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Summerfield, A.

Publications and source records attributed to Summerfield, A..

15 recordsLinked to original sources

An RNA replicon vaccine encoding HA and NA prevents shedding of antigen-drifted 2009 pandemic H1N1 influenza virus in the pig model

Seasonal influenza viruses escape the human immune response by antigenic drift, i.e. the positive selection of point mutations that prevent the binding of inhibitory antibodies to the influenza antigens HA and NA. The efficacy of seasonal influenza vaccines can be less than 50% if the selected influenza vaccine strain does not match the antigenic characteristics of the circulating seasonal influenza virus. In this study, we used the porcine model to evaluate the efficacy of an RNA replicon vaccine encoding the HA and NA antigens of A/Hamburg/4/2009 (H1N1) (H1N1HH4/09) in inducing cross-reactive immunity. We found that a single intramuscular immunization with this vaccine elicited high levels of antibodies with H1N1HH4/09-neutralizing activity and potent N1-sialidase inhibition. A second immunization with the same H1/N1 RNA replicon particles or with a live-attenuated influenza vaccine (LAIV) based on a modified H1N1HH4/09 virus boosted the inhibitory activity of the immune sera against the antigen-drifted A/Victoria/2570/2019 (H1N1) (H1N1Vic/19) strain. Interestingly, vaccination elicited N1-specific antibodies that also inhibited the activity of avian N1 sialidase and potently inhibited the replication of A/cattle/Texas/063224-24-1/2024 (H5N1) (H5N1Tex/24) in vitro. When challenged nasally with a H1N1HH4/09 /H1N1Vic/19 6:2 reassortant virus encoding the HA and NA antigens of H1N1Vic/19, immunized pigs did not shed infectious virus while the control animals did, suggesting that homologous prime/boost vaccination with H1/N1 replicon particles can block virus replication in the upper respiratory tract as efficiently as the heterologous RNA replicon prime/LAIV boost immunization regimen. In conclusion, RNA replicons encoding both HA and NA either used alone or in combination with LAIV mediate protection against antigen-drifted influenza viruses and reduce the risk of vaccination breakthroughs due to antigen mismatch. Furthermore, this vaccine may also limit the infection by zoonotic H5N1 viruses.

microbiology↗

Correlates of protection against African swine fever virus identified by a systems immunology approach

African swine fever virus (ASFV) causes a fatal hemorrhagic disease in domestic pigs and wild boars, which poses severe threats to the global pork industry. Despite the promise of live attenuated vaccines (LAVs), their narrow margin between efficacy and residual virulence presents major safety challenges. This study bridges a critical knowledge gap in ASF vaccinology by identifying innate and adaptive correlates of protection. This was achieved by using an established model with two groups of pigs differing in baseline immunological status (farm and specific pathogen-free [SPF]). The animals were immunized with an attenuated ASFV strain and subsequently challenged with a related, highly virulent genotype II strain. By applying a systems immunology approach, we correlated kinetic data, including serum cytokines, blood transcription modules (BTMs), T-cell responses, and antibody levels, with clinical outcomes to track protective and detrimental immune responses to the virus over time. Key innate correlates of protection included early and sustained IFN- response, activation of antigen presentation BTMs, and controlled IL-8 levels during immunization. Lower baseline immune activation observed in SPF pigs in steady state was linked to increased protection. Adaptive correlates encompassed cell cycle, plasma cell, and T-cell BTM responses lasting until day 15 post-immunization. Consequently, an effective response from ASFV-specific Th cells prior to challenge indicated protection. After the challenge, an early IFN- response, along with low levels of pro-inflammatory cytokines and a strong induction of memory Th and Tc cells, correlated with improved clinical outcomes. The model highlights the critical role of host-specific factors in vaccine efficacy and provides a valuable framework for optimizing ASFV vaccine design while distinguishing between protective and detrimental immune responses.

immunology↗

Dendritic-cell diversity in equine blood revealed by single-cell transcriptomics

Unbiased classification of equine dendritic cells (DC) is necessary to address various research questions such as the role of DC subsets in immune-mediated diseases of horses. We applied single-cell RNA sequencing (scRNA-seq) on DC enriched from the blood of two horses. All main DC subsets were detected by key gene expression, including conventional DC type 1 (cDC1; XCR1) and type 2 (cDC2; FCER1A, CD1E) as well as plasmacytoid DC (pDC; TCF4). In addition, we detected a small cluster of hematopoietic progenitors, as well as transitional DC (tDC; FCER1A, TCF4) and putative DC type 3 (DC3; FLT3, CD163). Our data confirms the previously reported phenotype of equine pDC (Flt3+MHC-IIlowCADM1lowCD172aint), cDC1 (Flt3+MHC-IIhighCADM1highCD172alow-int) and cDC2 (Flt3+MHC-IIhighCADM1intCD172ahigh), while also highlighting considerable CD14 expression for cDC2. Two subclusters of equine cDC2 were found to be enriched in FCER1A or CX3CR1 transcripts (cDC2.1 and cDC2.2, respectively), with suggested enhanced extravasation and T-cell stimulatory capacities of the latter. Conservation of DC subsets across species (horse, pig, human, mouse) was illustrated by enrichment analyses with subset-specific gene signatures and by cross-species data integration with publicly available scRNA-seq datasets. Our atlas of equine blood DC is a valuable resource for comparative analyses, and it forms the foundation for understanding the involvement of distinct DC subsets in infections and immune-mediated pathologies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/644174v2_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@bdce22org.highwire.dtl.DTLVardef@1285715org.highwire.dtl.DTLVardef@16d37c8org.highwire.dtl.DTLVardef@1695121_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Unraveling dendritic-cell diversity in blood of pigs: welcome tDC and DC3

Dendritic cells (DC) are professional antigen presenting cells playing a major role in orchestrating adaptative immune responses. To adapt to various immune challenges, such as different classes of pathogens, specialized subsets of DC have evolved across species. To date, DC are classified as conventional DC (cDC1, cDC2) and plasmacytoid DC (pDC), with the more recent addition of DC3 and transitional DC (tDC) that were discovered in human and mouse thanks to high-dimensional phenotyping and single-cell sequencing technologies. Here, by combining flow cytometry and RNA-seq on the bulk- and single-cell level, we identified the porcine equivalent of tDC in blood as CD14-CADM1-CD172a+CD4-cells expressing both Flt3 and CD123 (IL-3RA). This new subset forms a well-defined cluster when mapped onto scRNA-seq data of enriched DC and shares transcriptomic features and abundance with porcine blood cDC2 and pDC. Moreover, we describe putative porcine DC3 as transcriptionally overlapping cells in-between cDC2 and monocytes. With the core functions of tDC and DC3 remaining to be elucidated, our datasets provide a valuable resource for cross-species research on DC heterogeneity in various lymphoid and non-lymphoid tissues.

immunology↗

Bovine dendritic-cell subsets in lymphoid and non-lymphoid tissues: work in progress

Bovine dendritic-cell subsets can be readily identified in flow cytometry by staining for Flt3, CD4 and CD13. While this gating strategy could be confirmed by bulk RNA-seq of subsets sorted from peripheral blood mononuclear cells, it remains to be determined if the same gating strategy can be applied to gate on cDC1, cDC2 and pDC within lymphoid and non-lymphoid tissues. With this preprint we aim to inform on the current status of phenotyping experiments performed on Flt3+ cells in mesenteric lymph nodes, spleen and lung of cattle. Distinct DC subsets can be gated in all tissues based on CD4 and CD13, with high frequencies of Flt3+CD13+ cells (putative cDC1) detected in the lung. Further phenotyping performed on lymph node cells (in particular CADM1, CD26 and CD123) support the subset classification analogous to blood, with pDC being Flt3+CD4+CD13- and cDC1 being Flt3+CD4-CD13+. Heterogeneous expression of CADM1 and CD26 on Flt3+CD4-CD13- putative cDC2 warrants further investigations.

immunology↗

Expression of XCR1, CX3CR1, CSF1R and ADGRE1 on subsets of bovine blood dendritic cells and monocytes

Among dendritic cells (DC) and monocytes in blood of cattle we can distinguish conventional and plasmacytoid DC (cDC1, cDC2, pDC) and classical, intermediate and nonclassical monocytes (cM, intM, ncM), respectively. Phenotypic definitions of subsets rely on combinations of only a few markers such as CD13 and CD4 for Flt3+ dendritic cells, and CD14 and CD16 for CD172ahigh monocytes. Additional reagents for flow cytometry are urgently needed to refine these phenotypic classifications and account for heterogeneity of these cells, in particular cDC2 and intM. In the current study we have investigated expression of CX3CR1 and ADGRE1 on bovine blood DC and monocyte subsets, and have tested two newly generated bovine recombinant proteins (XCL1 and CSF1) for staining of XCR1 and CSF1R. Staining patterns obtained by multicolor flow cytometry of peripheral blood mononuclear cells from two cows were largely in line with gene expression data available from a previous study (bulk RNA-seq of sorted DC and monocyte subsets from bovine blood).

immunology↗

Peste des Petits Ruminants virus virulence is associated with an early inflammatory profile in the tonsils and cell cycle arrest in lymphoid tissue

Using a systems immunology approach, this study comprehensively explored the immunopathogenesis of Peste des Petits Ruminants (PPR) focussing on strain-dependent differences in virulence. Saanen goats were infected either with the highly virulent Morroco 2008 (MA08) or the low virulent Ivory Coast 1989 (IC89) strain of PPR virus (PPRV). As expected, MA08-infected goats exhibited higher clinical scores, pronounced lymphocyte depletion, and lesions affecting mucosal and lymphoid tissues. CD4 T cells were found to be most affected in terms of depletion and infection in the peripheral blood. Transcriptional analyses of the blood and lymphoid tissue demonstrated activation of interferon type I (IFN-I) responses at three days post infection (dpi) only with MA08, but comparable IFN-I expression levels with MA08 and IC89 at 6 dpi. In contrast, only the MA08 strain induced strong inflammatory and myeloid cell-related transcriptional responses which as observed in tonsils but not in the mesenteric lymph node. This inflammatory response in the tonsil was associated with an extensive damage and infection of the tonsillar epithelium in the crypts, pointing on a barrier defect as a possible cause of inflammation. The other prominent effect induced by MA08, but not IC89, was a strong and early downregulation of cell cycle gene networks in lymphoid tissues. This effect was found in the blood compartment and all analysed lymphoid tissues and can be interpreted as suppressed lymphocyte proliferation that may cause immunosuppression during the first week following MA08 infection. A proteome analysis confirmed elevated synthesis of IFN-I response proteins during infection with both strains, but only the MA08 strain additionally upregulated ribosomal and inflammation-related proteins. In conclusion, the present comprehensive investigation delineates strain-dependent differences in early immunopathological processes associated with severe inflammation disease and a blunted lymphocyte proliferation. Understanding such strain-specific differences is relevant for effective PPRV surveillance strategies. Author summaryField observations show that the severity of infection with Peste des Petits Ruminants virus (PPRV) is highly dependent on the viral strains and the host infected, but the mechanisms behind these variations are not well understood. Here we compare immune response in Saanen goats infected with high (MA08) and low (IC89) virulent PPRV strains. Analyses revealed a differential immune response: early activation of type I interferon (IFN-I) responses only with MA08, but comparable IFN-I expression levels with MA08 and IC89 at later stages. Additionally, only the MA08 strain triggered inflammatory and myeloid cell- related responses in the tonsils, as well as a disseminated early and marked suppression of lymphocyte proliferation evidenced by cell cycle arrest. CD4 T cells were found to be most affected in terms of depletion in the peripheral blood. Massive infection of the tonsils, particularly for the highly virulent strains, seems to induce epithelial lesions that promotes the inflammatory responses. These findings underscore the importance of understanding strain- specific differences for appropriate surveillance and control of PPR.

immunology↗

Intramuscular prime/intranasal boost vaccination to induce sterilizing immunity against influenza A virus infection

The most commonly used influenza vaccines are made from inactivated viruses and are administered via the intramuscular route. Although these vaccines can protect from severe lower respiratory tract disease, they do not completely prevent virus replication in the upper respiratory tract, and this may lead to virus excretion and dissemination. Therefore, nasally administered live-attenuated influenza vaccines (LAIV) that induce mucosal immunity have been developed, but finding an optimal balance between sufficient attenuation and immunogenicity remained challenging. These problems apply to both human and swine influenza vaccines. We have recently developed an LAIV candidate based on the 2009 pandemic H1N1 virus which encodes a truncated NS1 protein and lacks PA-X protein expression (NS1(1-126)-{Delta}PAX). This virus showed a blunted replication and elicited a strong innate immune response. In the present study, we took advantage of the pig animal model to evaluate this vaccine candidate in vivo and to identify a strategy for its improvement. Nasal infection of pigs with the NS1(1-126)-{Delta}PAX LAIV candidate did not cause disease but was associated with prolonged virus shedding from the upper respiratory tract. To increase safety of the vaccine candidate, we developed a novel prime/boost vaccination strategy consisting of a haemagglutinin-encoding propagation-defective vesicular stomatitis virus replicon vaccine for primary immunization via the intramuscular route, and the NS1(1-126)-{Delta}PAX LAIV for secondary immunization via the nasal route. This immunization strategy significantly reduced LAIV shedding, increased the production of specific serum IgG, neutralizing antibodies, Th1 memory cells, and induced virus-specific mucosal IgG and IgA. Of particular note, the immune response induced by this vaccination strategy completely blocked replication of the homologous challenge virus in the respiratory tract, indicating that sterilizing immunity was achieved. In summary, our novel intramuscular prime/intranasal boost vaccine combines the features of high efficacy and safety which are urgently needed to combat influenza epidemics and pandemics. Author summaryInactivated influenza vaccines which are administered intramuscularly are safe but offer only limited protection. In addition, they do not adequately prevent virus transmission by infected individuals. On the other hand, nasally administered live-attenuated influenza vaccines induce a mucosal immune response, which can effectively prevent primary infection and virus excretion. However, live-attenuated vaccines might not be sufficiently immunogenic if they are too attenuated or they trigger a robust immune response but are still too virulent. To overcome this challenge, we have developed a novel prime/boost vaccination strategy consisting of an initial intramuscular immunization with a propagation-defective RNA virus vector and a subsequent nasal immunization with a modified influenza virus that has lost its ability to counteract the hosts innate immune response. Using the pig model, we demonstrate that this approach elicited a more robust immune response both systemically and at mucosal surfaces. Importantly, replication of the vaccine virus in the respiratory tract was reduced, and challenge virus remained undetectable. In summary, our innovative vaccine, which combines intramuscular and intranasal routes of application, demonstrates high efficacy and safety and represents a valuable tool to control influenza epidemics and pandemics.

immunology↗

Fitness adaptations of Japanese encephalitis virus in pigs following vector-free serial passaging

Japanese encephalitis virus (JEV) is a zoonotic mosquito-transmitted Flavivirus circulating in birds and pigs. In humans, JEV can cause severe viral encephalitis with high mortality. Considering that vector-free direct virus transmission was observed in pigs, JEV introduction into an immunologically naive pig population could result in a series of direct transmissions disrupting the alternating host cycling between vertebrates and mosquitoes. To assess the potential consequences of such a realistic scenario, we passaged JEV ten times in pigs. This resulted in higher in vivo viral replication, increased shedding, and stronger innate immune responses in pigs. Nevertheless, the viral tissue tropism remained similar and frequency of direct transmission was not enhanced. Next generation sequencing showed single nucleotide deviations in 10% of the genome during passaging. In total, 25 point mutations were selected to reach a frequency of at least 35% in one of the passages. From these, six mutations resulted in amino acid changes located in the precursor of membrane, the envelope, the non-structural 3 and the non-structural 5 proteins. In a competition experiment with two lines of passaging, the mutation M374L in the envelope protein and N275D in the non-structural protein 5 showed a fitness advantage in pigs. Altogether, the interruption of the alternating host cycle of JEV caused a prominent selection of viral quasispecies as well as selection of de novo mutations associated with fitness gains in pigs, albeit without enhancing direct transmission frequency. Author summaryJapanese encephalitis virus (JEV) represents a major health threat in parts of Asia and Oceania. Primary vertebrate hosts are birds and pigs, but human infection also occurs and can cause severe encephalitis with high mortality. Like other Flaviviruses transmitted by insect bites, JEV requires replication in alternating cycles between mosquitoes on one side and birds or pigs on the other side. However, we previously reported that direct transmissions between pigs in absence of mosquitos can occur. Considering the increased risks for such events after the spread of JEV to a new region with immunologically naive pigs, the present study was performed to understand if and how a series of direct transmissions would promote JEV adaptations to pigs and change virus-host interactions. Pigs infected with JEV passaged ten times showed enhanced clinical symptoms and stronger antiviral immune response, but luckily no increase in direct transmission was observed. Nevertheless, genomic analysis demonstrated a complete change in dominant virus variants, as well as selection of six viral amino acid changes. This indicates that interruptions of the alternating lifestyle of JEV causes a strong evolutionary pressure, which through fitness adaptations can change the viral characteristics.

microbiology↗

Single-cell transcriptomics reveals striking heterogeneity and functional organization of dendritic and monocytic cells in the bovine mesenteric lymph node

Dendritic and monocytic cells co-operate to initiate and shape adaptive immune responses in secondary lymphoid tissue. The complexity of this system is poorly understood, also because of the high phenotypic and functional plasticity of monocytic cells. We have sequenced mononuclear phagocytes in mesenteric lymph nodes (LN) of three adult cows at the single-cell level, revealing ten dendritic-cell (DC) clusters and seven monocyte/macrophage clusters with clearly distinct transcriptomic profiles. Among DC, we defined LN-resident subsets and their progenitors, as well as subsets of highly activated migratory DC differing in transcript levels for T-cell attracting chemokines. Our analyses also revealed a potential differentiation path for cDC2, resulting in a cluster of inflammatory cDC2 with close transcriptional similarity to putative DC3 and monocyte-derived DC. Monocytes and macrophages displayed sub-clustering mainly driven by pro- or anti-inflammatory expression signatures, including a small cluster of cycling, presumably self-renewing, macrophages. With this transcriptomic snapshot of LN-derived mononuclear phagocytes, we reveal functional properties and differentiation trajectories in a "command center of immunity" that are likely to be conserved across species.

immunology↗

The baseline immunological and hygienic status of pigs impact disease severity of African swine fever

African Swine Fever virus (ASFV) is a large double-enveloped DNA virus of the Asfarviridae family that causes a lethal hemorrhagic disease in domestic pigs and wild boars. Since 2007, a highly virulent genotype II strain has emerged and spread in Europe and South-East Asia, where millions of animals succumbed to the disease. Field- and laboratory-attenuated strains of ASFV cause highly variable clinical disease severity and survival, and mechanisms remain unclear. We hypothesized that the immunological and hygienic status of pigs is a determinant of ASF disease course. Here we compared the immunological profile at baseline and in response to ASFV infection in specific pathogen-free (SPF) and farm-raised Large White domestic pigs. At steady state, SPF pigs showed lower white blood cell counts and a lower basal inflammatory and antiviral transcriptomic profile compared to farm pigs associated with profound differences in gut microbiome composition. After inoculation with a highly virulent ASFV genotype II strain (Armenia 2008), severe clinical signs, viremia and pro-inflammatory cytokines appeared sooner in SPF pigs, indicating a reduced capacity to control early virus replication. In contrast, during infection with an attenuated field isolate (Estonia 2014), SPF pigs presented a milder and shorter clinical disease with full recovery, whereas farm pigs presented severe protracted disease with 50% lethality. Interestingly, farm pigs showed higher production of inflammatory cytokines, whereas SPF pigs produced more anti-inflammatory IL-1ra early after infection, and presented a stronger expansion of leukocytes in the recovery phase. Altogether, our data indicate that the hygiene-dependent innate immune status has a double-edge sword impact on immune responses in ASF pathogenesis. While the higher baseline innate immune activity helps the host in reducing initial virus replication, it promotes immunopathological cytokine responses, and delays lymphocyte proliferation after infection with an attenuated strain. Such effects should be considered for live vaccine development and vigilance.

microbiology↗

Enhanced fitness of SARS-CoV-2 variant of concern B.1.1.7, but not B.1.351, in animal models

Emerging variants of concern (VOCs) drive the SARS-CoV-2 pandemic. We assessed VOC B.1.1.7, now prevalent in several countries, and VOC B.1.351, representing the greatest threat to populations with immunity to the early SARS-CoV-2 progenitors. B.1.1.7 showed a clear fitness advantage over the progenitor variant (wt-S614G) in ferrets and two mouse models, where the substitutions in the spike glycoprotein were major drivers for fitness advantage. In the "superspreader" hamster model, B.1.1.7 and wt-S614G had comparable fitness, whereas B.1.351 was outcompeted. The VOCs had similar replication kinetics as compared to wt-S614G in human airway epithelial cultures. Our study highlights the importance of using multiple models for complete fitness characterization of VOCs and demonstrates adaptation of B.1.1.7 towards increased upper respiratory tract replication and enhanced transmission in vivo. Summary sentenceB.1.1.7 VOC outcompetes progenitor SARS-CoV-2 in upper respiratory tract replication competition in vivo.

microbiology↗

Pulmonary mesenchymal stem cells are engaged in distinct steps of host response to respiratory syncytial virus infection

Lung-resident (LR) mesenchymal stem and stromal cells (MSCs) are key elements of the alveolar niche and fundamental regulators of homeostasis and regeneration. We interrogated their function during virus-induced lung injury using the highly prevalent respiratory syncytial virus (RSV) which causes severe outcomes in infants. We applied complementary approaches with primary pediatric LR-MSCs and a state-of-the-art model of human RSV infection in lamb. Remarkably, RSV-infection of pediatric LR-MSCs led to a robust activation, characterized by a strong antiviral and pro-inflammatory phenotype combined with mediators related to T cell function. In line with this, following in vivo infection, RSV invades and activates LR-MSCs, resulting in the expansion of the pulmonary MSC pool. Moreover, the global transcriptional response of LR-MSCs appears to follow RSV disease, switching from an early antiviral signature to repair mechanisms including differentiation, tissue remodeling, and angiogenesis. These findings demonstrate the involvement of LR-MSCs during virus-mediated acute lung injury and may have therapeutic implications. AUTHOR SUMMARYThis work identifies a novel function of lung-resident MSCs during virus-induced acute lung injury. These findings contribute to the understanding of host response and lung repair mechanisms during a highly prevalent clinical situation and may have therapeutic implications.

microbiology↗

No evidence for human monocyte-derived macrophage infection and antibody-mediated enhancement of SARS-CoV-2 infection

Vaccines are essential to control the spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and to protect the vulnerable population. However, one safety concern of vaccination is the possible development of antibody-dependent enhancement (ADE) of SARS-CoV-2 infection. The potential infection of Fc receptor bearing cells such as macrophages, would support continued virus replication and inflammatory responses, and thereby potentially worsen the clinical outcome of COVID-19. Here we demonstrate that SARS-CoV-2 and SARS-CoV-1 neither infect human monocyte-derived macrophages nor induce inflammatory cytokines in these cells, in sharp contrast to Middle East respiratory syndrome (MERS) coronavirus and the common cold human coronavirus 229E. Furthermore, serum from convalescent COVID-19 patients neither induced enhancement of SARS-CoV-2 infection nor innate immune response in human macrophages. These results support the view that ADE may not be involved in the immunopathological processes associated with COVID-19, however, more studies are necessary to understand the potential contribution of antibodies-virus complexes with other cells expressing FcR receptors.

immunology↗

Transcriptomic signature and metabolic programming of bovine classical and nonclassical monocytes indicate distinct functional specializations

Similar to human monocytes, bovine monocytes can be split into CD14+CD16- classical and CD14-CD16+ nonclassical monocytes (cM and ncM, respectively). Here, we present an in-depth analysis of their steady-state transcriptomes, highlighting pronounced functional specializations. Gene transcription indicates that pro-inflammatory and antibacterial processes are associated with cM, while ncM appear to be specialized in regulatory/anti-inflammatory functions and tissue repair, as well as antiviral responses and T-cell immunomodulation. In support of these functional differences, we found that oxidative phosphorylation prevails in ncM, whereas cM are clearly biased towards aerobic glycolysis. Furthermore, bovine monocyte subsets differed in their responsiveness to TLR ligands, supporting an antiviral role of ncM. Taken together, these data clearly indicate a variety of subset-specific functions in cM and ncM that are likely to be transferable to monocyte subsets of other species, including humans.

immunology↗