Clinical and molecular characterization of COVID-19 hospitalized patients

Abstract

Clinical and molecular characterization by Whole Exome Sequencing (WES) is reported in 35 COVID-19 patients attending the University Hospital in Siena, Italy, from April 7 to May 7, 2020. Eighty percent of patients required respiratory assistance, half of them being on mechanical ventilation. Fiftyone percent had hepatic involvement and hyposmia was ascertained in 3 patients. Searching for common genes by collapsing methods against 150 WES of controls of the Italian population failed to give straightforward statistically significant results with the exception of two genes. This result is not unexpected since we are facing the most challenging common disorder triggered by environmental factors with a strong underlying heritability (50%). The lesson learned from Autism-Spectrum-Disorders prompted us to re-analyse the cohort treating each patient as an independent case, following a Mendelian-like model. We identified for each patient an average of 2.5 pathogenic mutations involved in virus infection susceptibility and pinpointing to one or more rare disorder(s). To our knowledge, this is the first report on WES and COVID-19. Our results suggest a combined model for COVID-19 susceptibility with a number of common susceptibility genes which represent the favorite background in which additional host private mutations may determine disease progression.

Fig 1. Clinical characteristic and mutated genes.

The population is clustered into four qualitative severity groups indicated with different colors depending on the respiratory impairment and the need for ventilation. Red color is used for high care intensity group (those requiring invasive ventilation), orange for intermediate care intensity group (those requiring non invasive ventilation i.e. CPAP and BiPAP, and high-flows oxygen therapy), pink for low care intensity groups (those requiring conventional oxygen therapy) and light blue for very low care intensity groups (those not requiring oxygen therapy). Patients COV132-57 and COV133-58 are reported in grey because they are siblings. A detailed clinical characterization is provided (i.e multiple organs involvement, presence of comorbidity, clinical laboratory parameters, etc.) along with the genetic background for each patient. Liver and pancreas involvement is indicated in green color, heart involvement in magenta and kidney involvement in purple. The presence of hyposmia, classified from 0 to 10 using VAS score, is indicated in light blue. A darker shade of color represents a more severe organ damage. In-silico predicted deleterious variants in genes relevant for infection and pathogenic variants (both common and rare) reported in ClinVar Database are described and a further subdivision between genes involved in a mendelian disorder and/or viral infection susceptibility is provided. For all these gene categories, dark grey is used to identify the homozygous status of the variants while light grey for the heterozygous status. In the end, statistically significant genes obtained after Gene Burden analysis are listed: PRKRA and LAPTM4B mutational burden resulted to be enriched in the 35 COVID-19 patients compared to the controls, while OR4C5 and NDUFAF7 have proven to have an opposite trend, having a mutational burden more enriched in controls. For this reason, for NDUFAF7, OR4C5, genes the grey color and the white color are inverted because having less variants and by consequence a more functional gene represents a susceptibility factor. For this category, white color underlies a higher mutational burden while grey color indicates lower mutational burden. Clinical known co-morbidities: CHF (Congestive Heart Failure), Hy (Hypertension), CC (Colon Cancer), Le (Leukemia), DM (Diabetes mellitus), pHBV (Previous HBV infection), AMI (Acute myocardial infarction), BC (Breast Cancer), Ht (Hypothyroidism), IC (Ictus Cerebri), O (Obesity), Dy (Dyslipidemia), KF (Kidney Failure), CR (Congenital Rickets), AF (Atrial Fibrillation), Di (Diverticolosis), Br (Bronchiectasis), COPD (Chronic obstructive pulmonary disease), D (Depression), Tn (Thyroid Nodules), PC (Prostate Cancer), M (Melanoma), BCC (Basal cell carcinoma). Immunotherapy: T (Tocilizumab), R (Ruxolitinib), B (Baricitinib). Steroids: M (Methylprednisolone), D (Dexamethasone). Other anti-COVID19 drugs: HCQ (Hydroxicloroquine), A (Azithromycine), REM (Remdesevir), L/R (Lopinavir/Ritonavir), C (Cloroquine).

Fig 2. Mutational burden at the gene level.

The significance threshold including the Bonferroni correction is shown as a red line (α = 0.05, number of test, m = 7196). P-values for genes below the significance threshold are shown as grey dots. Black circles are used for the 4 genes that were identified as statistically different between COVID-19 samples and controls.