Disentangling the dynamical underpinnings of differences in SARS-CoV-2 pathology using within-host ecological models

Health outcomes following infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are remarkably variable. The way the virus spreads inside hosts, and how this spread interacts with host immunity and physiology, is likely to determine variation in health outcomes. Decades of data and dynamical analyses of how other viruses spread and interact with host cells could shed light on SARS-CoV-2 within-host trajectories. We review how common axes of variation in within-host dynamics and emergent pathology (such as age and sex) might be combined with ecological principles to understand the case of SARS-CoV-2. We highlight pitfalls in application of existing theoretical frameworks relevant to the complexity of the within-host context and frame the discussion in terms of growing knowledge of the biology of SARS-CoV-2. Viewing health outcomes for SARS-CoV-2 through the lens of ecological models underscores the value of repeated measures on individuals, especially since many lines of evidence suggest important contingence on trajectory.     

Environmental versus Anthropogenic Effects on Population Adaptive Divergence in the Freshwater Snail Lymnaea stagnalis

Repeated pesticide contaminations of lentic freshwater systems located within agricultural landscapes may affect population evolution in non-target organisms, especially in species with a fully aquatic life cycle and low dispersal ability. The issue of evolutionary impact of pollutants is therefore conceptually important for ecotoxicologists. The impact of historical exposure to pesticides on genetic divergence was investigated in the freshwater gastropod Lymnaea stagnalis, using a set of 14 populations from contrasted environments in terms of pesticide and other anthropogenic pressures. The hypothesis of population adaptive divergence was tested on 11 life-history traits, using Q _ST -F _ST comparisons. Despite strong neutral differentiation (mean F _ST = 0.291), five adult traits or parameters were found to be under divergent selection. Conversely, two early expressed traits showed a pattern consistent with uniform selection or trait canalization, and four adult traits appeared to evolve neutrally. Divergent selection patterns were mostly consistent with a habitat effect, opposing pond to ditch and channel populations. Comparatively, pesticide and other human pressures had little correspondence with evolutionary patterns, despite hatching rate impairment associated with global anthropogenic pressure. Globally, analyses revealed high genetic variation both at neutral markers and fitness-related traits in a species used as model in ecotoxicology, providing empirical support for the need to account for genetic and evolutionary components of population response in ecological risk assessment.     

Scale morphology and flexibility in the shortfin mako Isurus oxyrinchus and the blacktip shark Carcharhinus limbatus

We quantified placoid scale morphology and flexibility in the shortfin mako Isurus oxyrinchus and the blacktip shark Carcharhinus limbatus. The shortfin mako shark has shorter scales than the blacktip shark. The majority of the shortfin mako shark scales have three longitudinal riblets with narrow spacing and shallow grooves. In comparison, the blacktip shark scales have five to seven longitudinal riblets with wider spacing and deeper grooves. Manual manipulation of the scales at 16 regions on the body and fins revealed a range of scale flexibility, from regions of nonerectable scales such as on the leading edge of the fins to highly erectable scales along the flank of the shortfin mako shark body. The flank scales of the shortfin mako shark can be erected to a greater angle than the flank scales of the blacktip shark. The shortfin mako shark has a region of highly flexible scales on the lateral flank that can be erected to at least 50°. The scales of the two species are anchored in the stratum laxum of the dermis. The attachment fibers of the scales in both species appear to be almost exclusively collagen, with elastin fibers visible in the stratum laxum of both species. The most erectable scales of the shortfin mako shark have long crowns and relatively short bases that are wider than long. The combination of a long crown length to short base length facilitates pivoting of the scales. Erection of flank scales and resulting drag reduction is hypothesized to be passively driven by localized flow patterns over the skin. J. Morphol. 2012. © 2012 Wiley Periodicals, Inc.     

Assessing changes over time in healthcare provider performance: Addressing regression to the mean over multiple time points

In recent years, the evaluation of healthcare provider performance has become standard for governments, insurance companies, and other stakeholders. Often, performance is compared across providers using indicators in one time period, for example a year. However it is often important to assess changes in the performance of individual providers over time. Such analyses can be used to determine if any providers have significant improvements, deteriorations, unusual patterns or systematic changes in performance. Studies which monitor healthcare provider performance in this way have to date typically been limited to comparing performance in the most recent period with performance in a previous period. It is also important to consider a longer‐term view of performance and assess changes over more than two periods. In this paper, we develop test statistics that account for variable numbers of prior performance indicators, and show that these are particularly useful for assessing consecutive improvements or deteriorations in performance. We apply the tests to coronary artery bypass graft mortality rates in New York State hospitals, and mortality data from Australian and New Zealand intensive care units. Although our applications are to medical data, the new tests have broad application in other areas.     

Reproductive Dynamics and Potential Annual Fecundity of South Pacific Albacore Tuna (Thunnus alalunga)

The reproductive biology of albacore tuna, Thunnus alalunga, in the South Pacific Ocean was investigated with samples collected during broad-scale sampling between 2006 and 2011. Histology was done in a single laboratory according to standard protocols and the data analysed using generalized linear mixed-effects models. The sex ratio of albacore was female biased for fish smaller than approximately 60 cm FL and between 85 and 95 cm, and progressively more male biased above 95 cm FL. Spawning activity was synchronised across the region between 10°S and 25°S during the austral spring and summer where sea surface temperatures were ≥24 °C. The average gonad index varied among regions, with fish in easterly longitudes having heavier gonads for their size than fish in westerly longitudes. Albacore, while capable of spawning daily, on average spawn every 1.3 days during the peak spawning months of October to December. Spawning occurs around midnight and the early hours of the morning. Regional variation in spawning frequency and batch fecundity were not significant. The proportion of active females and the spawning fraction increased with length and age, and mature small and young fish were less active at either end of the spawning season than larger, older fish. Batch fecundity estimates ranged from 0.26 to 2.83 million oocytes with a mean relative batch fecundity of 64.4 oocytes per gram of body weight. Predicted batch fecundity and potential annual fecundity increased with both length and age. This extensive set of reproductive parameter estimates provides many of the first quantitative estimates for this population and will substantially improve the quality of biological inputs to the stock assessment for South Pacific albacore.