Vitamin D-related polymorphisms and vitamin D levels as risk biomarkers of COVID-19 infection severity
Ana Teresa Freitas, Conceição Calhau, Gonçalo Antunes, Beatriz Araújo, Matilde Bandeira, Sofia Barreira, Filipa Bazenga, Sandra Braz, Daniel Caldeira, Susana Constantino Rosa Santos, Ana Faria, Daniel Faria, Marta Fraga, Beatriz Nogueira-Garcia, Lúcia Gonçalves, Pavlo Kovalchuk, Luísa Lacerda, Hugo Lopes, Daniel Luís, Fábio Medeiros, Ana M P Melo, José Melo-Cristino, Ana Miranda, Clara Pereira, Ana Teresa Pinto, João Pinto, Helena Proença, Angélica Ramos, João P. R. Rato, Filipe Rocha, Júlio César Rocha, André Moreira-Rosário, Helena Vazão, Yuliya Volovetska, João-Tiago Guimarães, Fausto Pinto
doi:10.1101/2021.03.22.21254032
Biotechnology SA, declare that the company developed a genetic test, the MyVitDGenes®, that was used to evaluate all the polymorphisms under analysis in this work. All other authors have declared that no conflict of interest exists.
Data analysis. Clinical history, genotypic and phenotypic data was evaluated using statistical, machine learning and polygenic risk scores methodologies. Vitamin D polymorphisms prevalence in different populations was obtained from 1000 Genomes database (https://www.internationalgenome.org/) and from HeartGenetics's research database for the Portuguese population, with more than 8,000 Portuguese individuals. Regarding the methodological approach, the following steps were undertaken: 1. Data cleaning and validation: All variables were analysed for outliers and missing values. Some discrepancies, such as different units of measure and data entry errors, were identified and fixed. No imputation was made. Regarding data transformation, both disease severity and vitamin D levels were categorized in different levels, and the genetic variants were aggregated in PRSs.
Descriptive analysis: A complete, graphical descriptive analysis of the data was created for all variables of interest as univariate analysis. Data are presented as numbers or percentages for categorical variables, while continuous variables are shown as mean and standard deviation, and median and interquartile range (25th percentile -75th percentile).
Analysis of data distribution: The data normality was accessed using Shapiro-Wilk test and D'Agostino Pearson's test. Statistical normality testing is relevant in order to set up the category of statistical methods (parametric or non-parametric) used in further..
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doi:10.1210/jc.2016-2930DOI record:
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"abstract": "<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Vitamin D is a fundamental regulator of host defences by activating genes related to innate and adaptive immunity. Previous research shows a correlation between the levels of vitamin D in patients infected with SARS-CoV-2 and the degree of disease severity. This work investigates the impact of the genetic background related to vitamin D pathways on COVID-19 severity. For the first time, the Portuguese population was characterized regarding the prevalence of high impact variants in genes associated with the vitamin D pathways.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>This study enrolled 517 patients admitted to two tertiary Portuguese hospitals. The serum concentration of 25 (OH)D, was measured in the hospital at the time of patient admission. Genetic variants, 18 variants, in the genes <jats:italic>AMDHD1, CYP2R1, CYP24A1, DHCR7, GC, SEC23A</jats:italic>, and <jats:italic>VDR</jats:italic> were analysed.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The results show that polymorphisms in the vitamin D binding protein encoded by the <jats:italic>GC</jats:italic> gene are related to the infection severity (<jats:italic>p</jats:italic> = 0.005). There is an association between vitamin D polygenic risk score and the serum concentration of 25 (OH)D (<jats:italic>p</jats:italic> = 0.042). There is an association between 25 (OH)D levels and the survival and fatal outcomes (<jats:italic>p</jats:italic> = 1.5e-4). The Portuguese population has a higher prevalence of the <jats:italic>DHCR7</jats:italic> RS12785878 variant when compared with its prevalence in the European population (19% versus 10%).</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>This study shows a genetic susceptibility for vitamin D deficiency that might explain higher severity degrees in COVID-19 patients. These results reinforce the relevance of personalized strategies in the context of viral diseases.</jats:p></jats:sec><jats:sec><jats:title>Trial registration</jats:title><jats:p>NCT04370808</jats:p></jats:sec>",
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