Ecological Origins of Novel Human Pathogen

Centre for Infectious Diseases, University of Edinburgh, Edinburgh, United Kingdom.
Critical Reviews in Microbiology (Impact Factor: 6.02). 02/2007; 33(4):231-42. DOI: 10.1080/10408410701647560
Source: PubMed


A systematic literature survey suggests that there are 1399 species of human pathogen. Of these, 87 were first reported in humans in the years since 1980. The new species are disproportionately viruses, have a global distribution, and are mostly associated with animal reservoirs. Their emergence is often driven by ecological changes, especially with how human populations interact with animal reservoirs. Here, we review the process of pathogen emergence over both ecological and evolutionary time scales by reference to the "pathogen pyramid." We also consider the public health implications of the continuing emergence of new pathogens, focusing on the importance of international surveillance.

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    • "As a result of these discoveries, bats, rodents, and horses are now of significant interest to the hunt for the zoonotic origin of human hepaciviruses and pegiviruses, whereas in the past primates were the primary target of this research (Simmonds 2013). The potential for bat and rodent populations to act as reservoirs of viral infection and sources of cross-species transmission is well known; they have been estimated to be responsible for a quarter of all recently emerged human pathogens (Woolhouse and Gaunt 2007). The recent explosion in the known genetic diversity of the Hepacivirus and Pegivirus genera suggests that there may be many more viral species in novel host species yet to be discovered, hence the picture of hepacivirus and pegivirus evolution may yet change. "
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    ABSTRACT: The known genetic diversity of the hepaciviruses and pegiviruses has increased greatly in recent years through the discovery of viruses related to hepatitis C virus and human pegivirus in bats, bovines, equines, primates and rodents. Analysis of these new species is important for research into animal models of hepatitis C virus infection and into the zoonotic origins of human viruses. Here we provide the first systematic phylogenetic and evolutionary analysis of these two genera at the whole genome level. Phylogenies confirmed that hepatitis C virus is most closely related to viruses from horses while human pegiviruses clustered with viruses from African primates. Within each genus, several well-supported lineages were identified and viral diversity was structured by both host species and location of sampling. Recombination analyses provided evidence of inter-specific recombination in hepaciviruses, but none in the pegiviruses. Putative mosaic genome structures were identified in NS5B gene region and were supported by multiple tests. The identification of inter-specific recombination in the hepaciviruses represents an important evolutionary event that could be clarified by future sampling of novel viruses. We also identified parallel amino acid changes shared by distantly related lineages that infect similar types of host. Notable parallel changes were clustered in the NS3 and NS4B genes and provide a useful starting point for experimental studies of the evolution of Hepacivirus host-virus interactions.
    Full-text · Article · Oct 2015 · Genome Biology and Evolution
    • "Of the 1.5–5.1 million fungal species, an estimated 270,000 species are associated with plants, and 325 are known to infect humans (Blackwell 2011 ; Hawksworth and Rossman 1997 ; Robert and Casadevall 2009 ; Woolhouse and Gaunt 2007 ; Gauthier and Keller 2013 ). A small subset of plant pathogens such as E. rostratum can cross kingdoms and infect humans. "
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    ABSTRACT: Fungi have been recognized to be a major cause of disease in immunocompromised hosts: moreover, the loss of food and fodder crops through fungi has been unmatched since the last decade. Fungi colonize the plant cell and organs by modulating the host defense response. A number of different methods have been recently used to understand host–fungus interactions. With the advent of HiSeq approaches, more fungal genomes and transcriptomes are now sequenced, and their bioinformatics analyses have enriched and assisted our knowledge of the interplay between plant and fungi. The present chapter reviews the current biotechnological and bioinformatics approaches for the study of plant–fungus interactions.
    No preview · Article · Jan 2015
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    • "For such prevention to take place, timely and accurate prediction of outbreaks is critical. More than two thirds of emerging infectious diseases in recent decades are zoonotic in origin (crossing from animals to humans) [1, 2]. An example is the recent emergence of highly pathogenic avian influenza. "
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    ABSTRACT: Background Time series models can play an important role in disease prediction. Incidence data can be used to predict the future occurrence of disease events. Developments in modeling approaches provide an opportunity to compare different time series models for predictive power. Results We applied ARIMA and Random Forest time series models to incidence data of outbreaks of highly pathogenic avian influenza (H5N1) in Egypt, available through the online EMPRES-I system. We found that the Random Forest model outperformed the ARIMA model in predictive ability. Furthermore, we found that the Random Forest model is effective for predicting outbreaks of H5N1 in Egypt. Conclusions Random Forest time series modeling provides enhanced predictive ability over existing time series models for the prediction of infectious disease outbreaks. This result, along with those showing the concordance between bird and human outbreaks (Rabinowitz et al. 2012), provides a new approach to predicting these dangerous outbreaks in bird populations based on existing, freely available data. Our analysis uncovers the time-series structure of outbreak severity for highly pathogenic avain influenza (H5N1) in Egypt.
    Full-text · Article · Aug 2014 · BMC Bioinformatics
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