Multiplex PCR for bacterial, viral and protozoal pathogens in persistent diarrhoea or persistent abdominal pain in Côte d'Ivoire, Mali and Nepal.

In contrast to acute diarrhoea, the aetiology of persistent digestive disorders (≥ 14 days) is poorly understood in low-resource settings and conventional diagnostic approaches lack accuracy. In this multi-country study, we compared multiplex real-time PCR for enteric bacterial, parasitic and viral pathogens in stool samples from symptomatic patients and matched asymptomatic controls in Côte d'Ivoire, Mali and Nepal. Among 1826 stool samples, the prevalence of most pathogens was highest in Mali, being up to threefold higher than in Côte d'Ivoire and up to tenfold higher than in Nepal. In all settings, the most prevalent bacteria were EAEC (13.0-39.9%) and Campylobacter spp. (3.9-35.3%). Giardia intestinalis was the predominant intestinal protozoon (2.9-20.5%), and adenovirus 40/41 was the most frequently observed viral pathogen (6.3-25.1%). Significantly different prevalences between symptomatic and asymptomatic individuals were observed for Campylobacter, EIEC and ETEC in the two African sites, and for norovirus in Nepal. Multiple species pathogen infection was common in Côte d'Ivoire and Mali, but rarely found in Nepal. We observed that molecular testing detected multiple enteric pathogens and showed low discriminatory accuracy to distinguish between symptomatic and asymptomatic individuals. Yet, multiplex PCR allowed for direct comparison between different countries and revealed considerable setting-specificity.

Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease.

One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood1. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain-gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials.

The co-development and evaluation of an e-learning course on spinal cord injury physical activity counselling: a randomized controlled trial.

BACKGROUND: Health, fitness and lifestyle professionals can play important roles in promoting physical activity in groups at risk of developing an inactive lifestyle, such as people with spinal cord injury (SCI). Tailored counselling is a promising tool to promote and improve physical activity levels. To support professionals to effectively have a conversation about physical activity with clients with SCI, evidence-based training and resources are needed. This project aimed to (1) co-develop an e-learning course on best practices for SCI physical activity counselling and, (2) examine the effectiveness and usability of this course. METHODS: Guided by the technology-enhanced learning (TEL) evaluation framework, we used a systematic, multistep approach to co-develop and evaluate an e-learning course. The development process was informed by input and feedback from a diverse group of end-users and experts (n > 160) via online surveys and (think-aloud) interviews. A randomized controlled trial was used to compare learning outcomes (post-knowledge and self-efficacy) between participants who completed the course (intervention group) and the wait-listed control group. Usability, learning experiences, and satisfaction were assessed among all participants. RESULTS: Forty-one participants (21 intervention-group; 20 control-group) with various backgrounds (e.g., lifestyle counsellors, physiotherapists, occupational therapists, recreation therapists, fitness trainers) enrolled in the randomized controlled trial. After completing the course, participants in the intervention group showed significantly improved knowledge on the best practices for SCI physical activity counselling and higher self-efficacy for using these best practices in conversations with clients with SCI compared to the control group (p <.001). Participants reported above average usability scores, positive learning experiences, and high levels of satisfaction when completing the course. CONCLUSION: We used a systematic, multi-step, theory-informed approach to co-develop and evaluate an evidence-based e-learning course on SCI physical activity counselling to support professionals to promote physical activity in their daily practices. The overall positive findings demonstrate that the e-learning course is feasible and ready for further implementation in various health and community settings. Implementation of the e-learning course can help professionals improve the physical activity support they provide to their clients, and subsequently increase physical activity participation in people with SCI.

Tailoring Strength Training Prescriptions for People with Rheumatoid Arthritis: A Scoping Review.

Introduction: Prescribing strength training (ST) for people with rheumatoid arthritis (RA) is complicated by factors (barriers and facilitators) that affect participation. It is unclear whether guidelines include recommendations beyond prescription parameters (frequency, intensity, time, type, volume, and progression) and adequately incorporate participation factors tailored to people with RA. Objective: To summarize available recommendations to aid in the tailoring of ST prescriptions for people with RA. Methods: Medline, Embase, and CINAHL databases and gray literature were searched for guidelines, recommendations, and review articles containing ST prescription recommendations for RA. Article screening and data extraction were performed in duplicate by two reviewers. Results: Twenty-seven articles met the inclusion criteria. The recommendations address RA-specific ST participation factors including: knowledge gaps (of equipment, ST benefits, disease), memory problems, the management of joint deformity, comorbidity, the fluctuating nature of the disease and symptoms (pain, stiffness, flares), fear avoidance, motivation, need for referral to other professionals, and provision of RA-specific resources. Conclusion: This review summarizes recommendations for tailoring ST prescriptions for people with RA. Future research is required to understand how pain, symptom assessment, and unaddressed ST participation factors like sleep and medication side effects can be addressed to support ST participation amongst people with RA.

Role of multidrug-resistant bacteria in weaning from invasive mechanical ventilation.

BACKGROUND: Although multidrug-resistant bacteria (MDR) are common in patients undergoing prolonged weaning, there is little data on their impact on weaning and patient outcomes. METHODS: This is a retrospective analysis of consecutive patients who underwent prolonged weaning and were at a university weaning centre from January 2018 to December 2020. The influence of MDR colonisation and infection on weaning success (category 3a and 3b), successful prolonged weaning from invasive mechanical ventilation (IMV) with or without the need for non-invasive ventilation (NIV) compared with category 3c (weaning failure 3cI or death 3cII) was investigated. The pathogen groups considered were: multidrug-resistant gram-negative bacteria (MDRGN), methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus spp. (VRE). RESULTS: A total of 206 patients were studied, of whom 91 (44.2%) showed evidence of MDR bacteria (32% VRE, 1.5% MRSA and 16% MDRGN), with 25 patients also meeting the criteria for MDR infection. 70.9% of the 206 patients were successfully weaned from IMV, 8.7% died. In 72.2% of cases, nosocomial pneumonia and other infections were the main cause of death. Patients with evidence of MDR (infection and colonisation) had a higher incidence of weaning failure than those without evidence of MDR (48% vs. 34.8% vs. 21.7%). In multivariate analyses, MDR infection (OR 4.9, p = 0.004) was an independent risk factor for weaning failure, along with male sex (OR 2.3, p = 0.025), Charlson Comorbidity Index (OR 1.2, p = 0.027), pH (OR 2.7, p < 0.001) and duration of IMV before admission (OR 1.01, p < 0.001). In addition, MDR infection was the only independent risk factor for death (category 3cII), (OR 6.66, p = 0.007). CONCLUSION: Patients with MDR infection are significantly more likely to die during the weaning process. There is an urgent need to develop non-antibiotic approaches for the prevention and treatment of MDR infections as well as clinical research on antibiotic stewardship in prolonged weaning as well as in ICUs.

Mucosal and systemic immune correlates of viral control after SARS-CoV-2 infection challenge in seronegative adults.

Human infection challenge permits in-depth, early, and pre-symptomatic characterization of the immune response, enabling the identification of factors that are important for viral clearance. Here, we performed intranasal inoculation of 34 young adult, seronegative volunteers with a pre-Alpha severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain. Of these participants, 18 (53%) became infected and showed an interferon-dominated mediator response with divergent kinetics between nasal and systemic sites. Peripheral CD4+ and CD8+ T cell activation and proliferation were early and robust but showed distinct kinetic and phenotypic profiles; antigen-specific T cells were largely CD38+Ki67+ and displayed central and effector memory phenotypes. Both mucosal and systemic antibodies became detectable around day 10, but nasal antibodies plateaued after day 14 while circulating antibodies continued to rise. Intensively granular measurements in nasal mucosa and blood allowed modeling of immune responses to primary SARS-CoV-2 infection that revealed CD8+ T cell responses and early mucosal IgA responses strongly associated with viral control, indicating that these mechanisms should be targeted for transmission-reducing intervention.

Decision-Making Around COVID-19 Public Health Measures and Implications for Self-Care Activities: Experiences of Persons With Rheumatoid Arthritis.

OBJECTIVE: We aimed to advance understanding of how persons with rheumatoid arthritis (RA) experience decision-making about adopting public health measures during the COVID-19 pandemic. METHODS: Persons living with RA partnered throughout this nested qualitative study. One-to-one semistructured telephone interviews were conducted with participants with RA between December 2020 and December 2021. They were strategically sampled from a randomized controlled trial that was underway to test a physical activity counseling intervention. Analysis was guided by reflexive thematic analysis. RESULTS: Thirty-nine participants (aged 26-86 years; 36 women) in British Columbia, Canada were interviewed. We developed three themes. Participants described how their decision-making about public health measures related to 1) "upholding moral values of togetherness" because decisions were intertwined with moral values of neighborliness and reciprocity. Some adapted their self-care routines to uphold these moral values; 2) "relational autonomy-supports and challenges," because they sometimes felt supported and undermined in different relational settings (eg, by family, local community, or provincial government); and 3) "differing trust in information sources," in which decisions were shaped by the degree of faith they had in various information sources, including their rheumatologists. CONCLUSION: Across themes, experiences of decision-making about public health measures during the pandemic were embedded with moral concepts of solidarity, autonomy, and trust, with implications for how persons with RA chose and sustained their self-care activities. Insights gained help sensitize researchers and clinicians to moral issues experienced by persons with RA, which may inform support for self-care activities during and after the pandemic.

Assessing the reach, effectiveness, adoption, implementation, and maintenance of the ProACTIVE SCI physical activity counseling intervention among physiotherapists and SCI peer coaches during the transition from rehabilitation to community.

Introduction: Physical Activity (PA) levels for individuals with spinal cord injury (SCI) peak during rehabilitation and sharply decline post-discharge. The ProACTIVE SCI intervention has previously demonstrated very large-sized effects on PA; however, it has not been adapted for use at this critically understudied timepoint. The objective is to evaluate the reach, effectiveness, adoption, implementation, and maintenance of the ProACTIVE SCI intervention delivered by physiotherapists and SCI peer coaches during the transition from rehabilitation to community. Methods: A single-group, within-subjects, repeated measures design was employed. The implementation intervention consisted of PA counseling training, champion support, prompts and cues, and follow-up training/community of practice sessions. Physiotherapists conducted counseling sessions in hospital, then referred patients to SCI peer coaches to continue counseling for 1-year post-discharge in the community. The RE-AIM Framework was used to guide intervention evaluation. Results: Reach: 82.3% of patients at the rehabilitation hospital were reached by the intervention. Effectiveness: Interventionists (physiotherapists and SCI peer coaches) perceived that PA counseling was beneficial for patients. Adoption: 100% of eligible interventionists attended at least one training session. Implementation: Interventionists demonstrated high fidelity to the intervention. Intervention strategy highlights included a feasible physiotherapist to SCI peer coach referral process, flexibility in timepoint for intervening, and time efficiency. Maintenance: Ongoing training, PA counseling tracking forms, and the ability to refer to SCI peer coaches at discharge are core components needed to sustain this intervention. Discussion: The ProACTIVE SCI intervention was successfully adapted for use by physiotherapists and SCI peer coaches during the transition from rehabilitation to community. Findings are important for informing intervention sustainability and scale-up.

Delayed mucosal anti-viral responses despite robust peripheral inflammation in fatal COVID-19.

BACKGROUND: While inflammatory and immune responses to SARS-CoV-2 infection in peripheral blood are extensively described, responses at the upper respiratory mucosal site of initial infection are relatively poorly defined. We sought to identify mucosal cytokine/chemokine signatures that distinguished COVID-19 severity categories, and relate these to disease progression and peripheral inflammation. METHODS: We measured 35 cytokines and chemokines in nasal samples from 274 patients hospitalised with COVID-19. Analysis considered the timing of sampling during disease, as either the early (0-5 days post-symptom onset) or late (6-20 days post-symptom onset). RESULTS: Patients that survived severe COVID-19 showed IFN-dominated mucosal immune responses (IFN-γ, CXCL10 and CXCL13) early in infection. These early mucosal responses were absent in patients that would progress to fatal disease despite equivalent SARS-CoV-2 viral load. Mucosal inflammation in later disease was dominated by IL-2, IL-10, IFN-γ, and IL-12p70, which scaled with severity but did not differentiate patients who would survive or succumb to disease. Cytokines and chemokines in the mucosa showed distinctions from responses evident in the peripheral blood, particularly during fatal disease. CONCLUSIONS: Defective early mucosal anti-viral responses anticipate fatal COVID-19 but are not associated with viral load. Early mucosal immune responses may define the trajectory of severe COVID-19.

Impacts of Proximity to Primary Source Areas on Concentrations of POPs at Global Sampling Stations Estimated from Land Cover Information.

Given the considerable financial and logistical resources supporting long-term monitoring for air pollutants, and the use of these data for performance evaluation of mitigation measures, it is important to account for contributions from primary versus secondary sources. We demonstrate a simple approach for using open source Global land cover raster data from the National Mapping Organization from the Geospatial Information Authority of Japan to assess local source inputs for air measurements of legacy persistent organic pollutants (POPs)-polychlorinated biphenyls (PCBs) and organochlorine pesticides-reported under the Global atmospheric passive sampling (GAPS) Network at 119 locations for the time period 2005-2014. The land cover composition within a 10 km radius around the GAPS sites was identified to create source impact indicator (SII) vectors to quantify and rank the remoteness of the sites from human infrastructure. Using principal component analysis, three SII vectors were established to rank sites by impact of (i) general infrastructure/remoteness, (ii) urban infrastructure, and (iii) agricultural infrastructure. General infrastructure describes the combined effects of settlements and agricultural infrastructure. We found significant correlations (p < 0.05) between POP concentrations in air and specific SIIs. PCB levels in air had a statistically significant correlation to the SII ranking urban impacts around the sampling sites, while Endosulfan I, Endosulfan II, and Endosulfan sulfate had a statistically significant correlation with SII ranking agricultural impacts. The complete GAPS data set from 2004-2014 (1040 samples at 119 locations) was standardized based on the SII rankings to assess the global temporal trends of legacy POPs. SIIs were incorporated in the multiple regression analysis to determine global halving times. This includes short-term monitoring data from 79 locations that were previously excluded. Furthermore, the SII approach allows the integration of global monitoring data from different studies for broader global temporal trend analysis. This ability to link the results of independent and small-scale studies can enhance temporal trend analysis in support of the larger scale initiatives, such as inter alia, the Global Monitoring Plan and Effectiveness Evaluation of the Stockholm Convention in the case of POPs. This simple approach using open source data has a broad potential for application for other classes of air pollutants.

Trace Metals in Global Air: First Results from the GAPS and GAPS Megacities Networks.

Trace metals, as constituents of ambient air, can have impacts on human and environmental health. The Global Atmospheric Passive Sampling (GAPS) and GAPS Megacities (GAPS-MC) networks investigated trace metals in the air at 51 global locations by deploying polyurethane foam disk passive air samplers (PUF-PAS) for periods of 3-12 months. Aluminum and iron exhibited the highest concentrations in air (x̅ = 3400 and 4630 ng/m3, respectively), with notably elevated values at a rural site in Argentina thought to be impacted by resuspended soil. Urban sites had the highest levels of toxic Pb and Cd, with enrichment factors suggesting primarily anthropogenic influences. High levels of As at rural sites were also observed. Elevated trace metal concentrations in cities are associated with local emissions and higher PM2.5 and PM10 concentrations. Brake and tire wear-associated metals Sb, Cu, and Zn are significantly correlated and elevated at urban locations relative to those at background sites. These data demonstrate the versatility of PUF-PAS for measuring trace metals and other particle-associated pollutants in ambient air in a cost-effective and simple manner. The data presented here will serve as a global baseline for assessing future changes in ambient air associated with industrialization, urbanization, and population growth.

Applying state space grids methods to characterize counsellor-client interactions in a physical activity behavioural intervention for adults with disabilities.

BACKGROUND: Physical activity (PA) counselling research has mainly focused on identifying which behaviour change techniques (BCTs) are delivered by a counsellor. Less is known about how BCTs are received by clients. State Space Grids (SSGs) is a dynamic system method that can be used to study counsellor-client interactions by examining frequencies, durations and sequences of BCT delivery and receipt. In this methods paper, we show how SSG methods can be pragmatically used to characterize counsellor-client interactions during a PA behavioural support intervention for adults with disabilities. METHODS: Methods were demonstrated through a secondary analysis of data from adults with spinal cord injury (age: 45.79 ± 13.63; females: n = 5; males: n = 9) who received PA counselling. Transcripts of 30 audio-recorded counselling sessions (total duration: ∼8.3 h) were double-coded for BCT delivery and receipt statements using a reliable coding method (>84% agreement) and analyzed in two different ways using SSGs methods. RESULTS: Applying the SSG analyses to our data demonstrated that frequencies, durations, and sequences of BCT delivery and receipt varied largely within and between dyads. Across all sessions, the counsellor and client spent on average 32-34% of their time on talking about BCTs related to goals and planning, ∼29% of their time talking about other BCTs (e.g., self-belief, support strategies), and the remaining 27-29% of their time talking about other topics (not BCT-specific). CONCLUSION: This paper showed how dynamic system methods can be pragmatically used to characterize counsellor-client interactions and illustrate the variability of how BCTs are delivered by a counsellor and received by clients in a PA behavioural support intervention. We demonstrated that SSGs methods can facilitate the examination of frequencies, durations and sequences of BCT delivery and receipt can help advance our understanding of PA behavioural support for adults with and without disabilities.

Reduced Humoral and Cellular Immune Response to Primary COVID-19 mRNA Vaccination in Kidney Transplanted Children Aged 5-11 Years.

The situation of limited data concerning the response to COVID-19 mRNA vaccinations in immunocom-promised children hinders evidence-based recommendations. This prospective observational study investigated humoral and T cell responses after primary BNT162b2 vaccination in secondary immunocompromised and healthy children aged 5-11 years. Participants were categorized as: children after kidney transplantation (KTx, n = 9), proteinuric glomerulonephritis (GN, n = 4) and healthy children (controls, n = 8). Expression of activation-induced markers and cytokine secretion were determined to quantify the T cell response from PBMCs stimulated with peptide pools covering the spike glycoprotein of SARS-CoV-2 Wuhan Hu-1 and Omicron BA.5. Antibodies against SARS-CoV-2 spike receptor-binding domain were quantified in serum. Seroconversion was detected in 56% of KTx patients and in 100% of the GN patients and controls. Titer levels were significantly higher in GN patients and controls than in KTx patients. In Ktx patients, the humoral response increased after a third immunization. No differences in the frequency of antigen-specific CD4+ and CD8+ T cells between all groups were observed. T cells showed a predominant anti-viral capacity in their secreted cytokines; however, this capacity was reduced in KTx patients. This study provides missing evidence concerning the humoral and T cell response in immunocompromised children after COVID-19 vaccination.

Theory- and evidence-based best practices for physical activity counseling for adults with spinal cord injury.

OBJECTIVES: This project used a systematic and integrated knowledge translation (IKT) approach to co-create theory- and evidence-based best practices for physical activity counseling for adults with spinal cord injury (SCI). METHODS: Guided by the IKT Guiding Principles, we meaningfully engaged research users throughout this project. A systematic approach was used. An international, multidisciplinary expert panel (n = 15), including SCI researchers, counselors, and people with SCI, was established. Panel members participated in two online meetings to discuss the best practices by drawing upon new knowledge regarding counselor-client interactions, current evidence, and members' own experiences. We used concepts from key literature on SCI-specific physical activity counseling and health behavior change theories. An external group of experts completed an online survey to test the clarity, usability and appropriateness of the best practices. RESULTS: The best practices document includes an introduction, the best practices, things to keep in mind, and a glossary. Best practices focused on how to deliver a conversation and what to discuss during a conversation. Examples include: build rapport, use a client-centred approach following the spirit of motivational interviewing, understand your client's physical activity barriers, and share the SCI physical activity guidelines. External experts (n = 25) rated the best practices on average as clear, useful, and appropriate. CONCLUSION: We present the first systematically co-developed theory- and evidence-based best practices for SCI physical activity counseling. The implementation of the best practices will be supported by developing training modules. These new best practices can contribute to optimizing SCI physical activity counseling services across settings.

Per- and polyfluoroalkyl substances and volatile methyl siloxanes in global air: Spatial and temporal trends.

The study reports on the atmospheric concentrations of per- and polyfluoroalkyl substances (PFAS) and volatile methyl siloxanes (VMS) measured using sorbent-impregnated polyurethane foam disks (SIPs) passive air samplers. New results are reported for samples collected in 2017, which extends temporal trend information to the period 2009-2017, for 21 sites where SIPs have been deployed since 2009. Among neutral PFAS, fluorotelomer alcohols (FTOHs) had higher concentrations than perfluoroalkane sulfonamides (FOSAs) and perfluoroalkane sulfonamido ethanols (FOSEs) with levels of ND‒228, ND‒15.8, ND‒10.4 pg/m3, respectively. Among ionizable PFAS, the sum of perfluoroalkyl carboxylic acids (PFCAs) and perfluoroalkyl sulfonic acids (PFSAs) in air were 0.128-781 and 6.85-124 pg/m3, respectively. Longer-chain i.e. C9-C14 PFAS, which are relevant to the recent proposal by Canada for a listing of long-chain (C9-C21) PFCAs to the Stockholm Convention, were also detected in the environment at all site categories including Arctic sites. Cyclic and linear VMS ranged between 1.34‒452 and 0.01-12.1 ng/m3, respectively, showing dominance in urban areas. Despite the wide range of levels observed across different site categories, geometric means of the PFAS and VMS groups were fairly similar when grouped according to the five United Nations regions. Variable temporal trends in air (2009-2017) were observed for both PFAS and VMS. PFOS, which has been listed in the Stockholm Convention since 2009, is still showing increasing tendencies at several sites, indicating constant input from direct and/or indirect sources. These new data inform international chemicals management for PFAS and VMS.

SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination.

BACKGROUND: Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced. METHODS: In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data. FINDINGS: Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination. INTERPRETATION: The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity. FUNDING: This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript.

Nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination.

BackgroundMost studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced. MethodsPlasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data. FindingsStrong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months. Nasal and plasma anti-S IgG remained elevated for at least 12 months with high plasma neutralising titres against all variants. Of 180 with complete data, 160 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal. Samples 12 months after admission showed no association between nasal IgA and plasma IgG responses, indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination. InterpretationThe decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity. Research in contextO_ST_ABSEvidence before the studyC_ST_ABSWhile systemic immunity to SARS-CoV-2 is important in preventing severe disease, mucosal immunity prevents viral replication at the point of entry and reduces onward transmission. We searched PubMed with search terms "mucosal", "nasal", "antibody", "IgA", "COVID-19", "SARS-CoV-2", "convalescent" and "vaccination" for studies published in English before 20th July 2022, identifying three previous studies examining the durability of nasal responses that generally show nasal antibody to persist for 3 to 9 months. However, these studies were small or included individuals with mild COVID-19. One study of 107 care-home residents demonstrated increased salivary IgG (but not IgA) after two doses of mRNA vaccine, and another examined nasal antibody responses after infection and subsequent vaccination in 20 cases, demonstrating rises in both nasal IgA and IgG 7 to 10 days after vaccination. Added value of this studyStudying 446 people hospitalised for COVID-19, we show durable nasal and plasma IgG responses to ancestral (B.1 lineage) SARS-CoV-2, Delta and Omicron (BA.1) variants up to 12 months after infection. Nasal antibody induced by infection with pre-Omicron variants, bind Omicron virus in vitro better than plasma antibody. Although nasal and plasma IgG responses were enhanced by vaccination, Omicron binding responses did not reach levels equivalent to responses for ancestral SARS-CoV-2. Using paired plasma and nasal samples collected approximately 12 months after infection, we show that nasal IgA declines and shows a minimal response to vaccination whilst plasma antibody responses to S antigen are well maintained and boosted by vaccination. Implications of all the available evidenceAfter COVID-19 and subsequent vaccination, Omicron binding plasma and nasal antibody responses are only moderately enhanced, supporting the need for booster vaccinations to maintain immunity against SARS-CoV-2 variants. Notably, there is distinct compartmentalisation between nasal IgA and plasma IgA and IgG responses after vaccination. These findings highlight the need for vaccines that induce robust and durable mucosal immunity.

Enhanced incorporation of subnanometer tags into cellular proteins for fluorescence nanoscopy via optimized genetic code expansion.

With few-nanometer resolution recently achieved by a new generation of fluorescence nanoscopes (MINFLUX and MINSTED), the size of the tags used to label proteins will increasingly limit the ability to dissect nanoscopic biological structures. Bioorthogonal (click) chemical groups are powerful tools for the specific detection of biomolecules. Through the introduction of an engineered aminoacyl-tRNA synthetase/tRNA pair (tRNA: transfer ribonucleic acid), genetic code expansion allows for the site-specific introduction of amino acids with "clickable" side chains into proteins of interest. Well-defined label positions and the subnanometer scale of the protein modification provide unique advantages over other labeling approaches for imaging at molecular-scale resolution. We report that, by pairing a new N-terminally optimized pyrrolysyl-tRNA synthetase (chPylRS2020) with a previously engineered orthogonal tRNA, clickable amino acids are incorporated with improved efficiency into bacteria and into mammalian cells. The resulting enhanced genetic code expansion machinery was used to label ß-actin in U2OS cell filopodia for MINFLUX imaging with minimal separation of fluorophores from the protein backbone. Selected data were found to be consistent with previously reported high-resolution information from cryoelectron tomography about the cross-sectional filament bundling architecture. Our study underscores the need for further improvements to the degree of labeling with minimal-offset methods in order to fully exploit molecular-scale optical three-dimensional resolution.