Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR

Introduction

The declaration of the end of the Public Health Emergency for COVID-19 on May 11th, 2023, has shifted the global focus led by WHO and CDC towards monitoring the evolution of SARS-CoV-2. Augmenting these international endeavors with local initiatives becomes crucial to not only track the emergence of new variants but also to understand their spread. We present a cost-effective digital PCR-based pooled sample testing methodology tailored for early variant surveillance.

Methods

Using 1200 retrospective SARS-CoV-2 positive samples, either negative or positive for Delta or Omicron, we assessed the sensitivity and specificity of our detection strategy employing commercial TaqMan variant probes in a 1:9 ratio of variant-positive to variant-negative samples.

Results

The study achieved 100% sensitivity and 99% specificity in 10-sample pools, with an Area Under the Curve (AUC) exceeding 0.998 in ROC curves, using distinct commercial TaqMan variant probes.

Discussion

The employment of two separate TaqMan probes for both Delta and Omicron establishes dual validation routes, emphasizing the method's robustness. Although we used known samples to model realistic emergence scenarios of the Delta and Omicron variants, our main objective is to demonstrate the versatility of this strategy to identify future variant appearances. The utilization of two divergent variants and distinct probes for each confirms the method's independence from specific variants and probes. This flexibility ensures it can be tailored to recognize any subsequent variant emergence, given the availability of its sequence and a specific probe. Consequently, our approach stands as a robust tool for tracking and managing any new variant outbreak, reinforcing our global readiness against possible future SARS-CoV-2 waves.

Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR

Detection of SARS-CoV-2 has created an enormous workload for laboratories worldwide resulting in a restriction at the time of massive testing. Pool testing is a strategy that reduces time and costs. However, beyond the detection of infectious diseases in blood banks, this approach is rarely implemented in routine laboratories. Therefore, what was learned from the SARS-CoV-2 pool testing should represent an opportunity to increase diagnostic capabilities. The present work, carried out in the context of a diagnostic laboratory of a public hospital during the COVID-19 pandemic, represents a contribution to this end. The main limitation of pool testing is the risk of false negatives that could have been identified by individual tests. These limitations are the dilution of samples with a low virus load during pooling and that the integrity of the sample may be affected by the quality of the sample collection. Fortunately, both limitations coincide with the main strengths of droplet digital PCR (ddPCR). ddPCR is a third-generation PCR that splits the amplification into thousands of droplets that work in parallel, increasing sensitivity and resistance to inhibitors. Therefore, ddPCR is particularly useful for pool testing. Here we show how to factor between test sensitivity and savings in test time and resources. We have identified and optimized critical parameters for pool testing. The present study, which analyzed 1000 nasopharyngeal samples, showed that the pool testing could detect even a single positive sample with a CT value of up to 30 in pools of 34 samples. This test was performed using three different standard extraction methods, the simplest being heating only, which resulted in substantial savings of extraction reagents in addition to PCR reagents. Moreover, we show that pooling can be extended to use saliva, which is less invasive and allows self-collection, reducing the risk for health personnel.

Proinflammatory P2Y14 receptor inhibition protects against ischemic acute kidney injury in mice

Ischemic acute kidney injury (AKI), a complication that frequently occurs in hospital settings, is often associated with hemodynamic compromise, sepsis, cardiac surgery, or exposure to nephrotoxins. Here, using a murine renal ischemia/reperfusion injury (IRI) model, we show that intercalated cells (ICs) rapidly adopted a proinflammatory phenotype after IRI. Wwe demonstrate that during the early phase of AKI either blockade of the proinflammatory P2Y14 receptor located on the apical membrane of ICs or ablation of the gene encoding the P2Y14 receptor in ICs (a) inhibited IRI-induced increase of chemokine expression in ICs, (b) reduced neutrophil and monocyte renal infiltration, (c) reduced the extent of kidney dysfunction, and (d) attenuated proximal tubule damage. These observations indicate that the P2Y14 receptor participates in the very first inflammatory steps associated with ischemic AKI. In addition, we show that the concentration of the P2Y14 receptor ligand UDP-glucose (UDP-Glc) was higher in urine samples from intensive care unit patients who developed AKI compared with patients without AKI. In particular, we observed a strong correlation between UDP-Glc concentration and the development of AKI in cardiac surgery patients. Our study identifies the UDP-Glc/P2Y14 receptor axis as a potential target for the prevention and/or attenuation of ischemic AKI.

Tobacco exposure inhibits SPLUNC1-dependent antimicrobial activity

Background

Tobacco smoke exposure impairs the lung’s innate immune response, leading to an increased risk of chronic infections. SPLUNC1 is a secreted, multifunctional innate defense protein that has antimicrobial activity against Gram negative organisms. We hypothesize that tobacco smoke-induced SPLUNC1 dysfunction contributes to the observed defect in innate immunity in tobacco smokers and that this dysfunction can be used as a potential biomarker of harm.

Methods

We collected sputum from never-smokers and otherwise healthy smokers. We performed Western blotting to determine SPLUNC1 levels and determined antimicrobial activity against nontypeable Haemophilus influenzae. An in vitro exposure model was utilized to measure the effect of tobacco exposure on human bronchial epithelial culture (HBEC) antimicrobial activity against H. influenzae. The direct effects of cigarette and little cigar smoke exposure on SPLUNC1 function was determined using 24 h growth measurements and LPS binding assays.

Results

H. influenzae growth in cigarette smoker’s sputum was significantly greater compared to never-smokers sputum over 24 h. HBEC supernatants and lysates contained significantly higher numbers of H. influenzae following chronic cigarette and little cigar smoke exposure compared to air-exposed controls. Furthermore, SPLUNC1’s antimicrobial activity and LPS-binding capability against both H. influenzae and P. aeruginosa was attenuated following cigarette and little cigar exposure.

Conclusions

These data suggest that cigarette and little cigar exposure impairs SPLUNC1’s antimicrobial ability and that this inhibition may serve as a novel biomarker of harm that can be used to assess the toxicity of commercial tobacco products.

Cigarette smoke modifies and inactivates SPLUNC1, leading to airway dehydration

Chronic obstructive pulmonary disease (COPD) is a growing cause of morbidity and mortality worldwide. Cigarette smoke (CS) exposure, a major cause of COPD, dysregulates airway epithelial ion transport and diminishes airway surface liquid (ASL) volume. Short palate lung and nasal epithelial clone 1 (SPLUNC1) is secreted into the airway lumen where it maintains airway hydration via interactions with the epithelial Na+ channel (ENaC). Although ASL hydration is dysregulated in CS-exposed/COPD airways, effects of CS on SPLUNC1 have not been elucidated. We hypothesized that CS alters SPLUNC1 activity, therefore contributing to ASL dehydration. CS exposure caused irreversible SPLUNC1 aggregation and prevented SPLUNC1 from internalizing ENaC and maintaining ASL hydration. Proteomic analysis revealed αβ-unsaturated aldehyde modifications to SPLUNC1's cysteine residues. Removal of these cysteines prevented SPLUNC1 from regulating ENaC/ASL volume. In contrast, SPX-101, a peptide mimetic of natural SPLUNC1, that internalizes ENaC, but does not contain cysteines was unaffected by CS. SPX-101 increased ASL hydration and attenuated ENaC activity in airway cultures after CS exposure and prolonged survival in a chronic airway disease model. These findings suggest that the CS-induced defects in SPLUNC1 can be circumvented, thus making SPX-101 a novel candidate for the treatment of mucus dehydration in COPD. -Moore, P. J., Reidel, B., Ghosh, A., Sesma, J., Kesimer, M., Tarran, R. Cigarette smoke modifies and inactivates SPLUNC1, leading to airway dehydration.

SPX-101 Is a Novel Epithelial Sodium Channel-targeted Therapeutic for Cystic Fibrosis That Restores Mucus Transport

RATIONALE

Cystic fibrosis (CF) lung disease is caused by the loss of function of the cystic fibrosis transmembrane conductance regulator (CFTR) combined with hyperactivation of the epithelial sodium channel (ENaC). In the lung, ENaC is responsible for movement of sodium. Hyperactivation of ENaC, which creates an osmotic gradient that pulls fluid out of the airway, contributes to reduced airway hydration, causing mucus dehydration, decreased mucociliary clearance, and recurrent acute bacterial infections. ENaC represents a therapeutic target to treat all patients with CF independent of their underlying CFTR mutation.

OBJECTIVES

To investigate the in vitro and in vivo efficacy of SPX-101, a peptide mimetic of the natural regulation of ENaC activity by short palate, lung, and nasal epithelial clone 1, known as SPLUNC1.

METHODS

ENaC internalization by SPX-101 in primary human bronchial epithelial cells from healthy and CF donors was assessed by surface biotinylation and subsequent Western blot analysis. SPX-101's in vivo therapeutic effect was assessed by survival of β-ENaC-transgenic mice, mucus transport in these mice, and mucus transport in a sheep model of CF.

MEASUREMENTS AND MAIN RESULTS

SPX-101 binds selectively to ENaC and promotes internalization of the α-, β-, and γ-subunits. Removing ENaC from the membrane with SPX-101 causes a significant decrease in amiloride-sensitive current. The peptide increases survival of β-ENaC-transgenic mice to greater than 90% with once-daily dosing by inhalation. SPX-101 increased mucus transport in the β-ENaC mouse model as well as the sheep model of CF.

CONCLUSIONS

These data demonstrate that SPX-101 promotes durable reduction of ENaC membrane concentration, leading to significant improvements in mucus transport.

Late maternal hypothyroidism alters the expression of Camk4 in neocortical subplate neurons: a comparison with Nurr1 labeling

Maternal thyroid hormones (THs) are essential for normal offspring's neurodevelopment even after onset of fetal thyroid function. This is particularly relevant for preterm children who are deprived of maternal THs following birth, are at risk of suffering hypothyroxinemia, and develop attention-deficit/hyperactivity disorder. Expression of neocortical Ca(2+)/calmodulin kinase IV (Camk4), a genomic target of thyroid hormone, and nuclear receptor-related 1 protein (Nurr1), a postnatal marker of cortical subplate (SP) cells, was studied in euthyroid fetuses and in pups born to dams thyroidectomized in late gestation (LMH group, a model of prematurity), and compared with control and developmentally hypothyroid pups (C and MMI groups, respectively). In LMH pups, the extinction of heavy Camk4 expression in an SP was 1-2 days delayed postnatally compared with C pups. The heavy Camk4 and Nurr1 expression in the SP was prolonged in MMI pups, whereas heavy Camk4 and Nurr1 expression in layer VIb remains at P60. The abnormal expression of Camk4 in the cortical SP and in layer VIb might cause altered cortical connectivity affecting neocortical function.

[Research in urgent and emergency medicine]

Health research is consubstantial with clinical excellence, a fact that is also inherent in urgency and emergency medicine (UEM). Besides, the specific characteristics of the Spanish health CARE system and the organisation of hospital emergency CARE offer a probably unique scenario, offering unique opportunities for their scientific analysis and study. Although the indices of Spanish scientific production in UEM were traditionally below those registered for researchers of other medical specialties, as well for UEM researchers of other countries, there has been a dynamic of continuous growth since 1995: it is the highest with respect to the former and second amongst our European colleagues. Besides, there is a great deal of low level scientific activity (papers presented to conferences). To increase scientific production in UEM there is a need to solve some aspects that hinder this task, such as: the lack of a scientific culture, doubtless united to the lack of a recognised specialty; the limited training in research methodology; the lack of explicit recognition of scientific work; the limited scientific infrastructure; the practically 100% dedication to the work of care tasks; the scarce participation in national grants for research projects; and the absence in Spain of an indexed journal specialising in UEM. Besides, we believe that it is necessary to promote and interrelate the research groups of different hospitals and emergency medical systems, both locally and amongst the different autonomous communities, so that they work in a coordinated way and thus obtain the necessary critical mass that will enable the formation of a thematic network of cooperative research.

KIF4 mediates anterograde translocation and positioning of ribosomal constituents to axons

In this study, we have used a combination of biochemical and molecular biology techniques to demonstrate that the C-terminal tail domain of KIF4 directly interacts with P0, a major protein component of ribosomes. Besides, in dorsal root ganglion neurons, KIF4 and P0, as well as other ribosomal constituents, colocalize in clusters distributed along axons and neuritic tips. RNA interference suppression of KIF4 or expression of KIF4 variants lacking the tail domain or mutations of the ATP-binding site result in accumulation of P0 and other ribosomal proteins at the cell body and in their disappearance from axons. Our results also show one additional function for KIF4 involving an Ezrin-Radixin-Moesin-like domain in the second coiled-coiled region of KIF4. Expression of a KIF4 mutant lacking this domain abolishes the clustering of ribosomal constituents and prevents the anterograde translocation of the cell adhesion molecule L1. Taken together, the present results suggest that by binding to P0 through its tail domain and by using its motor activity, KIF4 is involved in the anterograde trafficking of ribosomal constituents to axons and that by means of its Ezrin-Radixin-Moesin-like domain interacts and transports L1.

Effect of intra-aortic occlusion balloon in external thoracic compressions during CPR in pigs

This study was performed to compare the effectiveness of external thoracic compressions with and without intra-aortic occlusion balloon with capnography and coronary and cerebral perfusion pressure (CPP) in the normothermic and traumatic-less cardiopulmonary arrest provoked by a ventricular fibrillation in pigs. This was an experimental study (cross-over study) in 14 pigs with similar characteristics (23 +/- 2 kg, 10-12 weeks of age). After an 8-minute nonintervention period, the cardiopulmonary resuscitation (CPR) consists of 4 periods of 5 minutes alternating CPR with and without intra-aortic occlusion balloon. Main outcomes measured are end-tidal CO(2) (ETCO(2)); intra-aortic, coronary, and cerebral perfusion pressures; blood gas analysis; and blood lactate concentration. At the end of each period, levels are obtained. Postmortem study was made. Inflation of the occlusion balloon provokes an expansion in the ETCO(2) of about 38%. The coronary perfusion pressure initially goes from 10.21 to 29.0 mm Hg after the occlusion of the aorta, which means an increase of 150%. The CPP goes from 12.54 to 39.71 mm Hg after the balloon was inflated, which means an increase of 200%. In all cases the differences are statistically significant (P <.0001). These increases are less important in the final periods. Intra-aortic balloon occlusion increased ETCO(2), coronary, and cerebral perfusion pressures. An early application of this technique was important.

[Use of troponin-I, CPK-MB and myoglobin in the diagnosis of myocardial infarct and processes of muscular necrosis of non-cardiac origin]

BACKGROUND

Thoracic pain is one of most frequent reasons for consultations at an Emergency Unit. Clinical description and the ECG are fundamental for its analysis, but a serious diagnostic problem arises when these do not provide typical data. Our aim is to analyse recently introduced biochemical parameters in order to test whether it is possible to discriminate between entities that are associated with myocardial necrosis and those others in which necrosis is due to striated muscle.

MATERIAL AND METHODS

We analysed troponin-I and the relation between CPK-MB and total CPK in the serum of 45 patients who attended the Emergency Services with different processes of striated muscle in whom the total CPK was elevated, and 50 patients with acute myocardial infarct. The serum was analysed through an immunotest by fluorescence with monoclonal antibodies.

RESULTS

Troponin-I proved to be above the normal value in the 50 patients with myocardial infarct an in 4 of the 45 in the muscular group. The total CPK/MB/CPK ratio was significantly higher in the infarct group than in the muscular group. In all of the patients of this latter group the relation was less than 5%.

CONCLUSIONS

Troponin-I rises above the normal value and is very sensitive in a myocardial infarct. The total CPK/MB/CPK relation discriminates between processes of muscular necrosis (value <5%) and processes with myocardial infarct (that are generally associated with value >5%). The increase of troponin-I supports the diagnosis of myocardial lesion when the pain suggests a coronary origin but the ratio does not reach 5%.