The severe acute respiratory syndrome coronavirus 2 pandemic is characterized by the emergence of novel variants of concern (VOCs) that replace ancestral strains. Here, we dissect the complex ...selective pressures by evaluating variant fitness and adaptation in human respiratory tissues. We evaluate viral properties and host responses to reconstruct forces behind D614G through Omicron (BA.1) emergence. We observe differential replication in airway epithelia, differences in cellular tropism, and virus-induced cytotoxicity. D614G accumulates the most mutations after infection, supporting zoonosis and adaptation to the human airway. We perform head-to-head competitions and observe the highest fitness for Gamma and Delta. Under these conditions, RNA recombination favors variants encoding the B.1.617.1 lineage 3′ end. Based on viral growth kinetics, Alpha, Gamma, and Delta exhibit increased fitness compared to D614G. In contrast, the global success of Omicron likely derives from increased transmission and antigenic variation. Our data provide molecular evidence to support epidemiological observations of VOC emergence.
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•The ancestral D614G is least adapted to the human airway compared to later variants•Gamma and Delta variants have the highest replicative fitness in human airway epithelia•Omicron displays poor replication and increased immune activation in the lower airway•Omicron success globally is likely due to increased transmission and antigenic variation
Meganck et al. recapitulate the drivers of evolution by evaluating SARS-CoV-2 variant fitness in primary human airway cells. Ancestral D614G displays pre-adaptation phenotypes, while Gamma and Delta variants have intrinsic high replicative fitness in the human airway. Omicron has poor replicative fitness and greater immune induction in the lower airway.
Effective models of support for HIV pre-exposure prophylaxis (PrEP) are needed for populations at elevated risk. In a hyperendemic Ugandan fishing community, PrEP counseling was provided through a ...situated Information, Motivation, and Behavioral Skills (sIMB)-based community health worker (CHW) intervention. We evaluated the intervention using a mixed-methods, implementation science design.
We surveyed all community members aged 15-49 through the Rakai Community Cohort Study. We used multivariable logistic regressions with generalized estimating equations to estimate the intervention's effect on PrEP knowledge and utilization. To understand intervention experiences and mechanisms, we conducted 74 qualitative interviews with 5 informant types (clients, CHWs, program staff, community leaders, health clinic staff) and analyzed data using an iterative, deductive approach. A mobile phone application provided intervention process implementation data.
Individuals self-reporting receipt of the CHW intervention showed significantly higher PrEP knowledge (N = 1848, PRR: 1.10, 95% CI: 1.06-1.14,
= <.0001), PrEP ever use (N = 1176, PRR: 1.77, 95% CI: 1.33-2.36,
= <.0001), and PrEP current use (N = 1176, PRR: 1.86, 95% CI: 1.22-2.82, p = 0.0039) compared to those who did not. Qualitative findings attributed positive PrEP outcomes to CHW counseling and effective use of motivational interviewing skills by CHWs. Salient themes across the RE-AIM framework included support for the CHW intervention and PrEP across clients, community, and implementers. Mobile application data demonstrated consistent delivery of the PrEP module throughout implementation.
CHWs improved PrEP knowledge and use among clients in an HIV hyperendemic fishing community. Mixed-methods, implementation science evaluations can inform adaptation of similar PrEP implementation strategies.
A new calibration curve for the conversion of radiocarbon ages to calibrated (cal) ages has been constructed and internationally ratified to replace IntCal98, which extended from 0–24 cal kyr BP ...(Before Present, 0 cal BP = AD 1950). The new calibration data set for terrestrial samples extends from 0–26 cal kyr BP, but with much higher resolution beyond 11.4 cal kyr BP than IntCal98. Dendrochronologically-dated tree-ring samples cover the period from 0–12.4 cal kyr BP. Beyond the end of the tree rings, data from marine records (corals and foraminifera) are converted to the atmospheric equivalent with a site-specific marine reservoir correction to provide terrestrial calibration from 12.4–26.0 cal kyr B P. A substantial enhancement relative to IntCal98 is the introduction of a coherent statistical approach based on a random walk model, which takes into account the uncertainty in both the calendar age and the 14C age to calculate the underlying calibration curve (Buck and Blackwell, this issue). The tree-ring data sets, sources of uncertainty, and regional offsets are discussed here. The marine data sets and calibration curve for marine samples from the surface mixed layer (Marine04) are discussed in brief, but details are presented in Hughen et al. (this issue a). We do not make a recommendation for calibration beyond 26 cal kyr BP at this time; however, potential calibration data sets are compared in another paper (van der Plicht et al., this issue).
The etiology for half of congenital hypopituitarism cases is unknown. Our long-term goal is to expand the molecular diagnoses for congenital hypopituitarism by identifying genes that contribute to ...this condition. We have previously shown that the forkhead box transcription factor, FOXO1, is present in approximately half of somatotropes at embryonic day (e) 18.5, suggesting it may have a role in somatotrope differentiation or function. To elucidate the role of FOXO1 in somatotrope differentiation and function, Foxo1 was conditionally deleted from the anterior pituitary (Foxo1Δpit). Uncommitted progenitor cells are maintained and able to commit to the somatotrope lineage normally based on the expression patterns of Sox2, a marker of uncommitted pituitary progenitors, and Pou1f1 (also known as Pit1), which marks committed progenitors. Interestingly, Foxo1Δpit embryonic mice exhibit delayed somatotrope differentiation as evidenced by an almost complete absence of GH immunoreactivity at e16.5 and reduced expression of Gh at e18.5 and postnatal day (P) 3. Consistent with this conclusion, expression of GHRH receptor, a marker of terminally differentiated somatotropes, is significantly reduced at e18.5 and P3 in the absence of FOXO1. The mechanism of FOXO1 regulation of somatotrope differentiation may involve the basic helix-loop-helix transcription factor, Neurod4, which has been implicated in somatotrope differentiation and is significantly reduced in Foxo1Δpit mice. Foxo1Δpit mice do not exhibit growth defects, and at P21 their pituitary glands exhibit a normal distribution of somatotropes. These studies demonstrate that FOXO1 is important for initial somatotrope specification embryonically but is dispensable for postnatal somatotrope expansion and growth.
New radiocarbon calibration curves, IntCal04 and Marine04, have been constructed and internationally ratified to replace the terrestrial and marine components of IntCal98. The new calibration data ...sets extend an additional 2000 yr, from 0–26 cal kyr BP (Before Present, 0 cal BP = AD 1950), and provide much higher resolution, greater precision, and more detailed structure than IntCal98. For the Marine04 curve, dendrochronologically-dated tree-ring samples, converted with a box diffusion model to marine mixed-layer ages, cover the period from 0–10.5 cal kyr BP. Beyond 10.5 cal kyr BP, high-resolution marine data become available from foraminifera in varved sediments and U/Th-dated corals. The marine records are corrected with site-specific 14C reservoir age information to provide a single global marine mixed-layer calibration from 10.5–26.0 cal kyr BP. A substantial enhancement relative to IntCal98 is the introduction of a random walk model, which takes into account the uncertainty in both the calendar age and the 14C age to calculate the underlying calibration curve (Buck and Blackwell, this issue). The marine data sets and calibration curve for marine samples from the surface mixed layer (Marine04) are discussed here. The tree-ring data sets, sources of uncertainty, and regional offsets are presented in detail in a companion paper by Reimer et al. (this issue).
The cycle of modules that lead from climate forcings to the fossil proxy data from which we try to infer past climate. Key climate forcings such as the Sun's energy are reflected in sensors such as ...the pollen produced by vegetation, which is then archived in lake sediment.
We review the statistical methods currently in use to estimate past changes in climate. These methods encompass the full gamut of statistical modeling approaches, ranging from simple regression up to nonparametric spatiotemporal Bayesian models. Often the full inferential challenge is broken down into many submodels each of which may involve multiple stochastic components, and occasionally mechanistic or process‐based models too. We argue that many of the traditional approaches are simplistic in their structure, handling, and presentation of uncertainty, and that newer models (which incorporate mechanistic aspects alongside statistical models) provide an exciting research agenda for the next decade. We hope that policy‐makers and those charged with predicting future climate change will increasingly use probabilistic paleoclimate reconstructions to calibrate their forecasts, learn about key natural climatological parameters, and make appropriate decisions concerning future climate change. Remarkably few statisticians have involved themselves with paleoclimate reconstruction, and we hope that this article inspires more to take up the challenge.
This article is categorized under:
Applications of Computational Statistics > Computational Climate Change and Numerical Weather Forecasting
Human norovirus infection is the leading cause of acute gastroenteritis. Genetic polymorphisms, mediated by the FUT2 gene (secretor enzyme), define strain susceptibility. Secretors express a diverse ...set of fucosylated histoblood group antigen carbohydrates (HBGA) on mucosal cells; nonsecretors (FUT2-/-) express a limited array of HBGAs. Thus, nonsecretors have less diverse norovirus strain infections, including resistance to the epidemiologically dominant GII.4 strains. Because future human norovirus vaccines will comprise GII.4 antigen and because secretor phenotype impacts GII.4 infection and immunity, nonsecretors may mimic young children immunologically in response to GII.4 vaccination, providing a needed model to study cross-protection in the context of limited pre-exposure.
By using specimens collected from the first characterized nonsecretor cohort naturally infected with GII.2 human norovirus, we evaluated the breadth of serologic immunity by surrogate neutralization assays, and cellular activation and cytokine production by flow cytometry.
GII.2 infection resulted in broad antibody and cellular immunity activation that persisted for at least 30 days for T cells, monocytes, and dendritic cells, and for 180 days for blocking antibody. Multiple cellular lineages expressing interferon-γ and tumor necrosis factor-α dominated the response. Both T-cell and B-cell responses were cross-reactive with other GII strains, but not GI strains. To promote entry mechanisms, inclusion of bile acids was essential for GII.2 binding to nonsecretor HBGAs.
These data support development of within-genogroup, cross-reactive antibody and T-cell immunity, key outcomes that may provide the foundation for eliciting broad immune responses after GII.4 vaccination in individuals with limited GII.4 immunity, including young children.
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Human noroviruses are non-enveloped, single-strand RNA viruses that cause pandemic outbreaks of acute gastroenteritis. A bivalent vaccine containing GI.1 and GII.4 virus-like particles (VLPs) has ...been shown to be safe and highly immunogenic, but its efficacy and durability have been limited. Here, we show that norovirus GI.1 VLPs are unstable and contain a substantial fraction of dissociated VLP components. Broadly reactive, non-neutralizing antibodies isolated from vaccinated donors bound to the dissociated components, but not to the intact VLPs. Engineering of interprotomer disulfide bonds within the shell domain prevented disassembly of the VLPs, while preserving antibody accessibility to blockade epitopes. Without adjuvant, mice immunized with stabilized GI.1 VLPs developed faster blockade antibody titers compared to immunization with wild-type GI.1 VLPs. In addition, immunization with stabilized particles focused immune responses toward surface-exposed epitopes and away from occluded epitopes. Overall, disulfide-stabilized norovirus GI.1 VLPs elicited improved responses over the non-disulfide-stabilized version, suggesting their promise as candidate vaccines.
Background
The nose is the portal for severe acute respiratory syndrome–coronavirus‐2 (SARS‐CoV‐2) infection, suggesting the nose as a target for topical antiviral therapies. The purpose of this ...study was to assess both the in vivo and in vitro efficacy of a detergent‐based virucidal agent, Johnson and Johnson's Baby Shampoo (J&J), in SARS‐CoV‐2–infected subjects.
Methods
Subjects were randomized into three treatment groups: (1) twice daily nasal irrigation with J&J in hypertonic saline, (2) hypertonic saline alone, and (3) no intervention. Complementary in vitro experiments were performed in cultured human nasal epithelia. The primary outcome measure in the clinical trial was change in SARS‐CoV‐2 viral load over 21 days. Secondary outcomes included symptom scores and change in daily temperature. Outcome measures for in vitro studies included change in viral titers.
Results
Seventy‐two subjects completed the clinical study (n = 24 per group). Despite demonstrated safety and robust efficacy in in vitro virucidal assays, J&J irrigations had no impact on viral titers or symptom scores in treated subjects relative to controls. Similar findings were observed administering J&J to infected cultured human airway epithelia using protocols mimicking the clinical trial regimen. Additional studies of cultured human nasal epithelia demonstrated that lack of efficacy reflected pharmacokinetic failure, with the most virucidal J&J detergent components rapidly absorbed from nasal surfaces.
Conclusion
In this randomized clinical trial of subjects with SARS‐CoV‐2 infection, a topical detergent‐based virucidal agent had no effect on viral load or symptom scores. Complementary in vitro studies confirmed a lack of efficacy, reflective of pharmacokinetic failure and rapid absorption from nasal surfaces.
Identification of fungal organisms often poses a problem for pathologists because the histomorphology of some fungal organisms is not specific, fresh tissues may not be available, and isolation and ...identification in culture may take a long time. The purpose of this study was to validate the use of panfungal PCR to identify fungal organisms from formalin-fixed paraffin-embedded (FFPE) tissues. FFPE curls were tested from 128 blocks containing canine, feline, equine, and bovine tissues with cutaneous, nasal, pulmonary, and systemic fungal infections, identified by the presence of fungi in histologic sections. Quantitative scoring of histologic sections identified rare (11.9%), occasional (17.5%), moderate (17.5%) or abundant (53%) fungal organisms. DNA was isolated from FFPE tissues and PCR was performed targeting the Internal Transcribed Spacer 2 (ITS-2) region, a segment of non-coding DNA found in all eukaryotes. PCR products were sequenced and identified at ≥97% identity match using the basic local alignment search tool (BLAST) and the NCBI database of ITS sequences. Of the 128 blocks, 117 (91.4%) yielded PCR products and high quality sequences were derived from 89 (69.5%). Sequence and histological identifications matched in 79 blocks (61.7%). This assay was capable of providing genus- and species-level identification when histopathology could not and thus is a beneficial complementary tool for diagnosis of fungal diseases.
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