Genetic Variants predisposition to Severe COVID-19 Illness Identified in a Healthy Nigerian Man, using Nebula Genomics Gene.iobio Platform

ABSTRACT

Background: The landscape of coronavirus disease in Nigeria is very undulating with established uncertainty due to blatant disregard to genomics research by government health care institutions. As other countries in the west are documenting Covid-19 disease genomics variations among her populace, few research efforts are made by a private university to replicate such data in Nigeria. The objective of this case study was to identify genetic variations associated with severe Covid-19 disease, by whole genome sequencing on a heathy adult Nigerian. Methods: Buccal swabs were self-collected and DNA extracted, quantified, normalised before sequencing on the high-throughput MGI DNBSEQ-T7 DNA sequencer using Nebula genomics platform. Raw sequences in FASTQ files were assembled in contigs or chromosomes using the Gene iobio pipeline. DNA sequences were aligned with integrated genome viewer (IGV) to the human reference genome GRCh38 (hg38) for single nucleotide polymorphism (SNP) variant calls, deletions and insertions. The genetic variations were compared with the recent genome wide association study (GWAS) implicating 8 genetic loci associated with critical covid-19 disease. Results: Five (5) out of the eight (8) genetic variants associated with severe covid-19 were identified in the healthy subject. The highest number of SNPs occurred in Leucine Zipper Transcription Factor Like 1 (LZTFL1) with 147 SNPs, followed by 100 SNPs observed in Oligoadenylate synthetase 1 (OAS1). Six (6) missense variants were observed in Coiled-Coil Alpha-Helical Rod Protein 1 (CCHCR1), all occurring in heterozygous pattern. The SNP in rs3131294 for variant Notch receptor 4 (NOTCH4) located at chr6:32220606 was present in 90% of the allele frequency, while the variant found in Dipeptidyl peptidase (DPP9) on rs2109069 located in chr19:4719431 implicated in GWAS and in this case study had 38% allele frequency. Conclusion: This case study has demonstrated the importance of genomics study that has the potential to play significant roles in mitigating risk factors associated with severe covid-19 disease for public health advise and personalized medicine.