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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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González-Plaza JJ, Furlan C, Rijavec T, Lapanje A, Barros R, Tamayo-Ramos JA, Suarez-Diez M. Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels. Front Microbiol 2022; 13:1006946. [PMID: 36519168 PMCID: PMC9744117 DOI: 10.3389/fmicb.2022.1006946] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/02/2022] [Indexed: 08/31/2023] Open
Abstract
The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.
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Affiliation(s)
- Juan José González-Plaza
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | - Cristina Furlan
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Tomaž Rijavec
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Aleš Lapanje
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Rocío Barros
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | | | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
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van der Kuyl AC. Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens. EPIDEMIOLOGIA (BASEL, SWITZERLAND) 2022; 3:443-464. [PMID: 36547255 PMCID: PMC9778136 DOI: 10.3390/epidemiologia3040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
Abstract
Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.
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Affiliation(s)
- Antoinette C. van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; ; Tel.: +31-205-666-778
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
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de Miranda JR, Brettell LE, Chejanovsky N, Childers AK, Dalmon A, Deboutte W, de Graaf DC, Doublet V, Gebremedhn H, Genersch E, Gisder S, Granberg F, Haddad NJ, Kaden R, Manley R, Matthijnssens J, Meeus I, Migdadi H, Milbrath MO, Mondet F, Remnant EJ, Roberts JMK, Ryabov EV, Sela N, Smagghe G, Somanathan H, Wilfert L, Wright ON, Martin SJ, Ball BV. Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970's Egypt. Virol J 2022; 19:12. [PMID: 35033134 PMCID: PMC8760790 DOI: 10.1186/s12985-022-01740-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/31/2021] [Indexed: 01/11/2023] Open
Abstract
In 1977, a sample of diseased adult honeybees (Apis mellifera) from Egypt was found to contain large amounts of a previously unknown virus, Egypt bee virus, which was subsequently shown to be serologically related to deformed wing virus (DWV). By sequencing the original isolate, we demonstrate that Egypt bee virus is in fact a fourth unique, major variant of DWV (DWV-D): more closely related to DWV-C than to either DWV-A or DWV-B. DWV-A and DWV-B are the most common DWV variants worldwide due to their close relationship and transmission by Varroa destructor. However, we could not find any trace of DWV-D in several hundred RNA sequencing libraries from a worldwide selection of honeybee, varroa and bumblebee samples. This means that DWV-D has either become extinct, been replaced by other DWV variants better adapted to varroa-mediated transmission, or persists only in a narrow geographic or host range, isolated from common bee and beekeeping trade routes.
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Affiliation(s)
- Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden.
| | - Laura E Brettell
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Renrith, NSW, 2751, Australia.,School of Environment and Life Sciences, University of Salford, Manchester, M5 4WT, UK.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Nor Chejanovsky
- Institute of Plant Protection, The Volcani Center, PO Box 15159, 7528809, Rishon Lezion, Israel
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Anne Dalmon
- Abeilles et Environnement, INRAE, 84914, Avignon, France
| | - Ward Deboutte
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, University of Leuven, 3000, Leuven, Belgium.,Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Dirk C de Graaf
- Laboratory of Molecular Entomology and Bee Pathology, Ghent University, 9000, Ghent, Belgium
| | - Vincent Doublet
- College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK.,Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Haftom Gebremedhn
- Laboratory of Molecular Entomology and Bee Pathology, Ghent University, 9000, Ghent, Belgium.,Tigray Agricultural Research Institute, P.O. Box 492, Mekelle, Ethiopia
| | - Elke Genersch
- Institut Für Mikrobiologie Und Tierseuchen, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany.,Department of Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Sebastian Gisder
- Department of Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Fredrik Granberg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden
| | - Nizar J Haddad
- Bee Research Department, National Agricultural Research Center, Baq'a, Jordan
| | - Rene Kaden
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden.,Clinical Microbiology, Department of Medical Sciences, Uppsala University, 753 09, Uppsala, Sweden
| | - Robyn Manley
- College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK
| | - Jelle Matthijnssens
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, University of Leuven, 3000, Leuven, Belgium
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Hussein Migdadi
- Bee Research Department, National Agricultural Research Center, Baq'a, Jordan
| | - Meghan O Milbrath
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden
| | - Fanny Mondet
- Abeilles et Environnement, INRAE, 84914, Avignon, France
| | - Emily J Remnant
- Behaviour, Ecology and Evolution (BEE) Lab, School of Life and Environmental Sciences, The University of Sydney, Camperdown, 2006, Australia
| | - John M K Roberts
- Commonwealth Scientific and Industrial Research Organisation, Canberra, 2601, Australia
| | - Eugene V Ryabov
- Bee Research Laboratory, Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Noa Sela
- Institute of Plant Protection, The Volcani Center, PO Box 15159, 7528809, Rishon Lezion, Israel
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Hema Somanathan
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, 695551, India
| | - Lena Wilfert
- College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK.,Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Owen N Wright
- Centre for Research in Animal Behaviour, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QG, UK
| | - Stephen J Martin
- School of Environment and Life Sciences, University of Salford, Manchester, M5 4WT, UK.,Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Brenda V Ball
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
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Houldcroft CJ, Ramond JB, Rifkin RF, Underdown SJ. Migrating microbes: what pathogens can tell us about population movements and human evolution. Ann Hum Biol 2017; 44:397-407. [PMID: 28511559 DOI: 10.1080/03014460.2017.1325515] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. The story of a pathogen's genetic code may, therefore, provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases. METHODS This study explores which pathogens leave traces in the archaeological record, and whether there are realistic prospects that these pathogens can be recovered from sub-Saharan African archaeological contexts. RESULTS Three stories are then presented of germs on a journey. The first is the story of HIV's spread on the back of colonialism and the railway networks over the last 150 years. The second involves the spread of Schistosoma mansoni, a parasite which shares its history with the trans-Atlantic slave trade and the origins of fresh-water fishing. Finally, we discuss the tantalising hints of hominin migration and interaction found in the genome of human herpes simplex virus 2. CONCLUSIONS Evidence from modern African pathogen genomes can provide data on human behaviour and migration in deep time and contribute to the improvement of human quality-of-life and longevity.
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Affiliation(s)
- Charlotte J Houldcroft
- a Department of Archaeology and Anthropology, Division of Biological Anthropology , University of Cambridge , Cambridge , UK.,b McDonald Institute of Archaeological Research, University of Cambridge , Cambridge , UK
| | - Jean-Baptiste Ramond
- c Department of Genetics , Centre for Microbial Ecology and Genomics, Genomic Research Institute, University of Pretoria , Hatfield , South Africa
| | - Riaan F Rifkin
- c Department of Genetics , Centre for Microbial Ecology and Genomics, Genomic Research Institute, University of Pretoria , Hatfield , South Africa
| | - Simon J Underdown
- d Department of Anthropology & Geography, Human Origins and Palaeoenvironmental Research Group (HOPE) , Oxford Brookes University , Oxford , UK.,e Leverhulme Centre for Human Evolutionary Studies , Henry Wellcome Building , Cambridge , UK
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