Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza

High-throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Crucially, there are an increasing number of molecular clock analyses using external evolutionary rate priors to infer evolutionary parameters. However, it is not clear which rate prior is appropriate for a given time window of observation due to the time-dependent nature of evolutionary rate estimates. Here, we characterize the molecular evolutionary dynamics of SARS-CoV-2 and 2009 pandemic H1N1 (pH1N1) influenza during the first 12 months of their respective pandemics. We use Bayesian phylogenetic methods to estimate the dates of emergence, evolutionary rates, and growth rates of SARS-CoV-2 and pH1N1 over time and investigate how varying sampling window and data set sizes affect the accuracy of parameter estimation. We further use a generalized McDonald–Kreitman test to estimate the number of segregating nonneutral sites over time. We find that the inferred evolutionary parameters for both pandemics are time dependent, and that the inferred rates of SARS-CoV-2 and pH1N1 decline by ∼50% and ∼100%, respectively, over the course of 1 year. After at least 4 months since the start of sequence sampling, inferred growth rates and emergence dates remain relatively stable and can be inferred reliably using a logistic growth coalescent model. We show that the time dependency of the mean substitution rate is due to elevated substitution rates at terminal branches which are 2–4 times higher than those of internal branches for both viruses. The elevated rate at terminal branches is strongly correlated with an increasing number of segregating nonneutral sites, demonstrating the role of purifying selection in generating the time dependency of evolutionary parameters during pandemics.     

Mapping bone cell distributions to assess ontogenetic origin of primate midfacial form

Midfacial reduction in primates has been explained as a byproduct of other growth patterns, especially the convergent orbits. This is at once an evolutionary and developmental explanation for relatively short snouts in most modern primates. Here, we use histological sections of perinatal nonhuman primates (tamarin, tarsier, loris) to investigate how orbital morphology emerges during ontogeny in selected primates compared to another euarchontan (Tupaia glis). We annotated serial histological sections for location of osteoclasts or osteoblasts, and used these to create three‐dimensional “modeling maps” showing perinatal growth patterns of the facial skeleton. In addition, in one specimen we transferred annotations from histological sections to CT slices, to create a rotatable 3D volume that shows orbital modeling. Our findings suggest that growth in the competing orbital and neurocranial functional matrices differs among species, influencing modeling patterns. Distinctions among species are observed in the frontal bone, at a shared interface between the endocranial fossa and the orbit. The medial orbital wall is extensively resorptive in primates, whereas the medial orbit is generally depositional in Tupaia. As hypothesized, the orbital soft tissues encroach on available interorbital space. However, eye size cannot, by itself, explain the extent of reduction of the olfactory recess. In Loris, the posterior portion of medial orbit differed from the other primates. It showed evidence of outward drift where the olfactory bulb increased in cross‐sectional area. We suggest the olfactory bulbs are significant to orbit position in strepsirrhines, influencing an expanded interorbital breadth at early stages of development. Am J Phys Anthropol 154:424–435, 2014. © 2014 Wiley Periodicals, Inc.     

Physician experience and outcomes among patients admitted to general internal medicine teaching wards

Background:

Physician scores on examinations decline with time after graduation. However, whether this translates into declining quality of care is unknown. Our objective was to determine how physician experience is associated with negative outcomes for patients admitted to hospital.

Methods:

We conducted a retrospective cohort study involving all patients admitted to general internal medicine wards over a 2-year period at all 7 teaching hospitals in Alberta, Canada. We used files from the Alberta College of Physicians and Surgeons to determine the number of years since medical school graduation for each patient’s most responsible physician. Our primary outcome was the composite of in-hospital death, or readmission or death within 30 days postdischarge.

Results:

We identified 10 046 patients who were cared for by 149 physicians. Patient characteristics were similar across physician experience strata, as were primary outcome rates (17.4% for patients whose care was managed by physicians in the highest quartile of experience, compared with 18.8% in those receiving care from the least experienced physicians; adjusted odds ratio [OR] 0.88, 95% confidence interval [CI] 0.72–1.06). Outcomes were similar between experience quartiles when further stratified by physician volume, most responsible diagnosis or complexity of the patient’s condition. Although we found substantial variability in length of stay between individual physicians, there were no significant differences between physician experience quartiles (mean adjusted for patient covariates and accounting for intraphysician clustering: 7.90 [95% CI 7.39–8.42] d for most experienced quartile; 7.63 [95% CI 7.13–8.14] d for least experienced quartile).

Interpretation:

For patients admitted to general internal medicine teaching wards, we saw no negative association between physician experience and outcomes commonly used as proxies for quality of inpatient care.Many jurisdictions have instituted compulsory recertification of physicians on the assumption that quality of care declines with experience. Although a systematic review reported that 32 of 62 studies found decreasing performance with increasing physician experience, most of these studies evaluated performance on examinations or hypothetical vignettes rather than actual quality of care provided to patients, and most of the studies were done decades ago, before the widespread availability of tools to readily facilitate evidence-based medicine.¹Experience is strongly related to better outcomes in surgery and obstetrics, but studies examining the association between physician experience and quality of care for medical patients have reported mixed results.^1–8 Many of the studies reporting an inverse association between experience and quality of care have focused on the provision of “guideline recommended tests or therapies” as a proxy for quality of care. However, guideline recommendations might not be appropriate in every situation.An evaluation of broader quality metrics may be more appropriate to answer this question. For example, in-hospital mortality and readmission rates or mortality postdischarge are commonly used as markers for quality of inpatient care, are endorsed by the Centers for Medicare & Medicaid Services and are included in the Patient Protection and Affordable Care Act.^9,10 However, to our knowledge, few studies have examined the association between these broader quality metrics and physician experience, and these studies have been limited. They either focused on single diagnoses,¹¹ excluded older adult patients,² examined data from only 1 hospital⁸ or combined data⁷ for both surgeons and physicians.Patients admitted to general internal medicine services at Alberta teaching hospitals are distributed between wards purely on the basis of bed availability, and attending physicians rotate every 1–4 weeks. For these reasons, the distribution of patients between attending physicians is quasirandom. We took advantage of this natural experiment to evaluate the association between attending physician experience (years since medical school graduation) and outcomes for patients admitted to general internal medicine wards in Alberta.     

Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission

Dengue is one of the most important infectious diseases of humans and has spread throughout much of the tropical and subtropical world. Despite this widespread dispersal, the determinants of dengue transmission in endemic populations are not well understood, although essential for virus control. To address this issue we performed a phylogeographic analysis of 751 complete genome sequences of dengue 1 virus (DENV-1) sampled from both rural (Dong Thap) and urban (Ho Chi Minh City) populations in southern Viet Nam during the period 2003-2008. We show that DENV-1 in Viet Nam exhibits strong spatial clustering, with likely importation from Cambodia on multiple occasions. Notably, multiple lineages of DENV-1 co-circulated in Ho Chi Minh City. That these lineages emerged at approximately the same time and dispersed over similar spatial regions suggests that they are of broadly equivalent fitness. We also observed an important relationship between the density of the human host population and the dispersion rate of dengue, such that DENV-1 tends to move from urban to rural populations, and that densely populated regions within Ho Chi Minh City act as major transmission foci. Despite these fluid dynamics, the dispersion rates of DENV-1 are relatively low, particularly in Ho Chi Minh City where the virus moves less than an average of 20 km/year. These low rates suggest a major role for mosquito-mediated dispersal, such that DENV-1 does not need to move great distances to infect a new host when there are abundant susceptibles, and imply that control measures should be directed toward the most densely populated urban environments.     

Synthesis of novel oxazolidinone antimicrobial agents

The oxazolidinone class of antimicrobials represents a promising advance in the fight against resistant Gram-positive bacterial infections. Four novel oxazolidinone antimicrobial compounds, each containing a benzodioxin ring system, have been prepared. The general synthesis of each compound begins with the construction of a benzodioxin ring system containing a nitro substituent that ultimately becomes the nitrogen of the oxazolidinone ring. Three of the compounds utilize high yielding 'click chemistry' in their final step. The antimicrobial activities of the new oxazolidinones have been measured and the MIC against Staphylococcus aureus for one of the antimicrobials was determined to be 2-3 microg/mL, which is comparable to the well-known oxazolidinone, linezolid.     

Root carbon flow from an invasive plant to belowground foodwebs

Aims

Soil foodwebs are based on plant production. This production enters belowground foodwebs via numerous pathways, with root pathways likely dominating supply. Indeed, root exudation may fuel 30–50?% of belowground activity with photosynthate fixed only hours earlier. Yet we have limited knowledge of root fluxes of recent-photosynthate from invasive plants to belowground foodwebs.

Methods

Using stable isotopes, we quantify the proportion of recent-photosynthate transferred belowground from the invasive grass Microstegium vimineum A. Camus, a widespread invader of forest understory. Given its minimal root biomass (～8?% of individual mass), we expected exudation to contribute little to belowground foodwebs.

Results

Within 2?days of ¹³C-labeling, we recover ～15?% of photosynthate carbon in microbial biomass. Recovery in root and dissolved organic carbon pools is consistently low (<2?%), suggesting these pools operate as ‘pipelines’ for carbon transport to soil microbes. The recovery of the label in wolf spiders – forest floor predators that feed on soil animals – highlights that root inputs of recent photosynthate can propagate rapidly through belowground foodwebs.

Conclusions

Our results suggest that root carbon-exudation, an unexplored process of invasive grass inputs to forest foodwebs, may be an important pathway through which invasive species affect the structure and function of recipient ecosystems.     

Laboratory evolution of catabolic enzymes and pathways

The laboratory evolution of environmentally relevant enzymes and proteins has resulted in the generation of optimized and stabilized enzymes, as well as enzymes with activity against new substrates. Numerous methods, including random mutagenesis, site-directed mutagenesis and DNA shuffling, have been widely used to generate variants of existing enzymes. These evolved catabolic enzymes have application for improving biodegradation pathways, generating engineered pathways for the degradation of particularly recalcitrant compounds, and for the development of biocatalytic processes to produce useful compounds. Regulatory proteins associated with catabolic pathways have been utilized to generate biosensors for the detection of bioavailable concentrations of environmentally relevant chemicals.