Deep mutational scanning reveals functional constraints and antibody-escape potential 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 the 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 used pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affected cell entry and antibody neutralization. Our experiments defined functional constraints throughout GPC. We quantified how GPC mutations affected neutralization with a panel of monoclonal antibodies. All antibodies tested were escaped by mutations that existed 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 the design of therapeutics and vaccines.

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 two H3N2 strains, A/Hong Kong/45/2019 and A/Perth/16/2009, 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 were fixed in influenza variants after 2020 cause greater escape from sera from younger individuals compared with adults. 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.

Anatomic total shoulder arthroplasty for posteriorly eccentric and concentric osteoarthritis: a comparison at minimum 5-year follow-up.

BACKGROUND: In patients with glenohumeral osteoarthritis and posteriorly eccentric wear patterns, the early to mid-term results of TSA using conservative glenoid reaming with no attempt at version correction have been favorable at early follow-up. The purpose of this study is to compare the clinical and radiographic outcomes of TSA using this technique for patients with and without eccentric wear patterns at a minimum 5-year follow-up. METHODS: Patients who underwent TSA with minimum 5-year follow-up were identified from an institutional registry. Preoperative and postoperative radiographs were used to determine humeroglenoid alignment (HGA-AP), humeroscapular alignment (HSA-AP), version, Walch classification and glenoid component seating. The outcome measures were the Simple Shoulder Test, glenoid component radiolucencies, and the occurrence of complications or revisions. RESULTS: Two hundred and ten patients were included in the study, of which 98 (47%) had posteriorly decentered humeral heads and 108 (51%) had centered humeral heads. There were 77 shoulders with Walch type A glenoids and 122 with Walch type B glenoids. At a mean 8-year follow-up, the final SST, change in SST and percentage of maximal improvement was not correlated with pre- and postoperative humeral head centering, Walch classification or glenoid version. There were no preoperative predictors of a low final SST. Two patients (1%) underwent open re-operations during the study period. In patients with Walch B1 and B2 glenoids (n=110), there were no differences in outcome measures between patients with postoperative retroversion of more and less than 15o. While 15 of 51 patients (29%) with minimum 5-year radiographs had glenoid radioluciences, these radiographic findings were not associated with inferior clinical outcomes. On multivariable analysis glenoid component radiolucencies were most strongly associated with incomplete component seating (OR 3.3, p = 0.082). CONCLUSION: The results of TSA with conservative glenoid reaming without attempt at version correction are favorable at minimum 5 year, mean 8-year follow-up. There were no differences in clinical and radiographic outcomes between patients with eccentric and concentric wear patterns. Incomplete glenoid component seating was the greatest predictor of glenoid component radiolucency, but these radiolucencies were not associated with inferior clinical outcomes.

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.

Does Adding Hydrogen Peroxide to Chlorhexidine Gluconate Increase the Effectiveness of Skin Preparation in Reducing Cutaneous Cutibacterium Levels? A Randomized Controlled Trial.

INTRODUCTION: Shoulder periprosthetic joint infection (PJI) is most commonly caused by Cutibacterium. Effective removal of these bacteria from the skin is difficult because Cutibacterium live protected in the dermal sebaceous glands beneath the skin surface to which surgical preparation solutions, such as chlorhexidine gluconate (CHG), are applied. There is conflicting evidence on the additional benefit of using hydrogen peroxide (H2O2) as an adjunct to CHG in eliminating Cutibacterium from the skin. A previous study demonstrated that after CHG skin preparation, repopulation of Cutibacterium from sebaceous glands onto the skin surface occurs in 90% of shoulders by 60 minutes after application. The objective of this randomized controlled study was to determine the effectiveness of adding H2O2 to CHG in reducing skin Cutibacterium. METHODS: Eighteen male volunteers (36 shoulders) were recruited for this study. The two shoulders of each volunteer were randomized to receive the control preparation ("CHG-only" - 2% CHG in 70% isopropyl alcohol [ISA] alone) or the study preparation ("H2O2+CHG" - 3% H2O2 followed by 2% CHG in 70% ISA). Skin swabs were taken from each shoulder prior to skin preparation and again at 60 minutes after preparation. Swabs were cultured for Cutibacterium and observed for 14 days. Cutibacterium skin load was reported using a semi-quantitative system based on the number of quadrants growing on the culture plate. RESULTS: Prior to skin preparation, 100% of the CHG-only shoulders and 100% of the H2O2+CHG shoulders had positive skin surface cultures for Cutibacterium. Repopulation of Cutibacterium on the skin at 60 minutes occurred in 78% of CHG-only and 78% of H2O2+CHG shoulders (p=1.00). Reduction of Cutibacterium skin levels occurred in 56% of CHG-only and 61% of H2O2+CHG shoulders (p=0.735). Cutibacterium levels were significantly decreased from before skin preparation to 60 minutes after preparation in both the CHG-only (2.1 ± 0.8 to 1.3 ± 0.9, p=0.003) and the H2O2+CHG groups (2.2 ± 0.7 to 1.4 ± 0.9, p<0.001). Substantial skin surface levels of Cutibacterium were present at 60 minutes after both preparations. CONCLUSIONS: In this randomized controlled study, there was no additional benefit of using hydrogen peroxide as an adjunct to chlorhexidine gluconate skin preparation in the reduction of cutaneous Cutibacterium levels. Neither preparation was able to eliminate repopulation of Cutibacterium on the skin surface from the dermal sebaceous glands.

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 4-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 < .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.

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.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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 TCRß 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.