Blood transcriptional biomarkers of acute viral infection for detection of pre-symptomatic SARS-CoV-2 infection: a nested, case-control diagnostic accuracy study

Background We hypothesised that host-response biomarkers of viral infections might contribute to early identification of individuals infected with SARS-CoV-2, which is critical to breaking the chains of transmission. We aimed to evaluate the diagnostic accuracy of existing candidate whole-blood transcriptomic signatures for viral infection to predict positivity of nasopharyngeal SARS-CoV-2 PCR testing.Methods We did a nested case-control diagnostic accuracy study among a prospective cohort of health-care workers (aged ≥18 years) at St Bartholomew’s Hospital (London, UK) undergoing weekly blood and nasopharyngeal swab sampling for whole-blood RNA sequencing and SARS-CoV-2 PCR testing, when fit to attend work. We identified candidate blood transcriptomic signatures for viral infection through a systematic literature search. We searched MEDLINE for articles published between database inception and Oct 12, 2020, using comprehensive MeSH and keyword terms for “viral infection”, “transcriptome”, “biomarker”, and “blood”. We reconstructed signature scores in blood RNA sequencing data and evaluated their diagnostic accuracy for contemporaneous SARS-CoV-2 infection, compared with the gold standard of SARS-CoV-2 PCR testing, by quantifying the area under the receiver operating characteristic curve (AUROC), sensitivities, and specificities at a standardised Z score of at least 2 based on the distribution of signature scores in test-negative controls. We used pairwise DeLong tests compared with the most discriminating signature to identify the subset of best performing biomarkers. We evaluated associations between signature expression, viral load (using PCR cycle thresholds), and symptom status visually and using Spearman rank correlation. The primary outcome was the AUROC for discriminating between samples from participants who tested negative throughout the study (test-negative controls) and samples from participants with PCR-confirmed SARS-CoV-2 infection (test-positive participants) during their first week of PCR positivity.Findings We identified 20 candidate blood transcriptomic signatures of viral infection from 18 studies and evaluated their accuracy among 169 blood RNA samples from 96 participants over 24 weeks. Participants were recruited between March 23 and March 31, 2020. 114 samples were from 41 participants with SARS-CoV-2 infection, and 55 samples were from 55 test-negative controls. The median age of participants was 36 years (IQR 27–47) and 69 (72%) of 96 were women. Signatures had little overlap of component genes, but were mostly correlated as components of type I interferon responses. A single blood transcript for IFI27 provided the highest accuracy for discriminating between test-negative controls and test-positive individuals at the time of their first positive SARS-CoV-2 PCR result, with AUROC of 0·95 (95% CI 0·91–0·99), sensitivity 0·84 (0·70–0·93), and specificity 0·95 (0·85–0·98) at a predefined threshold (Z score >2). The transcript performed equally well in individuals with and without symptoms. Three other candidate signatures (including two to 48 transcripts) had statistically equivalent discrimination to IFI27 (AUROCs 0·91–0·95).Interpretation Our findings support further urgent evaluation and development of blood IFI27 transcripts as a biomarker for early phase SARS-CoV-2 infection for screening individuals at high risk of infection, such as contacts of index cases, to facilitate early case isolation and early use of antiviral treatments as they emerge

Immune boosting by B.1.1.529 (Omicron) depends on previous SARS-CoV-2 exposure

The Omicron, or Pango lineage B.1.1.529, variant of SARS-CoV-2 carries multiple spike mutations with high transmissibility and partial neutralizing antibody (nAb) escape. Vaccinated individuals show protection from severe disease, often attributed to primed cellular immunity. We investigated T and B cell immunity against B.1.1.529 in triple mRNA vaccinated healthcare workers (HCW) with different SARS-CoV-2 infection histories. B and T cell immunity against previous variants of concern was enhanced in triple vaccinated individuals, but magnitude of T and B cell responses against B.1.1.529 spike protein was reduced. Immune imprinting by infection with the earlier B.1.1.7 (Alpha) variant resulted in less durable binding antibody against B.1.1.529. Previously infection-naïve HCW who became infected during the B.1.1.529 wave showed enhanced immunity against earlier variants, but reduced nAb potency and T cell responses against B.1.1.529 itself. Previous Wuhan Hu-1 infection abrogated T cell recognition and any enhanced cross-reactive neutralizing immunity on infection with B.1.1.529

Quantitative, multiplexed, targeted proteomics for ascertaining variant specific SARS-CoV-2 antibody response

Determining the protection an individual has to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VoCs) is crucial for future immune surveillance, vaccine development, and understanding of the changing immune response. We devised an informative assay to current ELISA-based serology using multiplexed, baited, targeted proteomics for direct detection of multiple proteins in the SARS-CoV-2 anti-spike antibody immunocomplex. Serum from individuals collected after infection or first- and second-dose vaccination demonstrates this approach and shows concordance with existing serology and neutralization. Our assays show altered responses of both immunoglobulins and complement to the Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.1) VoCs and a reduced response to Omicron (B1.1.1529). We were able to identify individuals who had prior infection, and observed that C1q is closely associated with IgG1 (r > 0.82) and may better reflect neutralization to VoCs. Analyzing additional immunoproteins beyond immunoglobulin (Ig) G, provides important information about our understanding of the response to infection and vaccination

Global, regional, and national burden of disorders affecting the nervous system, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BackgroundDisorders affecting the nervous system are diverse and include neurodevelopmental disorders, late-life neurodegeneration, and newly emergent conditions, such as cognitive impairment following COVID-19. Previous publications from the Global Burden of Disease, Injuries, and Risk Factor Study estimated the burden of 15 neurological conditions in 2015 and 2016, but these analyses did not include neurodevelopmental disorders, as defined by the International Classification of Diseases (ICD)-11, or a subset of cases of congenital, neonatal, and infectious conditions that cause neurological damage. Here, we estimate nervous system health loss caused by 37 unique conditions and their associated risk factors globally, regionally, and nationally from 1990 to 2021.MethodsWe estimated mortality, prevalence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs), with corresponding 95% uncertainty intervals (UIs), by age and sex in 204 countries and territories, from 1990 to 2021. We included morbidity and deaths due to neurological conditions, for which health loss is directly due to damage to the CNS or peripheral nervous system. We also isolated neurological health loss from conditions for which nervous system morbidity is a consequence, but not the primary feature, including a subset of congenital conditions (ie, chromosomal anomalies and congenital birth defects), neonatal conditions (ie, jaundice, preterm birth, and sepsis), infectious diseases (ie, COVID-19, cystic echinococcosis, malaria, syphilis, and Zika virus disease), and diabetic neuropathy. By conducting a sequela-level analysis of the health outcomes for these conditions, only cases where nervous system damage occurred were included, and YLDs were recalculated to isolate the non-fatal burden directly attributable to nervous system health loss. A comorbidity correction was used to calculate total prevalence of all conditions that affect the nervous system combined.FindingsGlobally, the 37 conditions affecting the nervous system were collectively ranked as the leading group cause of DALYs in 2021 (443 million, 95% UI 378–521), affecting 3·40 billion (3·20–3·62) individuals (43·1%, 40·5–45·9 of the global population); global DALY counts attributed to these conditions increased by 18·2% (8·7–26·7) between 1990 and 2021. Age-standardised rates of deaths per 100 000 people attributed to these conditions decreased from 1990 to 2021 by 33·6% (27·6–38·8), and age-standardised rates of DALYs attributed to these conditions decreased by 27·0% (21·5–32·4). Age-standardised prevalence was almost stable, with a change of 1·5% (0·7–2·4). The ten conditions with the highest age-standardised DALYs in 2021 were stroke, neonatal encephalopathy, migraine, Alzheimer's disease and other dementias, diabetic neuropathy, meningitis, epilepsy, neurological complications due to preterm birth, autism spectrum disorder, and nervous system cancer.InterpretationAs the leading cause of overall disease burden in the world, with increasing global DALY counts, effective prevention, treatment, and rehabilitation strategies for disorders affecting the nervous system are needed

Development and validation of a 3D-printed interfacial stress sensor for prosthetic applications

A novel capacitance-based sensor designed for monitoring mechanical stresses at the stump–socket interface of lower-limb amputees is described. It provides practical means of measuring pressure and shear stresses simultaneously. In particular, it comprises of a flexible frame (20 mm × 20 mm), with thickness of 4 mm. By employing rapid prototyping technology in its fabrication, it offers a low-cost and versatile solution, with capability of adopting bespoke shapes of lower-limb residua. The sensor was first analysed using finite element analysis (FEA) and then evaluated using lab-based electromechanical tests. The results validate that the sensor is capable of monitoring both pressure and shear at stresses up to 350 kPa and 80 kPa, respectively. A post-signal processing model is developed to induce pressure and shear stresses, respectively. The effective separation of pressure and shear signals can be potentially advantageous for sensor calibration in clinical applications. The sensor also demonstrates high linearity (approx. 5–8%) and high pressure (approx. 1.3 kPa) and shear (approx. 0.6 kPa) stress resolution performance. Accordingly, the sensor offers the potential for exploitation as an assistive tool to both evaluate prosthetic socket fitting in clinical settings and alert amputees in home settings of excessive loading at the stump–socket interface, effectively preventing stump tissue breakdown at an early stage

Analysis of lower limb prosthetic socket interface based on stress and motion measurements

The study was designed to establish a biomechanical assessment platform for the lower limb residuum/socket interface as a function of duration and speed of movement. The approach exploits an interface sensor which measures multi-directional stresses at the interface. The corresponding interface coupling motion was assessed using a 3D motion capture system. A longitudinal study, involving a trans-femoral amputee, was conducted with nine repeated level walking sessions over a 12-month period. The effect of walking speed on interface biomechanics was also assessed. Interface peak pressures and shear stresses in the range of 55–59 kPa and 12–19 kPa were measured, respectively, over all sessions in the 12 months study period at the posterior-proximal location of the residuum. The peak pressure and longitudinal shear values were found to fluctuate approximately 11% and 40% as against its maximum value, respectively, over 12 months. In addition, up to 12° of angular coupling and up to 28 mm of pistoning were recorded over a gait cycle, which was found to change by 29% and 45% respectively over the study period. The variation in walking speed, by altering self-selected cadence, resulted in changes of pressure and shear stresses at mid-stance of the gait cycle. In particular, as compared with self-selected cadence, for fast speed, peak pressure and peak longitudinal shear stress decreased by 5% and 33%, respectively. For slow speed, peak pressure and peak longitudinal shear stress increased by 7% and 17%, respectively. The corresponding angular and pistoning revealed a variation of up to 29% and 45%, respectively. This biomechanical assessment approach shows promise in the quantitative assessment of interface kinematics and kinetics for lower limb prosthetics, the usage of which could assist the clinical assessment of prosthetic socket fit

Characterisation of dynamic couplings at lower limb residuum/socket interface using 3D motion capture

Design and fitting of artificial limbs to lower limb amputees are largely based on the subjective judgement of the prosthetist. Understanding the science of three-dimensional (3D) dynamic coupling at the residuum/socket interface could potentially aid the design and fitting of the socket. A new method has been developed to characterise the 3D dynamic coupling at the residuum/socket interface using 3D motion capture based on a single case study of a trans-femoral amputee. The new model incorporated a Virtual Residuum Segment (VRS) and a Socket Segment (SS) which combined to form the residuum/socket interface. Angular and axial couplings between the two segments were subsequently determined. Results indicated a non-rigid angular coupling in excess of 10° in the quasi-sagittal plane and an axial coupling of between 21-35 mm. The corresponding angular couplings of less than 4° and 2° were estimated in the quasi-coronal and quasi-transverse plane, respectively.We propose that the combined experimental and analytical approach adopted in this case study could aid the iterative socket fitting process and could potentially lead to a new socket design. <br/

Development of a residuum/socket interface simulator for lower limb prosthetics

Mechanical coupling at the interface between lower limb residua and prosthetic sockets plays an important role in assessing socket fitting and tissue health. However, most research lab–based lower limb prosthetic simulators to-date have implemented a rigid socket coupling. This study describes the fabrication and implementation of a lower limb residuum/socket interface simulator, designed to reproduce the forces and moments present during the key loading phases of amputee walking. An artificial residuum made with model bones encased in silicone was used, mimicking the compliant mechanical loading of a real residuum/socket interface. A 6-degree-of-freedom load cell measured the overall kinetics, having previously been incorporated into an amputee’s prosthesis to collect reference data. The developed simulator was compared to a setup where a rigid pylon replaced the artificial residuum. A maximum uniaxial load of 850 N was applied, comparable to the peak vertical ground reaction force component during amputee walking. Load cell outputs from both pylon and residuum setups were compared. During weight acceptance, when including the artificial residuum, compression decreased by 10%, while during push off, sagittal bending and anterior–posterior shear showed a 25% increase and 34% decrease, respectively. Such notable difference by including a compliant residuum further highlighted the need for such an interface simulator. Subsequently, the simulator was adjusted to produce key load cell outputs briefly aligning with those from amputee walking. Force sensing resistors were deployed at load bearing anatomic locations on the residuum/socket interface to measure pressures and were compared to those cited in the literature for similar locations. The development of such a novel simulator provides an objective adjunct, using commonly available mechanical test machines. It could potentially be used to provide further insight into socket design, fit and the complex load transfer mechanics at the residuum/socket interface, as well as to evaluate the structural performance of prostheses

A pressure and shear sensor system for stress measurement at lower limb residuum/socket interface

A sensor system for measurement of pressure and shear at the lower limb residuum/socket interface is described. The system comprises of a flexible sensor unit and a data acquisition unit with wireless data transmission capability. Static and dynamic performance of the sensor system was characterised using a mechanical test machine. The static calibration results suggest that the developed sensor system presents high linearity (linearity error ~ 3.8%) and resolution (0.9kpa for pressure and 0.2kpa for shear). Dynamic characterisation of the sensor system shows hysteresis error of approximately 15% for pressure and 8% for shear. Subsequently, a pilot amputee walking test was conducted. Three sensors were placed at the residuum/socket interface of a knee disarticulation amputee and simultaneous measurements were obtained during pilot amputee walking test. The pressure and shear peak values as well as their temporal profiles are presented and discussed.In particular, peak pressure and shear of approximately 58kPa and 27kPa, respectively, were recorded. Their temporal profiles also provide dynamic coupling information at this critical residuum/socket interface. These preliminary amputee test results suggest strong potential of the developed sensor system for exploitation as an assistive technology to facilitate socket design, socket fit and effective monitoring of lower limb residuum health