Gene-Level Analyses of Novel Olfactory-Related Signal from Severe SARS-CoV-2 GWAS Reveal Association with Disease Mortality

TL;DR

This study identifies a genetic variant in the RTP5 gene linked to higher mortality in severe COVID-19 patients, suggesting a potential role in disease severity.

Contribution

The study discovers a novel SNP in RTP5 associated with mortality in severe COVID-19 and provides functional evidence via eQTL analysis.

Findings

The SNP rs7420371 G>A in RTP5 is significantly associated with 30- and 60-day mortality in severe COVID-19 patients.

The A allele of rs7420371 upregulates RTP5 mRNA expression in brain tissues.

RTP5 is a receptor transporter protein involved in olfactory and taste perception, potentially modulating SARS-CoV-2 infection responses.

Abstract

The coronavirus disease 2019 (COVID-19) was the third leading cause of mortality in the United States for three years in a row. The genetic contributions to disease severity remain unclear and many previously identified single nucleotide polymorphisms (SNPs) have not been replicated nor linked with functional significance.

To identify SNPs associated with mortality among hospitalized COVID-19 patients supplemented by expression quantitative trait loci (eQTL) evidence to infer plausible functional mechanisms related to COVID-19 severity.

A quality-controlled genome-wide association study (GWAS) supported by robust gene-level omnibus kernel association tests (SKAT-O), functional prediction, and eQTL analyses of the top GWAS signal.

Massachusetts General Hospital (MGH).

370 adult ICU patients with SARS-CoV-2 infection and acute hypoxemic respiratory failure and floor patients with mild hypoxemia managed with supplemental oxygen consecutively admitted to MGH between March and June 2020 (Surge 1), and January and March 2021 (Surge 2) with baseline clinical characteristics and demographics collected.

Low-pass genotyped SNPs from whole blood and aggregated SNP-sets of potential disease susceptibility loci with ±500 kb flanking regions.

Genome-wide individual SNP associations and SNP-set associations with mortality outcomes from 370 severe COVID-19 cases.

After LD pruning (<0.8) and false discovery rate adjustment (<0.05), we identified rs7420371 G>A of the receptor transporter protein 5 (RTP5) gene as the top independent signal significantly associated with 30- and 60-day mortality among severe COVID-19 patients (OR, 2.32; 95% CI, 1.59–3.39; p = 4.92 × 10−9 and OR, 2.06; 95% CI, 1.43–2.97; p = 5.43 × 10−8, respectively). SKAT-O analyses on the RTP5 SNP-set showed associations with both mortality outcomes (p = 5.90 × 10−5 and 6.17 × 10−5, respectively). eQTL analysis showed rs7420371 A allele significantly upregulated the mRNA expression of RTP5 in 266 cerebellum tissues, in 277 cerebellar hemisphere tissues, and in 270 cerebral cortex samples.

We discovered a novel, independent, and potentially functional SNP RTP5 rs7420371 G>A to be significantly associated with COVID-19 mortality. The A allele is significantly associated with elevated mRNA expression of RTP5 in the brain, an important protein coding gene that modulates olfactory binding and taste perceptions in response to SARS-CoV-2 infection.

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