A biophysical model of viral escape from polyclonal antibodies

A challenge in studying viral immune escape is determining how mutations combine to escape polyclonal antibodies, which can potentially target multiple distinct viral epitopes. Here we introduce a biophysical model of this process that partitions the total polyclonal antibody activity by epitope and then quantifies how each viral mutation affects the antibody activity against each epitope. We develop software that can use deep mutational scanning data to infer these properties for polyclonal antibody mixtures. We validate this software using a computationally simulated deep mutational scanning experiment and demonstrate that it enables the prediction of escape by arbitrary combinations of mutations. The software described in this paper is available at https://jbloomlab.github.io/polyclonal.

Drivers of inpatient hospitalization costs, joint-specific patient-reported outcomes, and health-related quality of life in shoulder arthroplasty for cuff tear arthropathy

BACKGROUND

Cuff tear arthropathy (CTA) can be successfully treated with various types of shoulder arthroplasty. While reverse total shoulder arthroplasty (RSA) is commonly used to treat CTA, CTA hemiarthroplasty (CTA-H, hemiarthroplasty with an extended humeral articular surface) can also be effective in patients with preserved glenohumeral elevation and an intact coracoacromial (CA) arch. As the value of arthroplasty is being increasingly scrutinized, cost containment has become a priority. The objective of this study was to assess hospitalization costs and improvements in joint-specific measures and health-related quality of life for these two types of shoulder arthroplasty in the management of CTA.

METHODS

Seventy-two patients (39 CTA-H and 33 RSA) were treated during the study time period using different selection criteria for each of the two procedures: CTA-H was selected in patients with retained active elevation, an intact CA arch, and an intact subscapularis, while RSA was selected in patients with pseudoparalysis or glenohumeral instability. The Simple Shoulder Test (SST) was used as a joint-specific patient-reported outcome measure. Improvement in quality-adjusted life years was measured using the Short Form 36. Costs associated with inpatient care were collected from hospital financial records. Univariate and multivariate analyses focused on determining predictors of hospitalization costs and improvements in patient-reported outcomes.

RESULTS

Significant improvements in SST and Short Form 36 physical component scores were seen in both groups. Inpatient hospitalization costs were significantly higher in the RSA group than that in the CTA-H group ($15,074 ± $1614 vs. $10,389 ± $1948, P < .001), driven primarily by supplies including the cost of the prosthesis ($9005 ± $2521 vs. $4715 ± $2091, P < .001). The diagnosis of diabetes was an independent predictor of higher inpatient hospitalization costs for both groups. There were no independent predictors for quality-adjusted life year improvements. SST improvement in the CTA-H group was significantly higher in patients with lower preoperative SST scores.

CONCLUSION

Using a standard algorithm of CTA-H for shoulders with retained active elevation and an intact CA arch and RSA for poor active elevation or glenohumeral instability, both procedures led to significant improvements in health-related quality of life and joint-specific measures. Costs were significantly lower for patients meeting the selection criteria for CTA-H. Further value analytics are needed to compare the relative cost effectiveness of RSA and CTA-H for patients with CTA having retained active elevation, intact CA arch, and intact subscapularis.

Inference of B cell clonal families using heavy/light chain pairing information

Next generation sequencing of B cell receptor (BCR) repertoires has become a ubiquitous tool for understanding the antibody-mediated immune response: it is now common to have large volumes of sequence data coding for both the heavy and light chain subunits of the BCR. However, until the recent development of high throughput methods of preserving heavy/light chain pairing information, these samples contained no explicit information on which heavy chain sequence pairs with which light chain sequence. One of the first steps in analyzing such BCR repertoire samples is grouping sequences into clonally related families, where each stems from a single rearrangement event. Many methods of accomplishing this have been developed, however, none so far has taken full advantage of the newly-available pairing information. This information can dramatically improve clustering performance, especially for the light chain. The light chain has traditionally been challenging for clonal family inference because of its low diversity and consequent abundance of non-clonal families with indistinguishable naive rearrangements. Here we present a method of incorporating this pairing information into the clustering process in order to arrive at a more accurate partition of the data into clonally related families. We also demonstrate two methods of fixing imperfect pairing information, which may allow for simplified sample preparation and increased sequencing depth. Finally, we describe several other improvements to the partis software package.

Culturing explants for Cutibacterium at revision shoulder arthroplasty: an analysis of explant and tissue samples at corresponding anatomic sites

BACKGROUND

Culturing of deep tissues obtained at revision arthroplasty for Cutibacterium is a key component of diagnosing a periprosthetic infection. The value of culturing explanted components has not been well described. This study sought to answer the following questions: (1) How does the culture positivity of explant cultures compare with that of deep tissue cultures? (2) How often are explant cultures positive when tissue cultures are not, and vice versa? (3) How does the bacterial density in explant cultures compare with that in tissue cultures?

METHODS

A total of 106 anatomic arthroplasties revised over a 7-year period were included. Explant (humeral head, humeral stem, and glenoid) and tissue (collar membrane, humeral canal tissue, and periglenoid tissue) specimens were sent for semiquantitative Cutibacterium culture. We compared culture positivity and bacterial density when cultures of an explant and tissue adjacent to the implant were both available.

RESULTS

Explants had positive cultures at a higher rate than adjacent tissue specimens for most anatomic sites. Of the shoulders that had Cutibacterium growth, a higher proportion of explants were culture positive when tissue samples were negative (23%-43%) than vice versa (0%-21%). The Cutibacterium density was higher in explants than in tissues. Considering only the results of tissue samples, 16% of the shoulders met our threshold for infection treatment (≥2 positive cultures); however, with the inclusion of the results for explant cultures, additional 14% of cases-a total of 30%-met the criteria for infection treatment.

CONCLUSIONS

In this group of patients, culturing explants in addition to tissue cultures increased the sensitivity for detecting Cutibacterium in revision shoulder arthroplasty.

Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency

Although the rates at which positions in the genome mutate are known to depend not only on the nucleotide to be mutated, but also on neighboring nucleotides, it remains challenging to do phylogenetic inference using models of context-dependent mutation. In these models, the effects of one mutation may in principle propagate to faraway locations, making it difficult to compute exact likelihoods. This article shows how to use bounds on the propagation of dependency to compute likelihoods of mutation of a given segment of genome by marginalizing over sufficiently long flanking sequence. This can be used for maximum likelihood or Bayesian inference. Protocols examining residuals and iterative model refinement are also discussed. Tools for efficiently working with these models are provided in an R package, which could be used in other applications. The method is used to examine context dependence of mutations since the common ancestor of humans and chimpanzee.

The minimal clinically important differences of the Simple Shoulder Test are different for different arthroplasty types

BACKGROUND

Preoperative and postoperative patient self-reported measures are the key to understanding the benefit of shoulder arthroplasty for patients with different diagnoses and having different surgical approaches. The minimal clinically important difference (MCID) for patient-reported outcomes such as the Simple Shoulder Test (SST) is often used to document the amount of improvement that is of importance to the patient; however, the MCID may differ for different types of shoulder arthroplasty. The objective of this study was to report the MCID of the SST and the MCID of the percentage of maximal possible improvement (%MPI) for 5 different arthroplasty types.

METHODS

Eight hundred eighty-seven patients undergoing shoulder arthroplasty with preoperative SST scores, 2-year postoperative SST scores, and patient satisfaction were included. The sample comprised 368 patients undergoing anatomic total shoulder arthroplasty (aTSA), 330 patients undergoing ream-and-run arthroplasty (R&R), 80 patients undergoing reverse total shoulder arthroplasty (rTSA), 53 patients undergoing cuff tear arthropathy arthroplasty, and 56 patients undergoing hemiarthroplasty. For each type of arthroplasty, the anchor-based method was used for calculating the MCID for both absolute SST scores and %MPI.

RESULTS

Significant improvements in SST values were seen for all arthroplasty types. The MCID for SST change was 2.3 overall but ranged from 1.6 for aTSA, to 2.6 for R&R, to 3.7 for rTSA. The MCID for %MPI was 32% overall but ranged from 22% for aTSA to 42% for hemiarthroplasty. The percentage of patients exceeding the MCID threshold was highest for aTSA at 96% and lowest for hemiarthroplasty at 61%.

CONCLUSION

The same MCID value may not be appropriate for different types of shoulder arthroplasty. This study reports MCID thresholds that can be used when assessing the effectiveness for each of the common types of shoulder arthroplasty.

What do positive and negative Cutibacterium culture results in periprosthetic shoulder infection mean? A multi-institutional control study

BACKGROUND

Deep tissue culture specimens obtained at the time of revision shoulder arthroplasty are commonly positive for Cutibacterium. Clinical interpretation of positive cultures can be difficult. This was a multi-institutional study evaluating the accuracy of cultures for Cutibacterium using positive control (PC) and negative control (NC) samples. The relationship between time to culture positivity and strength of culture positivity was also studied.

METHODS

Eleven different institutions were each sent 12 blinded samples (10 PC and 2 NC samples). The 10 PC samples included 2 sets of 5 different dilutions of a Cutibacterium isolate from a failed total shoulder arthroplasty with a probable periprosthetic infection. At each institution, the samples were handled as if they were received from the operating room. Specimen growth, time to culture positivity, and strength of culture positivity (based on semiquantitative assessment) were reported.

RESULTS

A total of 110 PC samples and 22 NC samples were tested. One hundred percent of specimens at the 4 highest dilutions were positive for Cutibacterium. At the lowest dilution, 91% of samples showed positive findings. Cutibacterium grew in 14% of NC samples. Cutibacterium grew in PC samples at an average of 4.0 ± 1.3 days, and all of these samples showed growth within 7 days. The time to positivity was significantly shorter (P < .001) and the strength of positivity was significantly higher (P < .001) in true-positive cultures compared with false-positive cultures.

CONCLUSIONS

This multi-institutional study suggests that different institutions may report highly consistent rates of culture positivity for revision shoulder arthroplasty samples with higher bacterial loads. In contrast, with lower bacterial loads, the results are somewhat less consistent. Clinicians should consider using a shorter time to positivity and a higher strength of positivity as adjuncts in determining whether a tissue culture sample is a true positive.

Distinct Antibody Responses to Endemic Coronaviruses Pre- and Post-SARS-CoV-2 Infection in Kenyan Infants and Mothers

Pre-existing antibodies that bind endemic human coronaviruses (eHCoVs) can cross-react with SARS-CoV-2, which is the betacoronavirus that causes COVID-19, but whether these responses influence SARS-CoV-2 infection is still under investigation and is particularly understudied in infants. In this study, we measured eHCoV and SARS-CoV-1 IgG antibody titers before and after SARS-CoV-2 seroconversion in a cohort of Kenyan women and their infants. Pre-existing eHCoV antibody binding titers were not consistently associated with SARS-CoV-2 seroconversion in infants or mothers; however, we observed a very modest association between pre-existing HCoV-229E antibody levels and a lack of SARS-CoV-2 seroconversion in the infants. After seroconversion to SARS-CoV-2, antibody binding titers to the endemic betacoronaviruses HCoV-OC43 and HCoV-HKU1, and the highly pathogenic betacoronavirus SARS-CoV-1, but not the endemic alphacoronaviruses HCoV-229E and HCoV-NL63, increased in the mothers. However, eHCoV antibody levels did not increase following SARS-CoV-2 seroconversion in the infants, suggesting the increase seen in the mothers was not simply due to cross-reactivity to naively generated SARS-CoV-2 antibodies. In contrast, the levels of antibodies that could bind SARS-CoV-1 increased after SARS-CoV-2 seroconversion in both the mothers and infants, both of whom were unlikely to have had a prior SARS-CoV-1 infection, supporting prior findings that SARS-CoV-2 responses cross-react with SARS-CoV-1. In summary, we found evidence of increased eHCoV antibody levels following SARS-CoV-2 seroconversion in the mothers but not the infants, suggesting eHCoV responses can be boosted by SARS-CoV-2 infection when a prior memory response has been established, and that pre-existing cross-reactive antibodies are not strongly associated with SARS-CoV-2 infection risk in mothers or infants.

Distinct antibody responses to endemic coronaviruses pre- and post-SARS-CoV-2 infection in Kenyan infants and mothers

Pre-existing antibodies that bind endemic human coronaviruses (eHCoVs) can cross-react with SARS-CoV-2, the betacoronavirus that causes COVID-19, but whether these responses influence SARS-CoV-2 infection is still under investigation and is particularly understudied in infants. In this study, we measured eHCoV and SARS-CoV-1 IgG antibody titers before and after SARS-CoV-2 seroconversion in a cohort of Kenyan women and their infants. Pre-existing eHCoV antibody binding titers were not consistently associated with SARS-CoV-2 seroconversion in infants or mothers, though we observed a very modest association between pre-existing HCoV-229E antibody levels and lack of SARS-CoV-2 seroconversion in infants. After seroconversion to SARS-CoV-2, antibody binding titers to endemic betacoronaviruses HCoV-OC43 and HCoV-HKU1, and the highly pathogenic betacoronavirus SARS-CoV-1, but not endemic alphacoronaviruses HCoV-229E and HCoV-NL63, increased in mothers. However, eHCoV antibody levels did not increase following SARS-CoV-2 seroconversion in infants, suggesting the increase seen in mothers was not simply due to cross-reactivity to naively generated SARS-CoV-2 antibodies. In contrast, the levels of antibodies that could bind SARS-CoV-1 increased after SARS-CoV-2 seroconversion in both mothers and infants, both of whom are unlikely to have had a prior SARS-CoV-1 infection, supporting prior findings that SARS-CoV-2 responses cross-react with SARS-CoV-1. In summary, we find evidence for increased eHCoV antibody levels following SARS-CoV-2 seroconversion in mothers but not infants, suggesting eHCoV responses can be boosted by SARS-CoV-2 infection when a prior memory response has been established, and that pre-existing cross-reactive antibodies are not strongly associated with SARS-CoV-2 infection risk in mothers or infants.

Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities

Every T cell receptor (TCR) repertoire is shaped by a complex probabilistic tangle of genetically determined biases and immune exposures. T cells combine a random V(D)J recombination process with a selection process to generate highly diverse and functional TCRs. The extent to which an individual’s genetic background is associated with their resulting TCR repertoire diversity has yet to be fully explored. Using a previously published repertoire sequencing dataset paired with high-resolution genome-wide genotyping from a large human cohort, we infer specific genetic loci associated with V(D)J recombination probabilities using genome-wide association inference. We show that V(D)J gene usage profiles are associated with variation in the TCRB locus and, specifically for the functional TCR repertoire, variation in the major histocompatibility complex locus. Further, we identify specific variations in the genes encoding the Artemis protein and the TdT protein to be associated with biasing junctional nucleotide deletion and N-insertion, respectively. These results refine our understanding of genetically-determined TCR repertoire biases by confirming and extending previous studies on the genetic determinants of V(D)J gene usage and providing the first examples of trans genetic variants which are associated with modifying junctional diversity. Together, these insights lay the groundwork for further explorations into how immune responses vary between individuals.

Oral and IV Antibiotic Administration After Single-Stage Revision Shoulder Arthroplasty: Study of Survivorship and Patient-Reported Outcomes in Patients without Clear Preoperative or Intraoperative Infection

BACKGROUND

Following revision shoulder arthroplasty, postoperative antibiotics are selected before the results of intraoperative cultures become available. We determined infection-free survival, revision-free survival, complications, and patient-reported outcomes for patients selected to receive oral or intravenous (IV) antibiotics after revision arthroplasty.

METHODS

This study included 92 patients who had revision shoulder arthroplasty. IV antibiotics were administered if the surgeon had a high index of suspicion for infection, and oral antibiotics were given if there was a low suspicion. Antibiotic therapy was modified based on intraoperative culture results. Patient-reported outcomes and adverse events were documented at a mean of 4.1 years.

RESULTS

In selecting antibiotic therapy, surgeons correctly predicted the presence or absence of multiple positive cultures of specimens from the revision surgery in 72% of the 92 cases. Subsequent re-revision surgery was required in 17 (18%) of the patients; 8 of these 17 patients had ≥2 positive cultures at re-revision. Patients who initially received IV antibiotics and those who initially received oral antibiotics had similar revision-free (p = 0.202) and infection-free (p = 0.155) survivorship. Patients requiring a change from oral to IV antibiotics based on positive cultures had similar survivorship compared with those initially treated with IV antibiotics. The IV and oral antibiotic groups had similar postoperative Simple Shoulder Test (SST), American Shoulder and Elbow Surgeons (ASES), and satisfaction scores. Patients receiving IV antibiotics had a higher rate of antibiotic-related adverse events.

CONCLUSIONS

Post-revision antibiotic therapy was associated with an infection-free survival rate of 91% at a mean of >4 years of follow-up. Infection-free survival, revision-free survival, and patient-reported outcomes were similar in high-risk patients placed on IV antibiotics and low-risk patients placed on oral antibiotics. Further study is needed to define the indications for IV or oral antibiotics after revision arthroplasty.

LEVEL OF EVIDENCE

Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.

Cutibacterium recovered from deep specimens at the time of revision shoulder arthroplasty samples has increased biofilm-forming capacity and hemolytic activity compared with Cutibacterium skin isolates from normal subjects

BACKGROUND

Biofilm formation and hemolytic activity are factors that may correlate with the virulence of Cutibacterium. We sought to compare the prevalence of these potential markers of pathogenicity between Cutibacterium recovered from deep specimens obtained at the time of surgical revision for failed shoulder arthroplasty and Cutibacterium recovered from skin samples from normal subjects.

METHODS

We compared 42 deep-tissue or explant isolates with 43 control Cutibacterium samples obtained from skin isolates from normal subjects. Subtyping information was available for all isolates. Biofilm-forming capacity was measured by inoculating a normalized amount of each isolate onto a 96-well plate. Planktonic bacteria were removed, the remaining adherent bacteria were stained with crystal violet, the crystal violet was re-solubilized in ethyl alcohol, and biofilm-forming capacity was quantitated by optical density (OD). Hemolytic activity was measured by plating a normalized amount of isolate onto agar plates. The area of the colony and the surrounding area of blood lysis were measured and reported as minimal, moderate, or severe hemolysis.

RESULTS

Biofilm-forming capacity was significantly higher in the tissue and explant samples compared with the control skin samples (OD of 0.34 ± 0.30 for deep tissue vs. 0.20 ± 0.28 for skin, P = .002). Hemolytic activity was also significantly higher in the tissue and explant samples than in the control skin samples (P < .0001). Samples with hemolytic activity had significantly higher biofilm-forming capacity compared with samples without hemolytic activity (OD of 0.27 ± 0.29 vs. 0.12 ± 0.15, P = .015). No difference in biofilm-forming capacity or hemolytic activity was found between subtypes.

CONCLUSIONS

Cutibacterium obtained from deep specimens at the time of revision shoulder arthroplasty has higher biofilm-forming capacity and hemolytic activity than Cutibacterium recovered from the skin of normal subjects. These data add support for the view that Cutibacterium harvested from deep tissues may have clinically significant virulence characteristics. The lack of correlation between these clinically relevant phenotypes and subtypes indicates that additional study is needed to identify genotypic markers that better correlate with biofilm and hemolytic activity.

Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection

Background:

Control of the COVID-19 pandemic will rely on SARS-CoV-2 vaccine-elicited antibodies to protect against emerging and future variants; an understanding of the unique features of the humoral responses to infection and vaccination, including different vaccine platforms, is needed to achieve this goal.

Methods:

The epitopes and pathways of escape for Spike-specific antibodies in individuals with diverse infection and vaccination history were profiled using Phage-DMS. Principal component analysis was performed to identify regions of antibody binding along the Spike protein that differentiate the samples from one another. Within these epitope regions, we determined potential sites of escape by comparing antibody binding of peptides containing wild-type residues versus peptides containing a mutant residue.

Results:

Individuals with mild infection had antibodies that bound to epitopes in the S2 subunit within the fusion peptide and heptad-repeat regions, whereas vaccinated individuals had antibodies that additionally bound to epitopes in the N- and C-terminal domains of the S1 subunit, a pattern that was also observed in individuals with severe disease due to infection. Epitope binding appeared to change over time after vaccination, but other covariates such as mRNA vaccine dose, mRNA vaccine type, and age did not affect antibody binding to these epitopes. Vaccination induced a relatively uniform escape profile across individuals for some epitopes, whereas there was much more variation in escape pathways in mildly infected individuals. In the case of antibodies targeting the fusion peptide region, which was a common response to both infection and vaccination, the escape profile after infection was not altered by subsequent vaccination.

Conclusions:

The finding that SARS-CoV-2 mRNA vaccination resulted in binding to additional epitopes beyond what was seen after infection suggests that protection could vary depending on the route of exposure to Spike antigen. The relatively conserved escape pathways to vaccine-induced antibodies relative to infection-induced antibodies suggests that if escape variants emerge they may be readily selected for across vaccinated individuals. Given that the majority of people will be first exposed to Spike via vaccination and not infection, this work has implications for predicting the selection of immune escape variants at a population level.

Funding:

This work was supported by NIH grants AI138709 (PI JMO) and AI146028 (PI FAM). JMO received support as the Endowed Chair for Graduate Education (FHCRC). The research of FAM was supported in part by a Faculty Scholar grant from the Howard Hughes Medical Institute and the Simons Foundation. Scientific Computing Infrastructure at Fred Hutch was funded by ORIP grant S10OD028685.

When SARS-CoV-2 – the virus that causes COVID-19 – infects our bodies, our immune system reacts by producing small molecules called antibodies that stick to a part of the virus called the spike protein. Vaccines are thought to work by triggering the production of similar antibodies without causing disease. Some of the most effective antibodies against SARS-CoV-2 bind a specific area of the spike protein called the ‘receptor binding domain’ or RBD.

When SARS-CoV-2 evolves it creates a challenge for our immune system: mutations, which are changes in the virus’s genetic code, can alter the shape of its spike protein, meaning that existing antibodies may no longer bind to it as effectively. This lowers the protection offered by past infection or vaccination, which makes it harder to tackle the pandemic.

As it stands, it is not clear which mutations to the virus’s genetic code can affect antibody binding, especially to portions outside the RBD. To complicate things further, the antibodies people produce in response to mild infection, severe infection, and vaccination, while somewhat overlapping, exhibit some differences. Studying these differences could help minimize emergence of mutations that allow the virus to ‘escape’ the antibody response.

A phage display library is a laboratory technique in which phages (viruses that infect bacteria) are used as a ‘repository’ for DNA fragments that code for a specific protein. The phages can then produce the protein (or fragments of it), and if the protein fragments bind to a target, it can be easily detected. Garrett, Galloway et al. exploited this technique to study how different portions of the SARS-CoV-2 spike protein were bound by antibodies. They made a phage library in which each phage encoded a portion of the spike protein with different mutations, and then exposed the different versions of the protein to antibodies from people who had experienced prior infection, vaccination, or both.

The experiment showed that antibodies produced during severe infection or after vaccination bound to similar parts of the spike protein, while antibodies from people who had experienced mild infection targeted fewer areas. Garrett, Galloway et al. also found that mutations that affected the binding of antibodies produced after vaccination were more consistent than mutations that interfered with antibodies produced during infection.

While these results show which mutations are most likely to help the virus escape existing antibodies, this does not mean that the virus will necessarily evolve in that direction. Indeed, some of the mutations may be impossible for the virus to acquire because they interfere with the virus’s ability to spread. Further studies could focus on revealing which of the mutations detected by Garrett, Galloway et al. are most likely to occur, to guide vaccine development in that direction. To help with this, Garrett, Galloway et al. have made the data accessible to other scientists and the public using a web tool.

Association Between Serum Testosterone Levels and Cutibacterium Skin Load in Patients Undergoing Elective Shoulder Arthroplasty: A Cohort Study

Cutibacterium periprosthetic joint infections are important complications of shoulder arthroplasty. Although it is known that these infections are more common among men and that they are more common in patients with high levels of Cutibacterium on the skin, the possible relationship between serum testosterone levels and skin Cutibacterium levels has not been investigated.

Macaque-human differences in SARS-CoV-2 Spike antibody response elicited by vaccination or infection

Macaques are a commonly used model for studying immunity to human viruses, including for studies of SARS-CoV-2 infection and vaccination. However, it is unknown whether macaque antibody responses recapitulate, and thus appropriately model, the response in humans. To answer this question, we employed a phage-based deep mutational scanning approach (Phage-DMS) to compare which linear epitopes are targeted on the SARS-CoV-2 Spike protein in humans and macaques following either vaccination or infection. We also used Phage-DMS to determine antibody escape pathways within each epitope, enabling a granular comparison of antibody binding specificities at the locus level. Overall, we identified some common epitope targets in both macaques and humans, including in the fusion peptide (FP) and stem helix-heptad repeat 2 (SH-H) regions. Differences between groups included a response to epitopes in the N-terminal domain (NTD) and C-terminal domain (CTD) in vaccinated humans but not vaccinated macaques, as well as recognition of a CTD epitope and epitopes flanking the FP in convalescent macaques but not convalescent humans. There was also considerable variability in the escape pathways among individuals within each group. Sera from convalescent macaques showed the least variability in escape overall and converged on a common response with vaccinated humans in the SH-H epitope region, suggesting highly similar antibodies were elicited. Collectively, these findings suggest that the antibody response to SARS-CoV-2 in macaques shares many features with humans, but with substantial differences in the recognition of certain epitopes and considerable individual variability in antibody escape profiles, suggesting a diverse repertoire of antibodies that can respond to major epitopes in both humans and macaques.

SARS-CoV-2 Antibody Binding and Neutralization in Dried Blood Spot Eluates and Paired Plasma

Wide-scale assessment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibodies is critical to understanding population seroprevalence, correlates of protection, and the longevity of vaccine-elicited responses. Most SARS-CoV-2 studies characterize antibody responses in plasma/sera. While reliable and broadly used, these samples pose several logistical restrictions, such as requiring venipuncture for collection and a cold chain for transportation and storage. Dried blood spots (DBS) overcome these barriers as they can be self-collected by fingerstick and mailed and stored at ambient temperature. Here, we evaluate the suitability of DBS for SARS-CoV-2 antibody assays by comparing several antibody responses between paired plasma and DBS from SARS-CoV-2 convalescent and vaccinated individuals. We found that DBS not only reflected plasma antibody binding by enzyme-linked immunosorbent assay (ELISA) and epitope profiles using phage display, but also yielded SARS-CoV-2 neutralization titers that highly correlated with paired plasma. Neutralization measurement was further streamlined by adapting assays to a high-throughput 384-well format. This study supports the adoption of DBS for numerous SARS-CoV-2 binding and neutralization assays. IMPORTANCE Plasma and sera isolated from venous blood represent conventional sample types used for the evaluation of SARS-CoV-2 antibody responses after infection or vaccination. However, collection of these samples is invasive and requires trained personnel and equipment for immediate processing. Once collected, plasma and sera must be stored and shipped at cold temperatures. To define the risk of emerging SARS-CoV-2 variants and the longevity of immune responses to natural infection and vaccination, it will be necessary to measure various antibody features in populations around the world, including in resource-limited areas. A sampling method that is compatible with these settings and is suitable for a variety of SARS-CoV-2 antibody assays is therefore needed to continue to understand and curb the COVID-19 pandemic.

Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein after infection and/or vaccination

Background:

Control of the COVID-19 pandemic will rely on SARS-CoV-2 vaccine-elicited antibodies to protect against emerging and future variants; an understanding of the unique features of the humoral responses to infection and vaccination, including different vaccine platforms, is needed to achieve this goal.

Methods:

The epitopes and pathways of escape for Spike-specific antibodies in individuals with diverse infection and vaccination history were profiled using Phage-DMS. Principal component analysis was performed to identify regions of antibody binding along the Spike protein that differentiate the samples from one another. Within these epitope regions we determined potential escape mutations by comparing antibody binding of peptides containing wildtype residues versus peptides containing a mutant residue.

Results:

Individuals with mild infection had antibodies that bound to epitopes in the S2 subunit within the fusion peptide and heptad-repeat regions, whereas vaccinated individuals had antibodies that additionally bound to epitopes in the N- and C-terminal domains of the S1 subunit, a pattern that was also observed in individuals with severe disease due to infection. Epitope binding appeared to change over time after vaccination, but other covariates such as mRNA vaccine dose, mRNA vaccine type, and age did not affect antibody binding to these epitopes. Vaccination induced a relatively uniform escape profile across individuals for some epitopes, whereas there was much more variation in escape pathways in in mildly infected individuals. In the case of antibodies targeting the fusion peptide region, which was a common response to both infection and vaccination, the escape profile after infection was not altered by subsequent vaccination.

Conclusions:

The finding that SARS-CoV-2 mRNA vaccination resulted in binding to additional epitopes beyond what was seen after infection suggests protection could vary depending on the route of exposure to Spike antigen. The relatively conserved escape pathways to vaccine-induced antibodies relative to infection-induced antibodies suggests that if escape variants emerge, they may be readily selected for across vaccinated individuals. Given that the majority of people will be first exposed to Spike via vaccination and not infection, this work has implications for predicting the selection of immune escape variants at a population level.

Subluxation in the Arthritic Shoulder

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The term "subluxation" means partial separation of the joint surfaces. In the arthritic shoulder, "arthritic glenohumeral subluxation" refers to displacement of the humeral head on the surface of the glenoid.

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The degree of arthritic glenohumeral subluxation can be measured using radiography with standardized axillary views or computed tomography (CT).

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Shoulders with a type-B1 or B2 glenoid may show more posterior subluxation on an axillary radiograph that is made with the arm in an elevated position than on a CT scan that is made with the arm at the side.

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The degree of arthritic glenohumeral subluxation is not closely related to glenoid retroversion.

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The position of the humeral head with respect to the plane of the scapula is related to glenoid retroversion and is not a measure of glenohumeral subluxation.

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Studies measuring glenohumeral subluxation before and after arthroplasty should clarify its importance to the clinical outcomes of shoulder reconstruction.

Shoulder Hemiarthroplasty with Nonprosthetic Glenoid Arthroplasty: The Ream-and-Run Procedure

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Glenoid component wear and loosening are the principal failure modes of anatomic total shoulder arthroplasty (aTSA).

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The ream-and-run (RnR) procedure is an alternative glenohumeral arthroplasty for patients who wish to avoid the risks and limitations of a prosthetic glenoid component.

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During the RnR procedure, the arthritic glenoid is conservatively reamed to a single concavity, while the prosthetic humeral component and soft tissues are balanced to provide both mobility and stability of the joint.

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The success of the RnR procedure depends on careful patient selection, preoperative education and engagement, optimal surgical technique, targeted rehabilitation, and close postoperative communication between the surgeon and the patient.

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While the RnR procedure allows high levels of shoulder function in most patients, the recovery can be longer and more arduous than with aTSA.

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Patients who have undergone an RnR procedure occasionally require a second closed or open procedure to address refractory shoulder stiffness, infection, or persistent glenoid-sided pain. These second procedures are more common after the RnR than with aTSA.

Drivers of lower inpatient hospital costs and greater improvements in health-related quality of life for patients undergoing total shoulder and ream-and-run arthroplasty

BACKGROUND

With increasing emphasis on value-based care and the heavy demands on the US health care budget, surgeons must be cognizant of factors that drive cost and quality of patient care. Our objective was to determine patient-level drivers of lower costs and improved health-related quality of life (HRQoL) in 2 anatomic shoulder arthroplasty procedures: total shoulder arthroplasty (TSA) and ream-and-run arthroplasty.

METHODS

This study included 222 TSAs and 211 ream-and-run arthroplasties. Simple Shoulder Test, Single Assessment Numeric Evaluation, and Short Form 36 scores were collected preoperatively and 2 years postoperatively. Quality-adjusted life-years (QALYs) were calculated as a measure of HRQoL. Univariate and multivariate analyses determined factors significantly associated with decreased hospitalization costs and improved HRQoL.

RESULTS

In the TSA group, female sex, lower American Society of Anesthesiologists class, diagnosis other than capsulorrhaphy arthropathy, lower pain score, and higher Single Assessment Numeric Evaluation score were associated with decreased total hospitalization costs; in addition, female sex was an independent predictor of lower total costs. Insurance other than workers' compensation, a diagnosis of chondrolysis, and higher optimism led to greater QALY gains, but a diagnosis of capsulorrhaphy arthropathy was the only independent predictor of greater QALY gains. In the ream-and-run arthroplasty group, older age, lower body mass index (BMI), lower American Society of Anesthesiologists class, insurance other than Medicaid, diagnosis other than capsulorrhaphy arthropathy, no history of surgery, higher preoperative Simple Shoulder Test score, and higher preoperative Short Form 36 Physical Component Summary score were associated with lower total costs; moreover, lower BMI was an independent predictor of lower costs. Higher preoperative optimism was an independent predictor of greater QALY gains.

CONCLUSIONS

Identifying factors associated with decreased costs and increased quality is becoming increasingly important in value-based care. This study identified fixed (sex and diagnosis) and modifiable (BMI) factors that drive decreased hospitalization costs and increased HRQoL improvements in shoulder arthroplasty patients. Higher preoperative patient optimism is a consistent predictor of improved HRQoL for both TSA patients and ream-and-run arthroplasty patients, and further study on optimizing the influence of patient expectations and optimism may be warranted.

Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection

Stimulating broadly neutralizing antibodies (bnAbs) directly from germline remains a barrier for HIV vaccines. HIV superinfection elicits bnAbs more frequently than single infection, providing clues of how to elicit such responses. We used longitudinal antibody sequencing and structural studies to characterize bnAb development from a superinfection case. BnAb QA013.2 bound initial and superinfecting viral Env, despite its probable naive progenitor only recognizing the superinfecting strain, suggesting both viruses influenced this lineage. A 4.15 Å cryo-EM structure of QA013.2 bound to native-like trimer showed recognition of V3 signatures (N301/N332 and GDIR). QA013.2 relies less on CDRH3 and more on framework and CDRH1 for affinity and breadth compared to other V3/glycan-specific bnAbs. Antigenic profiling revealed that viral escape was achieved by changes in the structurally-defined epitope and by mutations in V1. These results highlight shared and novel properties of QA013.2 relative to other V3/glycan-specific bnAbs in the setting of sequential, diverse antigens.

Epitope profiling reveals binding signatures of SARS-CoV-2 immune response in natural infection and cross-reactivity with endemic human CoVs

A major goal of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine efforts is to elicit antibody responses that confer protection. Mapping the epitope targets of the SARS-CoV-2 antibody response is critical for vaccine design, diagnostics, and development of therapeutics. Here, we develop a pan-coronavirus phage display library to map antibody binding sites at high resolution within the complete viral proteomes of all known human-infecting coronaviruses in patients with mild or moderate/severe coronavirus disease 2019 (COVID-19). We find that the majority of immune responses to SARS-CoV-2 are targeted to the spike protein, nucleocapsid, and ORF1ab and include sites of mutation in current variants of concern. Some epitopes are identified in the majority of samples, while others are rare, and we find variation in the number of epitopes targeted between individuals. We find low levels of SARS-CoV-2 cross-reactivity in individuals with no exposure to the virus and significant cross-reactivity with endemic human coronaviruses (CoVs) in convalescent sera from patients with COVID-19.

Assessing the Value to the Patient of New Technologies in Anatomic Total Shoulder Arthroplasty

BACKGROUND

Publications regarding anatomic total shoulder arthroplasty (TSA) have consistently reported that they provide significant improvement for patients with glenohumeral arthritis. New TSA technologies that have been introduced with the goal of further improving these outcomes include preoperative computed tomography (CT) scans, 3-dimensional preoperative planning, patient-specific instrumentation, stemless and short-stemmed humeral components, as well as metal-backed, hybrid, and augmented glenoid components. The benefit of these new technologies in terms of patient-reported outcomes is unknown.

METHODS

We reviewed 114 articles presenting preoperative and postoperative values for commonly used patient-reported metrics. The results were analyzed to determine whether patient outcomes have improved over the 20 years during which new technologies became available.

RESULTS

The analysis did not identify evidence that the results of TSA were statistically or clinically improved over the 2 decades of study or that any of the individual technologies were associated with significant improvement in patient outcomes.

CONCLUSIONS

Additional research is required to document the clinical value of these new technologies to patients with glenohumeral arthritis.

LEVEL OF EVIDENCE

Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.