People infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) show a wide range of clinical variations, from asymptomatic infection to lethal disease. In a recent study published on the preprint server bioRxiv*, and an international team of researchers investigated the genetic, immunological, and evolutionary factors that determine the wide variability observed in the clinical manifestations of coronavirus disease 2019 (COVID-19).
Study: environmental and genetic factors of population differences in immune responses to SARS-CoV-2. Image credit: Billion Photos / Shutterstock.com
background
Numerous epidemiological and genetic studies have elucidated the impact of genetic factors and variations in innate immunity, including innate errors or neutralizing autoantibodies against type I interferons (IFNs) in contributing to the different clinical manifestations associated with SARS-CoV -2. The importance of lineage-related differences in transcriptional responses to immune challenges has also been described.
Combined with evidence suggesting that viruses and other infectious agents have had an overwhelming impact on human evolution, there is still an urgent need for in-depth investigations of the magnitude of variation in immune responses to SARS-CoV -2 and its drivers in populations around the world.
For example, in East Asians, strong genetic adaptations starting around 25,000 years ago have been reported against multiple human proteins that interact with the coronavirus. In addition, many examples of human adaptation to ribonucleic acid (RNA) viruses as a source of population genetic differentiation have also been published.
There is also growing evidence of modulations of COVID-19 severity in modern Eurasians due to Neanderthal haplotypes, which are key determinants of their introgression and immunity. Taken together, these data have sparked curiosity in the scientific community about how these past events of natural selection and archaic admixture might influence the immune response to SARS-CoV-2 in contemporary humans.
About the study
In the present study, researchers used single-cell RNA sequencing (scRNA-seq) with population genetics approaches to characterize cell type-specific transcriptional responses in peripheral blood mononuclear cells (PBMCs) from 222 healthy donors of various ancestries stimulated by SARS-CoV-2 or influenza A virus. PBMCs treated for six hours showed strong immune responses and high cell viability, which in turn helped the team to capture more than one million high-quality single-cell transcriptomes.
The study population consisted of 80, 80, and 115 individuals of Central African, Western European, and East Asian ancestry, respectively, representing different genetic ancestries due to their exposure to different environmental conditions. The effects of human genetic variants on transcriptional variations were assessed by mapping expression quantitative trait loci (eQTLs) that focused on cis-regulatory variants.
The researchers also explored the contribution of natural selection to population differentiation of immune responses. To this end, they searched for overlaps between eQTLs or reQTLs and genome-wide local adaptation signals that were measured using the population branching statistic (PBS).
In addition, we determined the contribution of differences in cellular proportions to the observed interindividual variability of responses to SARS-CoV-2 focusing on individuals of Central African and Western European ancestry, all who were recruited during the same sampling campaign.
Finally, we studied the functional consequences of Neanderthal introgression on present-day immune responses to viral challenges. A set of 100,345 introgressed “archaic” alleles or archaic single nucleotide polymorphisms (aSNPs) was used to determine whether eQTLs were over- or under-represented among introgressed variants relative to randomly matched SNPs. Together, this information allowed the researchers to understand the contributions of genetic variants that alter responses to SARS-CoV-2 in vitro to the risk of COVID-19 in vivo.
Population-scale single-cell responses to SARS-CoV-2 and IAV. a, Study design. bic, Uniform manifold approximation and projection (UMAP) of 1,047,824 peripheral blood mononuclear cells: resting (unstimulated; NS), stimulated with SARS-CoV-2 (COV) or influenza A virus (IAV ) for six hours. b, Colors indicate the 22 different cell types that are inferred. c, Distribution of cells in NS, COV and IAV conditions in UMAP coordinates. The contour plot indicates the overall cell density and the colored areas delineate regions of high cell density in each condition (grey: NS, red: COV, blue: IAV). d, Comparison of transcriptional responses to SARS-CoV-2 and IAV across major immune lineages. Inflammatory and interferon-stimulated genes are highlighted in orange and blue, respectively. e, Relative expression of transcripts encoding IFN-α by each immune cell type in response to SARS-CoV-2 and IAV. Bar lengths indicate the mean number of IFN-α transcripts contributed by each cell type to the overall pool (frequency of cell type × mean number of IFN-α transcripts per cell) . Dotted area is proportional to the mean level of IFN-α transcripts in each cell type (counts per million). f, Correlation of ISG activity scores between individuals, after exposure to SARS-CoV-2 and IAV. Each point corresponds to a single individual (n = 222) and its color indicates the self-reported ancestry of the individual in question (AFB: Central Africa; EUB: Western Europe; ASH: East Asia).
Results of the study
Cell ratios that varied due to environmental exposures were the main drivers of population differences in immune responses to SARS-CoV-2. The higher proportions of memory cells detected in lymphoid lineages of Africans and their relationship with persistent cytomegalovirus (CMV) infections suggest that population-level differences in cellular activation states could be primarily driven by for lifetime exposure to the pathogen.
Socioenvironmental factors were also found to covary with an individual’s genetic ancestry, which in turn could lead to an overestimation of effects on immune responses to SARS-CoV-2, which is a phenotypic variation.
Common genetic alleles also contribute to the observed variability in immune responses to viral challenges. However, their effects tend to be limited to a subset of genes that exhibit strong population differentiation.
For example, the rs1142888-G variant is found at a higher frequency in Europeans than in Africans due to a selection event that occurred between 21,900 and 35,600 years ago. This variant represents more than 2.8-fold higher expression levels of guanylate binding protein 7 (GBP7) which facilitates IAV replication by suppressing innate immunity.
GBP7 also regulates IFN-γ-induced host oxidative defense that confers resistance to intracellular bacteria, such as Listeria monocytogenes and Mycobacterium tuberculosis, thus providing a feasible mechanism for positive selection at this genetic locus.
Viral evolution changed the genetic basis of infectious diseases over time. Thus, limited overlap was observed between the alleles selected during this period in East Asia and the genetic variants reported to underlie the risk of COVID-19.
However, the researchers found traces of a selection event targeting reQTLs specific to SARS-CoV-2 in East Asian ancestors that coincided with the proposed timing of an ancient epidemic about 25,000 years ago that affected the evolution of the proteins that interact with the coronavirus.
Delineating the genetic architecture of immune response variations in various cell types provided mechanistic insight into the effect of alleles associated with COVID-19. For example, the efficiency of IFN signaling was confirmed to be essential for favorable clinical outcomes of SARS-CoV-2 infection.
A Neanderthal introgressed eQTL at the mucin20 (MUC20) gene locus was found to increase its expression in SARS-CoV-2-stimulated CD4+ T cells and reduce susceptibility to COVID-19. Perhaps the Neanderthal haplotype conferred greater resistance to viral infections through a similar effect, as mucins form a barrier against infection in the nasal epithelium.
Conclusions
Overall, the study results highlight the importance of using sc-RNA-seq approaches to capture the diversity of the human immune response to RNA viruses, especially SARS-CoV-2. These observations provide new insights into the environmental, genetic, and evolutionary drivers of immune response variations among populations with genetic variations.
*Important news
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be considered conclusive, guide clinical practice/health-related behavior, or be treated as established information.