Employing a Systematic Approach to Biobanking and Analyzing Clinical and Genetic Data for Advancing COVID-19 Research

Abstract

Within the GEN-COVID Multicenter Study, biospecimens from more than 1,000 SARS-CoV-2-positive individuals have thus far been collected in the GEN-COVID Biobank (GCB). Sample types include whole blood, plasma, serum, leukocytes, and DNA. The GCB links samples to detailed clinical data available in the GEN-COVID Patient Registry (GCPR). It includes hospitalized patients (74.25%), broken down into intubated, treated by CPAP-biPAP, treated with O2 supplementation, and without respiratory support (9.5%, 18.4%, 31.55% and 14.8, respectively); and non-hospitalized subjects (25.75%), either pauci- or asymptomatic. More than 150 clinical patient-level data fields have been collected and binarized according to the organs/systems primarily affected by COVID-19: heart, liver, pancreas, kidney, chemosensors, innate or adaptive immunity, and clotting system, for further statistics. Hierarchical Clustering analysis identified five main clinical categories: i) severe multisystemic failure with either thromboembolic or pancreatic variant; ii) cytokine storm type either severe with liver involvement or moderate; iii) moderate heart type either with or without liver damage; iv) moderate multisystemic involvement either with or without liver damage; v) mild either with or without hyposmia. GCB and GCPR are further linked to the GEN-COVID Genetic Data Repository (GCGDR), which includes data from Whole Exome Sequencing and high-density SNP genotyping. The data are available for sharing through the Network for Italian Genomes, within the COVID-19 dedicated section. The study objective is to systematize this comprehensive data collection and start identifying multi-organ involvement in COVID-19, defining genetic parameters for infection susceptibility within the population, and mapping genetically COVID-19 severity and clinical complexity among patients.

Shorter androgen receptor polyQ alleles protect against life-threatening COVID-19 disease in males

“…Cases and controls were drawn from the Italian GENCOVID 2 cohort of 1178 subjects infected with SARS-CoV-2 diagnosed either by RT-PCR on nasopharyngeal swab, or by serology test. 2 Demographic characteristics of patients enrolled in the cohort are summarized in Table 1 according to their clinical status. In particular, the cohort was subdivided into 5 groups, based on the type of the respiratory and medical support that was given to the patients: i. endotracheal intubation; ii, CPAP-biPAP ventilation; iii.…”

“…1 After this initial study, we extended the cohort to more than 1,000 Italian SARS-CoV-2 PCR-positive subjects. 2 Among them, 25% were asymptomatic, 25% were very severe, and the remaining presented with different levels of respiratory failure and multi-organ involvement. 2 Alongside the mode of transmission, viral load, comorbidities, and demographic factors (such as age and sex), the host genetic background appears to play an important role in COVID-19 severity and progression.…”

“…2 Among them, 25% were asymptomatic, 25% were very severe, and the remaining presented with different levels of respiratory failure and multi-organ involvement. 2 Alongside the mode of transmission, viral load, comorbidities, and demographic factors (such as age and sex), the host genetic background appears to play an important role in COVID-19 severity and progression. 3 Two groups have recently identified rare variants in the interferon type I pathway that are responsible for inborn errors of immunity in a small percentage of patients and autoantibodies against type I interferon genes in up to 10% of with severe COVID-19 5,6,7 .…”

“…1 After this initial study, we extended the cohort to more than 1,000 Italian SARS-CoV-2 PCR-positive subjects. 2 Among them, 25% were asymptomatic, 25% were very severe, and the remaining presented with different levels of respiratory failure and multi-organ involvement. 2…”

“…2 Among them, 25% were asymptomatic, 25% were very severe, and the remaining presented with different levels of respiratory failure and multi-organ involvement. 2…”