A Unified Framework for the Infection Dynamics of Zoonotic Spillover and Spread.

A considerable amount of disease is transmitted from animals to humans and many of these zoonoses are neglected tropical diseases. As outbreaks of SARS, avian influenza and Ebola have demonstrated, however, zoonotic diseases are serious threats to global public health and are not just problems confined to remote regions. There are two fundamental, and poorly studied, stages of zoonotic disease emergence: 'spillover', i.e. transmission of pathogens from animals to humans, and 'stuttering transmission', i.e. when limited human-to-human infections occur, leading to self-limiting chains of transmission. We developed a transparent, theoretical framework, based on a generalization of Poisson processes with memory of past human infections, that unifies these stages. Once we have quantified pathogen dynamics in the reservoir, with some knowledge of the mechanism of contact, the approach provides a tool to estimate the likelihood of spillover events. Comparisons with independent agent-based models demonstrates the ability of the framework to correctly estimate the relative contributions of human-to-human vs animal transmission. As an illustrative example, we applied our model to Lassa fever, a rodent-borne, viral haemorrhagic disease common in West Africa, for which data on human outbreaks were available. The approach developed here is general and applicable to a range of zoonoses. This kind of methodology is of crucial importance for the scientific, medical and public health communities working at the interface between animal and human diseases to assess the risk associated with the disease and to plan intervention and appropriate control measures. The Lassa case study revealed important knowledge gaps, and opportunities, arising from limited knowledge of the temporal patterns in reporting, abundance of and infection prevalence in, the host reservoir.Natural Environment Research Council (project no.: NEJ001570-1), Department for International Development, Economic and Social Research Council, National Institute for Health Research, Science and Technology Directorate, Department of Homeland Security, Fogarty International Center USA, European Union FP7 (project ANTIGONE (contract number 278976)), Royal Society (Wolfson Research Merit Award), Alborada Trust, US National Institute of Health (P20GM103501, BAANIAID-DAIT-NIHQI2008031, HHSN272201000022C, HHSN272200900049C, 1U19AI109762, 1R01AI104621, 2R44AI088843), USAID/NIH PEER Health grant.This is the final version of the article. It first appeared from the Public Library of Science via http://dx.doi.org/10.1371/journal.pntd.000495

Using modelling to disentangle the relative contributions of zoonotic and anthroponotic transmission: the case of lassa fever.

BACKGROUND: Zoonotic infections, which transmit from animals to humans, form the majority of new human pathogens. Following zoonotic transmission, the pathogen may already have, or may acquire, the ability to transmit from human to human. With infections such as Lassa fever (LF), an often fatal, rodent-borne, hemorrhagic fever common in areas of West Africa, rodent-to-rodent, rodent-to-human, human-to-human and even human-to-rodent transmission patterns are possible. Indeed, large hospital-related outbreaks have been reported. Estimating the proportion of transmission due to human-to-human routes and related patterns (e.g. existence of super-spreaders), in these scenarios is challenging, but essential for planned interventions. METHODOLOGY/PRINCIPAL FINDINGS: Here, we make use of an innovative modeling approach to analyze data from published outbreaks and the number of LF hospitalized patients to Kenema Government Hospital in Sierra Leone to estimate the likely contribution of human-to-human transmission. The analyses show that almost [Formula: see text] of the cases at KGH are secondary cases arising from human-to-human transmission. However, we found much of this transmission is associated with a disproportionally large impact of a few individuals ('super-spreaders'), as we found only [Formula: see text] of human cases result in an effective reproduction number (i.e. the average number of secondary cases per infectious case) [Formula: see text], with a maximum value up to [Formula: see text]. CONCLUSIONS/SIGNIFICANCE: This work explains the discrepancy between the sizes of reported LF outbreaks and a clinical perception that human-to-human transmission is low. Future assessment of risks of LF and infection control guidelines should take into account the potentially large impact of super-spreaders in human-to-human transmission. Our work highlights several neglected topics in LF research, the occurrence and nature of super-spreading events and aspects of social behavior in transmission and detection.This work for the Dynamic Drivers of Disease in Africa Consortium, NERC project no. NE-J001570-1, was funded with support from the Ecosystem Services for Poverty Alleviation (ESPA) programme. The ESPA programme is funded by the Department for International Development (DFID), the Economic and Social Research Council (ESRC) and the Natural Environment Research Council (NERC). See more at: http://www.espa.ac.uk/about/identity/acknowledging-espafunding# sthash.UivKPObf.dpuf. GL, JLNW, AAC, CTW and EFC also benefit from the support of the small mammal disease working group, funded by the Research and Policy for Infectious Disease Dynamics (RAPIDD) programme of the Science and Technology Directorate, Department of Homeland Security, and Fogarty International Center, USA. JLNW and AC were also supported by the European Union FP7 project ANTIGONE (contract number 278976). AAC is supported by a Royal Society Wolfson Reearch Merit Award. JLNW is also supported by the Alborada Trust. JSS, LM, RG, and JGS were supported by the US National Institute of Health (JSS: NIH grant P20GM103501; LM, RG, JGS: NIH grant BAA-NIAID-DAIT-NIHQI2008031).This is the final published version. It first appeared at http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0003398

Author Correction: Impacts of environmental and socio-economic factors on emergence and epidemic potential of Ebola in Africa.

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Determining solar effects in Neptune’s atmosphere

Long-duration observations of Neptune’s brightness in two visible wavelengths provide a disk-averaged estimate of its atmospheric aerosol. Brightness variations were previously associated with the 11-year solar cycle, through solar-modulated mechanisms linked with either ultra-violet (UV) or galactic cosmic ray (GCR) effects on atmospheric particles. Here we use a recently extended brightness dataset (1972-2014), with physically realistic modelling to show that rather than alternatives, UV and GCR are likely to be modulating Neptune’s atmosphere in combination. The importance of GCR is further supported by the response of Neptune's atmosphere to an intermittent 1.5 to 1.9 year periodicity, which occurred preferentially in GCR (not UV) during the mid-1980s. This periodicity was detected both at Earth, and in GCR measured by Voyager 2, then near Neptune. A similar coincident variability in Neptune’s brightness suggests nucleation onto GCR ions. Both GCR and UV mechanisms may occur more rapidly than the subsequent atmospheric particle transport

Upper atmospheres and ionospheres of planets and satellites

The upper atmospheres of the planets and their satellites are more directly exposed to sunlight and solar wind particles than the surface or the deeper atmospheric layers. At the altitudes where the associated energy is deposited, the atmospheres may become ionized and are referred to as ionospheres. The details of the photon and particle interactions with the upper atmosphere depend strongly on whether the object has anintrinsic magnetic field that may channel the precipitating particles into the atmosphere or drive the atmospheric gas out to space. Important implications of these interactions include atmospheric loss over diverse timescales, photochemistry and the formation of aerosols, which affect the evolution, composition and remote sensing of the planets (satellites). The upper atmosphere connects the planet (satellite) bulk composition to the near-planet (-satellite) environment. Understanding the relevant physics and chemistry provides insight to the past and future conditions of these objects, which is critical for understanding their evolution. This chapter introduces the basic concepts of upper atmospheres and ionospheres in our solar system, and discusses aspects of their neutral and ion composition, wind dynamics and energy budget. This knowledge is key to putting in context the observations of upper atmospheres and haze on exoplanets, and to devise a theory that explains exoplanet demographics.Comment: Invited Revie

Saturn’s atmospheric response to the large influx of ring material inferred from Cassini INMS measurements

During the Grand Finale stage of the Cassini mission, organic-rich ring material was discovered to be flowing into Saturn’s equatorial upper atmosphere at a surprisingly large rate. Through a series of photochemical models, we have examined the consequences of this ring material on the chemistry of Saturn’s neutral and ionized atmosphere. We find that if a substantial fraction of this material enters the atmosphere as vapor or becomes vaporized as the solid ring particles ablate upon atmospheric entry, then the ring-derived vapor would strongly affect the composition of Saturn’s ionosphere and neutral stratosphere. Our surveys of Cassini infrared and ultraviolet remote-sensing data from the final few years of the mission, however, reveal none of these predicted chemical consequences. We therefore conclude that either (1) the inferred ring influx represents an anomalous, transient situation that was triggered by some recent dynamical event in the ring system that occurred a few months to a few tens of years before the 2017 end of the Cassini mission, or (2) a large fraction of the incoming material must have been entering the atmosphere as small dust particles less than 100 nm in radius, rather than as vapor or as large particles that are likely to ablate. Future observations or upper limits for stratospheric neutral species such as HCN, HCN, and CO at infrared wavelengths could shed light on the origin, timing, magnitude, and nature of a possible vapor-rich ring-inflow event

Atmospheric retrieval of exoplanets

Exoplanetary atmospheric retrieval refers to the inference of atmospheric properties of an exoplanet given an observed spectrum. The atmospheric properties include the chemical compositions, temperature profiles, clouds/hazes, and energy circulation. These properties, in turn, can provide key insights into the atmospheric physicochemical processes of exoplanets as well as their formation mechanisms. Major advancements in atmospheric retrieval have been made in the last decade, thanks to a combination of state-of-the-art spectroscopic observations and advanced atmospheric modeling and statistical inference methods. These developments have already resulted in key constraints on the atmospheric H2O abundances, temperature profiles, and other properties for several exoplanets. Upcoming facilities such as the JWST will further advance this area. The present chapter is a pedagogical review of this exciting frontier of exoplanetary science. The principles of atmospheric retrievals of exoplanets are discussed in detail, including parametric models and statistical inference methods, along with a review of key results in the field. Some of the main challenges in retrievals with current observations are discussed along with new directions and the future landscape

Atmospheric electrification in dusty, reactive gases in the solar system and beyond

Detailed observations of the solar system planets reveal a wide variety of local atmospheric conditions. Astronomical observations have revealed a variety of extrasolar planets none of which resembles any of the solar system planets in full. Instead, the most massive amongst the extrasolar planets, the gas giants, appear very similar to the class of (young) Brown Dwarfs which are amongst the oldest objects in the universe. Despite of this diversity, solar system planets, extrasolar planets and Brown Dwarfs have broadly similar global temperatures between 300K and 2500K. In consequence, clouds of different chemical species form in their atmospheres. While the details of these clouds differ, the fundamental physical processes are the same. Further to this, all these objects were observed to produce radio and X-ray emission. While both kinds of radiation are well studied on Earth and to a lesser extent on the solar system planets, the occurrence of emission that potentially originate from accelerated electrons on Brown Dwarfs, extrasolar planets and protoplanetary disks is not well understood yet. This paper offers an interdisciplinary view on electrification processes and their feedback on their hosting environment in meteorology, volcanology, planetology and research on extrasolar planets and planet formation

The Human Phenotype Ontology in 2024: phenotypes around the world

\ua9 The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs