Antigenic Profile Research Articles

Highly Defined Induced Pluripotent Stem Cell Lines Mimic Donor Red Blood Cell Antigen Profiles for Therapeutic and Diagnostic Use.

Our group generated two induced pluripotent stem cell (iPSC) lines for in vitro red blood cell (RBC) production from blood donors with extensively known erythrocyte antigen profiles. One line was intended to give rise to RBCs for transfusions in patients with sickle cell disease (SCD), while the other was developed to create RBC panel reagents. Two blood donors were selected based on their RBC phenotypes, further complemented by high-throughput DNA array analysis to obtain a more comprehensive erythrocyte antigen profile. Enriched erythroblast populations from the donors' peripheral blood mononuclear cells were reprogrammed into iPSCs using nonintegrative plasmid vectors. The iPSC lines were characterized and subsequently subjected to hematopoietic differentiation. iPSC PB02 and iPSC PB12 demonstrated in vitro and invivo iPSC features and retained the genotype of each blood donor's RBC antigen profile. Colony-forming cell assays confirmed that iPSC PB02 and iPSC PB12 generated hematopoietic progenitors. These two iPSC lines were generated with defined erythrocyte antigen profiles, self-renewal capacity, and hematopoietic differentiation potential. With improvements in hematopoietic differentiation, these cells could potentially be more efficiently differentiated into RBCs in the future. They could serve as a complementary approach for obtaining donor-independent RBCs and addressing specific demands for blood transfusions.

When and why is red blood cell genotyping applicable in transfusion medicine: a systematic review of the literature.

This review aims to provide a better understanding of when and why red blood cell (RBC) genotyping is applicable in transfusion medicine. Articles published within the last 8 years in peer-reviewed journals were reviewed in a systematic manner. RBC genotyping has many applications in transfusion medicine including predicting a patient's antigen profile when serologic methods cannot be used, such as in a recently transfused patient, in the presence of autoantibody, or when serologic reagents are not available. RBC genotyping is used in prenatal care to determine zygosity and guide the administration of Rh immune globulin in pregnant women to prevent hemolytic disease of the fetus and newborn. In donor testing, RBC genotyping is used for resolving ABO/D discrepancies for better donor retention or for identifying donors negative for high-prevalence antigens to increase blood availability and compatibility for patients requiring rare blood. RBC genotyping is helpful to immunohematology reference laboratory staff performing complex antibody workups and is recommended for determining the antigen profiles of patients and prospective donors for accurate matching for C, E, and K in multiply transfused patients. Such testing is also used to determine patients or donors with variant alleles in the Rh blood group system. Information from this testing aides in complex antibody identification as well as sourcing rare allele-matched RBC units. While RBC genotyping is useful in transfusion medicine, there are limitations to its implementation in transfusion services, including test availability, turn-around time, and cost.

Immunophenotypic clustering in paediatric acute myeloid leukaemia.

Acute myeloid leukaemia (AML) is a highly heterogeneous disease, exhibiting diverse subtypes according to the characteristics of tumour cells. The immunophenotype is one of the aspects acquired routinely through flow cytometry in the diagnosis of AML. Here, we characterized the antigen expression in paediatric AML cases across both morphological and molecular genetic subgroups. We discovered a subgroup of patients with unfavourable prognosis that can be immunologically characterized, irrespective of morphological FAB results or genetic aberrations. Cox regression analysis unveiled key antigens influencing the prognosis of AML patients. In terms of underlying genotypes, we observed that the antigenic profiles and outcomes of one specific group, primarily composed of CBFA2T3::GLIS2 and FUS::ERG, were analogous to the reported RAM phenotype. Overall, our data highlight the significance of immunophenotype to tailor treatment for paediatric AML.

An Early Dengue Virus Fever Diagnostic Tool

The dengue virus is a persistent and very prevalent pathogenic threat in underdeveloped nations such as India. In order to create effective management and treatment plans, it is necessary to continuously monitor the spread and diagnosis of dengue infections due to their variable types and frequencies. The dengue virus is a very complicated illness that presents in many ways. Using standard laboratory techniques to define the dengue virus infection is challenging. NS1, however, might be a useful diagnosis in the initial several days of fever. In this study, the presence of the dengue-specific NS1 antigen was examined in 88 patients from the Raipur regions of Chattisgarh who had been ill for one to thirty days.A kit based on ELISA was used. The collected data was analyzed and the percentage frequency of both IgM positive and negative and NS1 positive and negative results were expressed for each dengue fever patient. Notably, 36.3% of the population had dengue infection. Early in the infection period, the NS1 antigen was effectively measured. In every participant who tested positive for NS1 on the second day of fever, IgM was negative. Nevertheless, when the temperature increased, this correlation became less strong. It was determined through analysis that leuckocytopenia and thrombocytopenia were random states unrelated to NS1 positive. It is clear that diagnosing dengue is extremely difficult and that the antigenic profile drastically shifts as the fever progresses over a period of days.By using a diagnostic approach based on a thorough examination of the subjects, clinicians can reduce the possibility that dengue shock syndrome would cause hemorrhage. Key Words: India's dengue outbreak, dengue virus fever, or virally transmitted diseases

CountASAP: A Lightweight, Easy to Use Python Package for Processing ASAPseq Data.

Declining sequencing costs coupled with the increasing availability of easy-to-use kits for the isolation of DNA and RNA transcripts from single cells have driven a rapid proliferation of studies centered around genomic and transcriptomic data. Simultaneously, a wealth of new techniques have been developed that utilize single cell technologies to interrogate a broad range of cell-biological processes. One recently developed technique, transposase-accessible chromatin with sequencing (ATAC) with select antigen profiling by sequencing (ASAPseq), provides a combination of chromatin accessibility assessments with measurements of cell-surface marker expression levels. While software exists for the characterization of these datasets, there currently exists no tool explicitly designed to reformat ASAP surface marker FASTQ data into a count matrix which can then be used for these downstream analyses. To address this, we created CountASAP, an easy-to-use Python package purposefully designed to transform FASTQ files from ASAP experiments into count matrices compatible with commonly-used downstream bioinformatic analysis packages. CountASAP takes advantage of the independence of the relevant data structures to perform fully parallelized matches of each sequenced read to user-supplied input ASAP oligos and unique cell-identifier sequences.

Modification of deglycerolization procedure improves processing and post-thaw quality of cryopreserved sickle trait red cell concentrates

Red blood cell (RBC) transfusion is a critical therapy for those with sickle cell disease (SCD). Alloimmunization is frequent for those with SCD and may limit the availability of matched RBC. Cryopreserved RBCs, from family members or donors with a similar RBC antigen profile could provide a viable alternative to avoid further alloimmunization and prevent hemolytic transfusion-related events. However, cryopreserved SCD and Sickle Cell trait (S-trait) donor RBC units suffer from reduced recovery following deglycerolization. This study proposes and tests a modified deglycerolization protocol using an automated cell processor to mitigate RBC loss. Six red cell concentrates (RCC) from donors with S-trait and six control RCCs were glycerolized, frozen (<−65 °C) and deglycerolized on the ACP 215 using modified parameters (decreased hypertonic solution flow rate (100 mL/min) and hypertonic equilibration delay (120 s), and increased NaCl dilution volumes (500 mL). Quality testing included: hematocrit (HCT), hemolysis, indices, extracellular potassium, morphology, osmotic fragility, osmotic gradient ektacytometry, hemoglobin (HGB), and recovery. Canadian standards (CS) indicate that acceptable deglycerolized units for transfusion require a HCT ≤0.80 L/L, HGB ≥35 g/unit, and hemolysis <0.8 % in 90 % of units tested. No significant differences in HGB or RBC recovery were observed between study groups. Significant differences between study groups were identified in osmotic fragility and osmotic gradient ektacytometry parameters. Of the 6 S-trait RCCs, 3/6 units were within the HCT, HGB and hemolysis thresholds set by the CS. The modified deglycerolization protocol provides a path for the routine cryopreservation of S-trait RBCs.

Antigenic Characterization of Novel Human Norovirus GII.4 Variants San Francisco 2017 and Hong Kong 2019.

Norovirus is a major cause of acute gastroenteritis; GII.4 is the predominant strain in humans. Recently, 2 new GII.4 variants, Hong Kong 2019 and San Francisco 2017, were reported. Characterization using GII.4 monoclonal antibodies and serum demonstrated different antigenic profiles for the new variants compared with historical variants.

Evolutionary dynamics and comparative pathogenicity of clade 2.3.4.4b H5 subtype avian influenza viruses, China, 2021–2022

The recent concurrent emergence of H5N1, H5N6, and H5N8 avian influenza viruses (AIVs) has led to significant avian mortality globally. Since 2020, frequent human-animal interactions have been documented. To gain insight into the novel H5 subtype AIVs (i.e., H5N1, H5N6 and H5N8), we collected 6102 samples from various regions of China between January 2021 and September 2022, and identified 41 H5Nx strains. Comparative analyses on the evolution and biological properties of these isolates were conducted. Phylogenetic analysis revealed that the 41 H5Nx strains belonged to clade 2.3.4.4b, with 13 related to H5N1, 19 to H5N6, and 9 to H5N8. Analysis based on global 2.3.4.4b viruses showed that all the viruses described in this study were likely originated from H5N8, exhibiting a heterogeneous evolutionary history between H5N1 and H5N6 during 2015–2022 worldwide. H5N1 showed a higher rate of evolution in 2021–2022 and more sites under positive selection pressure in 2015–2022. The antigenic profiles of the novel H5N1 and H5N6 exhibited notable variations. Further hemagglutination inhibition assay suggested that some A(H5N1) viruses may be antigenically distinct from the circulating H5N6 and H5N8 strains. Mammalian challenge assays demonstrated that the H5N8 virus (21GD001_H5N8) displayed the highest pathogenicity in mice, followed by the H5N1 virus (B1557_H5N1) and then the H5N6 virus (220086_H5N6), suggesting a heterogeneous virulence profile of H5 AIVs in the mammalian hosts. Based on the above results, we speculate that A(H5N1) viruses have a higher risk of emergence in the future. Collectively, these findings unveil a new landscape of different evolutionary history and biological characteristics of novel H5 AIVs in clade 2.3.4.4b, contributing to a better understanding of designing more effective strategies for the prevention and control of novel H5 AIVs.

Antigenic distance between primary and secondary dengue infections correlates with disease risk.

Many pathogens continuously change their protein structure in response to immune-driven selection, resulting in weakened protection even in previously exposed individuals. In addition, for some pathogens, such as dengue virus, poorly targeted immunity is associated with increased risk of severe disease through a mechanism known as antibody-dependent enhancement. However, it remains unclear whether the antigenic distances between an individual's first infection and subsequent exposures dictate disease risk, explaining the observed large-scale differences in dengue hospitalizations across years. Here, we develop a framework that combines detailed antigenic and genetic characterization of viruses with details on hospitalized cases from 21 years of dengue surveillance in Bangkok, Thailand, to identify the role of the antigenic profile of circulating viruses in determining disease risk. We found that the risk of hospitalization depended on both the specific order of infecting serotypes and the antigenic distance between an individual's primary and secondary infections, with risk maximized at intermediate antigenic distances. These findings suggest that immune imprinting helps determine dengue disease risk and provide a pathway to monitor the changing risk profile of populations and to quantifying risk profiles of candidate vaccines.

Principles in the Management of Glioblastoma.

Glioblastoma, the most aggressive and common malignant primary brain tumour, is characterized by infiltrative growth, abundant vascularization, and aggressive clinical evolution. Patients with glioblastoma often face poor prognoses, with a median survival of approximately 15 months. Technological progress and the subsequent improvement in understanding the pathophysiology of these tumours have not translated into significant achievements in therapies or survival outcomes for patients. Progress in molecular profiling has yielded new omics data for a more refined classification of glioblastoma. Several typical genetic and epigenetic alterations in glioblastoma include mutations in genes regulating receptor tyrosine kinase (RTK)/rat sarcoma (RAS)/phosphoinositide 3-kinase (PI3K), p53, and retinoblastoma protein (RB) signalling, as well as mutation of isocitrate dehydrogenase (IDH), methylation of O6-methylguanine-DNA methyltransferase (MGMT), amplification of epidermal growth factor receptor vIII, and codeletion of 1p/19q. Certain microRNAs, such as miR-10b and miR-21, have also been identified as prognostic biomarkers. Effective treatment options for glioblastoma are limited. Surgery, radiotherapy, and alkylating agent chemotherapy remain the primary pillars of treatment. Only promoter methylation of the gene MGMT predicts the benefit from alkylating chemotherapy with temozolomide and it guides the choice of first-line treatment in elderly patients. Several targeted strategies based on tumour-intrinsic dominant signalling pathways and antigenic tumour profiles are under investigation in clinical trials. This review explores the potential genetic and epigenetic biomarkers that could be deployed as analytical tools in the diagnosis and prognostication of glioblastoma. Recent clinical advancements in treating glioblastoma are also discussed, along with the potential of liquid biopsies to advance personalized medicine in the field of glioblastoma, highlighting the challenges and promises for the future.

The Interplay Between Human Leukocyte Antigen Antibody Profile and COVID-19 Vaccination in Waitlisted Renal Transplant Patients.

Mass COVID-19 vaccination is mandated in vulnerable populations in our renal transplant waitlist cohort. However, the anti-human leukocyte antigen (anti-HLA) profile after COVID-19 vaccination is controversial, and the side effects are yet to be discerned. To evaluate the status of HLA antibodies in waitlist renal transplant patients before and 3 weeks after each vaccination and if comorbidities are associated with the HLA antibody profile. A total of 59 waitlisted kidney transplant patients were included in this study. The anti-HLA antibodies were analyzed before and 6 months after their last COVID-19 vaccination. The mean fluorescence intensity change in the anti-HLA antibody levels was used to classify patients into 3 groups: high inducers, low inducers, and noninducers. There were significant HLA antibody profile changes after COVID-19 vaccination, showing 21 antibodies generated against HLA class I antigens and 7 against HLA class II antigens to their baseline. Compared with the noninducers, the high and low inducers showed a higher prevalence of COVID-19 infection, COVID-19 vaccine type, and background hypertension history. Our data suggest that COVID-19 vaccination propagates anti-HLA class I and II antibodies for waitlisted renal transplant patients. The clinical significance of these antibodies needs further study. Furthermore, comorbidities, such as history of COVID-19 infection and hypertension, supplemented this effect. Anti-HLA antibody monitoring may be warranted in vaccinated, waitlisted renal transplant patients with COVID-19 vaccinations, and a history of COVID-19 infection or hypertension.

Comprehensive analysis of Salmonella in poultry meat and products in Türkiye: Prevalence, antibiotic susceptibility and genomic characterisation

SummaryThe study aimed to determine the prevalence and characteristics of Salmonella isolated from raw chicken meat and products. For this purpose, a total of 293 samples were collected, including chicken breast (n = 90), skinned drumstick (n = 80), skinned chicken chop (n = 42), wing (n = 32), chicken offal (n = 27) and chicken patty (n = 22). The samples were subjected to Salmonella enterica. detection and the obtained suspicious isolates were confirmed by conventional PCR. Their phenotypical antibiotic resistance profiles were subsequently determined. The prevalence of Salmonella Enteritidis and Typhimurium serovars among S. enterica isolates were investigated using TaqMan probe Real‐Time PCR (qPCR) analysis, and the detected serovars were evaluated with whole genome sequencing. In the study, 112 (38.22%) of the 293 chicken samples contained S. enterica, with five (4.46%) and one (0.89%) of the isolates identified as Salmonella Enteritidis and Typhimurium, respectively. Antibiotic resistance analysis revealed that all isolates were sensitive to Meropenem and Aztreonam, while the most resistant antibiotics were Doxycycline (96.42%) and Trimethoprim‐sulfamethoxazole (71.42%). Whole genome sequencing, specifically SNP‐based phylogenetic analyses, indicated that Salmonella Enteritidis and Typhimurium isolates were distinct clones. All Salmonella Enteritidis isolates shared the same antigenic profiles (9: g, m:‐) and cgMLST types of 11, while the Salmonella Typhimurium isolate had cgMLST type 19 and a 4:i:1,2 antigenic profile. It was observed that the phenotypic resistance profiles of the isolates were consistent with the whole genome characterisation. The data obtained in the study reveal the continued importance of Salmonella monitoring for the poultry industry across different regions of Türkiye to maintain food safety. Chicken meat and products are indispensable to public health in providing healthy nutrition and access to animal protein. The microbiological and epidemiological risks observed in mass production can be minimised, particularly by integrating epidemiological and molecular findings with an effective strategy.

Abstract 3361: Surfaceome and cancer testis antigen profiling of lung adenocarcinoma by large-scale transcriptomic analysis

Abstract Background: The emergence of improved modalities to target tumor specific and tumor associated antigens in solid tumors (e.g. antibody-drug conjugates, bi-specific antibodies, and adoptive cell therapy) underscores the need to efficiently identify and validate new therapeutic targets. Methods: We examined differential expression of surfaceome genes (Fonseca et al., 2016) and cancer testis (CT) antigen genes (Almeida et al., 2009) among major lung adenocarcinoma genomic subtypes; conducting comprehensive surfaceome/CT antigen profiling of 9002 NSCLC adenocarcinoma samples using data generated by RNA sequencing (whole transcriptome) at Caris Life Sciences (Phoenix, AZ). NSCLC tumors were stratified into 5 subgroups based on the presence of specific driver mutations: ALK fusion (N=325), EGFR mutant (N=1739), KRAS mutant (no STK11 or KEAP1 mutation; N=2561), KRAS + STK or KEAP1 mutation (N=1264), and Pan-WT (no mutation in ALK, EGFR, KRAS, STK11, or KEAP1 detected; N=3113). Fold-change in expression was calculated by dividing the median value for a specific subgroup by the median of all other groups combined. Significance was tested by Mann-Whitney U test, with p-values adjust for multiple hypothesis testing (Benjamini-Hochberg). Results: Surfaceome genes with the highest median expression overall included CD74, TMBIM6, and CD44, while the highest median expression among CT antigens was observed for SPAG9, KIAA0100, and RQCD1, yet the expression of these genes across the 5 driver mutation-based subgroups was similar (fold-changes ranged 0.93-1.06). To identify driver-associated candidate genes with relatively high expression, genes with subgroup-specific median expression &amp;gt;75th-percentile and with significant differences when compared to all other groups were ranked by fold-change. While several candidate surfaceome genes were associated with a specific subgroup, CLDN10 was identified among the top 3 candidates for both ALK fusion and KRAS + STK11/KEAP1 mutant subgroups: ALK fusion (GRIN2A, 3.03-fold; CLDN10, 2.53-fold; SLITRK6, 1.86-fold), EGFR mutant (SFTPC, 3.82-fold; MUC21, 1.99-fold; ATP13A4, 1.60-fold), KRAS mutant (VSIG1, 1.86-fold; AREG, 1.47-fold; C15orf48, 1.25-fold), and KRAS + STK11/KEAP1 mutant (ABCC2, 4.03-fold; MUC13, 3.21-fold; CLDN10, 3.00-fold). The top driver-associated CT antigen candidates included LEMD1 (1.42-fold) in ALK fusion, TMEM108 (1.27-fold) in EGFR mutant, XAGE1D (1.7-fold) in KRAS mutant, and CABYR (1.52-fold) in KRAS + STK11/KEAP1 mutant subgroups. Conclusion: Our analysis revealed several surfaceome and CT antigen candidate genes with relatively high expression across lung adenocarcinoma, as well as differential expression of candidate genes within specific genomic subtypes. These findings can help prioritize the validation and development of novel therapeutic targets in lung adenocarcinoma. Citation Format: Swartz Andrew, Andrew Elliott, George W. Sledge, Stephen V. Liu, Balazs Halmos, Vincent K. Lam, Taofeek K. Owonikoko. Surfaceome and cancer testis antigen profiling of lung adenocarcinoma by large-scale transcriptomic analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3361.

Physiological features of semen resistance of stallions to cooling with different antigenic profile of erythrocytes

The article shows the physiological features of the survival ability of stallion semen at a temperature of 2 to 5°C with different antigenic features according to blood group systems. It was shown that in the presence of the antigens cgm/ceg, ad/dk, cgm/dk, cgm/d, dg/di on D system erythrocytes, the semen survival ability at 2 to 5°C was observed for a maximum of 50 hours. The carriers of the antigens cegm/cgm, ad/de, cgm/cgm, аd/bcm, bcm/dg, ad/d, cegm/dg, bcm/cgm, bcm/de, cegm/d, de/cgm, cegm/dk, dk/d, de/d, de/dk, cgm/dg, dk/de antigens have obtained a medium sperm resistance to cooling with a semen survival time of 50 to 75 hours. Stallions with the antigens bcm/d, bcm/dk, ad/cgm, dg/dk, cgm/de, dg/cgm, dk/dk of the D blood group showed a high semen resistance to cooling at 2 to 5°C in the form of a survival time of more than 75 hours. When the experimental stallions inherited the a/- antigen of the K system, the semen survival ability was increased by 7.24 h (P &lt; 0.05) and the absolute survival ability by 24.18 standard units (P &lt; 0.05) compared to the absence of this system antigen. The absence of -/- erythrocytic antigens of the C blood group is associated with an increase (P &lt; 0.05) of 10.21 h in the survival ability and 30.29 standard units in the absolute semen survival ability compared to ejaculates from stallions with the a/- antigen of this erythrocytic system. The absence of the -/- antigen of the A system in stallions and the presence of the а/- antigen are followed by an increase in ejaculate resistance to cooling by 14 h (Р &lt; 0,05) as compared to the control. At the same time, the absolute semen survival ability is 38.69 and 45.94 standard units higher than the control values (P &lt; 0.01). Inheritance by stallions of the ad/- antigen by stallions was followed by a higher semen resistance to cooling as compared to the control by only 9.63 h (Р &lt; 0.05) and a lower resistance compared to а/- and -/- by 5 h. The practical application of the data obtained is that it becomes possible to predict the shelf life of freshly dissolved cooled semen before artificial insemination, which is especially important for long transport of semen doses.

Impact of ABO blood type on the risk of atrial fibrillation recurrence after catheter ablation

BackgroundBlood types are classified based on the specific antigenic characteristics they possess. Despite documented associations between antigens and inflammation, a scarcity of data exists concerning the impact of antigens on atrial fibrillation (AF). MethodsOSHOH-rhythm study is a multi-center, prospective observational study of 601 patients who underwent catheter ablation for AF. We examined the correlation between blood type groups and both the incidence and recurrence of AF. Additionally, we analyzed the recurrence of AF across antigenic profiles. ResultsThe frequencies of individual blood types were 239 (39.8 %), 190 (31.6 %), 122 (20.3 %), and 50 (8.3 %) for A, O, B, and AB, respectively, aligning closely with the prevalent blood type distribution among the Japanese populace. During follow-up period (18.8 months, median), AF recurrence occurred in 96 patients (22.4 %) lacking the B antigen (A and O), and 26 patients (15.1 %) possessing B antigen (B and AB), respectively (Log-rank test: P = 0.034). A multivariate analysis demonstrated that blood types lacking the B antigen (hazard ratio [HR], 1.55; 95 % CI, 1.01 to 2.42; P = 0.037), hypertension (HR, 1.51; 95 % CI, 1.05 to 2.17; P = 0.026) and non-paroxysmal AF (HR, 1.70; 95 % CI, 1.17 to 2.47; P = 0.005) were independently associated with the recurrence of AF. ConclusionsThis study elucidates that, despite the absence of direct correlation between blood types and the occurrence of AF, blood types devoid of the B antigen exhibit an enhanced predisposition to AF recurrence. Nonetheless, the intricate mechanism linking blood type to recurrence remains elusive, warranting further comprehensive foundational research on blood types.

Discordant Antigenic Properties of Soluble and Virion SARS-CoV-2 Spike Proteins.

Efforts to develop vaccine and immunotherapeutic countermeasures against the COVID-19 pandemic focus on targeting the trimeric spike (S) proteins of SARS-CoV-2. Vaccines and therapeutic design strategies must impart the characteristics of virion S from historical and emerging variants onto practical constructs such as soluble, stabilized trimers. The virus spike is a heterotrimer of two subunits: S1, which includes the receptor binding domain (RBD) that binds the cell surface receptor ACE2, and S2, which mediates membrane fusion. Previous studies suggest that the antigenic, structural, and functional characteristics of virion S may differ from current soluble surrogates. For example, it was reported that certain anti-glycan, HIV-1 neutralizing monoclonal antibodies bind soluble SARS-CoV-2 S but do not neutralize SARS-CoV-2 virions. In this study, we used single-molecule fluorescence correlation spectroscopy (FCS) under physiologically relevant conditions to examine the reactivity of broadly neutralizing and non-neutralizing anti-S human monoclonal antibodies (mAbs) isolated in 2020. Binding efficiency was assessed by FCS with soluble S trimers, pseudoviruses and inactivated wild-type virions representing variants emerging from 2020 to date. Anti-glycan mAbs were tested and compared. We find that both anti-S specific and anti-glycan mAbs exhibit variable but efficient binding to a range of stabilized, soluble trimers. Across mAbs, the efficiencies of soluble S binding were positively correlated with reactivity against inactivated virions but not pseudoviruses. Binding efficiencies with pseudoviruses were generally lower than with soluble S or inactivated virions. Among neutralizing mAbs, potency did not correlate with binding efficiencies on any target. No neutralizing activity was detected with anti-glycan antibodies. Notably, the virion S released from membranes by detergent treatment gained more efficient reactivity with anti-glycan, HIV-neutralizing antibodies but lost reactivity with all anti-S mAbs. Collectively, the FCS binding data suggest that virion surfaces present appreciable amounts of both functional and nonfunctional trimers, with neutralizing anti-S favoring the former structures and non-neutralizing anti-glycan mAbs binding the latter. S released from solubilized virions represents a nonfunctional structure bound by anti-glycan mAbs, while engineered soluble trimers present a composite structure that is broadly reactive with both mAb types. The detection of disparate antigenicity and immunoreactivity profiles in engineered and virion-associated S highlight the value of single-virus analyses in designing future antiviral strategies against SARS-CoV-2.

Body odours as putative chemosignals in the father-child relationship: New insights on paternal olfactory kin recognition and preference from infancy to adolescence

Children's body odours are effective chemical cues in the parent-child relationship. Mothers can recognize the odour of their child and prefer this odour over that of unfamiliar children. This effect is mediated by genetic similarity and developmental stage and is therefore suited to promote parental care at pre-pubertal stage, while facilitating incest avoidance at (post-)pubertal stage. The present study tested whether similar mechanisms apply to fathers. Therefore n = 56 fathers evaluated body odour samples of their own and of unfamiliar children in varying genetic and developmental stages. Genetic status was determined by human leucocyte antigen (HLA) profiling, developmental status by standardized assessment of pubertal status and steroid hormone concentration (estradiol, testosterone). Similar to mothers, fathers identified their own child's body odour above chance and preferred that odour. The paternal preference did not relate to HLA similarity but decreased with increasing age of the child. The decline was associated with higher pubertal stages in daughters only, which supports the hypothesis of odour-mediated incest prevention in opposite-sex parent-child dyads.

Recapitulation of the Powassan virus life cycle in cell culture.

Powassan virus (POWV) is a tick-borne flavivirus known for causing fatal neuroinvasive diseases in humans. Recently, there has been a noticeable increase in POWV infections, emphasizing the urgency of understanding viral replication, pathogenesis, and developing interventions. Notably, there are no approved vaccines or therapeutics for POWV, and its classification as a biosafety level-3 (BSL-3) agent hampers research. To overcome these obstacles, we developed a replicon system, a self-replicating RNA lacking structural proteins, making it safe to operate in a BSL-2 environment. We constructed a POWV replicon carrying the Gaussia luciferase (Gluc) reporter gene and blasticidin (BSD) selectable marker. Continuous BSD selection led to obtain a stable POWV replicon-carrying Huh7 cell lines. We identified cell culture adaptive mutations G4079A, G4944T and G6256A, resulting in NS2AR195K, NS3G122G, and NS3V560M, enhancing RNA replication. We demonstrated the utility of the POWV replicon system for high-throughput screening (HTS) assay to identify promising antivirals against POWV replication. We further explored the applications of the POWV replicon system, generating single-round infectious particles (SRIPs) by transfecting Huh7-POWV replicon cells with plasmids encoding viral capsid (C), premembrane (prM), and envelope (E) proteins, and revealed the distinct antigenic profiles of POWV with ZIKV. In summary, the POWV replicon and SRIP systems represent crucial platforms for genetic and functional analysis of the POWV life cycle and facilitating the discovery of antiviral drugs.IMPORTANCEIn light of the recent surge in human infections caused by POWV, a biosafety level-3 (BSL-3) classified virus, there is a pressing need to understand the viral life cycle and the development of effective countermeasures. To address this, we have pioneered the establishment of a POWV RNA replicon system and a replicon-based POWV SRIP system. Importantly, these systems are operable in BSL-2 laboratories, enabling comprehensive investigations into the viral life cycle and facilitating antiviral screening. In summary, these useful tools are poised to advance our understanding of the POWV life cycle and expedite the development of antiviral interventions.

Global evaluation of lineage-specific human papillomavirus capsid antigenicity using antibodies elicited by natural infection.

Human Papillomavirus (HPV) type variants have been classified into lineages and sublineages based upon their whole genome sequence. Here we have examined the specificity of antibodies generated following natural infection with lineage variants of oncogenic types (HPV16, 18, 31, 33, 45, 52 and 58) by testing serum samples assembled from existing archives from women residing in Africa, The Americas, Asia or Europe against representative lineage-specific pseudoviruses for each genotype. We have subjected the resulting neutralizing antibody data to antigenic clustering methods and created relational antigenic profiles for each genotype to inform the delineation of lineage-specific serotypes. For most genotypes, there was evidence of differential recognition of lineage-specific antigens and in some cases of a sufficient magnitude to suggest that some lineages should be considered antigenically distinct within their respective genotypes. These data provide compelling evidence for a degree of lineage specificity within the humoral immune response following natural infection with oncogenic HPV.

Comprehensive analysis of antigenic variations and genomic properties of hepatitis B virus in clinical samples in the mid-north east region of Bangladesh

This investigation delineates an exhaustive analysis of the clinical, immunological, and genomic landscapes of hepatitis B virus (HBV) infection across a cohort of 22 verified patients. The demographic analysis unveiled a pronounced male bias (77.27%), with patient ages spanning 20 to 85 years and durations of illness ranging from 10 days to 4 years. Predominant clinical manifestations included fever, fatigue, anorexia, abdominal discomfort, and arthralgia, alongside observed co-morbidities such as chronic renal disorders and hepatocellular carcinoma. Antigenic profiling of the HBV envelope proteins elucidated significant heterogeneity among the infected subjects, particularly highlighted by discordances in the detection capabilities of small and large HBsAg assays, suggesting antigenic diversity. Quantitative assessment of viral loads unveiled a broad spectrum, accompanied by atypical HBeAg reactivity patterns, challenging the reliability of existing serological markers. Correlative studies between viral burden and antigenicity of the envelope proteins unearthed phenomena indicative of diagnostic evasion. Notably, samples demonstrating robust viral replication were paradoxically undetectable by the large HBsAg ELISA kit, advocating for more sophisticated diagnostic methodologies. Genotypic examination of three HBV isolates classified them as genotype D (D2), with phylogenetic alignment to strains from various global origins. Mutational profiling identified pivotal mutations within the basic core promoter and preS2/S1 regions, associated with an augmented risk of hepatocellular carcinoma. Further, mutations discerned in the small HBsAg and RT/overlap regions were recognized as contributors to vaccine and/or diagnostic escape mechanisms. In summation, this scholarly discourse elucidates the intricate interplay of clinical presentations, antigenic diversity, and genomic attributes in HBV infection, accentuating the imperative for ongoing investigative endeavors to refine diagnostic and therapeutic modalities.