Seroprevalence of herpes simplex virus types 1 and 2 and correlates of infection in Jordan

Background Herpes infections are common infections among populations. Herein, a cross-sectional study was used to determine the seroprevalence of herpes simplex virus type 1 (HSV-1) and herpes simplex virus type 2 (HSV-2) IgG antibodies and their association with potential infection risk factors among Jordanians. Methods A total of 759 serum samples were collected (January to February 2020) and analyzed for HSV-1 and HSV-2 IgG antibodies by enzyme-linked immunosorbent assay. Estimates for population seropositivity were determined by weighting the age-specific seroprevalence by the size of the population in each age stratum. Results The population estimate for HSV-1 seroprevalence was 75.3%. After adjustment for possible confounders, regression analysis revealed higher seroprevalence with increase in age ( p < 0.005) and low household income ( p = 0.002). The population estimate for HSV-2 seroprevalence was 2.9%. No significant differences in HSV-2 seroprevalence were observed in association with age, gender, family size, educational level, and socioeconomic status, likely due to low seropositivity. Conclusions Jordanians have high HSV-1 and low HSV-2 seroprevalence. Periodical studies might be needed to evaluate changes in HSV-1 and HSV-2 seroprevalence over time. This study provides essential epidemiological data for Jordan and the Middle East and North Africa region.

History of COVID-19 Symptoms and Seroprevalence of SARS-CoV-2 Antibodies in HIV-Infected Patients in Northern France after the First Wave of the Pandemic

To assess the prevalence of COVID-19 in people living with HIV (PLWHIV), we performed an epidemiological survey from 1 April through 1 August 2020 in an HIV reference center in Northern France. PLWHIV completed a questionnaire about risk exposures and symptoms consistent with COVID-19 and performed a SARS-CoV-2 serology. Among the 600 PLWHIV included, 16 have been infected with SARS-CoV-2. Symptoms consistent with COVID-19 were frequent both in SARS-CoV-2 positive and negative patients (67% vs. 32%, p = 0.02). Among SARS-CoV-2 infected patients, one (6%) has been hospitalized and five (31%) have been asymptomatic. Close contact with a confirmed COVID-19 case was the only factor associated with COVID-19 acquisition (40% vs. 13%, p = 0.01). The prevalence of COVID-19 in PLWHIV was 2.5%, half of the overall population estimate after the first wave of the pandemic in France. In conclusion, proportion of asymptomatic COVID-19 was high in PLWHIV. The prevalence of COVID-19 in PLWHIV was two times lower than in the general population.

Updated range metrics and a global population estimate for the Critically Endangered Philippine Eagle using a spatial ensemble habitat model

Many range-restricted taxa are currently experiencing severe population declines yet lack fundamental biological information regarding distribution and population size. Establishing baseline estimates for both these key biological parameters is however critical for directing long-term monitoring and conservation planning for at-risk range-restricted species. The International Union for the Conservation of Nature (IUCN) Red List uses three spatial range metrics that define species distributions and inform extinction risk assessments: extent of occurrence (EOO), area of occupancy (AOO) and area of habitat (AOH). However, calculating all three metrics using standard IUCN approaches relies on a geographically representative sample of locations, which for rare species is often spatially biased. Here, we apply model-based interpolation using an ensemble Species Distribution Model (SDM), correlating occurrences with remote-sensing derived environmental covariates, to calculate IUCN range metrics and a global population estimate for the Critically Endangered Philippine Eagle (Pithecophaga jefferyi). Our ensemble averaged SDM had high predictive accuracy and was able to identify key areas of Philippine Eagle habitat across the species global range. We estimated an AOH = 49,426 km2 and from this metric calculated a maximum EOO = 609,697 km2 and a minimum EOO = 273,794 km2, with an AOO = 54,695 occupied cells. Based on inferred habitat from the AOH metric and territorial habitat area from home range estimates, we provide an updated global population estimate of 677 breeding pairs (range: 549-772 pairs), or 1354 mature individuals, across the entire Philippine Eagle range. We demonstrate that even when occurrence sampling is geographically biased, robust habitat models can be built which enable quantification of IUCN range metrics and a baseline population size estimate. In the absence of adequate location data for many rare and threatened taxa, our method is a promising spatial modelling tool with widespread applications, in particular for island endemics facing high extinction risk.

Population assessment and habitat associations of the Visayan Hornbill (Penelopides panini) in Northwest Panay, Philippines

Background Seven out of ten hornbill species in the Philippines are threatened with extinction. Among these is the endangered Visayan Hornbill (Penelopides panini), found on the islands of Panay and Negros. Threatened by habitat loss and hunting, its population size is thought to have declined from 1800 individuals 20 years ago to less than 1000. However, a recent study on Negros estimated 3564 individuals across three core forest blocks. This study aims to quantify the Visayan Hornbill population size in and around the Northwest Panay Peninsula Natural Park (NWPPNP) on Panay, the largest contiguous low-elevation forest landscape remaining across its range, and its broad habitat associations across a gradient of environmental degradation. Methods Hornbills were surveyed using 10-min distance sampling point counts (n = 367) along transects (average length 1.1 km). Environmental variables were recorded along transects, while habitat was classified into primary forest, secondary forest, plantation, or open habitat. Distance software was used to estimate population densities stratified by habitat, with the overall population estimate taken as a mean of habitat density estimates weighted by habitat area. Using generalized linear mixed models, hornbill occurrence was modelled using combinations of nine environmental variables as main and two-way fixed effects. Results Surveys covered 204.4 km2 of the 374.8 km2 Northwest Panay Peninsula. Hornbills were not recorded in plantations or open habitats. Hornbill density was significantly higher in primary forest (17.8 individuals/km2 ± 26.9% CV) than in secondary forest (3.7 individuals/km2 ± 33.2% CV; z = 15.212, P < 0.001). The overall population estimate for the NWPPNP and environs is 2109 individuals, and 2673 individuals for the entire Northwest Panay Peninsula. Hornbill presence was best explained by a model including distance from the Park boundary alongside five interaction effects and transect as a random effect. Distance, and the interaction between distance and medium-sized trees were significant predictors of hornbill presence. Conclusions Our study evidences the habitat preference of the Visayan Hornbill, highlights the importance of the NWPPNP for the species’ conservation, and provides strong evidence for re-assessing the global population size.

Tapirs in trouble: estimating Baird's tapir densities in the Sierra Madre de Chiapas, Mexico

Spatial capture–recapture models have been widely used to estimate densities of species where individuals can be uniquely identified, but alternatives have been developed for estimation of densities for unmarked populations. In this study we used camera-trap records from 2018 to estimate densities of a species that does not always have individually identifiable marks, Baird's tapir Tapirus bairdii, in the Sierra Madre de Chiapas, southern Mexico. We compared the performance of the spatial capture–recapture model with spatial mark–resight and random encounter models. The density of Baird's tapir did not differ significantly between the three models. The estimate of density was highest using the random encounter model (26/100 km2, 95% CI 12–41) and lowest using the capture–recapture model (8/100 km2, 95% CI 4–16). The estimate from the spatial mark–resight model was 10/100 km2 (95% CI 8–14), which had the lowest coefficient of variation, indicating a higher precision than with the other models. Using a second set of camera-trap data, collected in 2015–2016, we created occupancy models and extrapolated density to areas with potential occupancy of Baird's tapir, to generate a population estimate for the whole Sierra Madre de Chiapas. Our findings indicate the need to strengthen, and possibly expand, the protected areas of southern Mexico and to develop an action plan to ensure the conservation of Baird's tapir.

The fomite contribution to the transmission of COVID-19 in the UK: an evolutionary population estimate

A SEIR model with an added fomite term is used to constrain the contribution of fomites to the spread of COVID-19 under the Spring 2020 lockdown in the UK. Assuming uniform priors on the reproduction number in lockdown and the fomite transmission rate, an upper limit is found on the fomite transmission rate of less than 1 contaminated object in 7 per day per infectious person (95% CL). Basing the prior on the reproduction rate during lockdown instead on the CoMix study results for the reduction in social contacts under lockdown, and assuming the reproduction number scales with the number of social contacts, provides a much more restrictive upper limit on the transmission rate by contaminated objects of fewer than 1 in 30 per day per infectious person (95% CL). Applied to postal deliveries and groceries, the upper limit on the fomite transmission rate corresponds to a probability below 1 in 70 (95% CL) that a contaminated object transmits the infection. Fewer than about half (95% CL) of the total number of deaths during the lockdown are found to arise from fomites, and most likely fewer than a quarter. These findings apply only to fomites with a transmission rate that is unaffected by a lockdown.

Golden Eagle Abundance in Alaska: Migration Counts and Movement Data Generate a Conservative Population Estimate

ABSTRACT Estimating species density and abundance is challenging but important for establishing conservation and management strategies. Significant progress has been made toward estimating Golden Eagle (Aquila chrysaetos) abundance in the conterminous United States of America (USA) but much less is known about eagle abundance in Alaska. Here, we paired migration count and GPS-tracking data collected near Gunsight Mountain, Alaska, in a Bayesian framework to estimate the number of Golden Eagles in south-central Alaska. We estimated 1204 (95% credible interval: 866, 1526) potentially breeding (≥4 yr old) Golden Eagles annually moved through the Gunsight Mountain migration corridor and summered over an area of 150,325 km2 in south-central Alaska, equating to a density of 0.80 potentially breeding eagles/100 km2. By extrapolating across the species' nesting range in Alaska (1,180,489 km2) and incorporating published productivity and age-specific survival rates for eagles &lt;4 yr old into our hierarchical model, we estimated 12,717 (95% credible interval: 9043, 16,349) Golden Eagles of all ages occur in Alaska, annually. We propose this as a conservative statewide population estimate because we used methods that likely underestimated population size. Even so, our estimate is three to five times larger than previous estimates and likely represents about one quarter of the USA's population.