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Park SW, Cobey S, Metcalf CJE, Levine JM, Grenfell BT. Predicting pathogen mutual invasibility and co-circulation. Science 2024; 386:175-179. [PMID: 39388572 DOI: 10.1126/science.adq0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 09/05/2024] [Indexed: 10/12/2024]
Abstract
Observations of pathogen community structure provide evidence for both the coexistence and replacement of related strains. Despite many studies of specific host-pathogen systems, a unifying framework for predicting the outcomes of interactions among pathogens has remained elusive. We address this gap by developing a pathogen invasion theory (PIT) based on modern ecological coexistence theory and testing the resulting framework against empirical systems. Across major human pathogens, PIT predicts near-universal mutual susceptibility of one strain to invasion by another strain. However, predicting co-circulation from mutual invasion also depends on the degree to which susceptible abundance is reduced below the invasion threshold by overcompensatory epidemic dynamics, and the time it takes for susceptibles to replenish. The transmission advantage of an invading strain and the strength and duration of immunity are key determinants of susceptible dynamics. PIT unifies existing ideas about pathogen co-circulation, offering a quantitative framework for predicting the emergence of novel pathogen strains.
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Affiliation(s)
- Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
| | - Jonathan M Levine
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
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2
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Morreale R, Stenhouse S, Carvalho DO, Hahn DA, Bourtzis K, Lloyd A, Gale TW, Hoel DF. Seasonal insights for integrative mosquito management from multi-year baseline entomological data on Aedes aegypti in Lee County, Florida. PLoS One 2024; 19:e0311407. [PMID: 39392849 DOI: 10.1371/journal.pone.0311407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 09/18/2024] [Indexed: 10/13/2024] Open
Abstract
The spread of arboviruses like yellow fever, dengue, chikungunya, and Zika, transmitted by the invasive mosquito Aedes aegypti has led to the development of many strategies to suppress mosquito populations. Given the rapid development of resistance to common chemical larvicides and adulticides in some Ae. aegypti populations, as well as the ever-shrinking chemical options for mosquito control, there is a pressing need for new tools and deployment of those innovative tools as a component of integrative mosquito management programs. Prior to the adoption of any mosquito population intervention, be it conventional or innovative, understanding the baseline population is essential to evaluate the efficacy of the control measure. The Lee County Mosquito Control District in Florida has collected a three-year-long period of baseline entomological surveillance data collection for Ae. aegypti on Captiva and Sanibel Islands as foundational information prior to implementation of a new integrative mosquito management approach. We identified 18 mosquito species and described their population dynamics during the rainy and dry seasons. The two islands had no significant differences in species richness, diversity, dominance, or evenness overall. Yet, there were clear differences between the high rain season and low rain season in the Shannon diversity index, Simpson dominance index, and Pielou species evenness index within each site. Our data suggest that any innovative intervention should begin before mid to late April when the mosquito population is at its lowest and certainly before populations build up to their summer peak between June and September. These data also show the spatial distribution of Ae. aegypti is dynamic in space and time, identifying hotspots of mosquito abundance to focus on for future interventions. Overall, our study emphasizes the importance of entomological data collection to understand the population dynamics of Ae. aegypti mosquitoes, including the impact of environmental factors such as temperature and precipitation.
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Affiliation(s)
- Rachel Morreale
- Lee County Mosquito Control District, Lehigh Acres, FL, United States of America
| | - Steven Stenhouse
- Lee County Mosquito Control District, Lehigh Acres, FL, United States of America
| | - Danilo O Carvalho
- Department of Entomology & Nematology, University of Florida, Gainesville, FL, United States of America
| | - Daniel A Hahn
- Department of Entomology & Nematology, University of Florida, Gainesville, FL, United States of America
| | - Kostas Bourtzis
- Insect Pest Control Subprogramme, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, IAEA, Vienna, Austria
| | - Aaron Lloyd
- Lee County Mosquito Control District, Lehigh Acres, FL, United States of America
| | - Thomas Wayne Gale
- Lee County Mosquito Control District, Lehigh Acres, FL, United States of America
| | - David F Hoel
- Lee County Mosquito Control District, Lehigh Acres, FL, United States of America
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3
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McHugh SW, Donoghue MJ, Landis MJ. A Phylogenetic Model of Established and Enabled Biome Shifts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.30.610561. [PMID: 39282335 PMCID: PMC11398350 DOI: 10.1101/2024.08.30.610561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Where each species actually lives is distinct from where it could potentially survive and persist. This suggests that it may be important to distinguish established from enabled biome affinities when considering how ancestral species moved and evolved among major habitat types. We introduce a new phylogenetic method, called RFBS, to model how anagenetic and cladogenetic events cause established and enabled biome affinities (or, more generally, other discrete realized versus fundamental niche states) to shift over evolutionary timescale. We provide practical guidelines for how to assign established and enabled biome affinity states to extant taxa, using the flowering plant clade Viburnum as a case study. Through a battery of simulation experiments, we show that RFBS performs well, even when we have realistically imperfect knowledge of enabled biome affinities for most analyzed species. We also show that RFBS reliably discerns established from enabled affinities, with similar accuracy to standard competing models that ignore the existence of enabled biome affinities. Lastly, we apply RFBS to Viburnum to infer ancestral biomes throughout the tree and to highlight instances where repeated shifts between established affinities for warm and cold temperate forest biomes were enabled by a stable and slowly-evolving enabled affinity for both temperate biomes.
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4
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Herzog CM, Aklilu F, Sibhatu D, Shegu D, Belaineh R, Mohammed AA, Kidane M, Schulz C, Willett BJ, Cleaveland S, Bailey D, Peters AR, Cattadori IM, Hudson PJ, Asgedom H, Buza J, Forza MS, Chibssa TR, Gebre S, Juleff N, Bjørnstad ON, Baron MD, Kapur V. Empirical and model-based evidence for a negligible role of cattle in peste des petits ruminants virus transmission and eradication. Commun Biol 2024; 7:937. [PMID: 39095591 PMCID: PMC11297268 DOI: 10.1038/s42003-024-06619-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
Peste des petits ruminants virus (PPRV) is a multi-host pathogen with sheep and goats as main hosts. To investigate the role of cattle in the epidemiology of PPR, we simulated conditions similar to East African zero-grazing husbandry practices in a series of trials with local Zebu cattle (Bos taurus indicus) co-housed with goats (Capra aegagrus hircus). Furthermore, we developed a mathematical model to assess the impact of PPRV-transmission from cattle to goats. Of the 32 cattle intranasally infected with the locally endemic lineage IV strain PPRV/Ethiopia/Habru/2014 none transmitted PPRV to 32 co-housed goats. However, these cattle or cattle co-housed with PPRV-infected goats seroconverted. The results confirm previous studies that cattle currently play a negligible role in PPRV-transmission and small ruminant vaccination is sufficient for eradication. However, the possible emergence of PPRV strains more virulent for cattle may impact eradication. Therefore, continued monitoring of PPRV circulation and evolution is recommended.
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Affiliation(s)
- Catherine M Herzog
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA.
| | | | | | | | | | | | | | - Claudia Schulz
- Institute of Virology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sarah Cleaveland
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Andrew R Peters
- Supporting Evidence Based Interventions (SEBI), University of Edinburgh, Edinburgh, UK
| | - Isabella M Cattadori
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Peter J Hudson
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | | | - Joram Buza
- Nelson Mandela African Institute of Science and Technology, Arusha, Tanzania
| | | | | | | | - Nick Juleff
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Ottar N Bjørnstad
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | | | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA.
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5
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Wang F, Liu H, Yao H, Zhang B, Li Y, Jin S, Cao H. Reducing Application of Nitrogen Fertilizer Increases Soil Bacterial Diversity and Drives Co-Occurrence Networks. Microorganisms 2024; 12:1434. [PMID: 39065202 PMCID: PMC11278655 DOI: 10.3390/microorganisms12071434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Reducing nitrogen fertilizer application highlights its role in optimizing soil bacterial communities to achieve sustainable agriculture. However, the specific mechanisms of bacterial community change under these conditions are not yet clear. In this study, we employed long-term field experiments and high-throughput sequencing to analyze how varying levels of nitrogen application influence the soil bacterial community structure and co-occurrence networks. The results show that reducing the nitrogen inputs significantly enhances the diversity and evenness of the soil bacterial communities, possibly due to the diminished dominance of nitrogen-sensitive taxa, which in turn liberates the ecological niches for less competitive species. Furthermore, changes in the complexity and stability of the bacterial co-occurrence networks suggest increased community resilience and a shift toward more mutualistic interactions. These findings underline the potential of reduced nitrogen application to alleviate competitive pressures among bacterial species, thereby promoting a more diverse and stable microbial ecosystem, highlighting the role of competitive release in fostering microbial diversity. This research contributes to our understanding of how nitrogen management can influence soil health and offers insights into sustainable agricultural practices.
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Affiliation(s)
- Feng Wang
- Ningbo Key Laboratory of Testing and Control for Characteristic Agro-Product Quality and Safety, Ningbo Academy of Agricultural Sciences, Ningbo 315040, China; (F.W.); (H.Y.); (S.J.)
- Institute of Farmland Water Conservancy and Soil-Fertilizer, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (H.L.); (B.Z.); (Y.L.)
| | - Hongyan Yao
- Ningbo Key Laboratory of Testing and Control for Characteristic Agro-Product Quality and Safety, Ningbo Academy of Agricultural Sciences, Ningbo 315040, China; (F.W.); (H.Y.); (S.J.)
| | - Bo Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (H.L.); (B.Z.); (Y.L.)
| | - Yue Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (H.L.); (B.Z.); (Y.L.)
| | - Shuquan Jin
- Ningbo Key Laboratory of Testing and Control for Characteristic Agro-Product Quality and Safety, Ningbo Academy of Agricultural Sciences, Ningbo 315040, China; (F.W.); (H.Y.); (S.J.)
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (H.L.); (B.Z.); (Y.L.)
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6
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Bényei ÉB, Nazeer RR, Askenasy I, Mancini L, Ho PM, Sivarajan GAC, Swain JEV, Welch M. The past, present and future of polymicrobial infection research: Modelling, eavesdropping, terraforming and other stories. Adv Microb Physiol 2024; 85:259-323. [PMID: 39059822 DOI: 10.1016/bs.ampbs.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Over the last two centuries, great advances have been made in microbiology as a discipline. Much of this progress has come about as a consequence of studying the growth and physiology of individual microbial species in well-defined laboratory media; so-called "axenic growth". However, in the real world, microbes rarely live in such "splendid isolation" (to paraphrase Foster) and more often-than-not, share the niche with a plethora of co-habitants. The resulting interactions between species (and even between kingdoms) are only very poorly understood, both on a theoretical and experimental level. Nevertheless, the last few years have seen significant progress, and in this review, we assess the importance of polymicrobial infections, and show how improved experimental traction is advancing our understanding of these. A particular focus is on developments that are allowing us to capture the key features of polymicrobial infection scenarios, especially as those associated with the human airways (both healthy and diseased).
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Affiliation(s)
| | | | - Isabel Askenasy
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Leonardo Mancini
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Pok-Man Ho
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | | | - Jemima E V Swain
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom.
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Alseth EO, Custodio R, Sundius SA, Kuske RA, Brown SP, Westra ER. The impact of phage and phage resistance on microbial community dynamics. PLoS Biol 2024; 22:e3002346. [PMID: 38648198 PMCID: PMC11034675 DOI: 10.1371/journal.pbio.3002346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/19/2024] [Indexed: 04/25/2024] Open
Abstract
Where there are bacteria, there will be bacteriophages. These viruses are known to be important players in shaping the wider microbial community in which they are embedded, with potential implications for human health. On the other hand, bacteria possess a range of distinct immune mechanisms that provide protection against bacteriophages, including the mutation or complete loss of the phage receptor, and CRISPR-Cas adaptive immunity. While our previous work showed how a microbial community may impact phage resistance evolution, little is known about the inverse, namely how interactions between phages and these different phage resistance mechanisms affect the wider microbial community in which they are embedded. Here, we conducted a 10-day, fully factorial evolution experiment to examine how phage impact the structure and dynamics of an artificial four-species bacterial community that includes either Pseudomonas aeruginosa wild-type or an isogenic mutant unable to evolve phage resistance through CRISPR-Cas. Additionally, we used mathematical modelling to explore the ecological interactions underlying full community behaviour, as well as to identify general principles governing the impacts of phage on community dynamics. Our results show that the microbial community structure is drastically altered by the addition of phage, with Acinetobacter baumannii becoming the dominant species and P. aeruginosa being driven nearly extinct, whereas P. aeruginosa outcompetes the other species in the absence of phage. Moreover, we find that a P. aeruginosa strain with the ability to evolve CRISPR-based resistance generally does better when in the presence of A. baumannii, but that this benefit is largely lost over time as phage is driven extinct. Finally, we show that pairwise data alone is insufficient when modelling our microbial community, both with and without phage, highlighting the importance of higher order interactions in governing multispecies dynamics in complex communities. Combined, our data clearly illustrate how phage targeting a dominant species allows for the competitive release of the strongest competitor while also contributing to community diversity maintenance and potentially preventing the reinvasion of the target species, and underline the importance of mapping community composition before therapeutically applying phage.
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Affiliation(s)
- Ellinor O. Alseth
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, United Kingdom
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Rafael Custodio
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, United Kingdom
| | - Sarah A. Sundius
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Math, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Rachel A. Kuske
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Math, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Sam P. Brown
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Edze R. Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, United Kingdom
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Duda R, Betoulet JM, Besombes C, Mbrenga F, Borzykh Y, Nakouné E, Giles-Vernick T. A time of decline: An eco-anthropological and ethnohistorical investigation of mpox in the Central African Republic. PLOS GLOBAL PUBLIC HEALTH 2024; 4:e0002937. [PMID: 38517925 PMCID: PMC10959331 DOI: 10.1371/journal.pgph.0002937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/29/2024] [Indexed: 03/24/2024]
Abstract
The Central African Republic (CAR) has experienced repeated mpox outbreaks since 2001. Although several mpox epidemiological risk factors for zoonotic and interhuman transmission have been documented, the reasons for more frequent epidemic outbreaks are less well understood, relying on vague explanatory categories, including deforestation, hunting, and civil unrest. To gain insight into increasingly frequent outbreaks, we undertook an ethnohistorical, eco-anthropological analysis in two CAR regions: the Lobaye prefecture, experiencing one or more annual outbreaks in the past decade, and the Sangha-Mbaere prefecture, with a longer history of mpox but less frequent outbreaks. We comparatively examined changing political economies, forest use practices, and understandings of mpox. In 2022, we conducted 40 qualitative ethnohistorical, anthropological interviews and participant-observation of forest activities in two languages (Sango and French). We compared contemporary practices with hunting, trapping, and meet consumption practices, documented through quantitative and qualitative observation in one research site, over 6 months in 1993. We find increased rodent capture and consumption in both sites in the past 30 years and expanded practices of other potentially risky activities. Simultaneously, we also identify important differences in risky practices between our Lobaye and Sangha-Mbaere participants. In addition, Lobaye and Sangha participants underscored historical processes of decline producing mpox among other emergences, but they framed these declension processes diversely as economic, political, nutritional, and moral. Our findings are important because they mobilize new types of evidence to shed light on the processual dynamics of mpox outbreaks in the CAR. This study also reveals variability across two sites within the same country, highlighting the importance of comparative, fine-grained anthropological and historical research to identify underlying dynamics of mpox outbreaks. Finally, our study points to the need for mpox interventions and risk communication accounting for these regional differences, even within a single country.
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Affiliation(s)
- Romain Duda
- Anthropology & Ecology of Disease Emergence Unit, Department of Global Health, Institut Pasteur, Université Paris Cité, Paris, France
| | - José Martial Betoulet
- Ndima Kali, Baaka and Sangha-Sangha Youth Association, Bayanga, Central African Republic
- Dzanga-Sangha Protected Areas (DSPA-WWF), Bayanga, Central African Republic
| | - Camille Besombes
- Epidemiology of Emerging Diseases Unit, Department of Global Health, Institut Pasteur, Université Paris Cité, Paris, France
| | - Festus Mbrenga
- Department of Virology, Institut Pasteur de Bangui, Bangui, Central African Republic
| | - Yanina Borzykh
- Anthropology & Ecology of Disease Emergence Unit, Department of Global Health, Institut Pasteur, Université Paris Cité, Paris, France
| | - Emmanuel Nakouné
- Department of Virology, Institut Pasteur de Bangui, Bangui, Central African Republic
| | - Tamara Giles-Vernick
- Anthropology & Ecology of Disease Emergence Unit, Department of Global Health, Institut Pasteur, Université Paris Cité, Paris, France
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9
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Deng X, Tian Y, Zou J, Yang J, Sun K, Yu H. The risk of mpox importation and subsequent outbreak potential in Chinese mainland: a retrospective statistical modelling study. Infect Dis Poverty 2024; 13:21. [PMID: 38419040 PMCID: PMC10902966 DOI: 10.1186/s40249-024-01189-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND The 2022-2023 mpox (monkeypox) outbreak has spread rapidly across multiple countries in the non-endemic region, mainly among men who have sex with men (MSM). In this study, we aimed to evaluate mpox's importation risk, border screening effectiveness and the risk of local outbreak in Chinese mainland. METHODS We estimated the risk of mpox importation in Chinese mainland from April 14 to September 11, 2022 using the number of reported mpox cases during this multi-country outbreak from Global.health and the international air-travel data from Official Aviation Guide. We constructed a probabilistic model to simulate the effectiveness of a border screening scenario during the mpox outbreak and a hypothetical scenario with less stringent quarantine requirement. And we further evaluated the mpox outbreak potential given that undetected mpox infections were introduced into men who have sex with men, considering different transmissibility, population immunity and population activity. RESULTS We found that the reduced international air-travel volume and stringent border entry policy decreased about 94% and 69% mpox importations respectively. Under the quarantine policy, 15-19% of imported infections would remain undetected. Once a case of mpox is introduced into active MSM population with almost no population immunity, the risk of triggering local transmission is estimated at 42%, and would rise to > 95% with over six cases. CONCLUSIONS Our study demonstrates that the reduced international air-travel volume and stringent border entry policy during the COVID-19 pandemic reduced mpox importations prominently. However, the risk could be substantially higher with the recovery of air-travel volume to pre-pandemic level. Mpox could emerge as a public health threat for Chinese mainland given its large MSM community.
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Affiliation(s)
- Xiaowei Deng
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Yuyang Tian
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Junyi Zou
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Juan Yang
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.
| | - Hongjie Yu
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, 200032, China.
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10
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Lucena-Neto FD, Falcão LFM, Vieira-Junior AS, Moraes ECS, David JPF, Silva CC, Sousa JR, Duarte MIS, Vasconcelos PFC, Quaresma JAS. Monkeypox Virus Immune Evasion and Eye Manifestation: Beyond Eyelid Implications. Viruses 2023; 15:2301. [PMID: 38140542 PMCID: PMC10747317 DOI: 10.3390/v15122301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Monkeypox virus (MPXV), belonging to the Poxviridae family and Orthopoxvirus genus, is closely related to the smallpox virus. Initial prodromal symptoms typically include headache, fever, and lymphadenopathy. This review aims to detail various ocular manifestations and immune evasion associated with the monkeypox viral infection and its complications, making it appropriate as a narrative review. Common external ocular manifestations of MPXV typically involve a generalized pustular rash, keratitis, discharges, and dried secretions related to conjunctival pustules, photophobia, and lacrimation. Orthopoxviruses can evade host immune responses by secreting proteins that antagonize the functions of host IFNγ, CC and CXC chemokines, IL-1β, and the complement system. One of the most important transcription factors downstream of pattern recognition receptors binding is IRF3, which controls the expression of the crucial antiviral molecules IFNα and IFNβ. We strongly recommend that ophthalmologists include MPXV as part of their differential diagnosis when they encounter similar cases presenting with ophthalmic manifestations such as conjunctivitis, blepharitis, or corneal lesions. Furthermore, because non-vaccinated individuals are more likely to exhibit these symptoms, it is recommended that healthcare administrators prioritize smallpox vaccination for at-risk groups, including very young children, pregnant women, older adults, and immunocompromised individuals, especially those in close contact with MPXV cases.
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Affiliation(s)
- Francisco D. Lucena-Neto
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Luiz F. M. Falcão
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Adolfo S. Vieira-Junior
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Evelly C. S. Moraes
- Department of Infectious Disease, School of Medicine, Federal University of Pará, Belém 66075-110, PA, Brazil; (E.C.S.M.); (J.P.F.D.)
| | - Joacy P. F. David
- Department of Infectious Disease, School of Medicine, Federal University of Pará, Belém 66075-110, PA, Brazil; (E.C.S.M.); (J.P.F.D.)
| | - Camilla C. Silva
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Jorge R. Sousa
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Maria I. S. Duarte
- Department of Infectious Disease, School of Medicine, São Paulo University, São Paulo 01246-904, SP, Brazil;
| | - Pedro F. C. Vasconcelos
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Juarez A. S. Quaresma
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
- Department of Infectious Disease, School of Medicine, Federal University of Pará, Belém 66075-110, PA, Brazil; (E.C.S.M.); (J.P.F.D.)
- Department of Infectious Disease, School of Medicine, São Paulo University, São Paulo 01246-904, SP, Brazil;
- Virology Section, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil
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11
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Mohanto S, Faiyazuddin M, Dilip Gholap A, Jc D, Bhunia A, Subbaram K, Gulzar Ahmed M, Nag S, Shabib Akhtar M, Bonilla-Aldana DK, Sah S, Malik S, Haleem Al-Qaim Z, Barboza JJ, Sah R. Addressing the resurgence of global monkeypox (Mpox) through advanced drug delivery platforms. Travel Med Infect Dis 2023; 56:102636. [PMID: 37633474 DOI: 10.1016/j.tmaid.2023.102636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 08/28/2023]
Abstract
Monkeypox (Mpox) is a transmissible infection induced by the Monkeypox virus (a double-stranded DNA virus), recognised under the family orthopoxvirus genus. Monkeypox, like endemic diseases, is a substantial concern worldwide; thus, comprehending the pathogenesis and mutagenesis of amino acids is indispensable to combat the infection. According to the World Health Organization's report, about 89 thousand cases with 160 mortalities have been reported from 114 countries worldwide. The conventional orthopoxvirus vaccines developed on live attenuated viruses exempted any clinical validation from combating monkeypox due to inadequate immunogenicity, toxicity, instability, and multiple doses. Therefore, novel drug delivery systems come into the conception with high biological and mechanical characteristics to address the resurgence of Global Monkeypox. The edges of metallic biomaterials, novel molecules, and vaccine development in targeted therapy increase the modulation of the immune response and blockage of host-virus interaction, with enhanced stability for the antigens. Thus, this review strives to comprehend the viral cell pathogenesis concerning amino acid mutagenesis and current epidemiological standards of the Monkeypox disease across the globe. Furthermore, the review also recapitulates the various clinical challenges, current therapies, and progressive nanomedicine utilisation in the Monkeypox outbreak reinforced by various clinical trial reports. The contemporary challenges of novel drug delivery systems in Monkeypox treatment cannot be overlooked, and thus, authors have outlined the future strategies to develop successful nanomedicine to combat monkeypox. Future pandemics are inevitable but can be satisfactorily handled if we comprehend the crises, innovate, and develop cutting-edge technologies, especially by delving into frontiers like nanotechnology.
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Affiliation(s)
- Sourav Mohanto
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Md Faiyazuddin
- School of Pharmacy, Al-Karim University, Katihar, Bihar, 845106, India; Nano Drug Delivery®, Chapel Hill, NC, USA
| | - Amol Dilip Gholap
- Department of Pharmaceutics, St. John Institute of Pharmacy and Research, Palghar, Maharashtra, 401404, India
| | - Darshan Jc
- Department of Pharmacy Practice, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Adrija Bhunia
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Kannan Subbaram
- School of Medicine, The Maldives National University, Male', Maldives
| | - Mohammed Gulzar Ahmed
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Sagnik Nag
- Department of Bio-Sciences, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Mohammad Shabib Akhtar
- Department of Clinical Pharmacy, College of Pharmacy, Najran University, Najran, Kingdom of Saudi Arabia
| | | | - Sanjit Sah
- Global Consortium for Public Health and Research, Datta Meghe Institute of Higher Education and Research, Jawaharlal Nehru Medical College, Wardha, 442001, India; SR Sanjeevani Hospital, Kalyanpur-10, Siraha, Nepal
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University, Jharkhand, 834002, Ranchi, India; School of Applied Sciences, Uttaranchal University, Dehradun, India
| | - Zahraa Haleem Al-Qaim
- Department of Anesthesia Techniques, Al-Mustaqbal University College, 51001, Hillah, Babylon, Iraq
| | - Joshuan J Barboza
- Escuela de Medicina, Universidad César Vallejo, Trujillo, 13007, Peru
| | - Ranjit Sah
- Tribhuvan University Teaching Hospital, Kathmandu, 46000, Nepal; Department of Clinical Microbiology, DY Patil Medical College, Hospital and Research Centre, DY Patil Vidyapeeth, Pune, 411000, Maharashtra, India; Department of Public Health Dentistry, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, 411018, Maharashtra, India
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12
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Alseth EO, Custodio R, Sundius SA, Kuske RA, Brown SP, Westra ER. The impact of phage and phage resistance on microbial community dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559468. [PMID: 37808693 PMCID: PMC10557685 DOI: 10.1101/2023.09.26.559468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Where there are bacteria, there will be bacteriophages. These viruses are known to be important players in shaping the wider microbial community in which they are embedded, with potential implications for human health. On the other hand, bacteria possess a range of distinct immune mechanisms that provide protection against bacteriophages, including the mutation or complete loss of the phage receptor, and CRISPR-Cas adaptive immunity. Yet little is known about how interactions between phages and these different phage resistance mechanisms affect the wider microbial community in which they are embedded. Here, we conducted a 10-day, fully factorial evolution experiment to examine how phage impact the structure and dynamics of an artificial four-species bacterial community that includes either Pseudomonas aeruginosa wild type or an isogenic mutant unable to evolve phage resistance through CRISPR-Cas. Our results show that the microbial community structure is drastically altered by the addition of phage, with Acinetobacter baumannii becoming the dominant species and P. aeruginosa being driven nearly extinct, whereas P. aeruginosa outcompetes the other species in the absence of phage. Moreover, we find that a P. aeruginosa strain with the ability to evolve CRISPR-based resistance generally does better when in the presence of A. baumannii, but that this benefit is largely lost over time as phage is driven extinct. Combined, our data highlight how phage-targeting a dominant species allows for the competitive release of the strongest competitor whilst also contributing to community diversity maintenance and potentially preventing the reinvasion of the target species, and underline the importance of mapping community composition before therapeutically applying phage.
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Affiliation(s)
- Ellinor O Alseth
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rafael Custodio
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Sarah A Sundius
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Math, Georgia Institute of Technology, Atlanta, Georgia, USA
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rachel A Kuske
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Math, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sam P. Brown
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
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13
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Strona G, Bradshaw CJA, Cardoso P, Gotelli NJ, Guillaume F, Manca F, Mustonen V, Zaman L. Time-travelling pathogens and their risk to ecological communities. PLoS Comput Biol 2023; 19:e1011268. [PMID: 37498846 PMCID: PMC10374110 DOI: 10.1371/journal.pcbi.1011268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/13/2023] [Indexed: 07/29/2023] Open
Abstract
Permafrost thawing and the potential 'lab leak' of ancient microorganisms generate risks of biological invasions for today's ecological communities, including threats to human health via exposure to emergent pathogens. Whether and how such 'time-travelling' invaders could establish in modern communities is unclear, and existing data are too scarce to test hypotheses. To quantify the risks of time-travelling invasions, we isolated digital virus-like pathogens from the past records of coevolved artificial life communities and studied their simulated invasion into future states of the community. We then investigated how invasions affected diversity of the free-living bacteria-like organisms (i.e., hosts) in recipient communities compared to controls where no invasion occurred (and control invasions of contemporary pathogens). Invading pathogens could often survive and continue evolving, and in a few cases (3.1%) became exceptionally dominant in the invaded community. Even so, invaders often had negligible effects on the invaded community composition; however, in a few, highly unpredictable cases (1.1%), invaders precipitated either substantial losses (up to -32%) or gains (up to +12%) in the total richness of free-living species compared to controls. Given the sheer abundance of ancient microorganisms regularly released into modern communities, such a low probability of outbreak events still presents substantial risks. Our findings therefore suggest that unpredictable threats so far confined to science fiction and conjecture could in fact be powerful drivers of ecological change.
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Affiliation(s)
- Giovanni Strona
- European Commission, Joint Research Centre, Directorate D-Sustainable Resources, Ispra, Italy
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Corey J A Bradshaw
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research-LIBRe, Finnish Museum of Natural History Luomus, University of Helsinki, Helsinki, Finland
| | - Nicholas J Gotelli
- Department of Biology, University of Vermont, Burlington, Vermont, United States of America
| | - Frédéric Guillaume
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Federica Manca
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Ville Mustonen
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Luis Zaman
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, Michigan, United States of America
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14
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Brinkmann A, Kohl C, Pape K, Bourquain D, Thürmer A, Michel J, Schaade L, Nitsche A. Extensive ITR expansion of the 2022 Mpox virus genome through gene duplication and gene loss. Virus Genes 2023:10.1007/s11262-023-02002-1. [PMID: 37256469 DOI: 10.1007/s11262-023-02002-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/29/2023] [Indexed: 06/01/2023]
Abstract
Poxviruses are known to evolve slower than RNA viruses with only 1-2 mutations/genome/year. Rather than single mutations, rearrangements such as gene gain and loss, which have been discussed as a possible driver for host adaption, were described in poxviruses. In 2022 and 2023 the world is being challenged by the largest global outbreak so far of Mpox virus, and the virus seems to have established itself in the human community for an extended period of time. Here, we report five Mpox virus genomes from Germany with extensive gene duplication and loss, leading to the expansion of the ITR regions from 6400 to up to 24,600 bp. We describe duplications of up to 18,200 bp to the opposed genome end, and deletions at the site of insertion of up to 16,900 bp. Deletions and duplications of genes with functions of supposed immune modulation, virulence and host adaption as B19R, B21R, B22R and D10L are described. In summary, we highlight the need for monitoring rearrangements of the Mpox virus genome rather than for monitoring single mutations only.
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Affiliation(s)
- Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
| | - Claudia Kohl
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Katharina Pape
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Daniel Bourquain
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andrea Thürmer
- Genome Sequencing and Genomic Epidemiology, Methodology and Research Infrastructure, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Janine Michel
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
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15
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Taube JC, Rest EC, Lloyd-Smith JO, Bansal S. The global landscape of smallpox vaccination history and implications for current and future orthopoxvirus susceptibility: a modelling study. THE LANCET. INFECTIOUS DISEASES 2023; 23:454-462. [PMID: 36455590 PMCID: PMC10040439 DOI: 10.1016/s1473-3099(22)00664-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND More than four decades after the eradication of smallpox, the ongoing 2022 monkeypox outbreak and increasing transmission events of other orthopoxviruses necessitate a greater understanding of the global distribution of susceptibility to orthopoxviruses. We aimed to characterise the current global landscape of smallpox vaccination history and orthopoxvirus susceptibility. METHODS We characterised the global landscape of smallpox vaccination at a subnational scale by integrating data on current demography with historical smallpox vaccination programme features (coverage and cessation dates) from eradication documents and published literature. We analysed this landscape to identify the factors that were most associated with geographical heterogeneity in current vaccination coverage. We considered how smallpox vaccination history might translate into age-specific susceptibility profiles for orthopoxviruses under different vaccination effectiveness scenarios. FINDINGS We found substantial global spatial heterogeneity in the landscape of smallpox vaccination, with vaccination coverage estimated to range from 7% to 60% within admin-1 regions (ie, regions one administrative level below country) globally, with negligible uncertainty (99·6% of regions have an SD less than 5%). We identified that geographical variation in vaccination coverage was driven mostly by differences in subnational demography. Additionally, we found that susceptibility for orthopoxviruses was highly age specific based on age at cessation and age-specific coverage; however, the age profile was consistent across vaccine effectiveness values. INTERPRETATION The legacy of smallpox eradication can be observed in the current landscape of smallpox vaccine protection. The strength and longevity of smallpox vaccination campaigns globally, combined with current demographic heterogeneity, have shaped the epidemiological landscape today, revealing substantial geographical variation in orthopoxvirus susceptibility. This study alerts public health decision makers to non-endemic regions that might be at greatest risk in the case of widespread and sustained transmission in the 2022 monkeypox outbreak and highlights the importance of demography and fine-scale spatial dynamics in predicting future public health risks from orthopoxviruses. FUNDING US National Institutes of Health and US National Science Foundation.
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Affiliation(s)
- Juliana C Taube
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Eva C Rest
- Department of Biology, Georgetown University, Washington, DC, USA
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, DC, USA.
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16
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Patel CN, Mall R, Bensmail H. AI-driven drug repurposing and binding pose meta dynamics identifies novel targets for Monkeypox virus. J Infect Public Health 2023; 16:799-807. [PMID: 36966703 PMCID: PMC10014505 DOI: 10.1016/j.jiph.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/28/2023] [Accepted: 03/05/2023] [Indexed: 03/17/2023] Open
Abstract
Monkeypox virus (MPXV) was confirmed in May 2022 and designated a global health emergency by WHO in July 2022. MPX virions are big, enclosed, brick-shaped, and contain a linear, double-stranded DNA genome as well as enzymes. MPXV particles bind to the host cell membrane via a variety of viral-host protein interactions. As a result, the wrapped structure is a potential therapeutic target. DeepRepurpose, an artificial intelligence-based compound-viral proteins interaction framework, was used via a transfer learning setting to prioritize a set of FDA approved and investigational drugs which can potentially inhibit MPXV viral proteins. To filter and narrow down the lead compounds from curated collections of pharmaceutical compounds, we used a rigorous computational framework that included homology modeling, molecular docking, dynamic simulations, binding free energy calculations, and binding pose metadynamics. We identified Elvitegravir as a potential inhibitor of MPXV virus using our comprehensive pipeline.
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Affiliation(s)
- Chirag N. Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Science, Gujarat University, Ahmedabad-380009, India,Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD-21702, USA
| | - Raghvendra Mall
- Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee-38105, USA,Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi-9639, United Arab Emirates,Corresponding author at: Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee-38105, USA
| | - Halima Bensmail
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha-34110, Qatar,Corresponding author
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17
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Pan D, Nazareth J, Sze S, Martin CA, Decker J, Fletcher E, Déirdre Hollingsworth T, Barer MR, Pareek M, Tang JW. Transmission of monkeypox/mpox virus: A narrative review of environmental, viral, host, and population factors in relation to the 2022 international outbreak. J Med Virol 2023; 95:e28534. [PMID: 36708091 PMCID: PMC10107822 DOI: 10.1002/jmv.28534] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/05/2022] [Accepted: 01/24/2023] [Indexed: 01/29/2023]
Abstract
Monkeypox virus (MPXV) has spread globally. Emerging studies have now provided evidence regarding MPXV transmission, that can inform rational evidence-based policies and reduce misinformation on this topic. We aimed to review the evidence on transmission of the virus. Real-world studies have isolated viable viruses from high-touch surfaces for as long as 15 days. Strong evidence suggests that the current circulating monkeypox (mpox) has evolved from previous outbreaks outside of Africa, but it is yet unknown whether these mutations may lead to an inherently increased infectivity of the virus. Strong evidence also suggests that the main route of current MPXV transmission is sexual; through either close contact or directly, with detection of culturable virus in saliva, nasopharynx, and sperm for prolonged periods and the presence of rashes mainly in genital areas. The milder clinical presentations and the potential presence of presymptomatic transmission in the current circulating variant compared to previous clades, as well as the dominance of spread amongst men who have sex with men (MSMs) suggests that mpox has a developed distinct clinical phenotype that has increased its transmissibility. Increased public awareness of MPXV transmission modalities may lead to earlier detection of the spillover of new cases into other groups.
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Affiliation(s)
- Daniel Pan
- Department of Respiratory SciencesUniversity of LeicesterLeicesterUK
- Department of Infectious Diseases and HIV MedicineUniversity Hospitals of Leicester NHS TrustLeicesterUK
- Li Ka Shing Centre for Health Information and Discovery, Big Data InstituteUniversity of OxfordOxfordUK
- NIHR Leicester Biomedical Research CentreLiecesterUK
| | - Joshua Nazareth
- Department of Respiratory SciencesUniversity of LeicesterLeicesterUK
- Department of Infectious Diseases and HIV MedicineUniversity Hospitals of Leicester NHS TrustLeicesterUK
- NIHR Leicester Biomedical Research CentreLiecesterUK
| | - Shirley Sze
- Department of Cardiovascular SciencesUniversity of LeicesterLeicesterUK
| | - Christopher A. Martin
- Department of Respiratory SciencesUniversity of LeicesterLeicesterUK
- Department of Infectious Diseases and HIV MedicineUniversity Hospitals of Leicester NHS TrustLeicesterUK
- NIHR Leicester Biomedical Research CentreLiecesterUK
| | - Jonathan Decker
- Department of Respiratory SciencesUniversity of LeicesterLeicesterUK
| | - Eve Fletcher
- Department of Respiratory SciencesUniversity of LeicesterLeicesterUK
| | - T. Déirdre Hollingsworth
- Li Ka Shing Centre for Health Information and Discovery, Big Data InstituteUniversity of OxfordOxfordUK
| | - Michael R. Barer
- Department of Respiratory SciencesUniversity of LeicesterLeicesterUK
- Department of Clinical MicrobiologyUniversity Hospitals of Leicester NHS TrustLeicesterUK
| | - Manish Pareek
- Department of Respiratory SciencesUniversity of LeicesterLeicesterUK
- Department of Infectious Diseases and HIV MedicineUniversity Hospitals of Leicester NHS TrustLeicesterUK
- NIHR Leicester Biomedical Research CentreLiecesterUK
| | - Julian W. Tang
- Department of Respiratory SciencesUniversity of LeicesterLeicesterUK
- Department of VirologyUniversity Hospitals of Leicester NHS TrustLeicesterUK
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18
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Yuan P, Tan Y, Yang L, Aruffo E, Ogden NH, Bélair J, Heffernan J, Arino J, Watmough J, Carabin H, Zhu H. Assessing transmission risks and control strategy for monkeypox as an emerging zoonosis in a metropolitan area. J Med Virol 2023; 95:e28137. [PMID: 36089815 DOI: 10.1002/jmv.28137] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/11/2022] [Accepted: 08/26/2022] [Indexed: 01/11/2023]
Abstract
To model the spread of monkeypox (MPX) in a metropolitan area for assessing the risk of possible outbreaks, and identifying essential public health measures to contain the virus spread. The animal reservoir is the key element in the modeling of zoonotic disease. Using a One Health approach, we model the spread of the MPX virus in humans considering potential animal hosts such as rodents (e.g., rats, mice, squirrels, chipmunks, etc.) and emphasize their role and transmission of the virus in a high-risk group, including gay and bisexual men-who-have-sex-with-men (gbMSM). From model and sensitivity analysis, we identify key public health factors and present scenarios under different transmission assumptions. We find that the MPX virus may spill over from gbMSM high-risk groups to broader populations if the efficiency of transmission increases in the higher-risk group. However, the risk of outbreak can be greatly reduced if at least 65% of symptomatic cases can be isolated and their contacts traced and quarantined. In addition, infections in an animal reservoir will exacerbate MPX transmission risk in the human population. Regions or communities with a higher proportion of gbMSM individuals need greater public health attention. Tracing and quarantine (or "effective quarantine" by postexposure vaccination) of contacts with MPX cases in high-risk groups would have a significant effect on controlling the spreading. Also, monitoring for animal infections would be prudent.
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Affiliation(s)
- Pei Yuan
- Laboratory of Mathematical Parallel Systems (LAMPS), Department of Mathematics and Statistics, Centre for Diseases Modeling (CDM), York University, Toronto, Canada.,Centre for Diseases Modeling (CDM), York University, Toronto, Canada
| | - Yi Tan
- Laboratory of Mathematical Parallel Systems (LAMPS), Department of Mathematics and Statistics, Centre for Diseases Modeling (CDM), York University, Toronto, Canada.,Centre for Diseases Modeling (CDM), York University, Toronto, Canada
| | - Liu Yang
- Laboratory of Mathematical Parallel Systems (LAMPS), Department of Mathematics and Statistics, Centre for Diseases Modeling (CDM), York University, Toronto, Canada.,Centre for Diseases Modeling (CDM), York University, Toronto, Canada.,School of Mathematics and Statistics, Northeast Normal University, Changchun, Jilin, China
| | - Elena Aruffo
- Laboratory of Mathematical Parallel Systems (LAMPS), Department of Mathematics and Statistics, Centre for Diseases Modeling (CDM), York University, Toronto, Canada.,Centre for Diseases Modeling (CDM), York University, Toronto, Canada
| | - Nicholas H Ogden
- Centre for Diseases Modeling (CDM), York University, Toronto, Canada.,Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - Jacques Bélair
- Centre for Diseases Modeling (CDM), York University, Toronto, Canada.,Département de Mathématiques et de Statistique, Université de Montréal, Montréal, Québec, Canada
| | - Jane Heffernan
- Centre for Diseases Modeling (CDM), York University, Toronto, Canada.,Department of Mathematics and Statistics, York University, Toronto, Canada
| | - Julien Arino
- Centre for Diseases Modeling (CDM), York University, Toronto, Canada.,Department of Mathematics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - James Watmough
- Centre for Diseases Modeling (CDM), York University, Toronto, Canada.,Department of Mathematics and Statistics, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Hélène Carabin
- Département de Pathologie et Microbiologie, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada.,Département de médecine sociale et préventive, École de santé publique de l'université de Montréal, Montréal, Québec, Canada.,Centre de Recherche en Santé Publique (CReSP), de l'université de Montréal et du CIUSS du Centre Sud de Montréal, Montréal, Québec, Canada.,Groupe de Recherche en Épidémiologie des Zoonoses et Santé Publique (GREZOSP), Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Huaiping Zhu
- Laboratory of Mathematical Parallel Systems (LAMPS), Department of Mathematics and Statistics, Centre for Diseases Modeling (CDM), York University, Toronto, Canada.,Centre for Diseases Modeling (CDM), York University, Toronto, Canada
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19
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Weyer J, Blumberg LH. Monkeypox: Is the 'vacated niche' being filled? S Afr J Infect Dis 2022; 37:479. [PMID: 36568331 PMCID: PMC9772718 DOI: 10.4102/sajid.v37i1.479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Jacqueline Weyer
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lucille H. Blumberg
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
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Augsburger IB, Galanthay GK, Tarosky JH, Rychtář J, Taylor D. Voluntary vaccination may not stop monkeypox outbreak: A game-theoretic model. PLoS Negl Trop Dis 2022; 16:e0010970. [PMID: 36516113 PMCID: PMC9750030 DOI: 10.1371/journal.pntd.0010970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Monkeypox (MPX) is a viral zoonotic disease that was endemic to Central and West Africa. However, during the first half of 2022, MPX spread to almost 60 countries all over the world. Smallpox vaccines are about 85% effective in preventing MPX infections. Our objective is to determine whether the vaccines should be mandated or whether voluntary use of the vaccine could be enough to stop the MPX outbreak. We incorporate a standard SVEIR compartmental model of MPX transmission into a game-theoretical framework. We study a vaccination game in which individuals decide whether or not to vaccinate by assessing their benefits and costs. We solve the game for Nash equilibria, i.e., the vaccination rates the individuals would likely adopt without any outside intervention. We show that, without vaccination, MPX can become endemic in previously non-endemic regions, including the United States. We also show that to "not vaccinate" is often an optimal solution from the individual's perspective. Moreover, we demonstrate that, for some parameter values, there are multiple equilibria of the vaccination game, and they exhibit a backward bifurcation. Thus, without centrally mandated minimal vaccination rates, the population could easily revert to no vaccination scenario.
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Affiliation(s)
- Ian B Augsburger
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Grace K Galanthay
- Department of Mathematics and Computer Science, College of the Holy Cross, Worcester, Massachusetts, United States of America
| | - Jacob H Tarosky
- Department of Mathematical Sciences, High Point University, High Point, North Carolina, United States of America
| | - Jan Rychtář
- Department of Mathematics and Applied Mathematics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Dewey Taylor
- Department of Mathematics and Applied Mathematics, Virginia Commonwealth University, Richmond, Virginia, United States of America
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Ogunjo S, Olusola A, Orimoloye I. Association Between Weather Parameters and SARS-CoV-2 Confirmed Cases in Two South African Cities. GEOHEALTH 2022; 6:e2021GH000520. [PMID: 36348988 PMCID: PMC9635841 DOI: 10.1029/2021gh000520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 04/10/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Several approaches have been used in the race against time to mitigate the spread and impact of COVID-19. In this study, we investigated the role of temperature, relative humidity, and particulate matter in the spread of COVID-19 cases within two densely populated cities of South Africa-Pretoria and Cape Town. The role of different levels of COVID-19 restrictions in the air pollution levels, obtained from the Purple Air Network, of the two cities were also considered. Our results suggest that 26.73% and 43.66% reduction in PM2.5 levels were observed in Cape Town and Pretoria respectively for no lockdown (Level 0) to the strictest lockdown level (Level 5). Furthermore, our results showed a significant relationship between particulate matter and COVID-19 in the two cities. Particulate matter was found to be a good predictor, based on the significance of causality test, of COVID-19 cases in Pretoria with a lag of 7 days and more. This suggests that the effect of particulate matter on the number of cases can be felt after 7 days and beyond in Pretoria.
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Affiliation(s)
- Samuel Ogunjo
- Department of PhysicsFederal University of TechnologyAkureNigeria
| | - Adeyemi Olusola
- Faculty of Environmental and Urban ChangeYork UniversityTorontoCanada
- Department of GeographyUniversity of the Free StateBloemfonteinSouth Africa
| | - Israel Orimoloye
- Department of Geography, Faculty of Food and AgricultureThe University of the West Indies, St. Augustine CampusSt. AugustineTrinidad and Tobago
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22
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Caria J, Pinto R, Leal E, Almeida V, Cristóvão G, Gonçalves AC, Torres M, Santos MB, Pinheiro H, Póvoas D, Seixas D, Lino S, Cardoso O, Manata MJ, Virgolino A, Maltez F. Clinical and Epidemiological Features of Hospitalized and Ambulatory Patients with Human Monkeypox Infection: A Retrospective Observational Study in Portugal. Infect Dis Rep 2022; 14:810-823. [PMID: 36412741 PMCID: PMC9680313 DOI: 10.3390/idr14060083] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 12/14/2022] Open
Abstract
Monkeypox, a neglected and re-emergent zoonotic disease caused by monkeypox virus (MPXV) infection, has been endemic in Central and Western Africa for decades. More recently, an outbreak has spread to a global level, occurring in sites with no previous reported cases and being clustered among men who have sex with men, suggesting new modes of transmission. There is an urgent need for research for a better understanding of the genomic evolution and changing epidemiology of the Orthopoxvirus group. Our work aimed to characterize the clinical and epidemiological features of a cohort of patients with MPXV infection in a Portuguese hospital, admitted between 5 May and 26 July 2022. In this retrospective observational study, aggregate data of a case series on the presentation, clinical course, and outcomes of confirmed MPXV infections are reported. The study included 40 men and 1 woman, with a mean age of 37.2 years old; 92.7% identified as men who have sex with men, 90.2% had unprotected sex or sex with multiple or anonymous partners in the previous month, and 39.0% reported to have had sex with an MPXV-confirmed case; 59.5% had previously known human immunodeficiency virus (HIV) infection, all of whom were under antiretroviral therapy, and no patients had acquired immunodeficiency syndrome (AIDS) criteria. About a quarter of patients were observed only a week after symptom onset. All patients had skin or mucosal lesions and the anogenital region was the most frequent lesion site. There were no statistically significant clinical differences between HIV-positive and negative individuals. Four patients were admitted to the inpatient clinic, two of whom had proctitis with difficult-to-manage anal pain. There were no reported deaths. Our findings suggest the sexual route as a relevant mode of transmission of MPXV and confirm the mostly benign presentation of this disease.
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Affiliation(s)
- João Caria
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Raquel Pinto
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Ema Leal
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Vasco Almeida
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Gonçalo Cristóvão
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Ana Catarina Gonçalves
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Margarida Torres
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Maria Beatriz Santos
- Departamento de Medicina Interna, Hospital do Espírito Santo, Ilha Terceira, 9700-049 Angra do Heroísmo, Portugal
| | - Hélder Pinheiro
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
- Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal
| | - Diana Póvoas
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Diana Seixas
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Sara Lino
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Orlando Cardoso
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Maria José Manata
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Ana Virgolino
- Instituto de Saúde Ambiental (ISAMB), Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Laboratório Associado TERRA, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Fernando Maltez
- Departamento de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar de Lisboa Central, 1069-166 Lisboa, Portugal
- Instituto de Saúde Ambiental (ISAMB), Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Laboratório Associado TERRA, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Correspondence:
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23
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Brasil P, Martins EB, Calvet GA, Werneck GL. What do we need to know about the monkeypox virus infection in humans? CAD SAUDE PUBLICA 2022; 38:e00129222. [PMID: 36169515 DOI: 10.1590/0102-311xpt129222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Patrícia Brasil
- Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil
| | | | - Guilherme Amaral Calvet
- Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil
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Abstract
INTRODUCTION A monkeypox outbreak is spreading in territories where the virus is not generally prevalent. The rapid and sudden emergence of monkeypox in numerous nations at the same time means that unreported transmission may have persisted. The number of reported cases is on a constant increase worldwide. At least 20 non-African countries, like Canada, Portugal, Spain, and the United Kingdom, have reported more than 57662 as of September 9th suspected or confirmed cases. This is the largest epidemic seen outside of Africa. Scientists are struggling to determine the responsible genes for the higher virulence and transmissibility of the virus. Because the viruses are related, several countries have begun acquiring smallpox vaccinations, which are believed to be very effective against monkeypox. METHODS Bibliographic databases and web-search engines were used to retrieve studies that assessed monkeypox basic biology, life cycle, and transmission. Data were evaluated and used to explain the therapeutics that are under use or have potential. Finally, here is a comparison between how vaccines are being made now and how they were made in the past to stop the spread of new viruses. CONCLUSIONS Available vaccines are believed to be effective if administered within four days of viral exposure, as the virus has a long incubation period. As the virus is zoonotic, there is still a great deal of concern about the viral genetic shift and the risk of spreading to humans. This review will discuss the virus's biology and how dangerous it is. It will also look at how it spreads, what vaccines and treatments are available, and what technologies could be used to make vaccines quickly using mRNA technologies.
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Haider N, Guitian J, Simons D, Asogun D, Ansumana R, Honeyborne I, Velavan TP, Ntoumi F, Valdoleiros SR, Petersen E, Kock R, Zumla A. Increased outbreaks of monkeypox highlight gaps in actual disease burden in Sub-Saharan Africa and in animal reservoirs. Int J Infect Dis 2022; 122:107-111. [PMID: 35640830 PMCID: PMC9534138 DOI: 10.1016/j.ijid.2022.05.058] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 01/25/2023] Open
Abstract
We explain research gaps on Monkeypox (MPX) virus epidemiology in endemic countries and present hypotheses for the recent increase of MPX cases in West Africa as a possible explanation for the current epidemic in Europe, America, and Australia. The detection of >400 MPX cases in less than a month in May 2022, across many countries underscores the epidemic potential of MPX in humans and demonstrates several important research gaps. First, the true burden of MPX in West and Central Africa is poorly understood, although it is critical for prevention and control of future outbreaks. Second, the diversity and extent of the animal reservoir remain unknown. We hypothesize that the synanthropic rodent population has increased in recent years in Africa leading to more human-rodent interactions and thus increased transmission of MPXV. We further hypothesise that nearly 45 years after the end of routine smallpox vaccination, the larger and more interconnected immune-naïve population has crossed a threshold resulting in more sustainable human-to-human transmission of MPXV. The current epidemic in the Western World is possibly a consequence of increased local transmission of MPXV in Africa. A new estimation of the basic and effective reproduction rate (R0 and Re) in different populations is required. National, regional, and international collaborations are needed to address research gaps related to MPX outbreaks.
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Affiliation(s)
- Najmul Haider
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, United Kingdom.
| | - Javier Guitian
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, United Kingdom.
| | - David Simons
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, United Kingdom.
| | - Danny Asogun
- Irrua Specialized Teaching Hospital, Irrua, Nigeria.
| | - Rashid Ansumana
- School of Community Health Science, Njala University, Bo Campus, Sierra Leone.
| | - Isobella Honeyborne
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, United Kingdom.
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany; Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam.
| | - Francine Ntoumi
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany; Congolese Foundation for Medical Research, Brazzaville, Republic of Congo.
| | - Sofia R Valdoleiros
- Infectious Diseases Department, Centro Hospitalar Universitário de São João, Porto, Portugal; European Society for Clinical Microbiology and Infectious Diseases, Basel, Switzerland.
| | - Eskild Petersen
- European Society for Clinical Microbiology and Infectious Diseases, Basel, Switzerland; Institute for Clinical Medicine, Aarhus University, Aarhus, Denmark.
| | - Richard Kock
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, United Kingdom.
| | - Alimuddin Zumla
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, United Kingdom; NIHR-BRC, University College London Hospitals, London, United Kingdom.
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26
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Sieben AJ, Mihaljevic JR, Shoemaker LG. Quantifying mechanisms of coexistence in disease ecology. Ecology 2022; 103:e3819. [PMID: 35855596 DOI: 10.1002/ecy.3819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/22/2022] [Accepted: 04/20/2022] [Indexed: 11/06/2022]
Abstract
Pathogen coexistence depends on ecological processes operating at both within and between-host scales, making it difficult to quantify which processes may promote or prevent coexistence. Here, we propose that adapting modern coexistence theory-traditionally applied in plant communities-to pathogen systems provides an exciting approach for examining mechanisms of coexistence operating across different spatial scales. We first overview modern coexistence theory and its mechanistic decomposition; we subsequently adapt the framework to quantify how spatial variation in pathogen density, host resources and immunity, and their interaction may promote pathogen coexistence. We apply this derivation to an example two pathogen, multi-scale model comparing two scenarios with generalist and strain-specific immunity: one with demographic equivalency among pathogens and one with demographic trade-offs among pathogens. We then show how host-pathogen feedbacks generate spatial heterogeneity that promote pathogen coexistence and decompose those mechanisms to quantify how each spatial heterogeneity contributes to that coexistence. Specifically, coexistence of demographically equivalent pathogens occurs due to spatial variation in host resources, immune responses, and pathogen aggregation. With a competition-colonization trade-off, the superior colonizer requires spatial heterogeneity to coexist, whereas the superior competitor does not. Finally, we suggest ways forward for linking theory and empirical tests of coexistence in disease systems.
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Affiliation(s)
- Andrew J Sieben
- Department of Botany, University of Wyoming, Laramie, WY.,School of Medicine, Emory University, Atlanta, GA
| | - Joseph R Mihaljevic
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
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28
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Dai Y, Zhong J, Lan Y. Virus-virus interactions of febrile respiratory syndrome among patients in China based on surveillance data from February 2011 to December 2020. J Med Virol 2022; 94:4369-4377. [PMID: 35514049 DOI: 10.1002/jmv.27833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/17/2022] [Accepted: 05/02/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND The burden of acute respiratory infections is still considerable, and virus-virus interactions may affect their epidemics, but previous evidence is inconclusive. OBJECTIVE To quantitatively investigate the interactions among respiratory viruses at both the population and individual levels. METHODS Cases tested for influenza virus (IV), respiratory syncytial virus (RSV), human parainfluenza virus (PIV), human Adenovirus (AdV), human coronavirus (CoV), human bocavirus (BoV) and rhinoviruses (RV) were collected from the pathogen surveillance for febrile respiratory syndrome (FRS) in China from February 2011 to December 2020. We used spearman's rank correlation coefficients and binary logistic regression models to analyze the interactions between any two of the viruses at the population and individual levels, respectively. RESULTS Among 120,237 cases, 4.5% were co-infected with two or more viruses. Correlation coefficients showed 7 virus pairs were positively correlated, namely: IV and RSV, PIV and AdV, PIV and CoV, PIV and BoV, PIV and RV, AdV and BoV, CoV and RV. Regression models showed except for the negative interaction between IV and RV (OR=0.70, 95%CI: 0.61-0.81), all other virus pairs had positive interactions. CONCLUSION Most of the respiratory viruses interact positively, while IV and RV interact negatively. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yucen Dai
- Department of Epidemiology and Health Statistics, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China, 610041
| | - Jiao Zhong
- Department of Occupational and Environmental Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China, 610041.,Department of Osteoporosis, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China, 610041
| | - Yajia Lan
- Department of Occupational and Environmental Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China, 610041
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Brasil P, Martins EB, Calvet GA, Werneck GL. What do we need to know about the monkeypox virus infection in humans? CAD SAUDE PUBLICA 2022. [DOI: 10.1590/0102-311xen129222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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30
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Farrell MJ, Park AW, Cressler CE, Dallas T, Huang S, Mideo N, Morales-Castilla I, Davies TJ, Stephens P. The ghost of hosts past: impacts of host extinction on parasite specificity. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200351. [PMID: 34538147 PMCID: PMC8450631 DOI: 10.1098/rstb.2020.0351] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 11/29/2022] Open
Abstract
A growing body of research is focused on the extinction of parasite species in response to host endangerment and declines. Beyond the loss of parasite species richness, host extinction can impact apparent parasite host specificity, as measured by host richness or the phylogenetic distances among hosts. Such impacts on the distribution of parasites across the host phylogeny can have knock-on effects that may reshape the adaptation of both hosts and parasites, ultimately shifting the evolutionary landscape underlying the potential for emergence and the evolution of virulence across hosts. Here, we examine how the reshaping of host phylogenies through extinction may impact the host specificity of parasites, and offer examples from historical extinctions, present-day endangerment, and future projections of biodiversity loss. We suggest that an improved understanding of the impact of host extinction on contemporary host-parasite interactions may shed light on core aspects of disease ecology, including comparative studies of host specificity, virulence evolution in multi-host parasite systems, and future trajectories for host and parasite biodiversity. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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Affiliation(s)
- Maxwell J. Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | | | - Clayton E. Cressler
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Tad Dallas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70806, USA
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Shan Huang
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Ignacio Morales-Castilla
- Universidad de Alcalá, GloCEE - Global Change Ecology and Evolution Research Group, Departamento de Ciencias de la Vida, 28805 Alcalá de Henares, Madrid, Spain
| | - T. Jonathan Davies
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Department of Botany and Plant Biotechnology, African Centre for DNA Barcoding, University of Johannesburg, Johannesburg 2092, South Africa
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Senyonjo L, Addy J, Martin DL, Agyemang D, Yeboah-Manu D, Gwyn S, Marfo B, Asante-Poku A, Aboe A, Mensah E, Solomon AW, Bailey RL. Surveillance for peri-elimination trachoma recrudescence: Exploratory studies in Ghana. PLoS Negl Trop Dis 2021; 15:e0009744. [PMID: 34543293 PMCID: PMC8519445 DOI: 10.1371/journal.pntd.0009744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/15/2021] [Accepted: 08/18/2021] [Indexed: 11/26/2022] Open
Abstract
Introduction To date, eleven countries have been validated as having eliminated trachoma as a public health problem, including Ghana in 2018. Surveillance for recrudescence is needed both pre- and post-validation but evidence-based guidance on appropriate strategies is lacking. We explored two potential surveillance strategies in Ghana. Methodology/principal findings Amongst randomly-selected communities enrolled in pre-validation on-going surveillance between 2011 and 2015, eight were identified as having had trachomatous-inflammation follicular (TF) prevalence ≥5% in children aged 1–9 years between 2012 and 2014. These eight were re-visited in 2015 and 2016 and neighbouring communities were also added (“TF trigger” investigations). Resident children aged 1–9 years were then examined for trachoma and had a conjunctival swab to test for Chlamydia trachomatis (Ct) and a dried blood spot (DBS) taken to test for anti-Pgp3 antibodies. These investigations identified at least one community with evidence of probable recent Ct ocular transmission. However, the approach likely lacks sufficient spatio-temporal power to be reliable. A post-validation surveillance strategy was also evaluated, this reviewed the ocular Ct infection and anti-Pgp3 seroprevalence data from the TF trigger investigations and from the pre-validation surveillance surveys in 2015 and 2016. Three communities identified as having ocular Ct infection >0% and anti-Pgp3 seroprevalence ≥15.0% were identified, and along with three linked communities, were followed-up as part of the surveillance strategy. An additional three communities with a seroprevalence ≥25.0% but no Ct infection were also followed up (“antibody and infection trigger” investigations). DBS were taken from all residents aged ≥1 year and ocular swabs from all children aged 1–9 years. There was evidence of transmission in the group of communities visited in one district (Zabzugu-Tatale). There was no or little evidence of continued transmission in other districts, suggesting previous infection identified was transient or potentially not true ocular Ct infection. Conclusions/significance There is evidence of heterogeneity in Ct transmission dynamics in northern Ghana, even 10 years after wide-scale MDA has stopped. There is added value in monitoring Ct infection and anti-Ct antibodies, using these indicators to interrogate past or present surveillance strategies. This can result in a deeper understanding of transmission dynamics and inform new post-validation surveillance strategies. Opportunities should be explored for integrating PCR and serological-based markers into surveys conducted in trachoma elimination settings. The goal for trachoma programmes is elimination of trachoma as a public health problem. This means that ongoing low-level eye-to-eye transmission of the causative bacterium, Chlamydia trachomatis (Ct), is acceptable. Countries need to implement a suitable surveillance system to identify any return to higher transmission levels. The best methodology for doing this is not known. We first explored the approach used by Ghana in its standard programme, which involved monitoring a limited number of randomly selected communities for evidence of active (inflammatory) trachoma visible in children’s eyes on examination by trained observers. Although this strategy led to identification of at least one community that had probably had recent Ct transmission, the approach is unlikely to consistently identify places where return to higher levels of transmission is a risk. We also explored using information on infection (detected in eye swabs) and antibodies to Ct (detected in the blood) to identify communities at risk. We found evidence of both persistent eye-to-eye Ct transmission and areas where infection was transient and has now gone away. We conclude that the use of infection and antibody data for surveillance of trachoma appears promising.
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Affiliation(s)
- Laura Senyonjo
- Research Team, Sightsavers, Haywards Heath, United Kingdom
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - James Addy
- Eye Health Department, Ghana Health Service, Accra, Ghana
| | - Diana L. Martin
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, United States of America
| | | | - Dorothy Yeboah-Manu
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Sarah Gwyn
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Benjamin Marfo
- Neglected Tropical Diseases Division, Ghana Health Service, Accra, Ghana
| | - Adwoa Asante-Poku
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | | | | | - Anthony W. Solomon
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Robin L. Bailey
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Schatz AM, Park AW. Host and parasite traits predict cross-species parasite acquisition by introduced mammals. Proc Biol Sci 2021; 288:20210341. [PMID: 33947240 PMCID: PMC8097221 DOI: 10.1098/rspb.2021.0341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/01/2021] [Indexed: 01/02/2023] Open
Abstract
Species invasions and range shifts can lead to novel host-parasite communities, but we lack general rules on which new associations are likely to form. While many studies examine parasite sharing among host species, the directionality of transmission is typically overlooked, impeding our ability to derive principles of parasite acquisition. Consequently, we analysed parasite records from the non-native ranges of 11 carnivore and ungulate species. Using boosted regression trees, we modelled parasite acquisition within each zoogeographic realm of a focal host's non-native range, using a suite of predictors characterizing the parasites themselves and the host community in which they live. We found that higher parasite prevalence among established hosts increases the likelihood of acquisition, particularly for generalist parasites. Non-native host species are also more likely to acquire parasites from established host species to which they are closely related; however, the acquisition of several parasite groups is biased to phylogenetically specialist parasites, indicating potential costs of parasite generalism. Statistical models incorporating these features provide an accurate prediction of parasite acquisition, indicating that measurable host and parasite traits can be used to estimate the likelihood of new host-parasite associations forming. This work provides general rules to help anticipate novel host-parasite associations created by climate change and other anthropogenic influences.
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Affiliation(s)
- Annakate M. Schatz
- Odum School of Ecology, University of Georgia, Athens, GA, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Andrew W. Park
- Odum School of Ecology, University of Georgia, Athens, GA, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
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Kendig AE, Spear ER, Daws SC, Flory SL, Mordecai EA. Native perennial and non-native annual grasses shape pathogen community composition and disease severity in a California grassland. THE JOURNAL OF ECOLOGY 2021; 109:900-912. [PMID: 34158675 PMCID: PMC8215988 DOI: 10.1111/1365-2745.13515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/23/2020] [Indexed: 06/13/2023]
Abstract
The densities of highly competent plant hosts (i.e. those that are susceptible to and successfully transmit a pathogen) may shape pathogen community composition and disease severity, altering disease risk and impacts. Life history and evolutionary history can influence host competence; longer lived species tend to be better defended than shorter lived species and pathogens adapt to infect species with which they have longer evolutionary histories. It is unclear, however, how the densities of species that differ in competence due to life and evolutionary histories affect plant pathogen community composition and disease severity.We examined foliar fungal pathogens of two host groups in a California grassland: native perennial and non-native annual grasses. We first characterized pathogen community composition and disease severity of the two host groups to approximate differences in competence. We then used observational and manipulated gradients of native perennial and non-native annual grass densities to assess the effects of each host group on pathogen community composition and disease severity in 1-m2 plots.Native perennial and non-native annual grasses hosted distinct pathogen communities but shared generalist pathogens. Native perennial grasses experienced 26% higher disease severity than non-native annuals. Only the observational gradient of native perennial grass density affected disease severity; there were no other significant relationships between host group density and either disease severity or pathogen community composition.Synthesis. The life and evolutionary histories of grasses likely influence their competence for different pathogen species, exemplified by distinct pathogen communities and differences in disease severity. However, there was limited evidence that the density of either host group affected pathogen community composition or disease severity. Therefore, competence for different pathogens likely shapes pathogen community composition and disease severity but may not interact with host density to alter disease risk and impacts at small scales.
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Affiliation(s)
- Amy E. Kendig
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Erin R. Spear
- Smithsonian Tropical Research Institute, Panama City, Panama
| | | | - S. Luke Flory
- Agronomy Department, University of Florida, Gainesville, FL, USA
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Mummah RO, Hoff NA, Rimoin AW, Lloyd-Smith JO. Controlling emerging zoonoses at the animal-human interface. ONE HEALTH OUTLOOK 2020; 2:17. [PMID: 33073176 PMCID: PMC7550773 DOI: 10.1186/s42522-020-00024-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/09/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND For many emerging or re-emerging pathogens, cases in humans arise from a mixture of introductions (via zoonotic spillover from animal reservoirs or geographic spillover from endemic regions) and secondary human-to-human transmission. Interventions aiming to reduce incidence of these infections can be focused on preventing spillover or reducing human-to-human transmission, or sometimes both at once, and typically are governed by resource constraints that require policymakers to make choices. Despite increasing emphasis on using mathematical models to inform disease control policies, little attention has been paid to guiding rational disease control at the animal-human interface. METHODS We introduce a modeling framework to analyze the impacts of different disease control policies, focusing on pathogens exhibiting subcritical transmission among humans (i.e. pathogens that cannot establish sustained human-to-human transmission). We quantify the relative effectiveness of measures to reduce spillover (e.g. reducing contact with animal hosts), human-to-human transmission (e.g. case isolation), or both at once (e.g. vaccination), across a range of epidemiological contexts. RESULTS We provide guidelines for choosing which mode of control to prioritize in different epidemiological scenarios and considering different levels of resource and relative costs. We contextualize our analysis with current zoonotic pathogens and other subcritical pathogens, such as post-elimination measles, and control policies that have been applied. CONCLUSIONS Our work provides a model-based, theoretical foundation to understand and guide policy for subcritical zoonoses, integrating across disciplinary and species boundaries in a manner consistent with One Health principles.
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Affiliation(s)
- Riley O. Mummah
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E Young Dr S, Los Angeles, CA 90095 USA
- Department of Epidemiology, University of California, Los Angeles, CA 90095 USA
| | - Nicole A. Hoff
- Department of Epidemiology, University of California, Los Angeles, CA 90095 USA
| | - Anne W. Rimoin
- Department of Epidemiology, University of California, Los Angeles, CA 90095 USA
| | - James O. Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E Young Dr S, Los Angeles, CA 90095 USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892 USA
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Morens DM, Fauci AS. Emerging Pandemic Diseases: How We Got to COVID-19. Cell 2020; 182:1077-1092. [PMID: 32846157 PMCID: PMC7428724 DOI: 10.1016/j.cell.2020.08.021] [Citation(s) in RCA: 298] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/07/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022]
Abstract
Infectious diseases prevalent in humans and animals are caused by pathogens that once emerged from other animal hosts. In addition to these established infections, new infectious diseases periodically emerge. In extreme cases they may cause pandemics such as COVID-19; in other cases, dead-end infections or smaller epidemics result. Established diseases may also re-emerge, for example by extending geographically or by becoming more transmissible or more pathogenic. Disease emergence reflects dynamic balances and imbalances, within complex globally distributed ecosystems comprising humans, animals, pathogens, and the environment. Understanding these variables is a necessary step in controlling future devastating disease emergences.
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Affiliation(s)
- David M Morens
- Office of the Director, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Anthony S Fauci
- Office of the Director, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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COVID-19 in Light of Seasonal Respiratory Infections. BIOLOGY 2020; 9:biology9090240. [PMID: 32825427 PMCID: PMC7564908 DOI: 10.3390/biology9090240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 12/23/2022]
Abstract
A wide diversity of zoonotic viruses that are capable of overcoming host range barriers facilitate the emergence of new potentially pandemic viruses in the human population. When faced with a new virus that is rapidly emerging in the human population, we have a limited knowledge base to work with. The pandemic invasion of the new SARS-CoV-2 virus in 2019 provided a unique possibility to quickly learn more about the pathogenesis of respiratory viruses. In this review, the impact of pandemics on the circulation of seasonal respiratory viruses is considered. The emergence of novel respiratory viruses has often been accompanied by the disappearance of existing circulating strains. Some issues arising from the spread of pandemic viruses and underlying the choices of a strategy to fight the coronavirus infection are discussed.
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Guth S, Hanley KA, Althouse BM, Boots M. Ecological processes underlying the emergence of novel enzootic cycles: Arboviruses in the neotropics as a case study. PLoS Negl Trop Dis 2020; 14:e0008338. [PMID: 32790670 PMCID: PMC7425862 DOI: 10.1371/journal.pntd.0008338] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pathogens originating from wildlife (zoonoses) pose a significant public health burden, comprising the majority of emerging infectious diseases. Efforts to control and prevent zoonotic disease have traditionally focused on animal-to-human transmission, or "spillover." However, in the modern era, increasing international mobility and commerce facilitate the spread of infected humans, nonhuman animals (hereafter animals), and their products worldwide, thereby increasing the risk that zoonoses will be introduced to new geographic areas. Imported zoonoses can potentially "spill back" to infect local wildlife-a danger magnified by urbanization and other anthropogenic pressures that increase contacts between human and wildlife populations. In this way, humans can function as vectors, dispersing zoonoses from their ancestral enzootic systems to establish reservoirs elsewhere in novel animal host populations. Once established, these enzootic cycles are largely unassailable by standard control measures and have the potential to feed human epidemics. Understanding when and why translocated zoonoses establish novel enzootic cycles requires disentangling ecologically complex and stochastic interactions between the zoonosis, the human population, and the natural ecosystem. In this Review, we address this challenge by delineating potential ecological mechanisms affecting each stage of enzootic establishment-wildlife exposure, enzootic infection, and persistence-applying existing ecological concepts from epidemiology, invasion biology, and population ecology. We ground our discussion in the neotropics, where four arthropod-borne viruses (arboviruses) of zoonotic origin-yellow fever, dengue, chikungunya, and Zika viruses-have separately been introduced into the human population. This paper is a step towards developing a framework for predicting and preventing novel enzootic cycles in the face of zoonotic translocations.
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Affiliation(s)
- Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Kathryn A. Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Benjamin M. Althouse
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
- Epidemiology, Institute for Disease Modeling, Bellevue, Washington, United States of America
- Information School, University of Washington, Seattle, Washington, United States of America
| | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
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Simpson K, Heymann D, Brown CS, Edmunds WJ, Elsgaard J, Fine P, Hochrein H, Hoff NA, Green A, Ihekweazu C, Jones TC, Lule S, Maclennan J, McCollum A, Mühlemann B, Nightingale E, Ogoina D, Ogunleye A, Petersen B, Powell J, Quantick O, Rimoin AW, Ulaeato D, Wapling A. Human monkeypox - After 40 years, an unintended consequence of smallpox eradication. Vaccine 2020; 38:5077-5081. [PMID: 32417140 PMCID: PMC9533855 DOI: 10.1016/j.vaccine.2020.04.062] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/26/2020] [Indexed: 12/14/2022]
Abstract
Smallpox eradication, coordinated by the WHO and certified 40 years ago, led to the cessation of routine smallpox vaccination in most countries. It is estimated that over 70% of the world's population is no longer protected against smallpox, and through cross-immunity, to closely related orthopox viruses such as monkeypox. Monkeypox is now a re-emerging disease. Monkeypox is endemic in as yet unconfirmed animal reservoirs in sub-Saharan Africa, while its human epidemiology appears to be changing. Monkeypox in small animals imported from Ghana as exotic pets was at the origin of an outbreak of human monkeypox in the USA in 2003. Travellers infected in Nigeria were at the origin of monkeypox cases in the UK in 2018 and 2019, Israel in 2018 and Singapore in2019. Together with sporadic reports of human infections with other orthopox viruses, these facts invite speculation that emergent or re-emergent human monkeypox might fill the epidemiological niche vacated by smallpox. An ad-hoc and unofficial group of interested experts met to consider these issues at Chatham House, London in June 2019, in order to review available data and identify monkeypox-related research gaps. Gaps identified by the experts included:The experts further agreed on the need for a better understanding of the genomic evolution and changing epidemiology of orthopox viruses, the usefulness of in-field genomic diagnostics, and the best disease control strategies, including the possibility of vaccination with new generation non-replicating smallpox vaccines and treatment with recently developed antivirals.
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Affiliation(s)
- Karl Simpson
- JKS Bioscience Limited, 2 Midanbury Court, 44 Midanbury Lane, Southampton SO18 4HF, UK.
| | - David Heymann
- London School of Hygiene & Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, UK.
| | - Colin S Brown
- Public Health England, Colindale, 61 Colindale Avenue, London NW9 5EQ, UK.
| | - W John Edmunds
- London School of Hygiene & Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, UK.
| | - Jesper Elsgaard
- Bavarian Nordic A/S, Hejreskovvej 10A, DK-3490 Kvistgård, Denmark.
| | - Paul Fine
- London School of Hygiene & Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, UK.
| | | | - Nicole A Hoff
- Fielding School of Public Health, UCLA, 50 Charles E Young Dr S, Los Angeles, CA 90095, United States.
| | - Andrew Green
- Royal Centre of Defence Medicine, Level 2 QEHB, Mindelsohn Way, Edgbaston, Birmingham B15 2WB,UK.
| | - Chikwe Ihekweazu
- Nigeria CDC, Plot 801, Ebitu Ukiwe Street, Jabi, Abuja, Nigeria.
| | - Terry C Jones
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing St., Cambridge CB2 3EJ, UK; Institute of Virology, Charité, Universitätsmedizin Charitéplatz 1, 10117 Berlin, Germany.
| | - Swaib Lule
- University College London, Faculty of Population Health Sciences, 30 Guilford Street, London WC1N 1EH, UK.
| | - Jane Maclennan
- Bavarian Nordic GmbH, Fraunhoferstraße 13, 82152 Planegg, Germany.
| | - Andrea McCollum
- Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, CDC, Atlanta, GA 30333, USA.
| | - Barbara Mühlemann
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing St., Cambridge CB2 3EJ, UK; Institute of Virology, Charité, Universitätsmedizin Charitéplatz 1, 10117 Berlin, Germany.
| | - Emily Nightingale
- The Forge Veterinary Centre, 93b Head Street, Halstead, Essex CO9 2AZ, UK.
| | - Dimie Ogoina
- Niger Delta University/Niger Delta University Teaching Hospital, Bayelsa, Nigeria
| | - Adesola Ogunleye
- Nigeria CDC, Plot 801, Ebitu Ukiwe Street, Jabi, Abuja, Nigeria.
| | - Brett Petersen
- Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, CDC, Atlanta, GA 30333, USA.
| | - Jacqueline Powell
- Bavarian Nordic Inc, 3025 Carrington Mill Blvd, Morrisville, NC 27560, USA.
| | - Ollie Quantick
- SO1 Public Health and Health Protection, Army Headquarters, Ground Floor, Zone1, Blenheim Bd, Marlborough Lines, Monxton Road, Andover, Hampshire SP11 8HJ, UK.
| | - Anne W Rimoin
- Fielding School of Public Health, UCLA, 50 Charles E Young Dr S, Los Angeles, CA 90095, United States.
| | - David Ulaeato
- CBR Division, Defence Science & Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK.
| | - Andy Wapling
- Regional Head of Emergency Preparedness, Resilience and Response, NHS England (South West & South East), UK.
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Kowalska JD, Kazimierczak J, Sowińska PM, Wójcik EA, Siwicki AK, Dastych J. Growing Trend of Fighting Infections in Aquaculture Environment-Opportunities and Challenges of Phage Therapy. Antibiotics (Basel) 2020; 9:antibiotics9060301. [PMID: 32512805 PMCID: PMC7345527 DOI: 10.3390/antibiotics9060301] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 06/03/2020] [Indexed: 12/31/2022] Open
Abstract
Phage therapy, a promising alternative to antimicrobial treatment of bacterial diseases, is getting more and more popular, especially due to the rising awareness of antibiotic resistance and restrictions in antibiotics' use. During recent years, we observed a growing trend of bacteriophages' application in aquaculture, which in each year reports high losses due to bacterial diseases. This review provides an update of the status of bacteriophage therapy for the treatment and prevention of infections in the aquatic environment. As it is still mostly in the scientific stage, there are a few constraints that may prevent effective therapy. Therefore, specific characteristics of bacteriophages, that can act in favor or against their successful use in treatment, were described. We underlined aspects that need to be considered: specificity of phages, bacterial resistance, safety, immune response of the host organism, formulation, administration and stability of phage preparations as well as bacteriophages' influence on the environment. The biggest challenge to overcome is finding the right balance between the desired and problematic characteristics of bacteriophages. Finally, regulatory approval challenges may be encountered by bacteriophage manufacturers. Even though there are still some technical constraints connected with the global use of bacteriophage therapy, it was concluded that it can be successfully applied in aquaculture.
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Affiliation(s)
- Justyna D. Kowalska
- Proteon Pharmaceuticals, 90-364 Lodz, Poland; (J.K.); (P.M.S.); (E.A.W.); (J.D.)
- Correspondence:
| | - Joanna Kazimierczak
- Proteon Pharmaceuticals, 90-364 Lodz, Poland; (J.K.); (P.M.S.); (E.A.W.); (J.D.)
| | - Patrycja M. Sowińska
- Proteon Pharmaceuticals, 90-364 Lodz, Poland; (J.K.); (P.M.S.); (E.A.W.); (J.D.)
| | - Ewelina A. Wójcik
- Proteon Pharmaceuticals, 90-364 Lodz, Poland; (J.K.); (P.M.S.); (E.A.W.); (J.D.)
| | - Andrzej K. Siwicki
- Department of Microbiology and Clinical Immunology, Faculty of Veterinary Medicine, University of Warmia and Mazury, 10-719 Olsztyn, Poland;
| | - Jarosław Dastych
- Proteon Pharmaceuticals, 90-364 Lodz, Poland; (J.K.); (P.M.S.); (E.A.W.); (J.D.)
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Pastoral production is associated with increased peste des petits ruminants seroprevalence in northern Tanzania across sheep, goats and cattle. Epidemiol Infect 2020; 147:e242. [PMID: 31364555 DOI: 10.1017/s0950268819001262] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) causes a contagious disease of high morbidity and mortality in small ruminant populations globally. Using cross-sectional serosurvey data collected in 2016, our study investigated PPRV seroprevalence and risk factors among sheep, goats and cattle in 20 agropastoral (AP) and pastoral (P) villages in northern Tanzania. Overall observed seroprevalence was 21.1% (95% exact confidence interval (CI) 20.1-22.0) with 5.8% seroprevalence among agropastoral (95% CI 5.0-6.7) and 30.7% among pastoral villages (95% CI 29.3-32.0). Seropositivity varied significantly by management (production) system. Our study applied the catalytic framework to estimate the force of infection. The associated reproductive numbers (R0) were estimated at 1.36 (95% CI 1.32-1.39), 1.40 (95% CI 1.37-1.44) and 1.13 (95% CI 1.11-1.14) for sheep, goats and cattle, respectively. For sheep and goats, these R0 values are likely underestimates due to infection-associated mortality. Spatial heterogeneity in risk among pairs of species across 20 villages was significantly positively correlated (R2: 0.59-0.69), suggesting either cross-species transmission or common, external risk factors affecting all species. The non-negligible seroconversion in cattle may represent spillover or cattle-to-cattle transmission and must be investigated further to understand the role of cattle in PPRV transmission ahead of upcoming eradication efforts.
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Man I, Auranen K, Wallinga J, Bogaards JA. Capturing multiple-type interactions into practical predictors of type replacement following human papillomavirus vaccination. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180298. [PMID: 30955490 DOI: 10.1098/rstb.2018.0298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Current HPV vaccines target a subset of the oncogenic human papillomavirus (HPV) types. If HPV types compete during infection, vaccination may trigger replacement by the non-targeted types. Existing approaches to assess the risk of type replacement have focused on detecting competitive interactions between pairs of vaccine and non-vaccine types. However, methods to translate any inferred pairwise interactions into predictors of replacement have been lacking. In this paper, we develop practical predictors of type replacement in a multi-type setting, readily estimable from pre-vaccination longitudinal or cross-sectional prevalence data. The predictors we propose for replacement by individual non-targeted types take the form of weighted cross-hazard ratios of acquisition versus clearance, or aggregate odds ratios of coinfection with the vaccine types. We elucidate how the hazard-based predictors incorporate potentially heterogeneous direct and indirect type interactions by appropriately weighting type-specific hazards and show when they are equivalent to the odds-based predictors. Additionally, pooling type-specific predictors proves to be useful for predicting increase in the overall non-vaccine-type prevalence. Using simulations, we demonstrate good performance of the predictors under different interaction structures. We discuss potential applications and limitations of the proposed methodology in predicting type replacement, as compared to existing approaches. This article is part of the theme issue 'Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses'.
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Affiliation(s)
- Irene Man
- 1 Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven , The Netherlands.,2 Department of Medical Statistics and Bioinformatics, Leiden University Medical Center , Leiden , The Netherlands
| | - Kari Auranen
- 3 Department of Mathematics and Statistics, University of Turku , Vesilinnantie 5, 20500 Turku , Finland.,4 Department of Clinical Medicine, University of Turku , Vesilinnantie 5, 20500 Turku , Finland
| | - Jacco Wallinga
- 1 Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven , The Netherlands.,2 Department of Medical Statistics and Bioinformatics, Leiden University Medical Center , Leiden , The Netherlands
| | - Johannes A Bogaards
- 1 Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven , The Netherlands.,5 Department of Epidemiology and Biostatistics, Vrije Universiteit Amsterdam , UMC, Amsterdam , The Netherlands
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Man I, Vänskä S, Lehtinen M, Bogaards JA. Human Papillomavirus Genotype Replacement: Still Too Early to Tell? J Infect Dis 2020; 224:481-491. [PMID: 31985011 PMCID: PMC8328199 DOI: 10.1093/infdis/jiaa032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/23/2020] [Indexed: 12/19/2022] Open
Abstract
Background Although human papillomavirus (HPV) vaccines are highly efficacious in protecting against HPV infections and related diseases, vaccination may trigger replacement by nontargeted genotypes if these compete with the vaccine-targeted types. HPV genotype replacement has been deemed unlikely, based on the lack of systematic increases in the prevalence of nonvaccine-type (NVT) infection in the first decade after vaccination, and on the presence of cross-protection for some NVTs. Methods To investigate whether type replacement can be inferred from early postvaccination surveillance, we constructed a transmission model in which a vaccine type and an NVT compete through infection-induced cross-immunity. We simulated scenarios of different levels of cross-immunity and vaccine-induced cross-protection to the NVT. We validated whether commonly used measures correctly indicate type replacement in the long run. Results Type replacement is a trade-off between cross-immunity and cross-protection; cross-immunity leads to type replacement unless cross-protection is strong enough. With weak cross-protection, NVT prevalence may initially decrease before rebounding into type replacement, exhibiting a honeymoon period. Importantly, vaccine effectiveness for NVTs is inadequate for indicating type replacement. Conclusions Although postvaccination surveillance thus far is reassuring, it is still too early to preclude type replacement. Monitoring of NVTs remains pivotal in gauging population-level impacts of HPV vaccination.
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Affiliation(s)
- Irene Man
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands.,Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - Simopekka Vänskä
- Infectious Disease Control and Vaccinations, National Institute for Health and Welfare, Helsinki, Finland.,School of Health Sciences, University of Tampere, Finland
| | - Matti Lehtinen
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Division of Infections and Cancer Epidemiology, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Johannes A Bogaards
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands.,Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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Virus-virus interactions impact the population dynamics of influenza and the common cold. Proc Natl Acad Sci U S A 2019; 116:27142-27150. [PMID: 31843887 PMCID: PMC6936719 DOI: 10.1073/pnas.1911083116] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
When multiple pathogens cocirculate this can lead to competitive or cooperative forms of pathogen–pathogen interactions. It is believed that such interactions occur among cold and flu viruses, perhaps through broad-acting immunity, resulting in interlinked epidemiological patterns of infection. However, to date, quantitative evidence has been limited. We analyzed a large collection of diagnostic reports collected over multiple years for 11 respiratory viruses. Our analyses provide strong statistical support for the existence of interactions among respiratory viruses. Using computer simulations, we found that very short-lived interferences may explain why common cold infections are less frequent during flu seasons. Improved understanding of how the epidemiology of viral infections is interlinked can help improve disease forecasting and evaluation of disease control interventions. The human respiratory tract hosts a diverse community of cocirculating viruses that are responsible for acute respiratory infections. This shared niche provides the opportunity for virus–virus interactions which have the potential to affect individual infection risks and in turn influence dynamics of infection at population scales. However, quantitative evidence for interactions has lacked suitable data and appropriate analytical tools. Here, we expose and quantify interactions among respiratory viruses using bespoke analyses of infection time series at the population scale and coinfections at the individual host scale. We analyzed diagnostic data from 44,230 cases of respiratory illness that were tested for 11 taxonomically broad groups of respiratory viruses over 9 y. Key to our analyses was accounting for alternative drivers of correlated infection frequency, such as age and seasonal dependencies in infection risk, allowing us to obtain strong support for the existence of negative interactions between influenza and noninfluenza viruses and positive interactions among noninfluenza viruses. In mathematical simulations that mimic 2-pathogen dynamics, we show that transient immune-mediated interference can cause a relatively ubiquitous common cold-like virus to diminish during peak activity of a seasonal virus, supporting the potential role of innate immunity in driving the asynchronous circulation of influenza A and rhinovirus. These findings have important implications for understanding the linked epidemiological dynamics of viral respiratory infections, an important step towards improved accuracy of disease forecasting models and evaluation of disease control interventions.
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Mair C, Nickbakhsh S, Reeve R, McMenamin J, Reynolds A, Gunson RN, Murcia PR, Matthews L. Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models. PLoS Comput Biol 2019; 15:e1007492. [PMID: 31834896 PMCID: PMC6934324 DOI: 10.1371/journal.pcbi.1007492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 12/27/2019] [Accepted: 10/16/2019] [Indexed: 11/22/2022] Open
Abstract
It is well recognised that animal and plant pathogens form complex ecological communities of interacting organisms within their hosts, and there is growing interest in the health implications of such pathogen interactions. Although community ecology approaches have been used to identify pathogen interactions at the within-host scale, methodologies enabling robust identification of interactions from population-scale data such as that available from health authorities are lacking. To address this gap, we developed a statistical framework that jointly identifies interactions between multiple viruses from contemporaneous non-stationary infection time series. Our conceptual approach is derived from a Bayesian multivariate disease mapping framework. Importantly, our approach captures within- and between-year dependencies in infection risk while controlling for confounding factors such as seasonality, demographics and infection frequencies, allowing genuine pathogen interactions to be distinguished from simple correlations. We validated our framework using a broad range of synthetic data. We then applied it to diagnostic data available for five respiratory viruses co-circulating in a major urban population between 2005 and 2013: adenovirus, human coronavirus, human metapneumovirus, influenza B virus and respiratory syncytial virus. We found positive and negative covariances indicative of epidemiological interactions among specific virus pairs. This statistical framework enables a community ecology perspective to be applied to infectious disease epidemiology with important utility for public health planning and preparedness. Disease-causing microorganisms, including viruses, bacteria, protozoa and fungi, form complex communities within animals and plants. These microorganisms can coexist harmoniously or even beneficially, or they may competitively interact for host resources. Well-studied examples include interactions between viruses and bacteria in the respiratory tract. Whilst ecological studies have revealed that some pathogens do interact within their hosts, identifying interactions from available population scale data from health authorities is challenging. This is exacerbated by a lack of large-scale data describing the infection patterns of multiple pathogens within single populations over long time frames. Furthermore, methods for evaluating whether infection frequencies of different pathogens fluctuate together or not over time cannot readily account for alternative explanations. For example, human pathogens may have related seasonal patterns depending on the age groups they infect and the weather conditions they survive in, and not because they are interacting. We developed a robust statistical framework to identify pathogen-pathogen interactions from population scale diagnostic data. This framework serves as a crucial step in identifying such important interactions and will guide new studies to elucidate their underpinning mechanisms. This will have important consequences for public health preparedness and the design of effective disease control interventions.
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Affiliation(s)
- Colette Mair
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Mathematics and Statistics, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
| | - Sema Nickbakhsh
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jim McMenamin
- Health Protection Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Arlene Reynolds
- Health Protection Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Rory N. Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Pablo R. Murcia
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Louise Matthews
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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45
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Evans SE, Bell-Dereske LP, Dougherty KM, Kittredge HA. Dispersal alters soil microbial community response to drought. Environ Microbiol 2019; 22:905-916. [PMID: 31173453 DOI: 10.1111/1462-2920.14707] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 11/27/2022]
Abstract
Microbial communities will experience novel climates in the future. Dispersal is now recognized as a driver of microbial diversity and function, but our understanding of how dispersal influences responses to novel climates is limited. We experimentally tested how the exclusion of aerially dispersed fungi and bacteria altered the compositional and functional response of soil microbial communities to drought. We manipulated dispersal and drought by collecting aerially deposited microbes after precipitation events and subjecting soil mesocosms to either filter-sterilized rain (no dispersal) or unfiltered rain (dispersal) and to either drought (25% ambient) or ambient rainfall for 6 months. We characterized community composition by sequencing 16S and ITS rRNA regions and function using community-level physiological profiles. Treatments without dispersal had lower soil microbial biomass and metabolic diversity but higher bacterial and fungal species richness. Dispersal also altered soil community response to drought; drought had a stronger effect on bacterial (but not fungal) community composition, and induced greater functional loss, when dispersal was present. Surprisingly, neither immigrants nor drought-tolerant taxa had higher abundance in dispersal treatments. We show experimentally that natural aerial dispersal rate alters soil microbial responses to disturbance. Changes in dispersal rates should be considered when predicting microbial responses to climate change.
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Affiliation(s)
- S E Evans
- Kellogg Biological Station; Ecology, Evolutionary Biology, and Behavior Program, Department of Integrative Biology, 3700 E. Gull Lake Dr. Hickory Corners, MI, 49060, USA
| | - L P Bell-Dereske
- Kellogg Biological Station; Ecology, Evolutionary Biology, and Behavior Program, 3700 E. Gull Lake Dr. Hickory Corners, MI, 49060, USA
| | - K M Dougherty
- Kellogg Biological Station; Ecology, Evolutionary Biology, and Behavior Program, 3700 E. Gull Lake Dr. Hickory Corners, MI, 49060, USA
| | - H A Kittredge
- Kellogg Biological Station; Ecology, Evolutionary Biology, and Behavior Program, Department of Integrative Biology, 3700 E. Gull Lake Dr. Hickory Corners, MI, 49060, USA
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46
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Hochberg ME. An ecosystem framework for understanding and treating disease. EVOLUTION MEDICINE AND PUBLIC HEALTH 2018; 2018:270-286. [PMID: 30487969 PMCID: PMC6252061 DOI: 10.1093/emph/eoy032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/02/2018] [Indexed: 12/28/2022]
Abstract
Pathogens and cancers are pervasive health risks in the human population. I argue that if we are to better understand disease and its treatment, then we need to take an ecological perspective of disease itself. I generalize and extend an emerging framework that views disease as an ecosystem and many of its components as interacting in a community. I develop the framework for biological etiological agents (BEAs) that multiply within humans—focusing on bacterial pathogens and cancers—but the framework could be extended to include other host and parasite species. I begin by describing why we need an ecosystem framework to understand disease, and the main components and interactions in bacterial and cancer disease ecosystems. Focus is then given to the BEA and how it may proceed through characteristic states, including emergence, growth, spread and regression. The framework is then applied to therapeutic interventions. Central to success is preventing BEA evasion, the best known being antibiotic resistance and chemotherapeutic resistance in cancers. With risks of evasion in mind, I propose six measures that either introduce new components into the disease ecosystem or manipulate existing ones. An ecosystem framework promises to enhance our understanding of disease, BEA and host (co)evolution, and how we can improve therapeutic outcomes.
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Affiliation(s)
- Michael E Hochberg
- Institut des Sciences de l'Evolution, Université de Montpellier, 34095 Montpellier, France.,Santa Fe Institute, Santa Fe, NM 87501, USA.,Institute for Advanced Study in Toulouse, 31015 Toulouse, France
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47
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McMahon BJ, Morand S, Gray JS. Ecosystem change and zoonoses in the Anthropocene. Zoonoses Public Health 2018; 65:755-765. [PMID: 30105852 DOI: 10.1111/zph.12489] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/08/2018] [Accepted: 05/27/2018] [Indexed: 12/21/2022]
Abstract
Changes in land use, animal populations and climate, primarily due to increasing human populations, drive the emergence of zoonoses. Force of infection (FOI), which for these diseases is a measure of the ease with which a pathogen reaches the human population, can change with specific zoonoses and context. Here, we outline three ecosystem categories-domestic, peridomestic and sylvatic, where disease ecology alters the FOI of specific zoonoses. Human intervention is an overriding effect in the emergence of zoonoses; therefore, we need to understand the disease ecology and other influencing factors of pathogens and parasites that are likely to interact differently within ecological and cultural contexts. Planning for One Health and community ecology, such as an ecological impact assessment, is required to prepare and manage the emergence and impact of zoonoses in the Anthropocene.
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Affiliation(s)
- Barry J McMahon
- UCD School of Agriculture & Food Science, University College Dublin, Dublin 4, Ireland
| | - Serge Morand
- CNRS - CIRAD ASTRE, Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Jeremy S Gray
- UCD School of Biology & Environmental Science, University College Dublin, Dublin 4, Ireland
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48
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Ke R, Li H, Wang S, Ding W, Ribeiro RM, Giorgi EE, Bhattacharya T, Barnard RJO, Hahn BH, Shaw GM, Perelson AS. Superinfection and cure of infected cells as mechanisms for hepatitis C virus adaptation and persistence. Proc Natl Acad Sci U S A 2018; 115:E7139-E7148. [PMID: 29987026 PMCID: PMC6065014 DOI: 10.1073/pnas.1805267115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
RNA viruses exist as a genetically diverse quasispecies with extraordinary ability to adapt to abrupt changes in the host environment. However, the molecular mechanisms that contribute to their rapid adaptation and persistence in vivo are not well studied. Here, we probe hepatitis C virus (HCV) persistence by analyzing clinical samples taken from subjects who were treated with a second-generation HCV protease inhibitor. Frequent longitudinal viral load determinations and large-scale single-genome sequence analyses revealed rapid antiviral resistance development, and surprisingly, dynamic turnover of dominant drug-resistant mutant populations long after treatment cessation. We fitted mathematical models to both the viral load and the viral sequencing data, and the results provided strong support for the critical roles that superinfection and cure of infected cells play in facilitating the rapid turnover and persistence of viral populations. More broadly, our results highlight the importance of considering viral dynamics and competition at the intracellular level in understanding rapid viral adaptation. Thus, we propose a theoretical framework integrating viral and molecular mechanisms to explain rapid viral evolution, resistance, and persistence despite antiviral treatment and host immune responses.
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Affiliation(s)
- Ruian Ke
- Department of Mathematics, North Carolina State University, Raleigh, NC 27695
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Shuyi Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Wenge Ding
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
- Laboratory of Biomathematics, Faculty of Medicine, University of Lisbon, 1600-276 Lisbon, Portugal
| | - Elena E Giorgi
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
- Santa Fe Institute, Santa Fe, NM 87501
| | | | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545;
- Santa Fe Institute, Santa Fe, NM 87501
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49
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Tiee MS, Harrigan RJ, Thomassen HA, Smith TB. Ghosts of infections past: using archival samples to understand a century of monkeypox virus prevalence among host communities across space and time. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171089. [PMID: 29410823 PMCID: PMC5792900 DOI: 10.1098/rsos.171089] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 12/15/2017] [Indexed: 06/08/2023]
Abstract
Infectious diseases that originate from multiple wildlife hosts can be complex and problematic to manage. A full understanding is further limited by large temporal and spatial gaps in sampling. However, these limitations can be overcome, in part, by using historical samples, such as those derived from museum collections. Here, we screened over 1000 museum specimens collected over the past 120 years to examine the historical distribution and prevalence of monkeypox virus (MPXV) in five species of African rope squirrel (Funisciurus sp.) collected across Central Africa. We found evidence of MPXV infections in host species as early as 1899, half a century earlier than the first recognized case of MPXV in 1958, supporting the suggestion that historic pox-like outbreaks in humans and non-human primates may have been caused by MPXV rather than smallpox as originally thought. MPX viral DNA was found in 93 of 1038 (9.0%) specimens from five Funisciurus species (F. anerythrus, F. carruthersi, F. congicus, F. lemniscatus and F. pyrropus), of which F. carruthersi and pyrropus had not previously been identified as potential MPXV hosts. We additionally documented relative prevalence rates of infection in museum specimens of Funisciurus and examined the spatial and temporal distribution of MPXV in these potential host species across nearly a hundred years (1899-1993).
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Affiliation(s)
- Madeline S. Tiee
- Department of Ecology and Evolutionary Biology, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Henri A. Thomassen
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
- Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Thomas B. Smith
- Department of Ecology and Evolutionary Biology, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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50
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Rogalski MA, Gowler CD, Shaw CL, Hufbauer RA, Duffy MA. Human drivers of ecological and evolutionary dynamics in emerging and disappearing infectious disease systems. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0043. [PMID: 27920388 DOI: 10.1098/rstb.2016.0043] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2016] [Indexed: 01/03/2023] Open
Abstract
Humans have contributed to the increased frequency and severity of emerging infectious diseases, which pose a significant threat to wild and domestic species, as well as human health. This review examines major pathways by which humans influence parasitism by altering (co)evolutionary interactions between hosts and parasites on ecological timescales. There is still much to learn about these interactions, but a few well-studied cases show that humans influence disease emergence every step of the way. Human actions significantly increase dispersal of host, parasite and vector species, enabling greater frequency of infection in naive host populations and host switches. Very dense host populations resulting from urbanization and agriculture can drive the evolution of more virulent parasites and, in some cases, more resistant host populations. Human activities that reduce host genetic diversity or impose abiotic stress can impair the ability of hosts to adapt to disease threats. Further, evolutionary responses of hosts and parasites can thwart disease management and biocontrol efforts. Finally, in rare cases, humans influence evolution by eradicating an infectious disease. If we hope to fully understand the factors driving disease emergence and potentially control these epidemics we must consider the widespread influence of humans on host and parasite evolutionary trajectories.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
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Affiliation(s)
- Mary A Rogalski
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Camden D Gowler
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Clara L Shaw
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ruth A Hufbauer
- College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Meghan A Duffy
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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