Scalable RT-LAMP-based SARS-CoV-2 testing for infection surveillance with applications in pandemic preparedness.

Throughout the SARS-CoV-2 pandemic, limited diagnostic capacities prevented sentinel testing, demonstrating the need for novel testing infrastructures. Here, we describe the setup of a cost-effective platform that can be employed in a high-throughput manner, which allows surveillance testing as an acute pandemic control and preparedness tool, exemplified by SARS-CoV-2 diagnostics in an academic environment. The strategy involves self-sampling based on gargling saline, pseudonymized sample handling, automated RNA extraction, and viral RNA detection using a semiquantitative multiplexed colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay with an analytical sensitivity comparable with RT-qPCR. We provide standard operating procedures and an integrated software solution for all workflows, including sample logistics, analysis by colorimetry or sequencing, and communication of results. We evaluated factors affecting the viral load and the stability of gargling samples as well as the diagnostic sensitivity of the RT-LAMP assay. In parallel, we estimated the economic costs of setting up and running the test station. We performed > 35,000 tests, with an average turnover time of < 6 h from sample arrival to result announcement. Altogether, our work provides a blueprint for fast, sensitive, scalable, cost- and labor-efficient RT-LAMP diagnostics, which is independent of potentially limiting clinical diagnostics supply chains.

Rapid comparative evaluation of SARS-CoV-2 rapid point-of-care antigen tests.

PURPOSE: The objective of this study was to develop a scalable approach for direct comparison of the analytical sensitivities of commercially available SARS-CoV-2 antigen point-of-care tests (AgPOCTs) to rapidly identify poor-performing products. METHODS: We present a methodology for quick assessment of the sensitivity of SARS-CoV-2 AgPOCTs suitable for quality evaluation of many different products. We established reference samples with high, medium, and low SARS-CoV-2 viral loads along with a SARS-CoV-2 negative control sample. Test samples were used to semi-quantitatively assess the analytical sensitivities of 32 different commercial AgPOCTs in a head-to-head comparison. RESULTS: Among 32 SARS-CoV-2 AgPOCTs tested, we observe sensitivity differences across a broad range of viral loads (9.8 × 108 to 1.8 × 105 SARS-CoV-2 genome copies per ml). 23 AgPOCTs detected the Ct25 test sample (1.6 × 106 copies/ml), while only five tests detected the Ct28 test sample (1.8 × 105 copies/ml). In the low-range of analytical sensitivity, we found three saliva spit tests only delivering positive results for the Ct21 sample (2.7 × 107 copies/ml). Comparison with published data supports our AgPOCT ranking. Importantly, we identified an AgPOCT widely offered, which did not reliably recognize the sample with the highest viral load (Ct16 test sample with 9.8 × 108 copies/ml) leading to serious doubts about its usefulness in SARS-CoV-2 diagnostics. CONCLUSION: The results show that the rapid sensitivity assessment procedure presented here provides useful estimations on the analytical sensitivities of 32 AgPOCTs and identified a widely-spread AgPOCT with concerningly low sensitivity.

Differential modulation of parietal cortex activity by respiration and θ oscillations.

The simultaneous, local integration of information from widespread brain regions is an essential feature of cortical computation and particularly relevant for multimodal association areas such as the posterior parietal cortex. Slow, rhythmic fluctuations in the local field potentials (LFPs) are assumed to constitute a global signal aiding interregional communication through the long-range synchronization of neuronal activity. Recent work demonstrated the brain-wide presence of a novel class of slow neuronal oscillations that are entrained by nasal respiration. However, whether there are differences in the influence of the respiration-entrained rhythm (RR) and the endogenous theta (θ) rhythm over local networks is unknown. In this work, we aimed at characterizing the impact of both classes of oscillations on neuronal activity in the posterior parietal cortex of mice. We focused our investigations on a θ-dominated state (rapid eye movement sleep) and an RR-dominated state (wake immobility). Using linear silicon probes implanted along the dorsoventral cortical axis, we found that the LFP-depth distributions of both rhythms show differences in amplitude and coherence but no phase shift. Using tetrode recordings, we demonstrate that a substantial fraction of parietal neurons is modulated by either RR or θ or even by both rhythms simultaneously. Interestingly, the phase and cortical depth dependence of spike-field coupling differ for these oscillations. We further show through intracellular recordings in urethane-anesthetized mice that synaptic inhibition is likely to play a role in generating respiration-entrainment at the membrane potential level. We conclude that θ and respiration differentially affect neuronal activity in the parietal cortex.NEW & NOTEWORTHY Nasal respiration generates a rhythmic signal that entrains large portions of the mammalian brain into respiration-coupled field potentials. Here, we report the simultaneous presence of respiratory rhythm (RR) and θ oscillations in the parietal association cortex of mice. Despite their overlapping frequencies, both rhythms differ in their state-dependent power and differentially entrain the discharge behavior of units. We conclude that network activity in the parietal cortex is synchronized by two different physiological oscillation patterns.

Dysregulation of Npas4 and Inhba expression and an altered excitation-inhibition balance are associated with cognitive deficits in DBA/2 mice.

Differences in the learning associated transcriptional profiles between mouse strains with distinct learning abilities could provide insight into the molecular basis of learning and memory. The inbred mouse strain DBA/2 shows deficits in hippocampus-dependent memory, yet the transcriptional responses to learning and the underlying mechanisms of the impairments are unknown. Comparing DBA/2J mice with the reference standard C57BL/6N mouse strain we verify an enhanced susceptibility to kainic acid induced seizures, confirm impairments in hippocampus-dependent spatial memory tasks and uncover additional behavioral abnormalities including deficits in hippocampus-independent learning. Surprisingly, we found no broad dysfunction of the DBA/2J strain in immediate early gene (IEG) activation but instead report brain region-specific and gene-specific alterations. The learning-associated IEGs Arc, c-Fos, and Nr4a1 showed no DBA/2J deficits in basal or synaptic activity induced gene expression in hippocampal or cortical primary neuronal cultures or in the CA1, CA3, or retrosplenial cortex following spatial object recognition (SOR) training in vivo. However, the parietal cortex showed reduced and the dentate gyrus showed enhanced SOR-evoked induction of most IEGs. All DBA/2J hippocampal regions exhibited elevated basal expression of inhibin ß A (Inhba) and a learning-associated superinduction of the transcription factor neuronal Per-Arnt-Sim domain protein 4 (Npas4) known to regulate the synaptic excitation-inhibition balance. In line with this, CA1 pyramidal neurons of DBA/2J mice showed fewer inhibitory and more excitatory miniature postsynaptic currents but no alteration in most other electrophysiological properties or gross dendritic morphology. The dysregulation of Npas4 and Inhba expression and synaptic connectivity may underlie the cognitive deficits and increased susceptibility to seizures of DBA/2J mice.

A preliminary investigation of dispositional affect, the P300, and sentence processing.

We examined whether dispositional affect modulated the relation between sentence processing and the P300 Event Related Potential (ERP) component. We used sentence stimuli from our previous study, where sentences started with subject nouns that were quantified e.g., Every kid… or not, as in The kid…, and continued with a direct object which was either singular, as in a tree, or plural the trees. In this Stroop-like task, participants read sentences presented in 1- and 2-word chunks, and were asked to identify the number of words on the screen at the target word tree(s), which was always presented alone (and never sentence-final). We replicated previous findings of a P300 effect, at the target tree(s), however, actual by-condition effects differed from previous work. Of interest, clear individual differences were apparent. Participants with relatively lower Positive Affect scores (as measured by the Positive and Negative Affect Schedule; PANAS), showed differential P300 responses to the control condition, Every/The kid climbed the tree. Thus, the present ERP findings demonstrate that dispositional affect modulated P300 effects. These findings suggest that, rather than relying on global heuristic cues for sentence meaning interpretation, these participants may be differentially sensitive to local (grammatical) cues which signify task relevance. We discuss our results in terms of theories of positive affect, where less positive individuals are differentially sensitive to local (grammatical) information.