Human Leukocyte Antigen-G (HLA-G) is a key immunomodulatory molecule with multiple isoforms, including recently identified variants lacking the α1 domain (HLA-G Δα1). The absence of the α1 domain may reduce immune inhibition, particularly of Natural Killer (NK) cells, which are often suppressed during viral infections such as SARS-CoV-2. This suggests a novel immune regulatory mechanism that could mitigate COVID-19-related complications, including coagulopathies. This study investigates the influence of full-length and Δα1 HLA-G isoforms in NK-cell activity in vitro during SARS-CoV-2 infection and whether their expression associates with viral persistence and coagulopathy in COVID-19 patients, using vascular specimens retrieved from surgical procedures. RCC7 cell lines engineered to express either the full-length or Δα1 form of HLA-G were infected with Omicron SARS-CoV-2 to assess NK cell-mediated cytotoxicity in a co-culture system. Contrary to full-length, Δα1 HLA-G only partially inhibited NK activation, allowing greater cytotoxicity and higher IFN-I/II expression. To evaluate clinical relevance, vascular tissues from coagulopathic COVID-19 patients were analyzed for in situ SARS-CoV-2 persistence and HLA-G isoform expression. SARS-CoV-2 negative tissues more frequently expressed Δα1 and displayed higher systemic interferon (IFNs) levels. Among infection-positive cases, Δα1 expression was also associated with stronger IFN-β and IFN-γ responses. These in vivo trends mirror in vitro findings, supporting a model in which full-length HLA-G dampens NK-mediated clearance of infected vascular cells, favoring viral persistence and potentially contributing to immunothrombosis, while Δα1 permits enhanced antiviral immunity. Overall, these findings identify distinct immunomodulatory roles for HLA-G isoforms in SARS-CoV-2 infection. The Δα1 variant exhibits reduced inhibitory potency, partially preserving NK-cell antiviral functions and modulating interferon responses, whereas full-length HLA-G may facilitate vascular viral persistence and coagulopathy. HLA-G isoform profiling may thus represent a novel biomarker and therapeutic target in COVID-19 associated vascular pathology.

HLA-G encodes an immune checkpoint molecule with restricted expression in immune-privileged tissues and pathological conditions. It exhibits limited coding diversity but substantial regulatory-region variation influencing expression levels. Strong linkage disequilibrium across HLA-G creates a structured genetic architecture in which regulatory and coding variants co-segregate into well-defined haplotypes, enabling the imputation of complete HLA-G haplotypes from partial genomic data. We developed imputation models to predict HLA-G 4-field alleles, promoter, and 3'UTR haplotypes from whole-exome sequencing and SNP array data using HIBAG. Multi-ethnic reference panels were constructed from 5,347 individuals from three diverse cohorts (1000 Genomes, Human Genome Diversity Project, and Brazilian SABE cohort). Models were validated through cross-validation and independent datasets. Exome-based imputation achieved high accuracy (>99%) for common alleles (frequency>1%), with mean posterior probabilities exceeding 0.95. SNP array-based models showed slightly lower but still robust performance (>95% accuracy). Our approach enables simultaneous prediction of coding and regulatory sequences, providing comprehensive functional information from datasets that do not capture the complete HLA-G diversity. These models facilitate HLA-G analysis in widely available genomic datasets lacking introns and regulatory regions (tumor exomes, SNP arrays), enabling investigation of HLA-G's role in immune regulation, transplantation, cancer, and pregnancy complications without full-gene sequencing.