Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants

The emergence of successive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) during 2020 to 2022, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics-such as varying levels of immunity-can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform Coronavirus Disease 2019 (COVID-19) planning and response and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both interindividual variation in Ct values and complex host characteristics-such as vaccination status, exposure history, and age-we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least 5 prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs. Trial Registration: The Legacy study is a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening for SARS-CoV-2 at University College London Hospitals or at the Francis Crick Institute (NCT04750356) (22,23). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469) and is sponsored by University College London Hospitals. Written consent was given by all participants.

Preferences for Enhanced Primary Care Services Among Older Individuals and Primary Care Physicians

OBJECTIVE

We aimed to identify the factors that are most important for community-dwelling older individuals (i.e., users) and primary care (PC) providers to enhance PC services.

METHODS

Discrete choice experiment surveys were administered to 747 individuals aged ≥ 60 years and 242 PC physicians in Singapore between December 2020 and August 2021. Participants were asked to choose between two hypothetical PC clinics and their current clinic. Latent class models were used to estimate the relative attribute importance (RAI) and to calculate the predicted uptake for enhanced PC services.

RESULTS

Based on the attributes and levels used in this study, the out-of-pocket cost (RAI: 47%) and types of services offered (RAI: 25%) were the most important attributes for users while working hours (RAI: 28%) and patient load (RAI: 25%) were the most important for providers. For out-of-pocket visit costs ranging from Singapore dollars (S)$100 to S$5, users' predicted uptake for enhanced PC services ranged from 46 to 84%. For daily patient loads ranging from 60 to 20 patients, providers' predicted uptake ranged from 64 to 91%, assuming their income remains unchanged.

CONCLUSIONS

Our study provides timely insights for the development of strategies to support the government's new health care initiative (HealthierSG), which places PC at the center of Singapore's healthcare system. The ability to choose their preferred clinic, low out-of-pocket costs and types of services offered (for users), and reasonable working conditions (for providers) were the key factors for users and providers to participate in enhanced PC services.

The Kynurenine Pathway Metabolites in Cord Blood Positively Correlate With Early Childhood Adiposity

CONTEXT

The kynurenine pathway generates metabolites integral to energy metabolism, neurotransmission, and immune function. Circulating kynurenine metabolites positively correlate with adiposity in children and adults, yet it is not known whether this relationship is present already at birth.

OBJECTIVE

In this prospective longitudinal study, we investigate the relationship between cord blood kynurenine metabolites and measures of adiposity from birth to 4.5 years.

METHODS

Liquid chromatography-tandem mass spectrometry was used to quantify cord blood kynurenine metabolites in 812 neonates from the Growing Up in Singapore Towards healthy Outcomes (GUSTO) study. Fat percentage was measured by air displacement plethysmography and abdominal adipose tissue compartment volumes; superficial (sSAT) and deep subcutaneous (dSAT) and internal adipose tissue were quantified by magnetic resonance imaging at early infancy in a smaller subset of neonates, and again at 4 to 4.5 years of age.

RESULTS

Cord blood kynurenine metabolites appeared to be higher in female newborns, higher in Indian newborns compared with Chinese newborns, and higher in infants born by cesarean section compared with vaginal delivery. Kynurenine, xanthurenic acid, and quinolinic acid were positively associated with birthweight, but not with subsequent weight during infancy and childhood. Quinolinic acid was positively associated with sSAT at birth. Kynurenic acid and quinolinic acid were positively associated with fat percentage at 4 years.

CONCLUSION

Several cord blood kynurenine metabolite concentrations were positively associated with birthweight, with higher kynurenic acid and quinolinic acid correlating to higher percentage body fat in childhood, suggesting these cord blood metabolites as biomarkers of early childhood adiposity.

Derivation and measurement consistency of a novel biofluid dynamics measure of deglutitive bolus-driving function-pharyngeal swallowing power

BACKGROUND

The primary function of the pharyngeal swallowing mechanism is to drive ingested materials into the esophagus. Currently, a definitive measure of pharyngeal bolus-driving function that accounts for bolus movement remains lacking. The primary objectives of this study were to describe the derivation of a novel biofluid dynamics measure of deglutition-that is, pharyngeal swallowing power (PSP)-and to demonstrate the consistency of PSP in normal swallowing.

METHODS

The pharyngeal swallowing mechanism was conceptualized as a hydraulic power system with the upper esophageal sphincter (UES) as a conduit. PSP was calculated as the product of bolus pressure and flow across the UES. Thirty-four young healthy subjects swallowed materials consisting of two bolus volumes (10, 20 mL) and four bolus viscosities (thin liquid, nectar-thick liquid, honey-thick liquid, pudding). High-resolution impedance manometry was used for data collection. The consistency of PSP across specific bolus conditions was evaluated using standardized Cronbach's coefficient alpha.

KEY RESULTS

Standardized Cronbach's coefficient alphas in specific bolus conditions ranged between 0.85 and 0.93. Fisher weighted mean Cronbach's coefficient alphas for swallow trials across bolus volumes and across bolus viscosities ranged from 0.86 to 0.90. Fisher weighted mean Cronbach's coefficient alpha for overall consistency of PSP across all swallow trials was 0.88.

CONCLUSIONS AND INFERENCES

PSP estimates the output power of the pharyngeal bolus-driving mechanism during deglutition. PSP's high consistency indicates that it can be a useful biofluid dynamics measure of pharyngeal bolus-driving function. Current results also demonstrate that consistency in pharyngeal bolus propulsion is an important physiological target for the pharyngeal swallowing mechanism.

Pulses and waves of contractility

The nature of signal transduction networks in the regulation of cell contractility is not entirely clear. In this study, Graessl et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201706052) visualized and characterized pulses and waves of Rho activation in adherent cells and proposed excitable Rho signaling networks underlying cell contractility.

Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery

BACKGROUND

The relationship between monogenic and polygenic forms of epilepsy is poorly understood and the extent to which the genetic and acquired epilepsies share common pathways is unclear. Here, we use an integrated systems-level analysis of brain gene expression data to identify molecular networks disrupted in epilepsy.

RESULTS

We identified a co-expression network of 320 genes (M30), which is significantly enriched for non-synonymous de novo mutations ascertained from patients with monogenic epilepsy and for common variants associated with polygenic epilepsy. The genes in the M30 network are expressed widely in the human brain under tight developmental control and encode physically interacting proteins involved in synaptic processes. The most highly connected proteins within the M30 network were preferentially disrupted by deleterious de novo mutations for monogenic epilepsy, in line with the centrality-lethality hypothesis. Analysis of M30 expression revealed consistent downregulation in the epileptic brain in heterogeneous forms of epilepsy including human temporal lobe epilepsy, a mouse model of acquired temporal lobe epilepsy, and a mouse model of monogenic Dravet (SCN1A) disease. These results suggest functional disruption of M30 via gene mutation or altered expression as a convergent mechanism regulating susceptibility to epilepsy broadly. Using the large collection of drug-induced gene expression data from Connectivity Map, several drugs were predicted to preferentially restore the downregulation of M30 in epilepsy toward health, most notably valproic acid, whose effect on M30 expression was replicated in neurons.

CONCLUSIONS

Taken together, our results suggest targeting the expression of M30 as a potential new therapeutic strategy in epilepsy.