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Wesselmann KM, Postigo-Hidalgo I, Pezzi L, de Oliveira-Filho EF, Fischer C, de Lamballerie X, Drexler JF. Emergence of Oropouche fever in Latin America: a narrative review. THE LANCET. INFECTIOUS DISEASES 2024; 24:e439-e452. [PMID: 38281494 DOI: 10.1016/s1473-3099(23)00740-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 01/30/2024]
Abstract
Since its discovery in 1955, the incidence and geographical spread of reported Oropouche virus (OROV) infections have increased. Oropouche fever has been suggested to be one of the most important vector-borne diseases in Latin America. However, both literature on OROV and genomic sequence availability are scarce, with few contributing laboratories worldwide. Three reassortant OROV glycoprotein gene variants termed Iquitos, Madre de Dios, and Perdões virus have been described from humans and non-human primates. OROV predominantly causes acute febrile illness, but severe neurological disease such as meningoencephalitis can occur. Due to unspecific symptoms, laboratory diagnostics are crucial. Several laboratory tests have been developed but robust commercial tests are hardly available. Although OROV is mainly transmitted by biting midges, it has also been detected in several mosquito species and a wide range of vertebrate hosts, which likely facilitates its widespread emergence. However, potential non-human vertebrate reservoirs have not been systematically studied. Robust animal models to investigate pathogenesis and immune responses are not available. Epidemiology, pathogenesis, transmission cycle, cross-protection from infections with OROV reassortants, and the natural history of infection remain unclear. This Review identifies Oropouche fever as a neglected disease and offers recommendations to address existing knowledge gaps, enable risk assessments, and ensure effective public health responses.
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Affiliation(s)
- Konrad M Wesselmann
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Ignacio Postigo-Hidalgo
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Laura Pezzi
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France; Centre National de Référence (CNR) des Arbovirus, Marseille, France
| | - Edmilson F de Oliveira-Filho
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Carlo Fischer
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France; Centre National de Référence (CNR) des Arbovirus, Marseille, France
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; German Centre for Infection Research (DZIF), Berlin, Germany.
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Lehmann T, Kouam C, Woo J, Diallo M, Wilkerson R, Linton YM. The African mosquito-borne diseasosome: geographical patterns, range expansion and future disease emergence. Proc Biol Sci 2023; 290:20231581. [PMID: 38018102 PMCID: PMC10685135 DOI: 10.1098/rspb.2023.1581] [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: 08/21/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
Mosquito-borne diseases (MBDs) threaten public health and food security globally. We provide the first biogeographic description of the African mosquito fauna (677 species) and the 151 mosquito-borne pathogens (MBPs) they transmit. While mosquito species richness agrees with expectations based on Africa's land surface, African arboviruses and mammalian plasmodia are more speciose than expected. Species assemblages of mosquitoes and MBPs similarly separate sub-Saharan Africa from North Africa, and those in West and Central Africa from eastern and southern Africa. Similarities between mosquitoes and MBPs in diversity and range size suggest that mosquitoes are key in delimiting the range of MBPs. With approximately 25% endemicity, approximately 50% occupying one to three countries and less than 5% occupying greater than 25 countries, the ranges of mosquitoes and MBPs are surprisingly small, suggesting that most MBPs are transmitted by a single mosquito species. Exceptionally widespread mosquito species feed on people and livestock, and most are high-altitude-windborne migrants. Likewise, widespread MBPs are transmitted among people or livestock by widespread mosquitoes, suggesting that adapting to people or livestock and to widespread mosquito species promote range expansion in MBPs. Range size may predict range expansion and emergence risk. We highlight key knowledge gaps that impede prediction and mitigation of future emergence of local and global MBDs.
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Affiliation(s)
- Tovi Lehmann
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Cedric Kouam
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Joshua Woo
- Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Mawlouth Diallo
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar, Senegal
| | - Richard Wilkerson
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History, Washington, DC, USA
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History, Washington, DC, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
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3
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Bamford CGG, de Souza WM, Parry R, Gifford RJ. Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae). Virus Evol 2022; 8:veac085. [PMID: 36533146 PMCID: PMC9752770 DOI: 10.1093/ve/veac085] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/06/2022] [Accepted: 09/05/2022] [Indexed: 01/24/2023] Open
Abstract
Flavivirids (family Flaviviridae) are a group of positive-strand ribonucleic acid (RNA) viruses that pose serious risks to human and animal health on a global scale. Here, we use flavivirid-derived deoxyribonucleic acid (DNA) sequences, identified in animal genomes, to reconstruct the long-term evolutionary history of family Flaviviridae. We demonstrate that flavivirids are >100 million years old and show that this timing can be combined with dates inferred from co-phyletic analysis to produce a cohesive overview of their evolution, distribution, and diversity wherein the main flavivirid subgroups originate in early animals and broadly co-diverge with major animal phyla. In addition, we reveal evidence that the 'classical flaviviruses' of vertebrates, most of which are transmitted via blood-feeding arthropod vectors, originally evolved in haematophagous arachnids and later acquired the capacity to be transmitted by insects. Our findings imply that the biological properties of flavivirids have been acquired gradually over the course of animal evolution. Thus, broad-scale comparative analysis will likely reveal fundamental insights into their biology. We therefore published our results via an open, extensible, database (Flavivirid-GLUE), which we constructed to facilitate the wider utilisation of genomic data and evolution-related domain knowledge in flavivirid research.
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Shrivastava G, Valenzuela-Leon PC, Chagas AC, Kern O, Botello K, Zhang Y, Martin-Martin I, Oliveira MB, Tirloni L, Calvo E. Alboserpin, the Main Salivary Anticoagulant from the Disease Vector Aedes albopictus, Displays Anti-FXa-PAR Signaling In Vitro and In Vivo. Immunohorizons 2022; 6:373-383. [PMID: 35738824 PMCID: PMC10753553 DOI: 10.4049/immunohorizons.2200045] [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: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/19/2022] Open
Abstract
Blood-feeding arthropods secrete potent salivary molecules, which include platelet aggregation inhibitors, vasodilators, and anticoagulants. Among these molecules, Alboserpin, the major salivary anticoagulant from the mosquito vector Aedes albopictus, is a specific inhibitor of the human coagulation factor Xa (FXa). In this study, we investigated the anti-inflammatory properties of Alboserpin, in vitro and in vivo. In vitro, Alboserpin inhibited FXa-induced protease-activated receptor (PAR)-1, PAR-2, PAR-3, VCAM, ICAM, and NF-κB gene expression in primary dermal microvascular endothelial cells. Alboserpin also prevented FXa-stimulated ERK1/2 gene expression and subsequent inflammatory cytokine release (MCP-1, TNF-α, IL-6, IL-8, IL-1β, IL-18). In vivo, Alboserpin reduced paw edema induced by FXa and subsequent release of inflammatory cytokines (CCL2, MCP-1, IL-1α, IL-6, IL-1β). Alboserpin also reduced FXa-induced endothelial permeability in vitro and in vivo. These findings show that Alboserpin is a potent anti-inflammatory molecule, in vivo and in vitro, and may play a significant role in blood feeding.
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Affiliation(s)
- Gaurav Shrivastava
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Paola Carolina Valenzuela-Leon
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Andrezza Campos Chagas
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Olivia Kern
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Karina Botello
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Yixiang Zhang
- Protein Chemistry Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT; and
| | - Ines Martin-Martin
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Markus Berger Oliveira
- Tick-Pathogen Transmission Unit, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT
| | - Lucas Tirloni
- Tick-Pathogen Transmission Unit, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT
| | - Eric Calvo
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD;
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5
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Zhang F, Chase-Topping M, Guo CG, Woolhouse MEJ. Predictors of human-infective RNA virus discovery in the United States, China, and Africa, an ecological study. eLife 2022; 11:e72123. [PMID: 35666108 PMCID: PMC9278958 DOI: 10.7554/elife.72123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background The variation in the pathogen type as well as the spatial heterogeneity of predictors make the generality of any associations with pathogen discovery debatable. Our previous work confirmed that the association of a group of predictors differed across different types of RNA viruses, yet there have been no previous comparisons of the specific predictors for RNA virus discovery in different regions. The aim of the current study was to close the gap by investigating whether predictors of discovery rates within three regions-the United States, China, and Africa-differ from one another and from those at the global level. Methods Based on a comprehensive list of human-infective RNA viruses, we collated published data on first discovery of each species in each region. We used a Poisson boosted regression tree (BRT) model to examine the relationship between virus discovery and 33 predictors representing climate, socio-economics, land use, and biodiversity across each region separately. The discovery probability in three regions in 2010-2019 was mapped using the fitted models and historical predictors. Results The numbers of human-infective virus species discovered in the United States, China, and Africa up to 2019 were 95, 80, and 107 respectively, with China lagging behind the other two regions. In each region, discoveries were clustered in hotspots. BRT modelling suggested that in all three regions RNA virus discovery was better predicted by land use and socio-economic variables than climatic variables and biodiversity, although the relative importance of these predictors varied by region. Map of virus discovery probability in 2010-2019 indicated several new hotspots outside historical high-risk areas. Most new virus species since 2010 in each region (6/6 in the United States, 19/19 in China, 12/19 in Africa) were discovered in high-risk areas as predicted by our model. Conclusions The drivers of spatiotemporal variation in virus discovery rates vary in different regions of the world. Within regions virus discovery is driven mainly by land-use and socio-economic variables; climate and biodiversity variables are consistently less important predictors than at a global scale. Potential new discovery hotspots in 2010-2019 are identified. Results from the study could guide active surveillance for new human-infective viruses in local high-risk areas. Funding FFZ is funded by the Darwin Trust of Edinburgh (https://darwintrust.bio.ed.ac.uk/). MEJW has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 874735 (VEO) (https://www.veo-europe.eu/).
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Affiliation(s)
- Feifei Zhang
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
| | - Margo Chase-Topping
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghEdinburghUnited Kingdom
| | - Chuan-Guo Guo
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong KongHong KongChina
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6
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Gibb R, Albery GF, Mollentze N, Eskew EA, Brierley L, Ryan SJ, Seifert SN, Carlson CJ. Mammal virus diversity estimates are unstable due to accelerating discovery effort. Biol Lett 2022; 18:20210427. [PMID: 34982955 PMCID: PMC8727147 DOI: 10.1098/rsbl.2021.0427] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/29/2021] [Indexed: 11/29/2022] Open
Abstract
Host-virus association data underpin research into the distribution and eco-evolutionary correlates of viral diversity and zoonotic risk across host species. However, current knowledge of the wildlife virome is inherently constrained by historical discovery effort, and there are concerns that the reliability of ecological inference from host-virus data may be undermined by taxonomic and geographical sampling biases. Here, we evaluate whether current estimates of host-level viral diversity in wild mammals are stable enough to be considered biologically meaningful, by analysing a comprehensive dataset of discovery dates of 6571 unique mammal host-virus associations between 1930 and 2018. We show that virus discovery rates in mammal hosts are either constant or accelerating, with little evidence of declines towards viral richness asymptotes, even in highly sampled hosts. Consequently, inference of relative viral richness across host species has been unstable over time, particularly in bats, where intensified surveillance since the early 2000s caused a rapid rearrangement of species' ranked viral richness. Our results illustrate that comparative inference of host-level virus diversity across mammals is highly sensitive to even short-term changes in sampling effort. We advise caution to avoid overinterpreting patterns in current data, since it is feasible that an analysis conducted today could draw quite different conclusions than one conducted only a decade ago.
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Affiliation(s)
- Rory Gibb
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Nardus Mollentze
- Medical Research Council - University of Glasgow Centre for Virus Research, Glasgow, UK
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Evan A. Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | - Liam Brierley
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Sadie J. Ryan
- Department of Geography, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- College of Life Sciences, University of KwaZulu Natal, Durban 4041, South Africa
| | - Stephanie N. Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Colin J. Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA
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7
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Singh BB, Ward MP, Dhand NK. Inherent virus characteristics and host range drive the zoonotic and emerging potential of viruses. Transbound Emerg Dis 2021; 69:e799-e813. [PMID: 34710290 DOI: 10.1111/tbed.14361] [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: 09/09/2021] [Revised: 04/04/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022]
Abstract
Understanding the zoonotic and emerging potential of viruses is critical to prevent and control spread that can cause disease epidemics or pandemics. We developed a database using the most up-to-date information from the International Committee on Taxonomy of Viruses (4958 virus species) and identified 1479 vertebrate virus species and their host ranges. Viral traits and host ranges were then used as predictors in generalized linear mixed models for three host-associated outcomes - confirmed zoonotic, potential zoonotic and disease emergence. We identified significant interactions between host range and viral characteristics, not previously reported, that influence the zoonotic and emergence potential of viruses. Bat- and livestock-adapted viruses posed high risk, and the risk increased substantially if these viruses were also present in other vertebrates or were not reported from invertebrates. Our model predicted 39 viruses of interest that have never been reported to have zoonotic potential (27) or to potentially become emerging human viruses (12). We conclude that nucleic acid type is important in identifying the zoonotic and emerging potential of viruses. We recommend enhanced surveillance and monitoring of these virus species identified with a zoonotic and emerging potential to mitigate disease outbreaks and future epidemics.
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Affiliation(s)
- Balbir B Singh
- Sydney School of Veterinary Science, The University of Sydney, Camden, Australia.,Centre for One Health, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Michael P Ward
- Sydney School of Veterinary Science, The University of Sydney, Camden, Australia
| | - Navneet K Dhand
- Sydney School of Veterinary Science, The University of Sydney, Camden, Australia
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8
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Lu M, Gao L, Li H, He F. The patterns of vascular plant discoveries in China. Ecol Evol 2021; 11:12378-12388. [PMID: 34594506 PMCID: PMC8462150 DOI: 10.1002/ece3.7971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/12/2021] [Accepted: 07/15/2021] [Indexed: 11/11/2022] Open
Abstract
AIM (1) To understand geographic patterns of species discovery by examining the effect of growth form, range size, and geographic distribution on discovery probability of vascular plant species in China; (2) to find out which taxa harbor the largest number of undiscovered species and where those species locate; and (3) to find out the determinants of province-level mean discovery time and inventory completeness. LOCATION China. METHODS We compiled the discovery time and province-level geographic distributions of ~31,000 vascular plant species described between 1753 and 2013 from Flora of China. We used a Cox proportional hazard model to determine the biological and geographic correlates of discovery probability. Accumulation curves of species discoveries were fitted by a logistic discovery model to estimate inventory completeness of different growth forms and of different provinces. We then used linear regression to identify the determinants of mean discovery time and beta regression to identify the determinants of inventory completeness. RESULTS We found that species with larger range size and distributed in northeastern part of China have a higher discovery probability. Coastal species were discovered earlier than inland species. Trees and shrubs of seed plants have the highest discovery probability while ferns have the lowest discovery probability. Herbs have the largest number of undiscovered species in China. Most undiscovered species will be found in southwest China, where three global biodiversity hot spots locate. Spatial patterns of mean discovery time and inventory completeness are mainly driven by the total number of species, human population density in an area, and latitude and longitude of a province. MAIN CONCLUSIONS Socioeconomic factors primarily determine the discovery patterns of vascular plants in China. Undiscovered species are most likely to be narrow-ranged, inconspicuous endemic species such as herbs and ferns, which are prone to extinctions and locate in biodiversity hot spots in southwestern China.
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Affiliation(s)
- Muyang Lu
- ECNU‐Alberta Joint Lab for Biodiversity StudyTiantong National Station for Forest Ecosystem ResearchEast China Normal UniversityShanghaiChina
- Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Lianming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Hongtao Li
- Germplasm Bank of Wild Species in Southwest ChinaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Fangliang He
- ECNU‐Alberta Joint Lab for Biodiversity StudyTiantong National Station for Forest Ecosystem ResearchEast China Normal UniversityShanghaiChina
- Department of Renewable ResourcesUniversity of AlbertaEdmontonABCanada
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de Almeida JP, Aguiar ER, Armache JN, Olmo RP, Marques JT. The virome of vector mosquitoes. Curr Opin Virol 2021; 49:7-12. [PMID: 33991759 DOI: 10.1016/j.coviro.2021.04.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/05/2021] [Accepted: 04/05/2021] [Indexed: 11/30/2022]
Abstract
Mosquitoes are the major vectors for arthropod-borne viruses (arboviruses) of medical importance. Aedes aegypti and A. albopictus are the most prolific and widespread mosquito vectors being responsible for global transmission of dengue, Zika and Chikungunya viruses. Characterizing the collection of viruses circulating in mosquitoes, the virome, has long been of special interest. In addition to arboviruses, mosquitoes carry insect-specific viruses (ISVs) that do not directly infect vertebrates. Mounting evidence indicates that ISVs interact with arboviruses and may affect mosquito vector competence. Here, we review our current knowledge about the virome of vector mosquitoes and discuss the challenges for the field that may lead to novel strategies to prevent outbreaks of arboviruses.
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Affiliation(s)
- João Pp de Almeida
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte CEP 31270901, Minas Gerais, Brazil
| | - Eric Rgr Aguiar
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte CEP 31270901, Minas Gerais, Brazil; Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), State University of Santa Cruz (UESC), Rodovia Ilhéus-Itabuna km 16, Ilhéus 45652-900, Brazil
| | - Juliana N Armache
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte CEP 31270901, Minas Gerais, Brazil
| | - Roenick P Olmo
- Université de Strasbourg, CNRS UPR9022, INSERM U1257, Strasbourg 67084, France
| | - João T Marques
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte CEP 31270901, Minas Gerais, Brazil; Université de Strasbourg, CNRS UPR9022, INSERM U1257, Strasbourg 67084, France.
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10
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Fisher MC, Murray KA. Emerging infections and the integrative environment-health sciences: the road ahead. Nat Rev Microbiol 2021; 19:133-135. [PMID: 33432234 PMCID: PMC7797887 DOI: 10.1038/s41579-021-00510-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The integrative environment-health sciences including One Health, Conservation Medicine, EcoHealth and Planetary Health embody the transdisciplinary synthesis needed to understand the multitude of factors that underpin emerging infections and their management. Future successes in confronting and resolving the complex causal basis of disease emergence to generate robust, systems-oriented risk reduction strategies that preserve both human health as well as promoting sustainable futures represent the ‘Moon Shot’ for the integrative environment-health sciences.
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Affiliation(s)
- Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Imperial College School of Public Health, Imperial College London, London, UK.
| | - Kris A Murray
- MRC Centre for Global Infectious Disease Analysis, Imperial College School of Public Health, Imperial College London, London, UK.,MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
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11
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Zhang F, Chase-Topping M, Guo CG, van Bunnik BAD, Brierley L, Woolhouse MEJ. Global discovery of human-infective RNA viruses: A modelling analysis. PLoS Pathog 2020; 16:e1009079. [PMID: 33253277 PMCID: PMC7728385 DOI: 10.1371/journal.ppat.1009079] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 12/10/2020] [Accepted: 10/19/2020] [Indexed: 12/28/2022] Open
Abstract
RNA viruses are a leading cause of human infectious diseases and the prediction of where new RNA viruses are likely to be discovered is a significant public health concern. Here, we geocoded the first peer-reviewed reports of 223 human RNA viruses. Using a boosted regression tree model, we matched these virus data with 33 explanatory factors related to natural virus distribution and research effort to predict the probability of virus discovery across the globe in 2010–2019. Stratified analyses by virus transmissibility and transmission mode were also performed. The historical discovery of human RNA viruses has been concentrated in eastern North America, Europe, central Africa, eastern Australia, and north-eastern South America. The virus discovery can be predicted by a combination of socio-economic, land use, climate, and biodiversity variables. Remarkably, vector-borne viruses and strictly zoonotic viruses are more associated with climate and biodiversity whereas non-vector-borne viruses and human transmissible viruses are more associated with GDP and urbanization. The areas with the highest predicted probability for 2010–2019 include three new regions including East and Southeast Asia, India, and Central America, which likely reflect both increasing surveillance and diversity of their virome. Our findings can inform priority regions for investment in surveillance systems for new human RNA viruses. There is a lack of evidence on the factors driving the discovery of RNA viruses in general globally. Here, we recorded the initial discovery sites of all 223 human RNA viruses and revealed its global distribution pattern. By using a machine learning method, we found that the virus discovery was driven by a combination of variables describing socio-economic level, land use, climate and biodiversity, with GDP and GDP growth found to be the two leading predictors. We also predicted the probability of virus discovery in 2010–2019 across the globe, and identified three new areas (East and Southeast Asia, India, and Central America) in addition to the historical high-risk areas. The further stratified analyses (distinguishing viruses transmissible in humans or strictly zoonotic, and vector-borne or non-vector-borne) helped pinpoint the explanatory factors for the discovery of specific categories of viruses and confirm the plausibility of the model. The results of our study further understanding of the spatial distribution of human RNA virus discovery, and map the likelihood of further discoveries across the world. By identifying where new viruses are most likely to be discovered in the near future the study helps identify priority areas for surveillance.
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Affiliation(s)
- Feifei Zhang
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Margo Chase-Topping
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, United Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Chuan-Guo Guo
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Bram A. D. van Bunnik
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Liam Brierley
- Department of Biostatistics, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Mark E. J. Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, United Kingdom
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12
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Global Perspectives on Arbovirus Outbreaks: A 2020 Snapshot. Trop Med Infect Dis 2020; 5:tropicalmed5030142. [PMID: 32906771 PMCID: PMC7558566 DOI: 10.3390/tropicalmed5030142] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 11/21/2022] Open
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13
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Artika IM, Dewantari AK, Wiyatno A. Molecular biology of coronaviruses: current knowledge. Heliyon 2020; 6:e04743. [PMID: 32835122 PMCID: PMC7430346 DOI: 10.1016/j.heliyon.2020.e04743] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) late December 2019 in Wuhan, China, marked the third introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The constant spillover of coronaviruses from natural hosts to humans has been linked to human activities and other factors. The seriousness of this infection and the lack of effective, licensed countermeasures clearly underscore the need of more detailed and comprehensive understanding of coronavirus molecular biology. Coronaviruses are large, enveloped viruses with a positive sense single-stranded RNA genome. Currently, coronaviruses are recognized as one of the most rapidly evolving viruses due to their high genomic nucleotide substitution rates and recombination. At the molecular level, the coronaviruses employ complex strategies to successfully accomplish genome expression, virus particle assembly and virion progeny release. As the health threats from coronaviruses are constant and long-term, understanding the molecular biology of coronaviruses and controlling their spread has significant implications for global health and economic stability. This review is intended to provide an overview of our current basic knowledge of the molecular biology of coronaviruses, which is important as basic knowledge for the development of coronavirus countermeasures.
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Affiliation(s)
- I. Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor, 16680, Indonesia
| | - Aghnianditya Kresno Dewantari
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
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14
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Artika IM, Wiyatno A, Ma'roef CN. Pathogenic viruses: Molecular detection and characterization. INFECTION GENETICS AND EVOLUTION 2020; 81:104215. [PMID: 32006706 PMCID: PMC7106233 DOI: 10.1016/j.meegid.2020.104215] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Pathogenic viruses are viruses that can infect and replicate within human cells and cause diseases. The continuous emergence and re-emergence of pathogenic viruses has become a major threat to public health. Whenever pathogenic viruses emerge, their rapid detection is critical to enable implementation of specific control measures and the limitation of virus spread. Further molecular characterization to better understand these viruses is required for the development of diagnostic tests and countermeasures. Advances in molecular biology techniques have revolutionized the procedures for detection and characterization of pathogenic viruses. The development of PCR-based techniques together with DNA sequencing technology, have provided highly sensitive and specific methods to determine virus circulation. Pathogenic viruses potentially having global catastrophic consequences may emerge in regions where capacity for their detection and characterization is limited. Development of a local capacity to rapidly identify new viruses is therefore critical. This article reviews the molecular biology of pathogenic viruses and the basic principles of molecular techniques commonly used for their detection and characterization. The principles of good laboratory practices for handling pathogenic viruses are also discussed. This review aims at providing researchers and laboratory personnel with an overview of the molecular biology of pathogenic viruses and the principles of molecular techniques and good laboratory practices commonly implemented for their detection and characterization. The continous emergence and re-emergence of pathogenic viruses has become a major threat to public health. PCR-based techniques together with DNA sequencing technology have provided highly sensitive and specific methods to determine virus circulation. Southeast Asia is considered to be vulnerable to potential outbreaks of pathogenic viruses. A number of pathogenic viruses have been reported to circulate in this region. The 2019 novel coronavirus has also been identified in Southeast Asia. Development of local capacity to rapidly identify new viruses is very important.
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Affiliation(s)
- I Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia; Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia.
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
| | - Chairin Nisa Ma'roef
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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15
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Vasilakis N, Tesh RB, Popov VL, Widen SG, Wood TG, Forrester NL, Gonzalez JP, Saluzzo JF, Alkhovsky S, Lam SK, Mackenzie JS, Walker PJ. Exploiting the Legacy of the Arbovirus Hunters. Viruses 2019; 11:E471. [PMID: 31126128 PMCID: PMC6563318 DOI: 10.3390/v11050471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 12/13/2022] Open
Abstract
In recent years, it has become evident that a generational gap has developed in the community of arbovirus research. This apparent gap is due to the dis-investment of training for the next generation of arbovirologists, which threatens to derail the rich history of virus discovery, field epidemiology, and understanding of the richness of diversity that surrounds us. On the other hand, new technologies have resulted in an explosion of virus discovery that is constantly redefining the virosphere and the evolutionary relationships between viruses. This paradox presents new challenges that may have immediate and disastrous consequences for public health when yet to be discovered arboviruses emerge. In this review we endeavor to bridge this gap by providing a historical context for the work being conducted today and provide continuity between the generations. To this end, we will provide a narrative of the thrill of scientific discovery and excitement and the challenges lying ahead.
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Affiliation(s)
- Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Steve G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Naomi L Forrester
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Jean Paul Gonzalez
- Center of Excellence for Emerging & Zoonotic Animal Disease, Kansas State University, Manhattan, KS 66502, USA.
| | | | - Sergey Alkhovsky
- Ivanovsky Institute of Virology, N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, 18 Gamaleya str., Moscow, Russia.
| | - Sai Kit Lam
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - John S Mackenzie
- Faculty of Medical Sciences, Curtin University, Perth, Western Australia 6102, Australia.
| | - Peter J Walker
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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16
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Hedrick SM. The Imperative to Vaccinate. J Pediatr 2018; 201:259-263. [PMID: 30054163 PMCID: PMC7131101 DOI: 10.1016/j.jpeds.2018.06.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/01/2018] [Accepted: 06/13/2018] [Indexed: 11/16/2022]
Affiliation(s)
- Stephen M. Hedrick
- Reprint requests: Stephen M. Hedrick, PhD, UC San Diego, Molecular Biology, 9500 Gilman Dr, La Jolla, CA 92093-0377
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17
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Rosenberg R, Lindsey NP, Fischer M, Gregory CJ, Hinckley AF, Mead PS, Paz-Bailey G, Waterman SH, Drexler NA, Kersh GJ, Hooks H, Partridge SK, Visser SN, Beard CB, Petersen LR. Vital Signs: Trends in Reported Vectorborne Disease Cases - United States and Territories, 2004-2016. MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT 2018; 67:496-501. [PMID: 29723166 PMCID: PMC5933869 DOI: 10.15585/mmwr.mm6717e1] [Citation(s) in RCA: 491] [Impact Index Per Article: 81.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction Vectorborne diseases are major causes of death and illness worldwide. In the United States, the most common vectorborne pathogens are transmitted by ticks or mosquitoes, including those causing Lyme disease; Rocky Mountain spotted fever; and West Nile, dengue, and Zika virus diseases. This report examines trends in occurrence of nationally reportable vectorborne diseases during 2004–2016. Methods Data reported to the National Notifiable Diseases Surveillance System for 16 notifiable vectorborne diseases during 2004–2016 were analyzed; findings were tabulated by disease, vector type, location, and year. Results A total 642,602 cases were reported. The number of annual reports of tickborne bacterial and protozoan diseases more than doubled during this period, from >22,000 in 2004 to >48,000 in 2016. Lyme disease accounted for 82% of all tickborne disease reports during 2004–2016. The occurrence of mosquitoborne diseases was marked by virus epidemics. Transmission in Puerto Rico, the U.S. Virgin Islands, and American Samoa accounted for most reports of dengue, chikungunya, and Zika virus diseases; West Nile virus was endemic, and periodically epidemic, in the continental United States. Conclusions and Implications for Public Health Practice Vectorborne diseases are a large and growing public health problem in the United States, characterized by geographic specificity and frequent pathogen emergence and introduction. Differences in distribution and transmission dynamics of tickborne and mosquitoborne diseases are often rooted in biologic differences of the vectors. To effectively reduce transmission and respond to outbreaks will require major national improvement of surveillance, diagnostics, reporting, and vector control, as well as new tools, including vaccines.
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Affiliation(s)
- Ronald Rosenberg
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Nicole P Lindsey
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Marc Fischer
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Christopher J Gregory
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Alison F Hinckley
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Paul S Mead
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Gabriela Paz-Bailey
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Stephen H Waterman
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Naomi A Drexler
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Gilbert J Kersh
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Holley Hooks
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Susanna K Partridge
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Susanna N Visser
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Charles B Beard
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
| | - Lyle R Petersen
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Fort Collins, Colorado
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18
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Brault AC, Blitvich BJ. Continued Need for Comprehensive Genetic and Phenotypic Characterization of Viruses: Benefits of Complementing Sequence Analyses with Functional Determinations. Am J Trop Med Hyg 2018; 98:1213. [PMID: 29557334 PMCID: PMC5953397 DOI: 10.4269/ajtmh.18-0128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Aaron C Brault
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa
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19
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A Century in the Life of the Control of Communicable Diseases Manual: 1917 to 2017. JOURNAL OF PUBLIC HEALTH MANAGEMENT AND PRACTICE 2018; 22:597-602. [PMID: 27682728 DOI: 10.1097/phh.0000000000000435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The Control of Communicable Diseases Manual, a premier publication of the American Public Health Association, celebrates its centennial in 2017. The Control of Communicable Diseases Manual has evolved in format and content through 20 separate editions. This article is a follow-up to an earlier article, titled "Evolution of the Control of Communicable Disease Manual: 1917 to 2000," that appeared in the Journal of Public Health Management & Practice in 2001. Our update focuses on the period since the 17th edition, which is characterized by dramatic changes. The 20th edition (2014) added a few arboviral diseases (Banna, Cache Valley, Eyach, Heartland, severe fever with thrombocytopenia syndrome virus, Iquitos, and Me Tri), but mostly contracted, leaving 65 arboviral entries. Other categories of pathogens also declined in the most recent editions, indicating an apparent trend to make the manual less encyclopedic. We attempt to explain these and other changes and ask the reader to comment whether they are aware of other related facts or history based on personal experience.
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20
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Abstract
The recent Ebola and Zika epidemics demonstrate the need for the continuous surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast, affordable sequencing of pathogen genomes - now a staple of the public health microbiology laboratory in well-resourced settings - can affect each of these areas. Coupling genomic diagnostics and epidemiology to innovative digital disease detection platforms raises the possibility of an open, global, digital pathogen surveillance system. When informed by a One Health approach, in which human, animal and environmental health are considered together, such a genomics-based system has profound potential to improve public health in settings lacking robust laboratory capacity.
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Affiliation(s)
- Jennifer L. Gardy
- British Columbia Centre for Disease Control, Vancouver, V5Z 4R4 British Columbia Canada
- School of Population and Public Health, University of British Columbia, Vancouver, V6T 1Z3 British Columbia Canada
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT UK
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21
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Rascovan N, Duraisamy R, Desnues C. Metagenomics and the Human Virome in Asymptomatic Individuals. Annu Rev Microbiol 2017; 70:125-41. [PMID: 27607550 DOI: 10.1146/annurev-micro-102215-095431] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High-throughput sequencing technologies have revolutionized how we think about viruses. Investigators can now go beyond pathogenic viruses and have access to the thousands of viruses that inhabit our bodies without causing clinical symptoms. By studying their interactions with each other, with other microbes, and with host genetics and immune systems, we can learn how they affect health and disease. This article reviews current knowledge of the composition and diversity of the human virome in physiologically healthy individuals. It focuses on recent results from metagenomics studies and discusses the contribution of bacteriophages and eukaryotic viruses to human health.
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Affiliation(s)
- Nicolás Rascovan
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
| | - Raja Duraisamy
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
| | - Christelle Desnues
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
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22
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Artika IM, Ma'roef CN. Laboratory biosafety for handling emerging viruses. Asian Pac J Trop Biomed 2017; 7:483-491. [PMID: 32289025 PMCID: PMC7103938 DOI: 10.1016/j.apjtb.2017.01.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/24/2016] [Accepted: 12/13/2016] [Indexed: 11/05/2022] Open
Abstract
Emerging viruses are viruses whose occurrence has risen within the past twenty years, or whose presence is likely to increase in the near future. Diseases caused by emerging viruses are a major threat to global public health. In spite of greater awareness of safety and containment procedures, the handling of pathogenic viruses remains a likely source of infection, and mortality, among laboratory workers. There is a steady increase in both the number of laboratories and scientist handling emerging viruses for diagnostics and research. The potential for harm associated to work with these infectious agents can be minimized through the application of sound biosafety concepts and practices. The main factors to the prevention of laboratory-acquired infection are well-trained personnel who are knowledgable and biohazard aware, who are perceptive of the various ways of transmission, and who are professional in safe laboratory practice management. In addition, we should emphasize that appropriate facilities, practices and procedures are to be used by the laboratory workers for the handling of emerging viruses in a safe and secure manner. This review is aimed at providing researchers and laboratory personnel with basic biosafety principles to protect themselves from exposure to emerging viruses while working in the laboratory. This paper focuses on what emerging viruses are, why emerging viruses can cause laboratory-acquired infection, how to assess the risk of working with emerging viruses, and how laboratory-acquired infection can be prevented. Control measures used in the laboratory designed as such that they protect workers from emerging viruses and safeguard the public through the safe disposal of infectious wastes are also addressed.
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Affiliation(s)
- I. Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia
| | - Chairin Nisa Ma'roef
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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23
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24
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25
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Dennehy JJ. Evolutionary ecology of virus emergence. Ann N Y Acad Sci 2016; 1389:124-146. [PMID: 28036113 PMCID: PMC7167663 DOI: 10.1111/nyas.13304] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/24/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
Abstract
The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment.
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Affiliation(s)
- John J Dennehy
- Biology Department, Queens College of the City University of New York, Queens, New York and The Graduate Center of the City University of New York, New York, New York
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26
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Smith DR. Waiting in the wings: The potential of mosquito transmitted flaviviruses to emerge. Crit Rev Microbiol 2016; 43:405-422. [PMID: 27800692 DOI: 10.1080/1040841x.2016.1230974] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The sudden dramatic emergence of the mosquito transmitted flavivirus Zika virus has bought to the world's attention a relatively obscure virus that was previously only known to specialist researchers. The genus Flavivirus of the family Flaviviridae contains a number of well-known mosquito transmitted human pathogenic viruses including the dengue, yellow fever, Japanese encephalitis and West Nile viruses. However, the genus also contains a number of lesser known human pathogenic viruses transmitted by mosquitoes including Wesselsbron virus, Ilheus virus, St. Louis encephalitis virus and Usutu virus. This review summarizes our knowledge of these lesser known mosquito transmitted flaviviruses and highlights their potential to emerge.
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Affiliation(s)
- Duncan R Smith
- a Institute of Molecular Biosciences and Center for Emerging and Neglected Infectious Diseases, Mahidol University , Thailand
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27
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Villinger J, Mbaya MK, Ouso D, Kipanga PN, Lutomiah J, Masiga DK. Arbovirus and insect-specific virus discovery in Kenya by novel six genera multiplex high-resolution melting analysis. Mol Ecol Resour 2016; 17:466-480. [PMID: 27482633 DOI: 10.1111/1755-0998.12584] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 07/02/2016] [Accepted: 07/05/2016] [Indexed: 02/03/2023]
Abstract
A broad diversity of arthropod-borne viruses (arboviruses) of global health concern are endemic to East Africa, yet most surveillance efforts are limited to just a few key viral pathogens. Additionally, estimates of arbovirus diversity in the tropics are likely to be underestimated as their discovery has lagged significantly over past decades due to limitations in fast and sensitive arbovirus identification methods. Here, we developed a nearly pan-arbovirus detection assay that uses high-resolution melting (HRM) analysis of RT-PCR products from highly multiplexed assays to differentiate broad diversities of arboviruses. We differentiated 15 viral culture controls and seven additional synthetic viral DNA sequence controls, within Flavivirus, Alphavirus, Nairovirus, Phlebovirus, Orthobunyavirus and Thogotovirus genera. Among Bunyamwera, sindbis, dengue and Thogoto virus serial dilutions, detection by multiplex RT-PCR-HRM was comparable to the gold standard Vero cell plaque assays. We applied our low-cost method for enhanced broad-range pathogen surveillance from mosquito samples collected in Kenya and identified diverse insect-specific viruses, including a new clade in anopheline mosquitoes, and Wesselsbron virus, an arbovirus that can cause viral haemorrhagic fever in humans and has not previously been isolated in Kenya, in Culex spp. and Anopheles coustani mosquitoes. Our findings demonstrate how multiplex RT-PCR-HRM can identify novel viral diversities and potential disease threats that may not be included in pathogen detection panels of routine surveillance efforts. This approach can be adapted to other pathogens to enhance disease surveillance and pathogen discovery efforts, as well as the study of pathogen diversity and viral evolutionary ecology.
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Affiliation(s)
- Jandouwe Villinger
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772, Nairobi, 00100, Kenya
| | - Martin K Mbaya
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772, Nairobi, 00100, Kenya.,Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, Nairobi, Kenya
| | - Daniel Ouso
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772, Nairobi, 00100, Kenya.,Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, Nairobi, Kenya
| | - Purity N Kipanga
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772, Nairobi, 00100, Kenya.,Zoological Institute, Katholieke Universiteit, Naamsestraat 59, P.O. Box 3000, Leuven, Belgium
| | - Joel Lutomiah
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Daniel K Masiga
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772, Nairobi, 00100, Kenya
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Springer YP, Hoekman D, Johnson PTJ, Duffy PA, Hufft RA, Barnett DT, Allan BF, Amman BR, Barker CM, Barrera R, Beard CB, Beati L, Begon M, Blackmore MS, Bradshaw WE, Brisson D, Calisher CH, Childs JE, Diuk‐Wasser M, Douglass RJ, Eisen RJ, Foley DH, Foley JE, Gaff HD, Gardner SL, Ginsberg HS, Glass GE, Hamer SA, Hayden MH, Hjelle B, Holzapfel CM, Juliano SA, Kramer LD, Kuenzi AJ, LaDeau SL, Livdahl TP, Mills JN, Moore CG, Morand S, Nasci RS, Ogden NH, Ostfeld RS, Parmenter RR, Piesman J, Reisen WK, Savage HM, Sonenshine DE, Swei A, Yabsley MJ. Tick‐, mosquito‐, and rodent‐borne parasite sampling designs for the National Ecological Observatory Network. Ecosphere 2016. [DOI: 10.1002/ecs2.1271] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Discovery of replicating circular RNAs by RNA-seq and computational algorithms. PLoS Pathog 2014; 10:e1004553. [PMID: 25503469 PMCID: PMC4263765 DOI: 10.1371/journal.ppat.1004553] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/04/2014] [Indexed: 11/19/2022] Open
Abstract
Replicating circular RNAs are independent plant pathogens known as viroids, or act to modulate the pathogenesis of plant and animal viruses as their satellite RNAs. The rate of discovery of these subviral pathogens was low over the past 40 years because the classical approaches are technical demanding and time-consuming. We previously described an approach for homology-independent discovery of replicating circular RNAs by analysing the total small RNA populations from samples of diseased tissues with a computational program known as progressive filtering of overlapping small RNAs (PFOR). However, PFOR written in PERL language is extremely slow and is unable to discover those subviral pathogens that do not trigger in vivo accumulation of extensively overlapping small RNAs. Moreover, PFOR is yet to identify a new viroid capable of initiating independent infection. Here we report the development of PFOR2 that adopted parallel programming in the C++ language and was 3 to 8 times faster than PFOR. A new computational program was further developed and incorporated into PFOR2 to allow the identification of circular RNAs by deep sequencing of long RNAs instead of small RNAs. PFOR2 analysis of the small RNA libraries from grapevine and apple plants led to the discovery of Grapevine latent viroid (GLVd) and Apple hammerhead viroid-like RNA (AHVd-like RNA), respectively. GLVd was proposed as a new species in the genus Apscaviroid, because it contained the typical structural elements found in this group of viroids and initiated independent infection in grapevine seedlings. AHVd-like RNA encoded a biologically active hammerhead ribozyme in both polarities, and was not specifically associated with any of the viruses found in apple plants. We propose that these computational algorithms have the potential to discover novel circular RNAs in plants, invertebrates and vertebrates regardless of whether they replicate and/or induce the in vivo accumulation of small RNAs.
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Detecting the emergence of novel, zoonotic viruses pathogenic to humans. Cell Mol Life Sci 2014; 72:1115-25. [PMID: 25416679 PMCID: PMC4629502 DOI: 10.1007/s00018-014-1785-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 11/12/2014] [Accepted: 11/13/2014] [Indexed: 12/13/2022]
Abstract
RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. Despite great advances made in diagnostic technology since the 1950s, the annual rate at which novel virulent viruses have been found has remained at 2–3. Most emerging viruses are zoonoses; they have jumped from mammal or bird hosts to humans. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations.
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Abstract
Orthobunyaviruses, which have small, tripartite, negative-sense RNA genomes and structurally simple virions composed of just four proteins, can have devastating effects on human health and well-being, either by causing disease in humans or by causing disease in livestock and crops. In this Review, I describe the recent genetic and structural advances that have revealed important insights into the composition of orthobunyavirus virions, viral transcription and replication and viral interactions with the host innate immune response. Lastly, I highlight outstanding questions and areas of future research.
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Affiliation(s)
- Richard M Elliott
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, UK
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32
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Development of an algorithm for production of inactivated arbovirus antigens in cell culture. J Virol Methods 2014; 208:66-78. [PMID: 25102428 DOI: 10.1016/j.jviromet.2014.07.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/17/2014] [Accepted: 07/26/2014] [Indexed: 11/22/2022]
Abstract
Arboviruses are medically important pathogens that cause human disease ranging from a mild fever to encephalitis. Laboratory diagnosis is essential to differentiate arbovirus infections from other pathogens with similar clinical manifestations. The Arboviral Diseases Branch (ADB) reference laboratory at the CDC Division of Vector-Borne Diseases (DVBD) produces reference antigens used in serological assays such as the virus-specific immunoglobulin M antibody-capture enzyme-linked immunosorbent assay (MAC-ELISA). Antigen production in cell culture has largely replaced the use of suckling mice; however, the methods are not directly transferable. The development of a cell culture antigen production algorithm for nine arboviruses from the three main arbovirus families, Flaviviridae, Togaviridae, and Bunyaviridae, is described here. Virus cell culture growth and harvest conditions were optimized, inactivation methods were evaluated, and concentration procedures were compared for each virus. Antigen performance was evaluated by the MAC-ELISA at each step of the procedure. The antigen production algorithm is a framework for standardization of methodology and quality control; however, a single antigen production protocol was not applicable to all arboviruses and needed to be optimized for each virus.
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33
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Virgin HW. The virome in mammalian physiology and disease. Cell 2014; 157:142-50. [PMID: 24679532 DOI: 10.1016/j.cell.2014.02.032] [Citation(s) in RCA: 398] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 02/13/2014] [Accepted: 02/13/2014] [Indexed: 02/07/2023]
Abstract
The virome contains the most abundant and fastest mutating genetic elements on Earth. The mammalian virome is constituted of viruses that infect host cells, virus-derived elements in our chromosomes, and viruses that infect the broad array of other types of organisms that inhabit us. Virome interactions with the host cannot be encompassed by a monotheistic view of viruses as pathogens. Instead, the genetic and transcriptional identity of mammals is defined in part by our coevolved virome, a concept with profound implications for understanding health and disease.
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Affiliation(s)
- Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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34
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Affiliation(s)
- Lisa M. Gargano
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia 30322; ,
| | - James M. Hughes
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia 30322; ,
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35
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Myint KSA, Kosasih H, Artika IM, Perkasa A, Puspita M, Ma'roef CN, Antonjaya U, Ledermann JP, Powers AM, Alisjahbana B. West Nile virus documented in Indonesia from acute febrile illness specimens. Am J Trop Med Hyg 2014; 90:260-2. [PMID: 24420775 DOI: 10.4269/ajtmh.13-0445] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We report the presence of West Nile virus in a cryopreserved, dengue-negative serum specimen collected from an acute fever case on Java in 2004-2005. The strain belongs to genotype lineage 2, which has recently been implicated in human outbreaks in Europe.
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Affiliation(s)
- Khin Saw Aye Myint
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia; Universitas Padjadjaran, Bandung, Indonesia; Centers for Disease Control and Prevention, Fort Collins, Colorado; Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia
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