The Nature of Selection on the Major Histocompatibility Complex.

Only natural selection can account for the extreme genetic diversity of genes of the major histocompatibility complex (MHC). Although the structure and function of classic MHC genes is well understood at the molecular and cellular levels, there is controversy about how MHC diversity is selectively maintained. The diversifying selection can be driven by pathogen interactions and inbreeding avoidance mechanisms. Pathogen-driven selection can maintain MHC polymorphism based on heterozygote advantage or frequency-dependent selection due to pathogen evasion of MHC-dependent immune recognition. Empirical evidence demonstrates that specific MHC haplotypes are resistant to certain infectious agents, while susceptible to others. These data are consistent with both heterozygote advantage and frequency-dependent models. Additional research is needed to discriminate between these mechanisms. Infectious agents can precipitate autoimmunity and can potentially contribute to MHC diversity through molecular mimicry and by favoring immunodominance. MHC-dependent abortion and mate choice, based on olfaction, can also maintain MHC diversity and probably functions both to avoid genome-wide inbreeding and produce MHC-heterozygous offspring with increased immune responsiveness. Although this diverse set of hypotheses are often treated as competing alternatives, we believe that they all fit into a coherent, internally consistent thesis. It is likely that at least in some species, all of these mechanisms operate, leading to the extreme diversification found in MHC genes.

Experimental viral evolution to specific host MHC genotypes reveals fitness and virulence trade-offs in alternative MHC types.

The unprecedented genetic diversity found at vertebrate MHC (major histocompatibility complex) loci influences susceptibility to most infectious and autoimmune diseases. The evolutionary explanation for how these polymorphisms are maintained has been controversial. One leading explanation, antagonistic coevolution (also known as the Red Queen), postulates a never-ending molecular arms race where pathogens evolve to evade immune recognition by common MHC alleles, which in turn provides a selective advantage to hosts carrying rare MHC alleles. This cyclical process leads to negative frequency-dependent selection and promotes MHC diversity if two conditions are met: (i) pathogen adaptation must produce trade-offs that result in pathogen fitness being higher in familiar (i.e., host MHC genotype adapted to) vs. unfamiliar host MHC genotypes; and (ii) this adaptation must produce correlated patterns of virulence (i.e., disease severity). Here we test these fundamental assumptions using an experimental evolutionary approach (serial passage). We demonstrate rapid adaptation and virulence evolution of a mouse-specific retrovirus to its mammalian host across multiple MHC genotypes. Critically, this adaptive response results in trade-offs (i.e., antagonistic pleiotropy) between host MHC genotypes; both viral fitness and virulence is substantially higher in familiar versus unfamiliar MHC genotypes. These data are unique in experimentally confirming the requisite conditions of the antagonistic coevolution model of MHC evolution and providing quantification of fitness effects for pathogen and host. These data help explain the unprecedented diversity of MHC genes, including how disease-causing alleles are maintained.

Towards achieving the end of the HIV epidemic: Advances, challenges and scaling-up strategies.

We are entering the 5th decade of the HIV epidemic and although there is no cure, critical advances have been made in treatment, prevention and diagnostics, transforming HIV into a survivable disease. Due to these advances, the UNAIDS has set a goal of "90-90-90" target by 2020, which has been extended now to 2030, to have 90% of individuals infected with HIV diagnosed, 90% of those diagnosed linked to care and 90% of people receiving ART and 90% of those receiving ART achieving an undetectable viral load. Today, the focus is on U = U, "undetectable equals untransmittable", which takes advantage of improved diagnostics and treatment and preventive therapies that are combined with scale-up strategies. This article will review the advances in testing strategies and diagnostics, including rapid diagnostic tests and next generation sequencing, as well as the challenges that pre-exposure prophylaxis (PrEP) and post-exposure prophylaxis (PEP) now present for diagnosing and managing HIV infection.

Severe Acute Respiratory Syndrome Coronavirus 2 Serology Testing - A Laboratory Primer.

In 2019, an emerging coronavirus, SARS-COV-2, was first identified. In the months since, SARS-CoV-2 has become a global pandemic of unimaginable scale. In 2021, SARS-CoV-2 continues to be a huge public health burden and a dominating issue in health care. In addition, SARS-CoV-2 has placed a spotlight on laboratory medicine and its key role in infectious disease management. The SARS-CoV-2 antibody testing landscape is vast and consists of dozens of antibody tests that have received EUA. The laboratory is faced with choosing the right test, staying current with the rapidly evolving recommendations, and updating test information for clients and clinicians. This review addresses what we know about the humoral response in SARS-CoV-2 infection and how this knowledge translates into appropriate serology test choice, utility, and interpretation.

Evaluation of a Novel Multiplex Platform for Simultaneous Detection of IgG Antibodies Against the 4 Main SARS-CoV-2 Antigens.

BACKGROUND: Numerous serology assays are available for detection of SARS-CoV-2 antibodies but are limited in that only 1 or 2 target antigen(s) can be tested at a time. Here, we describe a novel multiplex assay that simultaneously detects and quantifies IgG antibodies to SARS-CoV-2 antigens, spike (S), nucleocapsid (N), receptor-binding domain (RBD), and N-terminal domain (NTD) in a single well. METHODS: Sensitivity was determined using samples (n = 124) from confirmed SARS-CoV-2 RT-PCR positive individuals. Prepandemic (n = 100) and non-COVID respiratory infection positive samples (n = 100) were used to evaluate specificity. Samples were analyzed using COVID-19 IgG multiplex serology assay from Meso Scale Discovery (MSD) and using commercial platforms from Abbott, EUROIMMUN, and Siemens. RESULTS: At >14 days post-PCR, MSD assay displayed >98.0% sensitivity [S 100% (95% CI 98.0%-100.0%); N 98.0% (95% CI 97.2%-98.9%); RBD 94.1% (95% CI 92.6%-95.6%); NTD 98.0% (95% CI, 97.2%-98.9%)] and 99% specificity (95% CI 99.3%-99.7%) for antibodies to all 4 antigens. Parallel assessment of antibodies to more than 1 antigen improved the sensitivity to 100% (95% CI 98.0%-100.0%) while maintaining 98% (95% CI 97.6%-98.4%) specificity regardless of the combinations used. When AU/mL concentrations of IgG antibodies from the MSD assay were compared against the corresponding IgG signals acquired from the single target commercial assays, the following correlations were observed: Abbott (vs MSD N, R2 = 0.73), Siemens (vs MSD RBD, R2 = 0.92), and EUROIMMUN (vs MSD S, R2 = 0.82). CONCLUSION: MSD assay offers an accurate and a comprehensive assessment of SARS-CoV-2 antibodies with higher sensitivity and equivalent specificity compared to the commercial IgG serology assays.

Evaluation of 3 SARS-CoV-2 IgG Antibody Assays and Correlation with Neutralizing Antibodies.

BACKGROUND: As serologic assays for SARS-CoV-2 become more widely utilized, it is important to understand their performance characteristics and correlation with neutralizing antibodies. We evaluated 3 commonly used SARS-CoV-2 IgG assays (Abbott, DiaSorin, and EUROIMMUN) for clinical sensitivity, specificity, and correlation with neutralizing antibodies, and then compared antibody kinetics during the acute phase of infection. METHODS: Three panels of samples were tested on every assay. Sensitivity was assessed using a panel of 35 specimens serially collected from 7 patients with RT-PCR-confirmed COVID-19. Specificity was determined using 100 sera samples collected in 2018 from healthy individuals prior to the outbreak. Analytical specificity was determined using a panel of 37 samples from individuals with respiratory illnesses other than COVID-19. RESULTS: Clinical sensitivity was 91.43% (95% CI 76.94-98.20%) for Abbott, and 88.57% (95% CI 73.26-96.80%) for both DiaSorin and EUROIMMUN. Clinical specificity was 99.00% (95% CI 94.55-99.97%) for Abbott and DiaSorin and 94.00% (95% CI 87.40-97.77%) for EUROIMMUN. The IgG assays demonstrated good qualitative agreement (minimum of 94%) and good correlation between the quantitative result for each combination of assays (r2 ≥ 0.90). The neutralizing antibody response did not necessarily follow the same temporal kinetics as the IgG response and did not necessarily correlate with IgG values. CONCLUSION: The 3 IgG antibody assays demonstrated comparable performance characteristics. Importantly, a qualitative positive IgG result obtained with any of the assays was associated with the presence of neutralizing antibodies; however, neutralizing antibody concentrations did not correlate well with signal to cutoff ratios.

Evaluation of a Surrogate Enzyme-Linked Immunosorbent Assay-Based Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) cPass Neutralization Antibody Detection Assay and Correlation With Immunoglobulin G Commercial Serology Assays.

CONTEXT.­: Emerging evidence shows correlation between the presence of neutralization antibodies (nAbs) and protective immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently available commercial serology assays lack the ability to specifically identify nAbs. An enzyme-linked immunosorbent assay-based nAb assay (GenScript cPass neutralization antibody assay) has recently received emergency use authorization from the Food and Drug Administration. OBJECTIVE.­: To evaluate the performance characteristics of this assay and compare and correlate it with the commercial assays that detect SARS-CoV-2-specific immunoglobulin G (IgG). DESIGN.­: Specimens from SARS-COV-2 infected patients (n = 124), healthy donors obtained prepandemic (n = 100), and patients with non-coronavirus disease 2019 (COVID-19) respiratory infections (n = 92) were analyzed using this assay. Samples with residual volume were also tested on 3 commercial serology platforms (Abbott, Euroimmun, Siemens). Twenty-eight randomly selected specimens from patients with COVID-19 and 10 healthy controls were subjected to a plaque reduction neutralization test. RESULTS.­: The cPass assay exhibited 96.1% (95% CI, 94.9%-97.3%) sensitivity (at >14 days post-positive PCR), 100% (95% CI, 98.0%-100.0%) specificity, and zero cross-reactivity for the presence of non-COVID-19 respiratory infections. When compared with the plaque reduction assay, 97.4% (95% CI, 96.2%-98.5%) qualitative agreement and a positive correlation (R2 = 0.76) was observed. Comparison of IgG signals from each of the commercial assays with the nAb results from plaque reduction neutralization test/cPass assays displayed greater than 94.7% qualitative agreement and correlations with R2 = 0.43/0.68 (Abbott), R2 = 0.57/0.85 (Euroimmun), and R2 = 0.39/0.63 (Siemens), respectively. CONCLUSIONS.­: The combined data support the use of cPass assay for accurate detection of the nAb response. Positive IgG results from commercial assays associated reasonably with nAbs presence and can serve as a substitute.

Pediatric reference intervals for random urine calcium, phosphorus and total protein.

The aim of this study was to establish age appropriate reference intervals for calcium (Ca), phosphorus (P) and total protein (UTP) in random urine samples. All analytes were measured using the Roche MODULAR P analyzer and normalized to creatinine (Cr). Our study cohort consisted of 674 boys and 728 girls between 7 and 17 years old (y.o.), which allowed us to determine the central 95% reference intervals with 90% confidence intervals by non-parametric analysis partitioned by both gender and 2-year age intervals for each analyte [i.e. boys in age group 7-9 years (7-9 boys); girls in age group 7-9 years (7-9 girls), etc.]. Results for the upper limits of the central 95% reference interval were: for Ca/Cr, 0.27 (16,17 y.o.) to 0.46 mg/mg (7-9 y.o.) for the girls and 0.26 (16,17 y.o.) to 0.43 mg/mg (7-9 y.o.) for the boys; for P/Cr, 0.85 (16,17 y.o.) to 1.44 mg/mg (7-9 y.o.) for the girls and 0.87 (16,17 y.o.) to 1.68 mg/mg (7-9 y.o.) for the boys; for UTP/Cr, 0.30 (7-9 y.o.) to 0.34 mg/mg (10-12 y.o.) for the girls and 0.19 (16,17, y.o.) to 0.26 mg/mg (13-15 y.o.) for the boys. Upper reference limits decreased with increasing age, and age was a statistically significant variable for all analytes. Eight separate age- and gender-specific reference intervals are proposed per analyte.

Sensory neurons with MHC-like peptide binding properties: disease consequences.

The recent discovery of specialized sensory neurons that bind peptides in an MHC-like fashion has revealed the long-sought odorants used to recognize the MHC genotype and phenotype of other individuals. The odorants are the same MHC peptides used during immune recognition, which provides the molecular logic linking selection acting on MHC-mediated behaviors with selection acting on immune recognition; both processes influence the evolving peptide binding properties of MHC molecules. The primary function of these chemosensory mechanisms for detecting MHC-mediated odors appears to be mating preferences (observed in humans and many vertebrates) that preferentially produce offspring more resistant to both infectious and genetic disease. Recent experiments are beginning to discriminate the relative importance of these different disease-reducing mechanisms.

Intermethod differences in results for total PSA, free PSA, and percentage of free PSA.

Serum prostate-specific antigen (PSA) assays differ in calibration and response to different PSA forms. We examined intermethod differences in total PSA (tPSA) and free PSA (fPSA) measurements. We tested 157 samples with tPSA concentrations of 2 to 10 ng/mL (2-10 microg/L) using 6 PSA/fPSA method pairs and 1 tPSA method: ADVIA Centaur (complexed and total; Siemens Diagnostics, Tarrytown, NY), ARCHITECT i 2000(SR) (Abbott Diagnostics, Abbott Park, IL), AxSYM (Abbott Diagnostics), IMMULITE 2000 (Siemens Diagnostics), Modular E170 (Roche Diagnostics, Indianapolis, IN), UniCel DxI 800 (Beckman Coulter, Brea, CA), and VITROS ECi (tPSA only; Ortho-Clinical Diagnostics, Raritan, NJ). Regression analysis was performed for PSA, fPSA, and percentage of fPSA with the ARCHITECT i 2000(SR) comparison method. Differences between test and comparison methods were estimated at 2.5, 4.0, and 10.0 ng/mL (2.5, 4.0, and 10.0 microg/L) for tPSA and 15%, 20%, and 25% for percentage of fPSA. Relative differences were more than 10% at 4.0 ng/mL (4.0 microg/L) tPSA for the Centaur, IMMULITE, ECi, and DxI methods. At 20% fPSA, the relative difference was more than 10% for all methods except the AxSYM. Additional harmonization is needed for tPSA and fPSA methods.

Efficacy of the detection of the alpha1-antitrypsin "Z" deficiency variant by routine serum protein electrophoresis.

Deficiency of alpha1-antitrypsin (AAT) is a common but underdiagnosed genetic disorder. Severe AAT deficiency may be detected by the absence of alpha1-globulin protein fraction by serum protein electrophoresis (SPEP). Routine SPEP may represent an underused resource for the identification of AAT deficiency. Total alpha1-globulin protein was measured in 47 MM, 24 MZ, and 19 ZZ phenotype serum samples by a Sebia CAPILLARYS (Norcross, GA) capillary electrophoresis system. Measured serum AAT concentrations by immunoassay exhibited moderate correlation with measured SPEP alpha1-globulin fraction concentrations. In this sample set, 16 (84%) of the ZZ, 7 (29%) of the MZ, and none of the MM sample phenotypes exhibited alpha1-globulin concentrations of less than 0.21 g/dL. From estimates of MZ and ZZ phenotype prevalence, it can be calculated that 1 ZZ phenotype should be present in approximately every 31 samples with alpha1-globulin concentrations of less than 0.21 g/dL. Clinicians should consider investigation of potential AAT deficiency in patients who exhibit low alpha1-globulin protein levels by routine SPEP.

Disease consequences of pathogen adaptation.

Experimental evolution studies demonstrate that pathogens evolve rapidly, have a large capacity for increased virulence and cause disease in many different ways. A large proportion of genetic diversity for host susceptibility to infectious, autoimmune and 'genetic' diseases, and to cancer, is probably caused by pathogens and/or host counteradaptations. Recent advances in diverse fields support this claim and suggest many underused approaches for identifying and experimentally dissecting the complicated host-pathogen interactions that often lead to disease.

Performance characteristics of 5 automated thyroglobulin autoantibody and thyroid peroxidase autoantibody assays.

BACKGROUND: Measurement of thyroid peroxidase autoantibodies (TPOAb) is useful in diagnosing patients with autoimmune thyroid disease. Measurement of thyroglobulin autoantibodies (TgAb) is used to detect potential interferences with thyroglobulin immunoassays and in limited situations for the diagnosis of autoimmune thyroid disease. METHODS: The limit of detection, imprecision, reference interval, method comparison and diagnostic concordance for the ADVIA Centaur, ARCHITECT i2000, AxSYM, Immulite 2000, Modular E170 (TPOAb only), and UniCel DxI 800 (TgAb only) methods were evaluated. The Advantage was used as the comparison method. RESULTS: Total imprecision ranged from 2.6% to 14.9% for TgAb and 2.1% to 15.8% for TPOAb. Passing-Bablok slopes ranged from 0.51 to 10.4 (TgAb) and 1.05 to 7.12 (TPOAb) with correlation coefficients of 0.48 to 0.82 (TgAb) and 0.66 to 0.78 (TPOAb). Assay cutoffs were adjusted using a common set of reference interval samples. Concordance with the Advantage assay using the new cutoffs was found to be improved and ranged from 68.5% to 84.7% (TgAb) and 77.5% to 84.7% (TPOAb). CONCLUSIONS: Although all assays generally performed well, assay concordance for a negative or positive result ranged from 54.2 to 84.7%. Quantitative agreement between methods was generally poor and methods could not be used interchangeably. Additional standardization efforts are required to improve inter-method agreement.

Performance characteristics of seven automated CA 15-3 assays.

Measurements of serum cancer antigen (CA) 15-3 are used to monitor tumor recurrence and treatment of advanced disease. We evaluated the performance characteristics, including limit of detection, linearity, method comparison, and reference intervals, of 7 automated methods for CA 15-3, including the Access 2 (Beckman Coulter, Brea, CA), ADVIA Centaur (Bayer Diagnostics, Tarrytown, NY), ARCHITECT i2000 and AxSYM (Abbott Diagnostics, Abbott Park, IL), Elecsys 2010 (Roche Diagnostics, Indianapolis, IN), IMMULITE 2000 (Diagnostic Products, Los Angeles, CA), and VITROS ECi (Ortho Clinical Diagnostics, Raritan, NJ) assays. The limit of detection for each assay was less than 1.0 kU/L. The maximum deviation for the target values for linearity samples was less than 10% for all methods. Method comparison studies revealed large differences for some individual samples. Overall slopes ranged from 0.50 to 1.48, and correlation coefficients were 0.90 to 0.96 when the ADVIA Centaur was the comparison method. The 97.5 percentile upper reference limit ranged from 23.3 to 51.7 kU/L. Additional standardization efforts are needed, and the availability of reference material is required. Substantial intermethod differences exist for some patient samples, indicating that redetermining the baseline is required when changing methods.

Specific Immunoglobulin (Ig) G Reference Intervals for Common Food, Insect, and Mold Allergens.

BACKGROUND: The clinical utility of serum IgG measurement in the diagnosis of allergy and food-induced hypersensitivity has been largely discredited. Recent studies, however, have shown that specific IgG can inhibit IgE mediated allergies, and may play a role in allergen specific desensitization. Accurate reference intervals for IgG specific allergens have not been widely established and are needed for better interpretation of serum antibody concentrations. In this study we established 64 IgG reference intervals for 48 common food allergens, 5 venoms, and 11 molds. DESIGN: Specific IgG concentrations were determined employing an automated fluorescent enzyme immunoassay on serum samples from 130 normal adults (65 males and 65 females), age range 18-69 y, mean 37.3 y. RESULTS: The lower reference interval limit for all allergens tested (n=64) was <2 mcg/mL. The median upper reference interval value for all 64 allergens was 12.9 mcg/mL, with Tuna (f40) having the lowest upper interval limit at 3.8 mcg/mL, and the mold Setomelanomma rostrate (m8) demonstrating the highest upper interval limit at 131 mcg/L. CONCLUSIONS: The considerable variation observed among the upper reference interval limits emphasizes the need for the establishment of allergen specific ranges for IgG. These newly established ranges should be a useful aid for clinicians in the interpretation of laboratory serum IgG results.

Copy number variation and incomplete linkage disequilibrium interfere with the HCP5 genotyping assay for abacavir hypersensitivity.

Carriers of HLA-B*57:01 are at risk for Abacavir hypersensitivity reaction (ABC-HSR). In Caucasians, a SNP (rs2395029) in the HCP5 gene is reported to be in linkage disequilibrium (LD) with HLA-B*57:01. Genotyping the HCP5 SNP has increasingly been adopted as a simple method to screen for susceptibility to ABC-HSR. We genotyped both the HCP5 SNP and HLA-B*57:01 in a set of 1888 samples and found a good correlation; significantly, however, one HLA-B*57:01-positive sample tested negative for the HCP5 SNP. In addition, HCP5 could not be amplified in two samples, both negative for HLA-B*57:01. Further investigation demonstrated both samples were homozygous for deletion of the HCP5 gene. The fact HCP5 occurs within a region of copy number variation and the fact LD is incomplete and may vary between ethnicities should be considered when using the HCP5 SNP as a surrogate marker for HLA-B*57:01.

Simultaneous genotyping of rs12979860 and rs8099917 variants near the IL28B locus associated with HCV clearance and treatment response.

Recent genome-wide association studies have identified two host single-nucleotide polymorphisms (SNPs) near the IL28B gene (rs12979860 C/T and rs8099917 T/G) that are associated with sustained virological response in patients infected with the hepatitis C virus. Herein, we describe a rapid multiplexed dual-color fluorescence resonance energy transfer (FRET) probe assay that accurately genotypes for both SNPs simultaneously. A single-nucleotide extension assay was also developed for verification of genotypes. Agreement (100%) was observed in genotype calls between the FRET and single-nucleotide extension methods for both SNPs, yielding 100% analytical sensitivity and specificity. By using the FRET assay, 443 samples of varying ethnic backgrounds were genotyped and six different compound genotypes (rs12979860/rs8099917) were detected in whites, Asians, Middle Easterners, Hispanics, and African Americans, at the following frequencies: CC/TT (39.2%, 78.9%, 40.0%, 33.9%, and 16.8%), CT/TT (20.8%, 0%, 40%, 9.3%, and 37.0%), TT/TT (2.4%, 0%, 0%, 3.4%, and 35.3%), CT/TG (24.0%, 19.7%, 20%, 39.8%, and 3.4%), TT/TG (8.0%, 1.4%, 0%, 3.4%, and 5.9%), and TT/GG (5.6%, 0%, 0%, 10.2%, and 1.7%), respectively. The multiplexed FRET assay can be used to effectively genotype for both SNPs in a single tube, with high analytical sensitivity and specificity.

Cerebrospinal fluid oligoclonal bands in childhood opsoclonus-myoclonus.

Oligoclonal bands in cerebrospinal fluid reflect local B-cell responses associated with various neuroinflammatory disorders. In opsoclonus-myoclonus syndrome, cerebrospinal fluid B-cell expansion was demonstrated, but no studies of oligoclonal bands are available. In a prospective case-control study of 132 children (103 with opsoclonus-myoclonus, 29 neurologic control subjects), cerebrospinal fluid oligoclonal bands, measured by isoelectric focusing with immunofixation, were observed in 35% with opsoclonus-myoclonus and none of the control subjects, with the highest frequency in severe cases (56%). In oligoclonal band-positive patients, the mean band number was 5 ± 3 S.D. (range, 2-10) and the total severity score was significantly higher than in band-negative patients, whereas the frequency of CD19(+) B cells, opsoclonus-myoclonus duration, neuroblastoma detection, and relapse history did not differ. The cerebrospinal fluid immunoglobulin G synthesis rate, immunoglobulin index, and Q albumin were normal. In 17 untreated children receiving adrenocorticotropic hormone, intravenous immunoglobulins, and rituximab, the number of oligoclonal band-positive decreased by 75%, and the mean band count fell by 80%. Oligoclonal band detection adds useful information to neuroimmunologic "staging" in opsoclonus-myoclonus. However, flow cytometry provides a more sensitive measure of B-cell infiltration. Cerebrospinal fluid oligoclonal bands warrant monitoring in long-term follow-up studies of disease-modifying drugs for opsoclonus-myoclonus.