Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

As SARS-CoV-2 becomes an endemic pathogen, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Aleutian Tern Onychoprion aleuticus abundance estimates at four globally significant colonies

Summary Aleutian Tern Onychoprion aleuticus numbers have been in steep decline at known Alaskan breeding colonies in recent decades (IUCN recently uplisted to ‘Vulnerable’). Available data suggest that most of the species may currently breed in Russia. Efforts to document global abundance and trends have been hampered by remoteness of colonies, lack of a formal monitoring programme, and the absence of reproducible population estimates with quantifiable errors, especially for large colonies. We surveyed four historically large colonies in Russia (2018) and Alaska (2019), which together may comprise 30–50% of the global breeding population. At each colony we obtained high resolution aerial photographs using a small Unmanned Aircraft System (sUAS). The large size of the colonies and the minimum altitude required to identify terns made it impractical to collect imagery of the entire colony. Instead, we employed a sampling approach, with sample locations selected based on spatially balanced acceptance sampling. Statistically sampled, low altitude sUAS images provided a fast, reproducible, and rigorous count of abundance for geographically large colonies, with low disturbance, and were generally consistent with concurrent ground-based observations. Concurrence among observers in photo counts indicated high precision in counts of attending birds and unattended nests, although species attribution in mixed tern colonies remains a source of significant uncertainty. Our results indicate that the four colonies surveyed here together supported <2,500 pairs of Aleutian Terns in the survey years. None of the colonies approached their peak size reported previously, likely due to recent predation, long-term decline, cold early season weather, or other factors. If these reduced colony sizes are representative of the current conditions, the implications for the global population would be dire.

Combining Fixed-Location Count Data and Movement Data to Estimate Abundance of a Lake Sturgeon Spawning Run: A Framework for Riverine Migratory Species

Estimating abundance of migrating fishes is challenging. While sonars can be deployed continuously, improper assumptions about unidirectional migration and complete spatial coverage can lead to inaccurate estimates. To address these challenges, we present a framework for combining fixed-location count data from a dual-frequency identification sonar (DIDSON) with movement data from acoustic telemetry to estimate spawning run abundance of lake sturgeon (Acipenser fulvescens). Acoustic telemetry data were used to estimate the probability of observing a lake sturgeon on the DIDSON and to determine the probability that a lake sturgeon passing the DIDSON site had passed the site previously during the season. Combining probabilities with DIDSON counts, using a Bayesian integrated model, we estimated the following abundances: 99 (42–215 CI) in 2017, 131 (82–248 CI) in 2018, and 92 (47–184 CI) in 2019. Adding movement data generated better inferences on count data by incorporating fish behavior (e.g., multiple migrations in a single season) and its uncertainty into abundance estimates. This framework can be applied to count and movement data to estimate abundance of spawning runs of other migratory fishes in riverine systems.

A Preliminary Abundance Estimate of an Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus) Contingent Within an Open Riverine System

Abundance estimates are essential for fisheries management, but estimating the abundance of open populations with low recapture rates has historically been unreliable. However, by using mark-recapture data modulated with survivability parameters obtained from analysis of acoustic telemetry data, more accurate abundance estimates can be made for species that exhibit these characteristics. One such species is the Atlantic sturgeon, for which abundance estimates were designated a research priority following precipitous population declines throughout the 20th century. We addressed this research need in the Saco River Estuary (SRE), a system where the Atlantic sturgeon has been extensively studied using mark-recapture and acoustic telemetry methods since 2009. These data were analyzed using Bayesian analysis of a Lincoln-Peterson estimator, constrained with parameters from a Cormack-Jolly-Seber model, to provide an initial abundance estimate for the system. The resulting estimate indicated that approximately 3 299 (95% Credible Interval: 1 462–6 828) Atlantic sturgeon utilize the SRE yearly, suggesting that the SRE provides critical foraging habitat to a large contingent of the species within the Gulf of Maine. The present study demonstrated the method utilized herein was effective in generating a reasonable estimate of abundance in an open system where recapture events are rare, and therefore may provide a valuable technique for supplying initial estimates of fish abundance in additional systems that display similar characteristics.

Quantitative insights into effects of intrapartum antibiotics and birth mode on infant gut microbiota in relation to well-being during the first year of life

Background and aims Caesarean section (CS)-birth and maternally administered intrapartum antibiotics (IP) affect colonization of the neonate. We compared the effects of CS delivery and IP antibiotics on infant gut microbiota development and wellbeing over the first year. To understand the developing community dynamics, we focused on absolute bacterial abundance estimates over relative abundances. Methods We studied 144 healthy infants born between gestational weeks 37-42 vaginally without antibiotics (N=58), with IP penicillin (N=25) or cephalosporin (N=13), or by CS with IP cephalosporin (N=34) or other antibiotics (N=14). Gut microbiota composition and temporal development was analysed at 5-7 time points during the first year of life using 16S rRNA gene amplicon sequencing, complemented with qPCR to obtain absolute abundance estimates in 92 infants. A mediation analysis was carried out to identify taxa linked to gastrointestinal function and discomfort (crying, defecation frequency and signs of gastrointestinal symptoms) and birth interventions. Results Based on absolute abundance estimates, depletion of Bacteroides spp. was specific to CS birth while decreased bifidobacteria and increased Bacilli were common to CS birth and exposure to IP antibiotics in vaginal delivery. Abundance of numerous taxa differed between the birth modes among cephalosporin-exposed infants. Penicillin had a milder impact on the infant gut microbiota than cephalosporin. The effects of both CS birth and IP antibiotics on infant gut microbiota associated with increased gastrointestinal symptoms during the first months. Conclusion CS birth and maternal IP antibiotics have both specific and overlapping effects on infant gut microbiota development. The resulting microbiota deviations were found to associate with gastrointestinal symptoms in infancy.

Chemical abundances in Seyfert galaxies– VIII. Argon abundance estimates

For the first time, the argon abundance relative to hydrogen abundance (Ar/H) in the narrow line region of a sample of Seyfert 2 nuclei has been derived. In view of this, optical narrow emission line intensities of a sample of 64 local Seyfert 2 nuclei (z &lt; 0.25) taken from Sloan Digital Sky Survey DR7 and measured by the MPA/JHU group were considered. We adopted the Te-method for AGNs, which is based on direct determination of the electron temperature, together with a grid of photoionization model results, built with the Cloudy code, to obtain a method for the derivation of the Ar/H abundance. We find that for a metallicity range of $\rm 0.2 \: \lesssim \: (Z/{\rm Z_{\odot }}) \: \lesssim \: 2.0$, Seyfert 2 nuclei present Ar/H abundance ranging from ∼0.1 to ∼3 times the argon solar value, adopting $\rm log(O/H)_{\odot }=-3.31$ and $\rm log(Ar/H)_{\odot }=-5.60$. These range of values correspond to $\rm 8.0 \: \lesssim \: (12+log(O/H) \: \lesssim \: 9.0$ and $\rm 5.4 \: \lesssim \: (12+log(Ar/H) \: \lesssim \: 6.9$, respectively. The range of Ar/H and Ar/O abundance values obtained from our sample are in consonance with estimations from extrapolations of the radial abundance gradients to the central parts of the disk for four spiral galaxies. We combined our abundance results with estimates obtained from a sample of H ii galaxies, which were taken from the literature, and found that the Ar/O abundance ratio decreases slightly as the O/H abundance increases.

Chemical abundances in Seyfert galaxies – VII. Direct abundance determination of neon based on optical and infrared emission lines

ABSTRACT For the first time, neon abundance has been derived in the narrow line region from a sample of Seyfert 2 nuclei. In view of this, we compiled from the literature fluxes of optical and infrared (IR) narrow emission lines for 35 Seyfert 2 nuclei in the local universe ($z \:\lesssim \:0.06$). The relative intensities of emission lines were used to derive the ionic and total neon and oxygen abundances through electron temperature estimations (Te-method). For the neon, abundance estimates were obtained by using both Te-method and IR-method. Based on photoionization model results, we found a lower electron temperature [$t_{\rm e}({\rm Ne\, \small {III}})$] for the gas phase where the Ne2 + is located in comparison with t3 for the O2 + ion. We find that the differences (D) between Ne2 +/H+ ionic abundances calculated from IR-method and Te-method (assuming t3 in the Ne2 +/H+ derivation) are similar to the derivations in star-forming regions (SFs) and they are reduced by a mean factor of ∼3 when $t_{\rm e}({\rm Ne\, \small {III}})$ is considered. We propose a semi-empirical Ionization Correction Factor (ICF) for the neon, based on [Ne ii]12.81$\rm{\mu m}$, [Ne iii]15.56$\rm{\mu m}$, and oxygen ionic abundance ratios. We find that the average Ne/H abundance for the Seyfert 2s sample is nearly 2 times higher than similar estimate for SFs. Finally, for the very high metallicity regime (i.e. [$\rm 12+log(O/H)\: \gtrsim \: 8.80$]) an increase in Ne/O with O/H is found, which likely indicates secondary stellar production for the neon.

Abundance and Potential Biological Removal of Common Dolphins Subject to Fishery Impacts in South Australian Waters

Conservation management of wildlife species should be underpinned by knowledge of their distribution and abundance, as well as impacts of human activities on their populations and habitats. Common dolphins (Delphinus delphis) are subject to incidental capture in a range of Australia’s commercial fisheries including gill netting, purse seining and mid-water trawling. The impact these fishery interactions have on common dolphin populations is uncertain, as estimates of abundance are lacking, particularly for the segments of the populations at risk of bycatch and in greater need of protection. Here we used double-observer platform aerial surveys and mark-recapture distance sampling methods to estimate the abundance of common dolphins in 2011 over an area of 42,438 km2 in central South Australia, where incidental mortality of common dolphins due to fisheries bycatch is the highest. We also used the potential biological removal (PBR) method to estimate sustainable levels of human-caused mortality for this segment of the population. The estimated abundance of common dolphins was 21,733 (CV = 0.25; 95% CI = 13,809–34,203) in austral summer/autumn and 26,504 in winter/spring (CV = 0.19; 95% CI = 19,488–36,046). Annual PBR estimates, assuming a conservative maximum population growth rate of Rmax = 0.02 and a recovery factor of Fr = 0.5 for species of unknown conservation status, ranged from 189 (summer/autumn) to 239 dolphins (winter/spring), and from 378 (summer/autumn) to 478 dolphins (winter/spring) with an Rmax = 0.04. Our results indicate that common dolphins are an abundant dolphin species in waters over the central South Australian continental shelf (up to 100 m deep). Based on the 2011 abundance estimates of this species, the highest estimated bycatch of common dolphins (423 mortalities in 2004/05) in the southern Australian region exceeded the precautionary PBR estimates for this population segment. Recent bycatch levels appear to be below PBR estimates, but low observer coverage and underreporting of dolphin mortalities by fishers means that estimates of dolphin bycatch rates are not robust. The effects of cumulative human impacts on common dolphins are not well understood, and thus we recommend a precautionary management approach to manage common dolphin bycatch based on local abundance estimates.

Closer to Carrying Capacity: Analysis of the Internal Demographic Structure Associated with the Management and Density Dependence of a Controlled Wolf Population in Latvia

Large carnivores are essential components of natural ecosystems. In populated areas, their conservation depends on preserving a favorable status in coexistence with humans, which may require the elimination of excess carnivores to minimize public concerns. As the Baltic region currently hosts a thriving wolf population, locally sustainable management of wolves is important for preserving biodiversity at a European scale. In this paper, we provide a dynamic assessment of the Latvian wolf subpopulation from 1998 until 2020. This study is based on age composition and fecundity data from teeth, uteri, and ovaria inspections obtained from samples of legally culled or accidentally killed individuals. The abundance estimates indicated population growth that exceeded the previously predicted carrying capacity. The proportion of juveniles among the culled individuals increased in recent years, but the mean age of culled adults exhibited a stable trend. In presumably nonselective hunting, the juveniles and individuals older than 3 years had greater culling mortality estimates in comparison with other age classes, and the culling rates for adult females of particular age classes were higher than for males of the same age. While creating significant hunting pressure, wolf management in Latvia may have contributed to the population growth by affecting its demographic processes.