with confirmed COVID-19. Quantitative Synthetic SARS-CoV-2 RNA cycle threshold values were used to calculate the viral load in log10 copies/mL. Disease severity at the end of follow-up was categorized into mild, moderate, and severe. Primary endpoint was a composite of ICU admission and/or death, for which univariable and multivariable logistic regression analyses were performed. Since IFN-β seemed to be an attractive drug for repurposing and use in the treatment of COVID-19, based on its in vitro antiviral activity and the encouraging results from clinical trials, we elaborated a fourth article Impact of early interferon-β treatment on the prognosis of patients with COVID-19 in the first wave: A post hoc analysis from a multicenter cohort published in Biomedicine & Pharmacotherapy (doi: 10.1016/j.biopha.2021.112572) that analyzed the impact of early IFN-β treatment in patients admitted with COVID-19 during the first wave of the pandemic. This was post hoc analysis of a COVID-19@Spain multicenter cohort including 3808 consecutive adult patients hospitalized with COVID-19 from 1 January to 17 March 2020. The primary endpoint was 30-day all-cause mortality, and the main exposure of interest was subcutaneous administration of IFN-β, defined as early if started ≤ 3 days from admission. Multivariate logistic and Cox regression analyses were conducted to identify the associations of different variables with receiving early IFN-β therapy and to assess its impact on 30-day mortality. A PS was calculated and used to both control for confounders and perform a matched cohort analysis. The fundamental implication of our first article is the identification of specific and independent predictors (age ≥ 70 years, respiratory rate > 20 bpm, lymphocytes < 1 x 1000/μL, and lactate dehydrogenase ≥ 300 U/L) for unfavorable outcomes in hospitalized SOTRs with COVID-19, which could ease the development of future research and guidelines targeted at high-risk transplanted populations. Furthermore, we showed that an interval shorter than six months between transplantation and COVID-19 diagnosis has a negative impact on mortality and ICU admission rates, which is a risk that should be considered when deciding which patients should proceed with transplantation. Finally, although analogous to the general population, mortality in SOTRs hospitalized with SARS-CoV-2 infection is dramatically high, and the promotion of preventive strategies and treatments will be crucial to mitigate the adverse impacts of the COVID-19 pandemic in these patients. Our second article is the first analyzing the interplay among the SARS-CoV-2 RNAemia, IFN-α, and IFN-γ serum levels at the first clinical evaluation of COVID-19 in a cohort of 455 adult patients. We showed that undetectable IFN-γ in serum at hospital admission was independently associated with 30-day all-cause mortality in COVID-19, specifically in non SOTRs. However, undetectable IFN-α in serum was not associated with mortality neither in SOTRs or non SOTRs. RNAemia at hospital admission was also as a robust predictor of 30-day all-cause mortality in all adult COVID-19 inpatients, SOTRs and non SOTRs. The main finding of our third article was that patients with SARS-CoV-2 infection, regardless of their illness severity, have a high rate of viral replication in the upper respiratory airways. Consequently, this parameter cannot be used as a predictor of COVID-19 unfavorable outcome, defined as admission to ICU and/or death. There is not a clear viral load cut-off point capable of discriminating between the various levels of COVID-19 severity and, contrary to expectations, a higher number of SARS-CoV-2 copies in NP swabs at first patient’s evaluation is not predictive of whether ICU admission or death might occur. Our fourth article is, to the best of our knowledge, the biggest study providing information on the effectiveness of systemic early IFN-β administration vs. standard treatment alone in patients with moderate-to-severe COVID-19 addressing the confounding effects of other potential targeted drugs. We did not find an association between early IFN-β therapy after hospital admission and any mortality benefit in patients admitted because of COVID-19. Conclusions: 1. Among hospitalized SOTR with COVID-19, ICU admission and death rates were high, and they were similar to those reported in the general population. 2. Unfavorable outcomes were mainly driven by respiratory failure (represented by a high breathing rate), older age, and two laboratory features at presentation, namely lymphopenia and elevated level of lactate dehydrogenase, as inflammatory biomarker. 3. An earlier post-transplant SARS-CoV-2 infection was established as a novel risk factor for ICU need and mortality. 4. Undetectable IFN-γ in serum, at hospital admission, is a predictor of 30-day all-cause mortality in adult COVID-19 inpatients. 5. In SOTRs, there is an association between undetectable IFN-γ and unfavorable clinical outcomes. 6. RNAemia at hospital admission is the most robust predictor of 30-day all-cause mortality in all adult COVID-19 inpatients. 7. RNAemia and IFN-γ serum levels determinations at hospital admission should be used to guide the management of patients and to assess the antiviral therapy efficacy. 8. Higher values of SARS-CoV-2 viral load in NP samples at first hospital evaluation are more frequent in patients with unfavorable in hospital outcome, but they are not an independent predictor of ICU admission or death among adult patients with COVID- 19. 9. The administration of early IFN-β therapy after hospital admission does not have a survival benefit in patients with moderate-to-severe COVID-19. Whether the drug would be useful specifically in patients with low IFN production needs to be investigated.