How Trustworthy Is Your Tree? Bayesian Phylogenetic Effective Sample Size Through the Lens of Monte Carlo Error

Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judge how well a given Bayesian Markov chain Monte Carlo (MCMC) run explores the space of phylogenetic trees. In this paper, we investigate the Monte Carlo error of phylogenies, focusing on high-dimensional summaries of the posterior distribution, including variability in estimated edge/branch (known in phylogenetics as "split") probabilities and tree probabilities, and variability in the estimated summary tree. Specifically, we ask if there is any measure of effective sample size (ESS) applicable to phylogenetic trees which is capable of capturing the Monte Carlo error of these three summary measures. We find that there are some ESS measures capable of capturing the error inherent in using MCMC samples to approximate the posterior distributions on phylogenies. We term these tree ESS measures, and identify a set of three which are useful in practice for assessing the Monte Carlo error. Lastly, we present visualization tools that can improve comparisons between multiple independent MCMC runs by accounting for the Monte Carlo error present in each chain. Our results indicate that common post-MCMC workflows are insufficient to capture the inherent Monte Carlo error of the tree, and highlight the need for both within-chain mixing and between-chain convergence assessments.

Minimum 10-year follow-up of anatomic total shoulder arthroplasty and ream-and-run arthroplasty for primary glenohumeral osteoarthritis

BACKGROUND

Reports on long term outcomes and failures of shoulder arthroplasty are uncommon. The purpose of this study is to present minimum 10-year outcomes in consecutive patients undergoing ream-and-run and anatomic total shoulder arthroplasty (TSA) for primary glenohumeral arthritis.

METHODS

This study analyzed consecutive patients who had undergone a ream-and-run or TSA with minimum 10-year follow-up. Pain scores and Simple Shoulder Test (SST) values were obtained preoperatively and at a minimum of 10 years postoperatively via e-mail or mail-in response. Percentage of maximum possible improvement (%MPI) was also calculated.

RESULTS

Of 127 eligible patients, 63 (50%) responded to a 10-year survey. This included 34 patients undergoing ream-and-run arthroplasty and 29 patients undergoing TSA. The ream-and-run patients were significantly younger than the TSA patients (60 ± 7 vs. 68 ± 8, P < .001), predominantly male (97% vs. 41%, P < .001), and had a lower American Society of Anesthesiologists classification (P = .018). In the ream-and-run group, the mean pain score improved from a preoperative value of 6.5 ± 1.9 to 0.9 ± 1.3 (P < .001), and the mean SST score improved from 5.4 ± 2.4 to 10.3 ± 2.1 at 10-year follow-up (P < .001). Twenty-eight (82%) achieved an SST improvement above the minimally clinically important difference (MCID) of 2.6. Four patients (12%) underwent single-stage exchange to another hemiarthroplasty, whereas 1 (3%) required manipulation under anesthesia. In the TSA group, the pain score improved from a preoperative value of 6.6 ± 2.2 to 1.2 ± 2.3 (P < .001), and the SST score improved from 3.8 ± 2.6 to 8.9 ± 2.6 at 10-year follow-up (P < .001). Of the 29 patients who underwent a TSA, 27 (93%) achieved an SST improvement above the MCID of 1.6. No patient in the TSA group required reoperation.

CONCLUSION

Although the characteristics of the patients differ between the 2 groups, excellent functional results can be obtained with the ream-and-run arthroplasty and TSA for glenohumeral osteoarthritis.

Anatomic shoulder arthroplasty: the correlation between patient resilience, mental health, and outcome

BACKGROUND

Recovery from anatomic shoulder arthroplasty may be enhanced in patients with good mental health and the resilience to participate in the prescribed postoperative rehabilitation program. To test this concept, we utilized validated and reliable scales in determining whether resilience and mental health are associated with the outcome of anatomic arthroplasty.

METHODS

Three hundred ninety-nine patients (195 ream and run [RnR] and 204 anatomic total shoulder arthroplasty [aTSA]) were surveyed at a mean follow-up of 6.3 ± 3.3 years. Preoperative variables included age, sex, body mass index, history of prior shoulder surgery, diabetes, visual analog scale for pain, Simple Shoulder Test (SST) scores, and Veteran's RAND 12 Mental Component Score (VR-12 MCS). Outcomes collected included the SST, American Shoulder and Elbow Surgeons (ASES) score, revision rate, and patient satisfaction. Resilience was documented using the Connor-Davidson Resilience Scale 10 (CD-RISC 10) at latest follow-up. Univariable and multivariable regression analyses were used to identify factors significantly associated with follow-up postoperative SST, ASES, and satisfaction.

RESULTS

In the univariable analysis, CD-RISC 10 was positively correlated with postoperative SST, ASES, and satisfaction after both RnR and aTSA. The mean CD-RISC 10 scores were higher in the RnR cohort (34.3 ± 4.8 vs. 32.5 ± 6.2 for aTSA, P < .001). Male sex and lower preoperative visual analog scale for pain were correlated with higher ASES after RnR; VR-12 MCS was positively correlated with all outcomes except SST after RnR. In the multivariable linear regression analysis, CD-RISC 10 was independently associated with postoperative SST, ASES and satisfaction scores in aTSA patients. In the RnR cohort, CD-RISC 10 was only correlated with satisfaction. VR-12 MCS was correlated with ASES and satisfaction after RnR.

DISCUSSION

In this study of anatomic arthroplasties, increased resilience and better mental health were correlated with better outcomes. RnR patients had higher resilience than aTSA patients. Greater resilience was associated with better outcomes after aTSA. Better mental health was associated with superior outcomes after the ream and run procedure.

Anatomic Total Shoulder: Predictors of Excellent Outcomes at Five Years after Arthroplasty

PURPOSE

The objectives of this study were to: report minimum 5-year outcomes in patients undergoing TSA and determine characteristics predictive of patients achieving an excellent functional outcome.

METHODS

Pre-operative demographic variables and Simple Shoulder Test (SST) scores were obtained pre-operatively and at a minimum of five years after surgery. A final SST ≥ 10 and percentage of maximal possible improvement (% MPI) of ≥ 66.7% were determined to be the thresholds for excellent outcomes. Univariate and multivariate analysis were performed to identify factors associated with excellent five year clinical outcomes.

RESULTS

Of 233 eligible patients, 188 (81%) had adequate follow-up for inclusion in this study. Mean SST scores improved from 3.4 ± 2.4 to 9.7 ± 2.2 (p < 0.001). Male sex was an independent predictor of both SST ≥ 10 (OR 3.46, 95% CI 1.70-7.31; p < 0.001) and %MPI ≥ 66.7 (OR 2.27, 95% CI 1.11-4.81, p = 0.027). Workers' Compensation insurance was predictive of not obtaining SST ≥ 10 (OR 0.12, 95% 0.02-0.60; p = 0.016) or %MPI ≥ 66.7 (OR 0.16, 95% CI 0.03-0.77, p = 0.025). MCID was passed by the vast majority (95%) of patients undergoing TSA and did not necessarily indicate an excellent, satisfactory outcome.

CONCLUSION

Male sex and commercial insurance coverage were significantly associated with these excellent outcomes, while Workers' Compensation insurance was associated with failure to achieve this result. Thresholds for excellent outcomes, such as final SST ≥ 10 and %MPI ≥ 66.7, may be useful in identifying the characteristics of patients who benefit most from TSA.

Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses

The recurring spillover of pathogenic coronaviruses and demonstrated capacity of sarbecoviruses, such SARS-CoV-2, to rapidly evolve in humans underscores the need to better understand immune responses to this virus family. For this purpose, we characterized the functional breadth and potency of antibodies targeting the receptor binding domain (RBD) of the spike glycoprotein that exhibited cross-reactivity against SARS-CoV-2 variants, SARS-CoV-1 and sarbecoviruses from diverse clades and animal origins with spillover potential. One neutralizing antibody, C68.61, showed remarkable neutralization breadth against both SARS-CoV-2 variants and viruses from different sarbecovirus clades. C68.61, which targets a conserved RBD class 5 epitope, did not select for escape variants of SARS-CoV-2 or SARS-CoV-1 in culture nor have predicted escape variants among circulating SARS-CoV-2 strains, suggesting this epitope is functionally constrained. We identified 11 additional SARS-CoV-2/SARS-CoV-1 cross-reactive antibodies that target the more sequence conserved class 4 and class 5 epitopes within RBD that show activity against a subset of diverse sarbecoviruses with one antibody binding every single sarbecovirus RBD tested. A subset of these antibodies exhibited Fc-mediated effector functions as potent as antibodies that impact infection outcome in animal models. Thus, our study identified antibodies targeting conserved regions across SARS-CoV-2 variants and sarbecoviruses that may serve as therapeutics for pandemic preparedness as well as blueprints for the design of immunogens capable of eliciting cross-neutralizing responses.

2023 Neer Award for Basic Science: Genetics of Cutibacterium acnes in Revision Shoulder Arthroplasty: A Large-Scale Bacterial Whole-Genome Sequencing Study

BACKGROUND

Cutibacterium acnes is the bacterium most commonly responsible for shoulder periprosthetic joint infection (PJI) and is often cultured from samples obtained at the time of revision for failed shoulder arthroplasty. We sought to determine whether these bacteria originate from the patient or from exogenous sources. We also sought to identify which C. acnes genetic traits were associated with the development of shoulder PJI.

METHODS

We performed bacterial whole-genome sequencing of C. acnes from a single-institution repository of cultures obtained before or during primary and revision shoulder arthroplasty and correlated the molecular epidemiology and genetic content of strains with clinical features of infection.

RESULTS

A total of 341 isolates collected over a four-year period from 88 patients were sequenced. C. acnes cultured from surgical specimens demonstrated significant similarity to the strains colonizing the skin of the same patient (p<0.001). Infrequently, there was evidence of strains shared across unrelated patients, suggesting that exogenous sources of C. acnes culture-positivity were uncommon. Phylotypes IB and II were modestly associated with clinical features of PJI, but all phylotypes appeared inherently capable of causing disease. Chronic shoulder PJI was associated with the absence of common C. acnes genes involved in bacterial quorum-sensing (luxS, tqsA).

CONCLUSION

C. acnes strains cultured from deep intraoperative sources during revision shoulder arthroplasty demonstrate strong genetic similarity to the strains colonizing a patient's skin. Some phylotypes of C. acnes commonly colonizing human skin are modestly more virulent than others, but all phylotypes have a capacity for PJI. C. acnes cultured from cases of PJI commonly demonstrated genetic hallmarks associated with adaptation from acute to chronic phases of infection. This is the strongest evidence to date supporting the role of the patient's own, cutaneous C. acnes strains in the pathogenesis of shoulder arthroplasty infection. Our findings support the importance of further research focused on perioperative decolonization and management of endogenous bacteria that are likely to be introduced into the arthroplasty wound at the time of skin incision.

Managing rotator cuff tear arthropathy: a role for cuff tear arthropathy hemiarthroplasty as well as reverse total shoulder arthroplasty

BACKGROUND

Disabling cuff tear arthropathy (CTA) is commonly managed with reverse shoulder arthroplasty (RSA). However, for patients with CTA having preserved active elevation, cuff tear arthropathy hemiarthroplasty (CTAH) may offer a cost-effective alternative that avoids the complications unique to RSA. We sought to determine the characteristics and outcomes of a series of patients with CTA managed with these procedures.

MATERIALS AND METHODS

We retrospectively reviewed 103 patients with CTA treated with shoulder arthroplasty, the type of which was determined by the patient's ability to actively elevate the arm. Outcome measures included the change in the Simple Shoulder Test (SST), the percent maximum improvement in SST (%MPI), and the percentage of patients exceeding the minimal clinically important difference for the change in SST and %MPI. Postoperative x-rays were evaluated to assess the positions of the center of rotation and the greater tuberosity for each implant.

RESULTS

Forty-four percent of the 103 patients were managed with CTAH while 56% were managed with RSA. Both arthroplasties resulted in clinically significant improvement. Patients having RSA improved from a mean preoperative SST score of 1.7 (interquartile range [IQR], 0.0-3.0) to a postoperative score of 6.3 (IQR, 2.3-10.0) (P < .01). Patients having CTAH improved from a preoperative SST score of 3.1 (IQR, 1.0-4.0) to a postoperative score of 7.6 (IQR, 5.0-10.) (P < .001). These improvements exceeded the minimal clinically important difference. Instability accounted for most of the RSA complications; however, it did not account for any CTAH complications. The postoperative position of the center of rotation and greater tuberosity on anteroposterior radiographs did not correlate with the clinical outcomes for either procedure.

CONCLUSION

For 103 patients with CTA, clinically significant improvement was achieved with appropriately indicated CTAH and RSA. In view of the lower cost of the CTAH implant, it may provide a cost-effective alternative to RSA for patients with retained active elevation.

Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex

Lassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host, Mastomys rodents. Efforts to create vaccines and antibody therapeutics must account for the evolutionary variability of Lassa virus's glycoprotein complex (GPC), which mediates viral entry into cells and is the target of neutralizing antibodies. To map the evolutionary space accessible to GPC, we use pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affect cell entry and antibody neutralization. Our experiments define functional constraints throughout GPC. We quantify how GPC mutations affect neutralization by a panel of monoclonal antibodies and show that all antibodies are escaped by mutations that exist among natural Lassa virus lineages. Overall, our work describes a biosafety-level-2 method to elucidate the mutational space accessible to GPC and shows how prospective characterization of antigenic variation could aid design of therapeutics and vaccines.

Many-core algorithms for high-dimensional gradients on phylogenetic trees

MOTIVATION

Advancements in high-throughput genomic sequencing are delivering genomic pathogen data at an unprecedented rate, positioning statistical phylogenetics as a critical tool to monitor infectious diseases globally. This rapid growth spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters of these phylogenetic models where the dimensions of the parameters increase with the number of sequences N. HMC requires repeated calculation of the gradient of the data log-likelihood with respect to (wrt) all branch-length-specific (BLS) parameters that traditionally takes O(N2) operations using the standard pruning algorithm. A recent study proposes an approach to calculate this gradient in O(N), enabling researchers to take advantage of gradient-based samplers such as HMC. The CPU implementation of this approach makes the calculation of the gradient computationally tractable for nucleotide-based models but falls short in performance for larger state-space size models, such as Markov-modulated and codon models. Here, we describe novel massively parallel algorithms to calculate the gradient of the log-likelihood wrt all BLS parameters that take advantage of graphics processing units (GPUs) and result in many fold higher speedups over previous CPU implementations.

RESULTS

We benchmark these GPU algorithms on three computing systems using three evolutionary inference examples exploring complete genomes from 997 dengue viruses, 62 carnivore mitochondria and 49 yeasts, and observe a >128-fold speedup over the CPU implementation for codon-based models and >8-fold speedup for nucleotide-based models. As a practical demonstration, we also estimate the timing of the first introduction of West Nile virus into the continental Unites States under a codon model with a relaxed molecular clock from 104 full viral genomes, an inference task previously intractable.

AVAILABILITY AND IMPLEMENTATION

We provide an implementation of our GPU algorithms in BEAGLE v4.0.0 (https://github.com/beagle-dev/beagle-lib), an open-source library for statistical phylogenetics that enables parallel calculations on multi-core CPUs and GPUs. We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (https://github.com/beast-dev/beast-mcmc).

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

Human influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral mutations vary across the human population, and how this heterogeneity affects virus evolution. Here we use deep mutational scanning to map how mutations to the hemagglutinin (HA) proteins of the A/Hong Kong/45/2019 (H3N2) and A/Perth/16/2009 (H3N2) strains affect neutralization by serum from individuals of a variety of ages. The effects of HA mutations on serum neutralization differ across age groups in ways that can be partially rationalized in terms of exposure histories. Mutations that fixed in influenza variants after 2020 cause the greatest escape from sera from younger individuals. Overall, these results demonstrate that influenza faces distinct antigenic selection regimes from different age groups, and suggest approaches to understand how this heterogeneous selection shapes viral evolution.

Which Components of the Simple Shoulder Test Show Improvement After Scapulothoracic Fusion for Recalcitrant Scapular Winging? Clinical Results at a Minimum of 5 Years of Follow-up

BACKGROUND

Scapular winging is an uncommon but important cause of shoulder pain and disability. Surgical management can include soft tissue procedures such as split pectoralis major transfer, the Eden-Lange procedure, or a triple tendon transfer. When these procedures do not alleviate symptomatic winging or are inappropriate, scapulothoracic fusion is an alternative, but data on its longer-term effectiveness are sparse.

QUESTIONS/PURPOSES

(1) What changes in outcome scores were observed (VAS, Single Assessment Numeric Evaluation [SANE], and Simple Shoulder Test [SST] scores), and what proportion of the patients improved by an amount larger than the minimum clinically important difference (MCID) for the outcome tool in question? (2) Which components of the SST are patients able to perform at a minimum of 5 years? (3) What complications occurred after surgery?

METHODS

We performed a retrospective study in a single, large, urban referral medical center of patients who underwent scapulothoracic fusion. Between January 2011 and November 2016, 15 patients underwent scapulothoracic fusion to treat symptomatic scapular winging. Only patients with nondystrophic etiology were included in the analysis (n = 13). Of the 13 remaining patients, one patient was lost to follow-up and another patient died during data collection, leaving 11 patients for the final analysis. Six patients had brachial plexus injuries affecting multiple nerve roots and periscapular muscles, and five had persistent symptoms despite prior tendon transfer. The median age of the patients was 43 years (range 20 to 67 years), and there were six male and five female patients. All patients had a minimum of 5 years of follow-up. There was a median follow-up of 79 months (range 61 to 128 months). The VAS pain score (range 0 to 10, higher scores represent more pain; MCID = 2), SST score (range 0 to 12, higher scores represent less pain and better shoulder function; MCID = 2.3), and SANE score (range 0 to 100, higher scores represent better shoulder function; MCID = 28) were recorded before surgery and at the most recent follow-up. We compared scores from before surgery with those taken at the most recent follow-up and ascertained the proportion of patients whose improvement exceeded the MCID. The number of patients achieving fusion (as confirmed by a CT image), complications, and reoperations was recorded via a record review as well as direct patient query by telephone.

RESULTS

The median VAS pain score improved from 7 (range 3 to 10) preoperatively to 3 (range 2 to 5) at the latest follow-up (p < 0.001). The median SANE score improved from 30 (range 0 to 60) preoperatively to 65 (range 40 to 85) at the latest follow-up (p < 0.001). The median SST score improved from 0 (range 0 to 9) to 8 (range 5 to 10) at the latest follow-up (p < 0.001). Ten of 11 patients had improvements exceeding the MCID for VAS, six of 11 had improvements for SANE scores, and nine of 11 had improvements for SST. Preoperative to postoperative improvements in these components of the SST were seen (responses of "yes"): comfort at rest (three of 11 improved to 11 of 11; p < 0.001), sleep comfortably (three of 11 improved to 11 of 11; p < 0.001), place coin on shelf (two of 11 improved to 10 of 11; p < 0.001), lift 1 pound above shoulder (two of 11 improved to eight of 11; p = 0.03), and carry 20 pounds with the arm at side (one of 11 improved to nine of 11; p < 0.001). All 11 patients had successful fusion noted on CT images. There were three complications (progression of glenohumeral arthritis, broken wires, and perioperative chest tube placement) and one reoperation for progression of glenohumeral arthritis with subsequent total shoulder arthroplasty.

CONCLUSION

Patients with recalcitrant symptomatic scapular winging often undergo an exhaustive course of clinical examinations, diagnostic tests, physical therapy, and multiple surgical procedures. Those with brachial plexus palsy with involvement of multiple nerves may continue to have symptoms despite nonoperative management and subsequent soft tissue tendon transfers. Scapulothoracic fusion could be considered for patients with persistent pain and decreased function because of recalcitrant scapular winging who are either not candidates for the procedure or have persistent symptoms despite prior soft tissue procedures.

LEVEL OF EVIDENCE

Level IV, therapeutic study.

Using viral sequence diversity to estimate time of HIV infection in infants

Age at HIV acquisition may influence viral pathogenesis in infants, and yet infection timing (i.e. date of infection) is not always known. Adult studies have estimated infection timing using rates of HIV RNA diversification, however, it is unknown whether adult-trained models can provide accurate predictions when used for infants due to possible differences in viral dynamics. While rates of viral diversification have been well defined for adults, there are limited data characterizing these dynamics for infants. Here, we performed Illumina sequencing of gag and pol using longitudinal plasma samples from 22 Kenyan infants with well-characterized infection timing. We used these data to characterize viral diversity changes over time by designing an infant-trained Bayesian hierarchical regression model that predicts time since infection using viral diversity. We show that diversity accumulates with time for most infants (median rate within pol = 0.00079 diversity/month), and diversity accumulates much faster than in adults (compare previously-reported adult rate within pol = 0.00024 diversity/month [1]). We find that the infant rate of viral diversification varies by individual, gene region, and relative timing of infection, but not by set-point viral load or rate of CD4+ T cell decline. We compare the predictive performance of this infant-trained Bayesian hierarchical regression model with simple linear regression models trained using the same infant data, as well as existing adult-trained models [1]. Using an independent dataset from an additional 15 infants with frequent HIV testing to define infection timing, we demonstrate that infant-trained models more accurately estimate time since infection than existing adult-trained models. This work will be useful for timing HIV acquisition for infants with unknown infection timing and for refining our understanding of how viral diversity accumulates in infants, both of which may have broad implications for the future development of infant-specific therapeutic and preventive interventions.

phippery: a software suite for PhIP-Seq data analysis

SUMMARY

We present the phippery software suite for analyzing data from phage display methods that use immunoprecipitation and deep sequencing to capture antibody binding to peptides, often referred to as PhIP-Seq. It has three main components that can be used separately or in conjunction: (i) a Nextflow pipeline, phip-flow, to process raw sequencing data into a compact, multidimensional dataset format and allows for end-to-end automation of reproducible workflows. (ii) a Python API, phippery, which provides interfaces for tasks such as count normalization, enrichment calculation, multidimensional scaling, and more, and (iii) a Streamlit application, phip-viz, as an interactive interface for visualizing the data as a heatmap in a flexible manner.

AVAILABILITY AND IMPLEMENTATION

All software packages are publicly available under the MIT License. The phip-flow pipeline: https://github.com/matsengrp/phip-flow. The phippery library: https://github.com/matsengrp/phippery. The phip-viz Streamlit application: https://github.com/matsengrp/phip-viz.

Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers

Infant antibody responses to viral infection can differ from those in adults. However, data on the specificity and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in infants, and direct comparisons between infants and adults are limited. Here, we characterize antibody binding and functionality against Wuhan-Hu-1 (B lineage) strain SARS-CoV-2 in convalescent plasma from 36 postpartum women and 14 of their infants infected with SARS-CoV-2 from a vaccine-naïve prospective cohort in Nairobi, Kenya. We find significantly higher antibody titers against SARS-CoV-2 Spike, receptor binding domain and N-terminal domain, and Spike-expressing cell-surface staining levels in infants versus mothers. Plasma antibodies from mothers and infants bind to similar regions of the Spike S2 subunit, including the fusion peptide (FP) and stem helix-heptad repeat 2. However, infants display higher antibody levels and more consistent antibody escape pathways in the FP region compared to mothers. Finally, infants have significantly higher levels of antibody-dependent cellular cytotoxicity (ADCC), though, surprisingly, Spike pseudovirus neutralization titers between infants and mothers are similar. These results suggest infants develop distinct SARS-CoV-2 binding and functional antibody activities and reveal age-related differences in humoral immunity to SARS-CoV-2 infection that could be relevant to protection and COVID-19 disease outcomes.

A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm

Bayesian phylogenetics is a computationally challenging inferential problem. Classical methods are based on random-walk Markov chain Monte Carlo (MCMC), where random proposals are made on the tree parameter and the continuous parameters simultaneously. Variational phylogenetics is a promising alternative to MCMC, in which one fits an approximating distribution to the unnormalized phylogenetic posterior. Previous work fit this variational approximation using stochastic gradient descent, which is the canonical way of fitting general variational approximations. However, phylogenetic trees are special structures, giving opportunities for efficient computation. In this paper we describe a new algorithm that directly generalizes the Felsenstein pruning algorithm (a.k.a. sum-product algorithm) to compute a composite-like likelihood by marginalizing out ancestral states and subtrees simultaneously. We show the utility of this algorithm by rapidly making point estimates for branch lengths of a multi-tree phylogenetic model. These estimates accord with a long MCMC run and with estimates obtained using a variational method, but are much faster to obtain. Thus, although generalized pruning does not lead to a variational algorithm as such, we believe that it will form a useful starting point for variational inference.

Passively Acquired Constant Region 5-Specific Antibodies Associated With Improved Survival in Infants Who Acquire Human Immunodeficiency Virus

Studying vertical human immunodeficiency virus (HIV) transmission enables the impact of passively transferred antibodies on HIV transmission and pathogenesis to be examined. Using phage display of HIV envelope peptides and peptide enzyme-linked immunosorbent assay (ELISA), we found that, in infants who acquired HIV, passive antibody responses to constant region 5 (C5) were associated with improved survival in 2 cohorts. In a combined analysis, C5 peptide ELISA activity was correlated directly with survival and estimated infection time and inversely with set point viral load. These results suggest that preexisting C5-specific antibodies may be correlated with the survival of infants living with HIV, motivating additional research into their protective potential.

Dynamics of Cutibacterium repopulation onto the skin surface of the shoulder after chlorhexidine application

PURPOSE

The objective of this study was to characterize the temporal dynamics of Cutibacterium repopulation of the skin surface after application of chlorhexidine to the shoulder.

METHODS

Ten shoulders in five male subjects were used. A skin swab was taken prior to (0 minutes) and then at three, 30, 60, 120, and 240 minutes after skin preparation with 2% chlorhexidine gluconate and 70% isopropyl alcohol. Semi-quantitative bacterial load was measured for each timepoint.

RESULTS

From zero minutes (pre-treatment) to three minutes, chlorhexidine-isopropyl alcohol reduced the skin bacterial load in eight out of ten shoulders. Of these eight shoulders, four (50%) had growth by 30 minutes, seven (88%) had growth by 60 minutes, and all eight (100%) had growth by 240 minutes. Compared to the three minutes after chlorhexidine application, bacterial load had significantly increased by 60 minutes but were still significantly lower than the pre-prep bacterial load (0 minutes).

CONCLUSION

Following standard surgical skin preparation with chlorhexidine-isopropyl alcohol, the surface of the shoulder is repopulated with Cutibacterium within one hour, presumably from reservoirs in sebaceous glands not penetrated by topical antiseptic agents. Since these dermal glands are transected by skin incision for shoulder arthroplasty, this study suggests that they may be sources of wound contamination during surgery in spite of skin preparation with chlorhexidine.

Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming

To appropriately defend against a wide array of pathogens, humans somatically generate highly diverse repertoires of B cell and T cell receptors (BCRs and TCRs) through a random process called V(D)J recombination. Receptor diversity is achieved during this process through both the combinatorial assembly of V(D)J-genes and the junctional deletion and insertion of nucleotides. While the Artemis protein is often regarded as the main nuclease involved in V(D)J recombination, the exact mechanism of nucleotide trimming is not understood. Using a previously published TCRβ repertoire sequencing data set, we have designed a flexible probabilistic model of nucleotide trimming that allows us to explore various mechanistically interpretable sequence-level features. We show that local sequence context, length, and GC nucleotide content in both directions of the wider sequence, together, can most accurately predict the trimming probabilities of a given V-gene sequence. Because GC nucleotide content is predictive of sequence-breathing, this model provides quantitative statistical evidence regarding the extent to which double-stranded DNA may need to be able to breathe for trimming to occur. We also see evidence of a sequence motif that appears to get preferentially trimmed, independent of GC-content-related effects. Further, we find that the inferred coefficients from this model provide accurate prediction for V- and J-gene sequences from other adaptive immune receptor loci. These results refine our understanding of how the Artemis nuclease may function to trim nucleotides during V(D)J recombination and provide another step toward understanding how V(D)J recombination generates diverse receptors and supports a powerful, unique immune response in healthy humans.

Reconstruction of a polyclonal ADCC antibody repertoire from an HIV-1 non-transmitting mother

Human natural history and vaccine studies support a protective role of antibody dependent cellular cytotoxicity (ADCC) activity against many infectious diseases. One setting where this has consistently been observed is in HIV-1 vertical transmission, where passively acquired ADCC activity in HIV-exposed infants has correlated with reduced acquisition risk and reduced pathogenesis in HIV+ infants. However, the characteristics of HIV-specific antibodies comprising a maternal plasma ADCC response are not well understood. Here, we reconstructed monoclonal antibodies (mAbs) from memory B cells from late pregnancy in mother MG540, who did not transmit HIV to her infant despite several high-risk factors. Twenty mAbs representing 14 clonal families were reconstructed, which mediated ADCC and recognized multiple HIV Envelope epitopes. In experiments using Fc-defective variants, only combinations of several mAbs accounted for the majority of plasma ADCC of MG540 and her infant. We present these mAbs as evidence of a polyclonal repertoire with potent HIV-directed ADCC activity.

Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses

Sequential dengue virus (DENV) infections often generate neutralizing antibodies against all four DENV serotypes and sometimes, Zika virus. Characterizing cross-flavivirus broadly neutralizing antibody (bnAb) responses can inform countermeasure strategies that avoid infection enhancement associated with non-neutralizing antibodies. Here, we used single cell transcriptomics to mine the bnAb repertoire following secondary DENV infection. We identified several new bnAbs with comparable or superior breadth and potency to known bnAbs, and with distinct recognition determinants. Unlike all known flavivirus bnAbs, which are IgG1, one newly identified cross-flavivirus bnAb (F25.S02) was derived from IgA1. Both IgG1 and IgA1 versions of F25.S02 and known bnAbs displayed neutralizing activity, but only IgG1 enhanced infection in monocytes expressing IgG and IgA Fc receptors. Moreover, IgG-mediated enhancement of infection was inhibited by IgA1 versions of bnAbs. We demonstrate a role for IgA in flavivirus infection and immunity with implications for vaccine and therapeutic strategies.

Risk Factors for Stiffness Requiring Intervention After Ream-and-Run Arthroplasty

Ream-and-run arthroplasty can improve pain and function in patients with glenohumeral arthritis while avoiding the complications and activity restrictions associated with a prosthetic glenoid component. However, stiffness is a known complication after ream-and-run arthroplasty and can lead to repeat procedures such as a manipulation under anesthesia (MUA) or open surgical revision. The objective of this study was to determine risk factors associated with repeat procedures indicated for postoperative stiffness after ream-and-run arthroplasty.

Methods

We conducted a retrospective review of our shoulder arthroplasty database to identify patients who underwent ream-and-run arthroplasty and determined which patients underwent subsequent repeat procedures (MUA and/or open revision) indicated for postoperative stiffness. The minimum follow-up was 2 years. We collected baseline demographic information and preoperative and 2-year patient-reported outcome scores and analyzed preoperative radiographs. Univariate and multivariate analyses determined the factors significantly associated with repeat procedures to treat postoperative stiffness.

Results

There were 340 patients who underwent ream-and-run arthroplasty. The mean Simple Shoulder Test (SST) scores for all patients improved from 5.0 ± 2.4 preoperatively to 10.2 ± 2.6 postoperatively (p < 0.001). Twenty-six patients (7.6%) underwent open revision for stiffness. An additional 35 patients (10.3%) underwent MUA. Univariate analysis found younger age (p = 0.001), female sex (p = 0.034), lower American Society of Anesthesiologists (ASA) class (p = 0.045), posterior decentering on preoperative radiographs (p = 0.010), and less passive forward elevation at the time of discharge after ream-and-run arthroplasty (p < 0.001) to be significant risk factors for repeat procedures. Multivariate analysis found younger age (p = 0.040), ASA class 1 compared with class 3 (p = 0.020), and less passive forward elevation at discharge (p < 0.001) to be independent risk factors for repeat procedures. Of the patients who underwent open revision for stiffness, 69.2% had multiple positive cultures for Cutibacterium.

Conclusions

Younger age, ASA class 1 compared with class 3, and less passive forward elevation in the immediate postoperative period were independent risk factors for repeat procedures to treat postoperative stiffness after ream-and-run arthroplasty.

Level of Evidence

Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.

What is the optimal management of a loose glenoid component after anatomic total shoulder arthroplasty: a systematic review

BACKGROUND

Total shoulder arthroplasty (TSA) provides excellent long-term clinical outcomes in the treatment of glenohumeral arthritis. However, symptomatic glenoid polyethylene loosening can be seen at intermediate follow-up and can lead to shoulder pain and dysfunction. The purpose of this study was to perform a systematic review of the available literature to determine the optimal management of symptomatic glenoid loosening with regard to reoperation and patient satisfaction following various approaches to symptomatic glenoid loosening.

METHODS

This study was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Studies investigating revision arthroplasty for the treatment of glenoid loosening with clinical outcomes were identified. Clinical failure was defined as a repeat procedure after revision arthroplasty.

RESULTS

Overall, 14 studies met inclusion criteria that included 483 patients with a mean age of 66.5 ± 3.0 years who underwent revision arthroplasty for symptomatic glenoid loosening. There were 8 studies that discussed conversion to a hemiarthroplasty (HA, 148 patients), 7 studies that discussed glenoid reimplantation in a single setting (1-stage TSA, 157 patients), 2 studies that discussed glenoid reimplantation in a staged setting (2-stage TSA, 18 patients), and 2 studies that discussed conversion to a reverse shoulder arthroplasty (RSA, 164 patients). All patients underwent glenoid component removal. The length of follow-up was significantly shorter in the RSA group (41 months for RSA vs. 56 months for HA vs. 55 months for 1-stage TSA vs. 62 months for 2-stage TSA, P < .001). The reoperation rate at the final follow-up was 19% for the HA cohort, 20% for the 1-stage TSA cohort, 22% for the 2-stage TSA cohort, and 21% for the RSA cohort (P = .971). Patient satisfaction rate at the final follow-up was 62% for the HA cohort, 66% for the 1-stage TSA cohort, 71% for the 2-stage TSA cohort, and 86% for the RSA cohort (P = .045). Positive cultures were noted in 15% of patients with Cutibacterium acnes comprising 72% of positive cultures.

CONCLUSIONS

Overall, the optimal management of symptomatic glenoid loosening remains unclear. All 4 types of revision arthroplasty (HA, 1-stage TSA, 2-stage TSA, and RSA) had a similar reoperation rate (20%) at the latest follow-up. Conversion to RSA provided a higher proportion of patients satisfied with the procedure. However, the length of follow-up was significantly shorter than other groups, and therefore longer-term follow-up of this group is needed to determine if results are durable.

Factors Associated with Success of Ream-and-Run Arthroplasty at a Minimum of Five Years

BACKGROUND

Ream-and-run arthroplasty offers improvement in shoulder pain and function for patients with primary glenohumeral arthritis who wish to avoid limitations associated with a polyethylene glenoid component. Longer-term clinical outcome assessments of the ream-and-run procedure are sparse in the literature. This study aims to present minimum 5-year functional outcomes in a large cohort following ream-and-run arthroplasty to determine factors associated with clinical success and reoperation.

METHODS

Patients undergoing ream-and-run surgery with a minimum of 5-years and mean of 7.6 ± 2.1 years of follow-up were collected through a retrospective review of a prospectively maintained database from a single academic institution. To assess clinical outcomes, the Simple Shoulder Test (SST) was administered and assessed for minimum clinically important difference achievement as well as the necessity for open revision surgery. Factors associated with a p<0.1 on univariate analysis were included in a multivariate analysis.

RESULTS

A total of 201 patients of 228 patients (88%) consented for long-term follow-up were included in our analysis. Average age was 59.4 ± 8.8 years, and 93% of patients were male with the majority having the diagnosis of osteoarthritis (79%) or capsulorrhaphy arthropathy (10%). SST scores improved from a mean of 4.9 ± 2.5 preoperatively to a mean of 10.2 ± 2.6 at latest follow-up. 165 patients (82%) reached the minimal clinically important difference of the SST of 2.6. Male sex (p=0.020), non-diabetes (p=0.080), and lower preoperative SST (p<0.001) were included in the multivariate analysis. Male sex (p=0.010) and lower preoperative SST scores (p≤0.001) were associated with clinically important improvements in SST scores on the multivariate analysis. Twenty-two patients (11%) required open revision surgery. Younger age (p<0.001), female sex (p=0.055), and higher preoperative pain scores (p=0.023) were included in the multivariate analysis. Only younger age was predictive of open revision surgery (p=0.003).

CONCLUSIONS

Ream and run arthroplasty can provide significant and clinically important improvements in clinical outcomes at minimum 5-year follow-up. Successful clinical outcomes were significantly associated with male sex and lower preoperative SST scores. Reoperation was more common in younger patients.

Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers

Infant antibody responses to viral infection can differ from those in adults. However, data on the specificity and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in infants, and direct comparisons between infants and adults are limited. We characterized antibody binding and functionality in convalescent plasma from postpartum women and their infants infected with SARS-CoV-2 from a vaccine-naïve prospective cohort in Nairobi, Kenya. Antibody titers against SARS-CoV-2 Spike, receptor binding domain and N-terminal domain, and Spike-expressing cell-surface staining levels were significantly higher in infants than in mothers. Plasma antibodies from mothers and infants bound to similar regions of the Spike S2 subunit, including the fusion peptide (FP) and stem helix-heptad repeat 2. However, infants displayed higher antibody levels and more consistent antibody escape pathways in the FP region compared to mothers. Finally, infants had significantly higher levels of antibody-dependent cellular cytotoxicity (ADCC), though, surprisingly, neutralization titers between infants and mothers were similar. These results suggest infants develop distinct SARS-CoV-2 binding and functional antibody repertoires and reveal age-related differences in humoral immunity to SARS-CoV-2 infection that could be relevant to protection and COVID-19 disease outcomes.

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.

High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies

Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, spike (S). Here, we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using coronavirus disease 2019 (COVID-19) convalescent plasma. Antibody binding was common in two regions, the fusion peptide and the linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.