HLA predictions from the bronchoalveolar lavage fluid and blood samples of eight COVID-19 patients at the pandemic onset

Abstract

MOTIVATION\nWe are in the midst of a global viral pandemic, one with no clear cure and a high mortality rate. The Human Leukocyte Antigen (HLA) gene complex plays a critical role in host immunity. Here we analyse data from eight patient samples from the initial COVID-19 outbreak, and report on their HLA profiles. Our analysis paradigm may help provide future insights on disease susceptibility.\n\n\nRESULTS\nWe predicted HLA class I and II alleles from the transcriptome sequencing data prepared from the bronchoalveolar lavage (BAL) fluid samples of five patients and from the peripheral blood mononuclear cells (PBMC) of three patients at the early stage of the COVID-19 outbreak in Wuhan, China. We observe certain HLA allele overlap between the patients of those small cohorts, including the HLA-I A*24:02 allele predicted in four out of the five patients of the first cohort and HLA-II haplotype DPA1*02:02-DPB1*05:01 predicted in seven out of the eight patient samples analysed. Our analysis demonstrates the technical feasibility of HLA typing from BAL and PMBC metatranscriptomic samples. We stress that these are small cohorts, and although informative with respect to uncovering possible host defence genes shared between patients, additional work on larger cohorts is warranted to yield new and actionable knowledge on host susceptibility to SARS-CoV-2.\n\n\nAVAILABILITY\nThe tool used to perform the reported analysis results, HLAminer, is available from https://github.com/bcgsc/hlaminer. Predictions are available for download from https://www.bcgsc.ca/downloads/btl/SARS-CoV-2/BAL.\n\n\nSUPPLEMENTARY INFORMATION\nSupplementary data are available at Bioinformatics online.