Synthetic coevolution reveals adaptive mutational trajectories of neutralizing antibodies and SARS-CoV-2 (preprint)

The Covid-19 pandemic showcases a coevolutionary race between the human immune system and SARS-CoV-2, mirroring the Red Queen hypothesis of evolutionary biology. The immune system generates neutralizing antibodies targeting the SARS-CoV-2 spike protein's receptor binding domain (RBD), crucial for host cell invasion, while the virus evolves to evade antibody recognition. Here, we establish a synthetic coevolution system combining high-throughput screening of antibody and RBD variant libraries with protein mutagenesis, surface display, and deep sequencing. Additionally, we train a protein language machine learning model that predicts antibody escape to RBD variants. Synthetic coevolution reveals antagonistic and compensatory mutational trajectories of neutralizing antibodies and SARS-CoV-2 variants, enhancing the understanding of this evolutionary conflict.

Neutralisation sensitivity of the SARS-CoV-2 BA.2.87.1 variant (preprint)

Against the backdrop of the rapid global takeover and dominance of BA.1/BA.2 and subsequently BA.2.86 lineages, the emergence of a highly divergent SARS-CoV-2 variant warrants characterization and close monitoring. Recently, another such BA.2 descendent, designated BA.2.87.1, was detected in South Africa. Here, we show using spike-pseudotyped viruses that BA.2.87.1 is less resistant to neutralisation by prevailing antibody responses in Sweden than other currently circulating variants such as JN.1. Further we show that a monovalent XBB.1.5-adapted booster enhanced neutralising antibody titers to BA.2.87.1 by almost 4-fold. While BA.2.87.1 may not outcompete other currently-circulating lineages, the repeated emergence and transmission of highly diverged variants suggests that another large antigenic shift, similar to the replacement by Omicron, may be likely in the future.

Tracking inflammation resolution signatures in lungs after SARS-CoV-2 omicron BA.1 infection of K18-hACE2 mice (preprint)

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19), which can result in severe disease often characterised by a 'cytokine storm' and the associated acute respiratory distress syndrome. However, many infections with SARS-CoV-2 are mild or asymptomatic throughout the course of infection. Although blood biomarkers of severe disease are well studied, less well understood are the inflammatory signatures in lung tissues associated with mild disease or silent infections, wherein infection and inflammation are rapidly resolved leading to sequelae-free recovery. Herein we described RNA-Seq and histological analyses of lungs over time in an omicron BA.1/K18-hACE2 mouse infection model, which displays these latter features. Although robust infection was evident at 2 days post infection (dpi), viral RNA was largely cleared by 10 dpi. Acute inflammatory signatures showed a slightly different pattern of cytokine signatures compared with severe infection models, but where much diminished 30 dpi and absent by 66 dpi. Cellular deconvolution identified significantly increased abundance scores for a number of anti-inflammatory pro-resolution cell types at 5/10 dpi. These included type II innate lymphoid cells, T regulatory cells, and interstitial macrophages. Genes whose expression trended downwards over 2 - 66 dpi included biomarkers of severe disease and were associated with 'cytokine storm' pathways. Genes whose expression trended upward during this period were associated with recovery of ciliated cells, AT2 to AT1 transition, reticular fibroblasts and innate lymphoid cells, indicating a return to homeostasis. Very few differentially expressed host genes were identified at 66 dpi, suggesting near complete recovery. The parallels between mild or subclinical infections in humans and those observed in this BA.1/K18-hACE2 mouse model are discussed.

Doublethink: simultaneous Bayesian-frequentist model-averaged hypothesis testing (preprint)

Bayesian model-averaged hypothesis testing is an important technique in regression because it addresses the problem that the evidence one variable directly affects an outcome often depends on which other variables are included in the model. This problem is caused by confounding and mediation, and is pervasive in big data settings with thousands of variables. However, model-averaging is under-utilized in fields, like epidemiology, where classical statistical approaches dominate. Here we show that simultaneous Bayesian and frequentist model-averaged hypothesis testing is possible in large samples, for a family of priors. We show that Bayesian model-averaged regression is a closed testing procedure, and use the theory of regular variation to derive interchangeable posterior odds and $p$-values that jointly control the Bayesian false discovery rate (FDR), the frequentist type I error rate, and the frequentist familywise error rate (FWER). These results arise from an asymptotic chi-squared distribution for the model-averaged deviance, under the null hypothesis. We call the approach 'Doublethink'. In a related manuscript (Arning, Fryer and Wilson, 2024), we apply it to discovering direct risk factors for COVID-19 hospitalization in UK Biobank, and we discuss its broader implications for bridging the differences between Bayesian and frequentist hypothesis testing.

Humoral immune responses to the monovalent XBB.1.5-adapted BNT162b2 mRNA booster (preprint)

Continued SARS-CoV-2 evolution and immune escape necessitated the development of updated vaccines, and a monovalent vaccine incorporating the XBB.1.5 variant spike protein is currently being rolled out. Amidst the emergence of the highly mutated BA.2.86 lineage and against the backdrop of pronounced immune imprinting, it is important to characterize the antibody responses following vaccination, particularly in the elderly. Here, we show that the monovalent XBB.1.5-adapted booster vaccination substantially enhanced both binding and neutralising antibody responses against a panel of variants, including BA.2.86, in an older population with four or more previous vaccine doses. Furthermore, neutralizing antibody titers to XBB.1.5 and BA.2.86 were boosted more strongly than titers to historical variants were. Our findings thereby suggest increased vaccine induced protection against both antigenically matched variants, as well as the more distant BA.2.86 variant, and support current vaccine policies recommending a monovalent XBB.1.5 booster dose to older individuals.

Microplastics dysregulate innate immunity in the SARS-CoV-2 infected lung (preprint)

Global microplastic (MP) pollution is now well recognized, with humans and animals consuming and inhaling MPs on a daily basis. Herein we described the effects of azide-free, 1 {micro}m polystyrene MP beads co-delivered into lungs with a SARS-CoV-2 omicron BA.5 inoculum using a mouse model of mild COVID-19. Lung virus titres and viral RNA levels were not significantly affected by MPs, with overt clinical or histopathological changes also not observed. However, RNA-Seq of infected lungs revealed that MP exposure suppressed innate immune responses at 2 days post infection (dpi) and increased pro-inflammatory signatures at 6 dpi. The cytokine profile at 6 dpi showed a significant correlation with the cytokine release syndrome signature seen in some severe COVID-19 patients. This study adds to a growing body of literature suggesting that MPs can dysregulate inflammation in specific disease settings. Graphical Abstract HIGHLIGHTSO_LIA single inoculation of microplastics dysregulated SARS-CoV-2 lung inflammation C_LIO_LIAt the peak of SARS-CoV-2 infection microplastics decreased early innate responses C_LIO_LILater post infection microplastics promoted a "cytokine release syndrome" signature C_LIO_LIA key mechanism may involve the inhibition of the phagocytosis of infected cells C_LIO_LIAzide-free microplastics were used, with no elevated ROS responses identified C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/567745v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@73eefborg.highwire.dtl.DTLVardef@14eb683org.highwire.dtl.DTLVardef@b0638aorg.highwire.dtl.DTLVardef@571512_HPS_FORMAT_FIGEXP M_FIG Postulated mechanisms whereby microplastics might decrease the proinflammatory responses 2 days after SARS-CoV-2 infection, yet promote the proinflammatory cytokine release syndrome signature at 6 days post infection. C_FIG

Association of Cognitive Deficits with Sociodemographic Characteristics among Adults with Post-COVID Conditions: Findings from the United States Household Pulse Survey (preprint)

BackgroundPeople infected with COVID-19 may continue to experience symptoms for several weeks or even months after acute infection, a condition known as long COVID. Cognitive problems such as memory loss are among the most commonly reported symptoms of long COVID. However, a comprehensive evaluation on the risks of cognitive decline following COVID infection among different sociodemographic groups has not been undertaken at the national level in the United States. MethodsWe conducted a secondary analysis on the datasets from U.S. Census Bureau Household Pulse Survey, encompassing the data collected from June 1, 2022 to December 19, 2022. Based on a cohort of 385,370 individuals aged 18 or older, we employed logistic regression analyses to examine the association between self-reported cognitive deficits and different sociodemographic factors among individuals with long COVID conditions. ResultsAmong individuals aged 18 or older, 44.7% percent of survey respondents report having been diagnosed with COVID in the past, and 29.0% of those with previous COVID infection experienced long COVID symptoms lasting for more than 3 months. We have demonstrated that individuals with long COVID had significantly higher risk of experiencing cognitive deficits compared to those with no history of COVID infection. Furthermore, females, young adults, people with multiple races, or low levels of education attainment are at high risk of cognitive deficits if they experience long COVID. At the state level, the prevalence of cognitive deficits among long COVID patients varied across different US states, with the highest prevalence in West Virginia and Kentucky, and the lowest prevalence in Connecticut and Maryland. The variation could be due to differences in racial composition and education level among long COVID patients in the four states. ConclusionsThe risks of cognitive deficits among adults with post-COVID conditions are substantial. Various sociodemographic groups can have different risks of developing cognitive deficits after experiencing long COVID. Findings of this large-scale study can help identify sociodemographic groups at higher risk of cognitive deficits, and facilitate medical interventions and guide resource allocation to target populations at risk and to prioritize areas with a high rate of cognitive decline.

Sensitivity of BA.2.86 to prevailing neutralising antibody responses (preprint)

A new SARS-CoV-2 variant, designated BA.2.86, has recently emerged with over 30 spike mutations relative to its parental BA.2, raising questions about its degree of resistance to neutralising antibodies. Using a spike-pseudotyped virus model we characterise neutralisation of BA.2.86 by clinically relevant monoclonal antibodies and by two cohorts of serum sampled from Stockholm, including both a recent cohort, and one sampled prior to the arrival of XBB in Sweden.

Comparative Study of Chemosensory Dysfunction in COVID-19 in 2 Geographically Distinct Regions.

OBJECTIVE: To directly compare the prevalence of chemosensory dysfunction (smell and taste) in geographically distinct regions with the same questionnaires. METHODS: A cross-sectional study was performed to evaluate the self-reported symptoms among adults (older than 18 years) who underwent COVID-19 testing at an ambulatory assessment center in Canada and at a hospital in Israel between March 16, 2020, and August 19, 2020. The primary outcome was the prevalence of self-reported chemosensory dysfunction (anosmia/hypomsia and dysgeusia/ageusia). Subgroup analysis was performed to evaluate the prevalence of chemosensory deficits among the outpatients. RESULTS: We identified a total of 350 COVID-19-positive patients (138 Canadians and 212 Israelis). The overall prevalence of chemosensory dysfunction was 47.1%. There was a higher proportion of chemosensory deficits among Canadians compared to Israelis (66.7% vs 34.4%, P < .01). A subgroup analysis for outpatients (never hospitalized) still identified a higher prevalence of chemosensory dysfunction among Canadians compared to Israelis (68.2% vs 36.1%, P < 0.01). A majority of patients recovered their sense of smell after 4 weeks of symptom onset. CONCLUSION: Although the prevalence of chemosensory deficit in COVID-19 was found to be similar to previously published reports, the prevalence can vary significantly across different geographical regions. Therefore, it is important to obtain regionally specific data so that the symptom of anosmia/dysgeusia can be used as a guide for screening for the clinical diagnosis of COVID-19.

Development of a Definition of Postacute Sequelae of SARS-CoV-2 Infection.

Importance: SARS-CoV-2 infection is associated with persistent, relapsing, or new symptoms or other health effects occurring after acute infection, termed postacute sequelae of SARS-CoV-2 infection (PASC), also known as long COVID. Characterizing PASC requires analysis of prospectively and uniformly collected data from diverse uninfected and infected individuals. Objective: To develop a definition of PASC using self-reported symptoms and describe PASC frequencies across cohorts, vaccination status, and number of infections. Design, Setting, and Participants: Prospective observational cohort study of adults with and without SARS-CoV-2 infection at 85 enrolling sites (hospitals, health centers, community organizations) located in 33 states plus Washington, DC, and Puerto Rico. Participants who were enrolled in the RECOVER adult cohort before April 10, 2023, completed a symptom survey 6 months or more after acute symptom onset or test date. Selection included population-based, volunteer, and convenience sampling. Exposure: SARS-CoV-2 infection. Main Outcomes and Measures: PASC and 44 participant-reported symptoms (with severity thresholds). Results: A total of 9764 participants (89% SARS-CoV-2 infected; 71% female; 16% Hispanic/Latino; 15% non-Hispanic Black; median age, 47 years [IQR, 35-60]) met selection criteria. Adjusted odds ratios were 1.5 or greater (infected vs uninfected participants) for 37 symptoms. Symptoms contributing to PASC score included postexertional malaise, fatigue, brain fog, dizziness, gastrointestinal symptoms, palpitations, changes in sexual desire or capacity, loss of or change in smell or taste, thirst, chronic cough, chest pain, and abnormal movements. Among 2231 participants first infected on or after December 1, 2021, and enrolled within 30 days of infection, 224 (10% [95% CI, 8.8%-11%]) were PASC positive at 6 months. Conclusions and Relevance: A definition of PASC was developed based on symptoms in a prospective cohort study. As a first step to providing a framework for other investigations, iterative refinement that further incorporates other clinical features is needed to support actionable definitions of PASC.

Hospital at Home: An Evolving Model for Comprehensive Healthcare.

Hospital at Home (HaH) is a sustainable, innovative, and next-generation model of healthcare. From the healthcare management point of view, this model provides cost benefits and quality improvement, and from the physicians' point of view, it helps in providing patient-centered medical care and keeps patients away from hospital admission and its complications. The HaH model was first introduced at John Hopkins in the United States in 1995, which showed very promising results in context to the length of stay, readmission rates, patient satisfaction, and hospital-acquired infections. The HaH model of care provides acute critical care to patients at home and reduces unnecessary hospitalization and related complications. The identified patients for this model of care are elderly patients with chronic conditions and multiple comorbidities. The emergence of technology in today's world and the impact of coronavirus disease 2019 (COVID-19) have increased the demand for the HaH model of care. Although there are many benefits and advantages, the HaH model of care has significant barriers and limitations, such as reimbursement for payment, physician and patient resistance, patient safety, and lack of quantifying research data to support the use of this model. Specific training for the physician, nursing, and other members of the HaH multidisciplinary team is necessary for HaH treatment protocols, along with patient and family caregiver education for those who elect the HaH model of care. HaH is the future of comprehensive healthcare services and helps in achieving the triple aim of access to healthcare, improved quality of care, and reduced cost for healthcare.

Machine learning analysis of humoral and cellular responses to SARS-CoV-2 infection in young adults.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces B and T cell responses, contributing to virus neutralization. In a cohort of 2,911 young adults, we identified 65 individuals who had an asymptomatic or mildly symptomatic SARS-CoV-2 infection and characterized their humoral and T cell responses to the Spike (S), Nucleocapsid (N) and Membrane (M) proteins. We found that previous infection induced CD4 T cells that vigorously responded to pools of peptides derived from the S and N proteins. By using statistical and machine learning models, we observed that the T cell response highly correlated with a compound titer of antibodies against the Receptor Binding Domain (RBD), S and N. However, while serum antibodies decayed over time, the cellular phenotype of these individuals remained stable over four months. Our computational analysis demonstrates that in young adults, asymptomatic and paucisymptomatic SARS-CoV-2 infections can induce robust and long-lasting CD4 T cell responses that exhibit slower decays than antibody titers. These observations imply that next-generation COVID-19 vaccines should be designed to induce stronger cellular responses to sustain the generation of potent neutralizing antibodies.

Creation of 21st century anatomy facilities: designing facilities for integrated preclinical education in the Middle East.

BACKGROUND: The establishment of new anatomy facilities needs to accommodate a combination of modern teaching modalities that best align with evidence-based best teaching practices. This article describes the process in which our state-of-the-art anatomy laboratories were designed and implemented, and how these facilities support aspects of modern anatomy education. METHODS: A list of best practices for anatomy education in a modern medical curriculum was summarized from the literature. To assess student satisfaction, a survey related to student perception of the anatomy facilities (5-point Likert scale) was conducted. RESULTS: Our educational modalities include a broad range of teaching approaches. The Instructional Studio houses prosected and plastinated specimens, and cadaveric dissections are performed. Each of our three Dry Laboratories allow for active learning and interaction between small student groups. The Webinar Room acts as a conference room for departmental and online meetings, discussions with students, and dialogues with affiliated hospitals via the internet. The Imaging Center is equipped with a Sectra® medical educational platform, CAE Vimedix® Virtual Medical Imaging Ultrasound Training System, and Philipps Lumify® Ultrasound devices to train students to conduct and interpret sonographic images. Moreover, the Complete Anatomy® program is made available to all our students. CONCLUSION: The layout of our newly created Anatomy Facilities allows for all aspects of modern medical education mentioned in the literature. These educational modalities and teaching approaches are highly appreciated by our faculty and students. Moreover, these technologies allowed for a smooth transition from on-site anatomy teaching to online education during the COVID pandemic.

Eco-friendly and effective antimicrobial Melaleuca alternifolia essential oil Pickering emulsions stabilized with cellulose nanofibrils against bacteria and SARS-CoV-2.

Melaleuca alternifolia essential oil (MaEO) is a green antimicrobial agent suitable for confection eco-friendly disinfectants to substitute conventional chemical disinfectants commonly formulated with toxic substances that cause dangerous environmental impacts. In this contribution, MaEO-in-water Pickering emulsions were successfully stabilized with cellulose nanofibrils (CNFs) by a simple mixing procedure. MaEO and the emulsions presented antimicrobial activities against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). Moreover, MaEO deactivated the SARS-CoV-2 virions immediately. FT-Raman and FTIR spectroscopies indicate that the CNF stabilizes the MaEO droplets in water by the dipole-induced-dipole interactions and hydrogen bonds. The factorial design of experiments (DoE) indicates that CNF content and mixing time have significant effects on preventing the MaEO droplets' coalescence during 30-day shelf life. The bacteria inhibition zone assays show that the most stable emulsions showed antimicrobial activity comparable to commercial disinfectant agents such as hypochlorite. The MaEO/water stabilized-CNF emulsion is a promissory natural disinfectant with antibacterial activity against these bacteria strains, including the capability to damage the spike proteins at the SARS-CoV-2 particle surface after 15 min of direct contact when the MaEO concentration is 30 % v/v.

Coronavirus sampling and surveillance in bats from 1996-2019: a systematic review and meta-analysis.

The emergence of SARS-CoV-2 highlights a need for evidence-based strategies to monitor bat viruses. We performed a systematic review of coronavirus sampling (testing for RNA positivity) in bats globally. We identified 110 studies published between 2005 and 2020 that collectively reported positivity from 89,752 bat samples. We compiled 2,274 records of infection prevalence at the finest methodological, spatiotemporal and phylogenetic level of detail possible from public records into an open, static database named datacov, together with metadata on sampling and diagnostic methods. We found substantial heterogeneity in viral prevalence across studies, reflecting spatiotemporal variation in viral dynamics and methodological differences. Meta-analysis identified sample type and sampling design as the best predictors of prevalence, with virus detection maximized in rectal and faecal samples and by repeat sampling of the same site. Fewer than one in five studies collected and reported longitudinal data, and euthanasia did not improve virus detection. We show that bat sampling before the SARS-CoV-2 pandemic was concentrated in China, with research gaps in South Asia, the Americas and sub-Saharan Africa, and in subfamilies of phyllostomid bats. We propose that surveillance strategies should address these gaps to improve global health security and enable the origins of zoonotic coronaviruses to be identified.

Rheumatology and Long COVID: lessons from the study of fibromyalgia.

Rheumatology, such as other subspecialties, has both a unique perspective to offer as well as an evolving role to play in the global COVID-19 pandemic. Our field has already contributed meaningfully to the development and repurposing of many of the immune-based therapeutics which are now standard treatments for severe forms of the disease as well as to the understanding of the epidemiology, risk factors and natural history of COVID-19 in immune-mediated inflammatory diseases. Still in evolution is our potential to contribute to burgeoning research efforts in the next phase of the pandemic: the syndrome of postacute sequelae of COVID-19 or Long COVID. While our field brings many assets to the study of Long COVID including our expertise in the investigation of chronic inflammation and autoimmunity, our Viewpoint focuses on the strong similarities between fibromyalgia (FM) and Long COVID. While one can speculate on how embracing and confident practising rheumatologists already are regarding these interrelationships, we assert that in the emerging field of Long COVID the potential lessons from the field of fibromyalgia care and research have been underappreciated and marginalised and most importantly now deserve a critical appraisal.