Poking COVID-19: Insights on Genomic Constraints among Immune-Related Genes between Qatari and Italian Populations
Open Access
- 22 November 2021
- Vol. 12 (11), 1842
- https://doi.org/10.3390/genes12111842
Abstract
Host genomic information, specifically genomic variations, may characterize susceptibility to disease and identify people with a higher risk of harm, leading to better targeting of care and vaccination. Italy was the epicentre for the spread of COVID-19 in Europe, the first country to go into a national lockdown and has one of the highest COVID-19 associated mortality rates. Qatar, on the other hand has a very low mortality rate. In this study, we compared whole-genome sequencing data of 14398 adults and Qatari-national to 925 Italian individuals. We also included in the comparison whole-exome sequence data from 189 Italian laboratory-confirmed COVID-19 cases. We focused our study on a curated list of 3619 candidate genes involved in innate immunity and host-pathogen interaction. Two population-gene metric scores, the Delta Singleton-Cohort variant score (DSC) and Sum Singleton-Cohort variant score (SSC), were applied to estimate the presence of selective constraints in the Qatari population and in the Italian cohorts. Results based on DSC and SSC metrics demonstrated a different selective pressure on three genes (MUC5AC, ABCA7, FLNA) between Qatari and Italian populations. This study highlighted the genetic differences between Qatari and Italian populations and identified a subset of genes involved in innate immunity and host-pathogen interaction.Funding Information
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo" (5X1000 funding)
- Rome Foundation (Italy, Prot 317A/I)
- Regione Lazio (Italy, Progetti di Gruppi di Ricerca 2020 A0375-2020-36663 GecoBiomark)
This publication has 51 references indexed in Scilit:
- A global reference for human genetic variationNature, 2015
- Looking for a needle in a haystack: Cellular proteins that may interact with the tyrosine-based sorting signal of the TGEV S proteinVirus Research, 2015
- Second-generation PLINK: rising to the challenge of larger and richer datasetsGigaScience, 2015
- Correction: Genic Intolerance to Functional Variation and the Interpretation of Personal GenomesPLoS Genetics, 2013
- Genic Intolerance to Functional Variation and the Interpretation of Personal GenomesPLoS Genetics, 2013
- Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversityEuropean Journal of Human Genetics, 2012
- Overexpressing mouse model demonstrates the protective role of Muc5ac in the lungsProceedings of the National Academy of Sciences of the United States of America, 2012
- Robust relationship inference in genome-wide association studiesBioinformatics, 2010
- ABCA7 expression is regulated by cellular cholesterol through the SREBP2 pathway and associated with phagocytosisJournal of Lipid Research, 2006
- ATP-binding cassette transporter A7 enhances phagocytosis of apoptotic cells and associated ERK signaling in macrophagesThe Journal of cell biology, 2006