1
|
Condori RE, Kartskhia N, Avaliani L, Donduashvili M, Elbakidze T, Kapanadze A, Pieracci EG, Maghlakelidze G, Wadhwa A, Morgan CN, Reynolds M, Li Y, Ninidze L. Comparing the genetic typing methods for effective surveillance and rabies control in Georgia. Front Microbiol 2023; 14:1243510. [PMID: 38107855 PMCID: PMC10722154 DOI: 10.3389/fmicb.2023.1243510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/31/2023] [Indexed: 12/19/2023] Open
Abstract
A full nucleoprotein gene sequencing of 68 isolates collected from passive rabies surveillance system in Georgia between 2015 and 2016 identified two distinct dog rabies phylogroups, GEO_V1 and GEO_V2, which both belonged to the cosmopolitan dog clade. GEO_V1 was found throughout the country and was further divided into four sub-phylogroups that overlapped geographically; GEO_V2 was found in the southeast region and was closely related to dog rabies in Azerbaijan. A sequence analysis of the full N gene, partial nucleoprotein gene of N-terminal and C-terminal, and the amplicon sequences of pan-lyssavirus RT-qPCR LN34 showed that all four sequencing approaches provided clear genetic typing results of canine rabies and could further differentiate GEO_V1 and GEO_V2. The phylogenetic analysis results vary and were affected by the length of the sequences used. Amplicon sequencing of the LN34 assay positive samples provided a rapid and cost-effective method for rabies genetic typing, which is important for improving rabies surveillance and canine rabies eradication globally.
Collapse
Affiliation(s)
- Rene E. Condori
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Natia Kartskhia
- Veterinary Department, National Food Agency, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
| | - Lasha Avaliani
- Veterinary Department, National Food Agency, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
| | - Marina Donduashvili
- State Laboratory of Agriculture, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
| | - Tinatin Elbakidze
- State Laboratory of Agriculture, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
| | - Ana Kapanadze
- State Laboratory of Agriculture, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
| | - Emily G. Pieracci
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Giorgi Maghlakelidze
- Center for Global Health, Centers for Disease Control and Prevention, Tbilisi, Georgia
| | - Ashutosh Wadhwa
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Clint N. Morgan
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Mary Reynolds
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Yu Li
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lena Ninidze
- Veterinary Department, National Food Agency, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
| |
Collapse
|
2
|
Urban L, Perlas A, Francino O, Martí‐Carreras J, Muga BA, Mwangi JW, Boykin Okalebo L, Stanton JL, Black A, Waipara N, Fontsere C, Eccles D, Urel H, Reska T, Morales HE, Palmada‐Flores M, Marques‐Bonet T, Watsa M, Libke Z, Erkenswick G, van Oosterhout C. Real-time genomics for One Health. Mol Syst Biol 2023; 19:e11686. [PMID: 37325891 PMCID: PMC10407731 DOI: 10.15252/msb.202311686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.
Collapse
Affiliation(s)
- Lara Urban
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Albert Perlas
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
| | - Olga Francino
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Joan Martí‐Carreras
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Brenda A Muga
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | | | | | | | - Amanda Black
- Bioprotection AotearoaLincoln UniversityLincolnNew Zealand
| | | | - Claudia Fontsere
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
| | - David Eccles
- Hugh Green Cytometry CentreMalaghan Institute of Medical ResearchWellingtonNew Zealand
| | - Harika Urel
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Tim Reska
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Hernán E Morales
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
- Department of Biology, Ecology BuildingLund UniversityLundSweden
| | - Marc Palmada‐Flores
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
| | - Tomas Marques‐Bonet
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAGCentre of Genomic AnalysisBarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaBarcelonaSpain
| | | | - Zane Libke
- Instituto Nacional de BiodiversidadQuitoEcuador
- Fundación Sumak Kawsay In SituCantón MeraEcuador
| | | | | |
Collapse
|
3
|
Capin JBG, Sanque AJC, Eng MNJ, Lagare A, Sepulveda MCB, Murao LAE. Emerging Genomic Trends on Rabies Virus in Davao Region, Philippines, 2018-2021. Viruses 2023; 15:1658. [PMID: 37632001 PMCID: PMC10459148 DOI: 10.3390/v15081658] [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: 06/26/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/27/2023] Open
Abstract
Rabies, caused by the rabies virus (RABV), remains a significant public health issue in the Philippines despite efforts to control it. To eliminate rabies by 2030, effective surveillance strategies are crucial. In this study, we examined RABV evolution and phylodynamics in the Davao Region using genome sequences from Davao City and nearby provinces. We adapted the RABV ARTIC Protocol for Oxford Nanopore High-Throughput Sequencing to optimize workflow efficiency under limited resources. Comparing new virus samples collected from June 2019 to June 2021 (n = 38) with baseline samples from June 2018 to May 2019 (n = 49), new sub-clades were observed in the phylogenetic tree, suggesting divergence from older variants that were previously undetected. Most of the new viruses belonged to the Asian SEA4_A1.1.1 lineage, but new (SEA4_B1 and SEA4_B1.1) and emerging (SEA4_B1.1_E1) lineages that have never been reported in the Philippines were also identified. The baseline study reported phylogeographic clustering of RABV isolates from the same areas. However, this pattern was disrupted in the current biosurveillance, with variants detected in areas outside the original cluster. Furthermore, our findings revealed significant transmission routes between Davao City and neighboring provinces, contrasting with the predominantly intra-city transmission observed in the baseline study. These results underscore the need for ongoing and timely genomic surveillance to monitor genetic diversity changes and the emergence of novel strains, as well as to track alterations in transmission pathways. Implementing cost-effective next-generation sequencing workflows will facilitate the integration of genomic surveillance into rabies control programs, particularly in resource-limited settings. Collaborations between different sectors can empower local laboratories and experts in genomic technologies and analysis.
Collapse
Affiliation(s)
- Jessel Babe G. Capin
- Department of Biological Science and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Davao City 8000, Philippines; (J.B.G.C.); (A.J.C.S.)
| | - Angela Jahn C. Sanque
- Department of Biological Science and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Davao City 8000, Philippines; (J.B.G.C.); (A.J.C.S.)
| | - Maria Noreen J. Eng
- Davao City Veterinarian’s Office, Davao City 8000, Philippines; (M.N.J.E.); (A.L.); (M.C.B.S.)
| | - Arlene Lagare
- Davao City Veterinarian’s Office, Davao City 8000, Philippines; (M.N.J.E.); (A.L.); (M.C.B.S.)
| | | | - Lyre Anni E. Murao
- Department of Biological Science and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Davao City 8000, Philippines; (J.B.G.C.); (A.J.C.S.)
| |
Collapse
|
4
|
Viana M, Benavides JA, Broos A, Ibañez Loayza D, Niño R, Bone J, da Silva Filipe A, Orton R, Valderrama Bazan W, Matthiopoulos J, Streicker DG. Effects of culling vampire bats on the spatial spread and spillover of rabies virus. SCIENCE ADVANCES 2023; 9:eadd7437. [PMID: 36897949 PMCID: PMC10005164 DOI: 10.1126/sciadv.add7437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Controlling pathogen circulation in wildlife reservoirs is notoriously challenging. In Latin America, vampire bats have been culled for decades in hopes of mitigating lethal rabies infections in humans and livestock. Whether culls reduce or exacerbate rabies transmission remains controversial. Using Bayesian state-space models, we show that a 2-year, spatially extensive bat cull in an area of exceptional rabies incidence in Peru failed to reduce spillover to livestock, despite reducing bat population density. Viral whole genome sequencing and phylogeographic analyses further demonstrated that culling before virus arrival slowed viral spatial spread, but reactive culling accelerated spread, suggesting that culling-induced changes in bat dispersal promoted viral invasions. Our findings question the core assumptions of density-dependent transmission and localized viral maintenance that underlie culling bats as a rabies prevention strategy and provide an epidemiological and evolutionary framework to understand the outcomes of interventions in complex wildlife disease systems.
Collapse
Affiliation(s)
- Mafalda Viana
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Julio A. Benavides
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
- Doctorado en Medicina de la Conservación y Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440 Santiago, Chile
| | - Alice Broos
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | | | - Ruby Niño
- Colegio Médico Veterinario de Apurímac, Abancay, Perú
| | - Jordan Bone
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | | | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - William Valderrama Bazan
- ILLARIY (Asociación para el Desarrollo y Conservación de los Recursos Naturales), Lima, Perú
- Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jason Matthiopoulos
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Daniel G. Streicker
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| |
Collapse
|
5
|
From Field Tests to Molecular Tools-Evaluating Diagnostic Tests to Improve Rabies Surveillance in Namibia. Viruses 2023; 15:v15020371. [PMID: 36851585 PMCID: PMC9966532 DOI: 10.3390/v15020371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Rabies is endemic in Namibia and is present both in wildlife carnivores and domestic free-roaming dogs. The disease thus represents a challenge for public human and veterinary disease control. Namibia has implemented a national strategic plan to control rabies and the country's activities are supported by international organizations. To this end, rabies diagnosis at the Central Veterinary Laboratory (CVL) was improved in the frame of a World Organization for Animal Health (WOAH) laboratory twinning program: from practical sampling techniques and the use of lateral flow devices to a novel universal and discriminatory quantitative real-time Reverse transcription polymerase chain reaction (RT-qPCR), which easily identify dog-associated rabies viruses. The procedures applied and the results can be used as a template to improve rabies laboratory diagnosis.
Collapse
|
6
|
Elimination of human rabies in Goa, India through an integrated One Health approach. Nat Commun 2022; 13:2788. [PMID: 35589709 PMCID: PMC9120018 DOI: 10.1038/s41467-022-30371-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 04/27/2022] [Indexed: 01/13/2023] Open
Abstract
Dog-mediated rabies kills tens of thousands of people each year in India, representing one third of the estimated global rabies burden. Whilst the World Health Organization (WHO), World Organization for Animal Health (OIE) and the Food and Agriculture Organization of the United Nations (FAO) have set a target for global dog-mediated human rabies elimination by 2030, examples of large-scale dog vaccination programs demonstrating elimination remain limited in Africa and Asia. We describe the development of a data-driven rabies elimination program from 2013 to 2019 in Goa State, India, culminating in human rabies elimination and a 92% reduction in monthly canine rabies cases. Smartphone technology enabled systematic spatial direction of remote teams to vaccinate over 95,000 dogs at 70% vaccination coverage, and rabies education teams to reach 150,000 children annually. An estimated 2249 disability-adjusted life years (DALYs) were averted over the program period at 526 USD per DALY, making the intervention 'very cost-effective' by WHO definitions. This One Health program demonstrates that human rabies elimination is achievable at the state level in India.
Collapse
|
7
|
Campbell K, Gifford RJ, Singer J, Hill V, O’Toole A, Rambaut A, Hampson K, Brunker K. Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination. PLoS Pathog 2022; 18:e1010023. [PMID: 35500026 PMCID: PMC9162366 DOI: 10.1371/journal.ppat.1010023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/02/2022] [Accepted: 03/30/2022] [Indexed: 12/17/2022] Open
Abstract
The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 96 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, as well as areas of persistence and routes of virus movement, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as countries work towards eliminating dog-mediated rabies, as well as having potential for broader application to the surveillance of other viruses.
Collapse
Affiliation(s)
- Kathryn Campbell
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Joshua Singer
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Aine O’Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|