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Chadwick FJ, Haydon DT, Husmeier D, Ovaskainen O, Matthiopoulos J. LIES of omission: complex observation processes in ecology. Trends Ecol Evol 2024; 39:368-380. [PMID: 37949794 DOI: 10.1016/j.tree.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Advances in statistics mean that it is now possible to tackle increasingly sophisticated observation processes. The intricacies and ambitious scale of modern data collection techniques mean that this is now essential. Methodological research to make inference about the biological process while accounting for the observation process has expanded dramatically, but solutions are often presented in field-specific terms, limiting our ability to identify commonalities between methods. We suggest a typology of observation processes that could improve translation between fields and aid methodological synthesis. We propose the LIES framework (defining observation processes in terms of issues of Latency, Identifiability, Effort and Scale) and illustrate its use with both simple examples and more complex case studies.
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Affiliation(s)
- Fergus J Chadwick
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK; Centre for Research Into Ecological and Environmental Monitoring, School of Mathematics and Statistics, University of St Andrews, St. Andrews, Scotland, UK.
| | - Daniel T Haydon
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Dirk Husmeier
- School of Mathematics and Statistics, University of Glasgow, Glasgow, G12 8TA, UK
| | - Otso Ovaskainen
- Department of Biological and Environmental Science, P.O. Box 35 FI-40014, University of Jyväskylä, Jyväskylä, Finland
| | - Jason Matthiopoulos
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
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Moorthy GS, Rubach MP, Maze MJ, Refuerzo RP, Shirima GM, Lukambagire AS, Bodenham RF, Cash-Goldwasser S, Thomas KM, Sakasaka P, Mkenda N, Bowhay TR, Perniciaro JL, Nicholson WL, Kersh GJ, Kazwala RR, Mmbaga BT, Buza JJ, Maro VP, Haydon DT, Crump JA, Halliday JEB. Prevalence and risk factors for Q fever, spotted fever group rickettsioses, and typhus group rickettsioses in a pastoralist community of northern Tanzania, 2016-2017. Trop Med Int Health 2024. [PMID: 38480005 DOI: 10.1111/tmi.13980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
BACKGROUND In northern Tanzania, Q fever, spotted fever group (SFG) rickettsioses, and typhus group (TG) rickettsioses are common causes of febrile illness. We sought to describe the prevalence and risk factors for these zoonoses in a pastoralist community. METHODS Febrile patients ≥2 years old presenting to Endulen Hospital in the Ngorongoro Conservation Area were enrolled from August 2016 through October 2017. Acute and convalescent blood samples were collected, and a questionnaire was administered. Sera were tested by immunofluorescent antibody (IFA) IgG assays using Coxiella burnetii (Phase II), Rickettsia africae, and Rickettsia typhi antigens. Serologic evidence of exposure was defined by an IFA titre ≥1:64; probable cases by an acute IFA titre ≥1:128; and confirmed cases by a ≥4-fold rise in titre between samples. Risk factors for exposure and acute case status were evaluated. RESULTS Of 228 participants, 99 (43.4%) were male and the median (interquartile range) age was 27 (16-41) years. Among these, 117 (51.3%) had C. burnetii exposure, 74 (32.5%) had probable Q fever, 176 (77.2%) had SFG Rickettsia exposure, 134 (58.8%) had probable SFG rickettsioses, 11 (4.8%) had TG Rickettsia exposure, and 4 (1.8%) had probable TG rickettsioses. Of 146 participants with paired sera, 1 (0.5%) had confirmed Q fever, 8 (5.5%) had confirmed SFG rickettsioses, and none had confirmed TG rickettsioses. Livestock slaughter was associated with acute Q fever (adjusted odds ratio [OR] 2.54, 95% confidence interval [CI] 1.38-4.76) and sheep slaughter with SFG rickettsioses case (OR 4.63, 95% CI 1.08-23.50). DISCUSSION Acute Q fever and SFG rickettsioses were detected in participants with febrile illness. Exposures to C. burnetii and to SFG Rickettsia were highly prevalent, and interactions with livestock were associated with increased odds of illness with both pathogens. Further characterisation of the burden and risks for these diseases is warranted.
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Affiliation(s)
- Ganga S Moorthy
- Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, North Carolina, USA
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Matthew P Rubach
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, USA
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
- Kilimanjaro Christian Medical University College, Tumaini University, Moshi, Tanzania
| | - Michael J Maze
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Regina P Refuerzo
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Gabriel M Shirima
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - AbdulHamid S Lukambagire
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- EcoHealth Alliance, New York, New York, USA
| | | | | | - Kate M Thomas
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | | | - Nestory Mkenda
- Endulen Hospital, Ngorongoro Conservation Area, Endulen, Tanzania
| | - Thomas R Bowhay
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Jamie L Perniciaro
- Rickettsial Zoonoses Branch, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - William L Nicholson
- Rickettsial Zoonoses Branch, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gilbert J Kersh
- Rickettsial Zoonoses Branch, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rudovick R Kazwala
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Blandina T Mmbaga
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Joram J Buza
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Venance P Maro
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Daniel T Haydon
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - John A Crump
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, USA
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Jo E B Halliday
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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Mbwambo GA, van Zwetselaar M, Sonda T, Lukambagire AS, Njau JS, Wadugu B, Ignass IP, Amani NB, Hugho EA, Rubach MP, Sakasaka P, Oisso RS, Mkenda N, Shirima G, Ashford RT, Haydon DT, Maro VP, Kazwala RR, Kumburu HH, Mmbaga BT, Halliday JEB. Complete genome sequence of Brucella abortus isolated from a human blood culture sample in Tanzania. Microbiol Resour Announc 2024; 13:e0093023. [PMID: 38289053 PMCID: PMC10871059 DOI: 10.1128/mra.00930-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/07/2024] [Indexed: 02/16/2024] Open
Abstract
Brucella abortus causes infections in humans and livestock. Bacterial isolates are challenging to obtain, and very little is known about the genomic epidemiology of this species in Africa. Here, we report the complete genome sequence of a Brucella abortus isolate cultured from a febrile human in northern Tanzania.
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Affiliation(s)
| | | | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | - Judith S. Njau
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Boaz Wadugu
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | | | - Ephrasia A. Hugho
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Institute of Public Health, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Matthew P. Rubach
- Department of Medicine, Division of Infectious Disease and International Health, Duke Global Health Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Rose S. Oisso
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | - Gabriel Shirima
- Nelson Mandela Africa Institute of Science and Technology, Arusha, Tanzania
| | - Roland T. Ashford
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Daniel T. Haydon
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Venance P. Maro
- Department of Internal Medicine, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Rudovick R. Kazwala
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Happiness H. Kumburu
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Jo E. B. Halliday
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
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Kabalika Z, Haydon DT, McGill RAR, Morales JM, Morrison TA, Newton J, Hopcraft JGC. Using sulfur stable isotope ratios (δ 34 S) for animal geolocation: Estimating the delay mechanisms between diet ingestion and isotope incorporation in tail hair. Rapid Commun Mass Spectrom 2024; 38:e9674. [PMID: 38124168 PMCID: PMC10909487 DOI: 10.1002/rcm.9674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 12/23/2023]
Abstract
RATIONALE Metabolism and diet quality play an important role in determining delay mechanisms between an animal ingesting an element and depositing the associated isotope signal in tissue. While many isotope mixing models assume instantaneous reflection of diet in an animal- tissue, this is rarely the case. Here we use data from wildebeest to measure the lag time between ingestion of 34 S and its detection in tail hair. METHODS We use time-lagged regression analysis of δ34 S data from GPS-collared blue wildebeest from the Serengeti ecosystem in combination with δ34 S isoscape data to estimate the lag time between an animal ingesting and depositing 34 S in tail hair. RESULTS The best fitting regression model of δ34 S in tail hair and an individual- position on the δ34 S isoscape is generated assuming an average time delay of 78 days between ingestion and detection in tail hair. This suggests that sulfur may undergo multiple metabolic transitions before being deposited in tissue. CONCLUSION Our findings help to unravel the underlying complexities associated with sulfur metabolism and are broadly consistent with results from other species. These findings will help to inform research aiming to apply the variation of δ34 S in inert biological material for geolocation or understanding dietary changes, especially for fast moving migratory ungulates such as wildebeest.
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Affiliation(s)
- Zabibu Kabalika
- School of Biodiversity, One Health and Veterinary Medicine, Graham Kerr Building, University of Glasgow, Glasgow, UK
| | - Daniel T Haydon
- School of Biodiversity, One Health and Veterinary Medicine, Graham Kerr Building, University of Glasgow, Glasgow, UK
| | - Rona A R McGill
- National Environmental Isotope Facility, Scottish Universities Environmental Research Centre, University of Glasgow, Glasgow, UK
| | - Juan M Morales
- School of Biodiversity, One Health and Veterinary Medicine, Graham Kerr Building, University of Glasgow, Glasgow, UK
| | - Thomas A Morrison
- School of Biodiversity, One Health and Veterinary Medicine, Graham Kerr Building, University of Glasgow, Glasgow, UK
| | - Jason Newton
- National Environmental Isotope Facility, Scottish Universities Environmental Research Centre, University of Glasgow, Glasgow, UK
| | - J Grant C Hopcraft
- School of Biodiversity, One Health and Veterinary Medicine, Graham Kerr Building, University of Glasgow, Glasgow, UK
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Maze MJ, Shirima GM, Lukambagire AHS, Bodenham RF, Rubach MP, Cash-Goldwasser S, Carugati M, Thomas KM, Sakasaka P, Mkenda N, Allan KJ, Kazwala RR, Mmbaga BT, Buza JJ, Maro VP, Galloway RL, Haydon DT, Crump JA, Halliday JEB. Prevalence and risk factors for human leptospirosis at a hospital serving a pastoralist community, Endulen, Tanzania. PLoS Negl Trop Dis 2023; 17:e0011855. [PMID: 38117858 PMCID: PMC10766184 DOI: 10.1371/journal.pntd.0011855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/04/2024] [Accepted: 12/11/2023] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND Leptospirosis is suspected to be a major cause of illness in rural Tanzania associated with close contact with livestock. We sought to determine leptospirosis prevalence, identify infecting Leptospira serogroups, and investigate risk factors for leptospirosis in a rural area of Tanzania where pastoralist animal husbandry practices and sustained livestock contact are common. METHODS We enrolled participants at Endulen Hospital, Tanzania. Patients with a history of fever within 72 hours, or a tympanic temperature of ≥38.0°C were eligible. Serum samples were collected at presentation and 4-6 weeks later. Sera were tested using microscopic agglutination testing with 20 Leptospira serovars from 17 serogroups. Acute leptospirosis cases were defined by a ≥four-fold rise in antibody titre between acute and convalescent serum samples or a reciprocal titre ≥400 in either sample. Leptospira seropositivity was defined by a single reciprocal antibody titre ≥100 in either sample. We defined the predominant reactive serogroup as that with the highest titre. We explored risk factors for acute leptospirosis and Leptospira seropositivity using logistic regression modelling. RESULTS Of 229 participants, 99 (43.2%) were male and the median (range) age was 27 (0, 78) years. Participation in at least one animal husbandry practice was reported by 160 (69.9%). We identified 18 (7.9%) cases of acute leptospirosis, with Djasiman 8 (44.4%) and Australis 7 (38.9%) the most common predominant reactive serogroups. Overall, 69 (30.1%) participants were Leptospira seropositive and the most common predominant reactive serogroups were Icterohaemorrhagiae (n = 20, 29.0%), Djasiman (n = 19, 27.5%), and Australis (n = 17, 24.6%). Milking cattle (OR 6.27, 95% CI 2.24-7.52) was a risk factor for acute leptospirosis, and milking goats (OR 2.35, 95% CI 1.07-5.16) was a risk factor for Leptospira seropositivity. CONCLUSIONS We identified leptospirosis in approximately one in twelve patients attending hospital with fever from this rural community. Interventions that reduce risks associated with milking livestock may reduce human infections.
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Affiliation(s)
- Michael J. Maze
- Department of Medicine, University of Otago, Christchurch, New Zealand
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Gabriel M. Shirima
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | | | - Matthew P. Rubach
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina, United States
| | - Shama Cash-Goldwasser
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States
| | - Manuela Carugati
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina, United States
| | - Kate M. Thomas
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Philoteus Sakasaka
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Nestory Mkenda
- Endulen Hospital, Ngorongoro Conservation Area, Endulen, Tanzania
| | - Kathryn J. Allan
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rudovick R. Kazwala
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Blandina T. Mmbaga
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Joram J. Buza
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Venance P. Maro
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Renee L. Galloway
- Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Daniel T. Haydon
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - John A. Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Jo E. B. Halliday
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Nuvey FS, Hanley N, Simpson K, Haydon DT, Hattendorf J, Mensah GI, Addo KK, Bonfoh B, Zinsstag J, Fink G. Farmers' valuation and willingness to pay for vaccines to protect livestock resources against priority infectious diseases in Ghana. Prev Vet Med 2023; 219:106028. [PMID: 37774497 DOI: 10.1016/j.prevetmed.2023.106028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/06/2023] [Accepted: 09/21/2023] [Indexed: 10/01/2023]
Abstract
INTRODUCTION Livestock vaccination coverage rates remain low in many lower and middle income countries despite effective vaccines being commonly available. Consequently, many preventable infectious livestock diseases remain highly prevalent, causing significant animal mortalities and threatening farmers' livelihood and food security. This study sought to assess farmers' maximum willingness to pay (WTP) for contagious bovine pleuropneumonia (CBPP), and peste-des-petits-ruminants (PPR) vaccination of cattle, and sheep and goats, respectively. METHODS Overall, 350 ruminant livestock farmers were randomly selected from three districts located in the northern, middle and southern farming belts of Ghana. We implemented a double-bounded dichotomous contingent valuation experiment, where farmers indicated their WTP for vaccinating each livestock specie(s) owned at randomly assigned price points. WTP responses were analyzed using maximum likelihood estimation, and factors influencing WTP were assessed using censored regression analysis accounting for village-level clustering. RESULTS Mean WTP for CBPP vaccination was USD 1.43 or Ghanaian Cedi (GHC) 8.63 (95% CI: GHC 7.08-GHC 10.19) per cattle. Mean WTP for PPR vaccination was USD 1.17 or GHC 7.02 (95% CI: GHC 5.99-GHC 8.05) per sheep, and USD 1.1 or GHC 6.66 (95% CI: GHC 5.89-GHC 7.44) per goat. WTP was positively associated with resilience, limited knowledge about vaccines (assessed prior to WTP experiment), farmland size, and male gender, after adjusting for other covariates. To attain 70% vaccination coverage in Ghana, vaccination costs should be no larger than GHC 5.30 (USD 0.88) for CBPP per cattle and GHC 3.89 (USD 0.65) and GHC 3.67 (USD 0.61), respectively, for PPR vaccines per sheep and goat. CONCLUSIONS Ruminant livestock farmers in Ghana value vaccination highly, and are, on average, willing to pay vaccination costs that exceed the prevailing market prices (GHC 6 for CBPP and GHC 5 for PPR vaccination) to protect their livestock resources. To achieve 70% coverage, only minor subsidies would likely be required. These results suggest that effective disease control in these settings should be possible with appropriate distribution strategies.
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Affiliation(s)
- Francis Sena Nuvey
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland; Faculty of Medicine, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan BP 1303, Cote d'Ivoire.
| | - Nick Hanley
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, UK
| | - Katherine Simpson
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, UK
| | - Daniel T Haydon
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, UK
| | - Jan Hattendorf
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland; Faculty of Science, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Gloria Ivy Mensah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, P.O. Box LG 581, Ghana
| | - Kennedy Kwasi Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, P.O. Box LG 581, Ghana
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan BP 1303, Cote d'Ivoire
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland; Faculty of Science, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Günther Fink
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland; Faculty of Economics, University of Basel, Peter Merian-Weg 6, 4052 Basel, Switzerland
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Nuvey FS, Haydon DT, Hattendorf J, Addo KK, Mensah GI, Fink G, Zinsstag J, Bonfoh B. Relationship between animal health and livestock farmers' wellbeing in Ghana: beyond zoonoses. BMC Public Health 2023; 23:1353. [PMID: 37452274 PMCID: PMC10347735 DOI: 10.1186/s12889-023-16287-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023] Open
Abstract
INTRODUCTION Livestock production is a key livelihood source for many people in developing countries. Poor control of livestock diseases hamper livestock productivity, threatening farmers' wellbeing and food security. This study estimates the effect of livestock mortalities attributable to disease on the wellbeing of livestock farmers. METHODS Overall, 350 ruminant livestock farmers were randomly selected from three districts located in the north, middle and southern belts of Ghana. Mixed-effect linear regression models were used to estimate the relationship between animal health and farmer wellbeing. Farmer wellbeing was assessed using the WHOQOL-BREF tool, as the mean quality-of-life in four domains (physical, psychological, social, and environmental). Animal health was assessed as annual livestock mortalities to diseases adjusted for herd size, and standardized in tropical livestock units to account for different ruminant livestock species. We adjusted for the potential confounding effect of farmers' age, sex, educational attainment, farmland size, socio-economic status, perception of disease risk to herd, satisfaction with health, previous experience of disease outbreaks in herds, and social support availability by including these as fixed effects, and community as random effects, in a pre-specified model. RESULTS Our results showed that farmers had a median score of 65.5 out of 100 (IQR: 56.6 to 73.2) on the wellbeing scale. The farmers' reported on average (median) 10% (IQR: 0 to 23) annual herd mortalities to diseases. There was a significantly negative relationship between increasing level of animal disease-induced mortality in herds and farmers' wellbeing. Specifically, our model predicted an expected difference in farmers' wellbeing score of 7.9 (95%CI 1.50 to 14.39) between a farmer without any herd mortalities to diseases compared to a (hypothetical) farmer with 100% of herd mortalities caused by diseases in a farming year. Thus, there is a reduction of approximately 0.8 wellbeing points of farmers, for the average of 10% disease-induced herd mortalities experienced. CONCLUSIONS Disease-induced livestock mortalities have a significant negative effect on farmers' wellbeing, particularly in the physical and psychological domains. This suggests that veterinary service policies addressing disease risks in livestock, could contribute to improving the wellbeing of livestock dependent populations, and public food security.
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Affiliation(s)
- Francis Sena Nuvey
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, Allschwil, 4123, Switzerland.
- Faculty of Medicine, University of Basel, Klingelbergstrasse 61, Basel, 4056, Switzerland.
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, BP, 1303, Côte d'Ivoire.
| | - Daniel T Haydon
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland
| | - Jan Hattendorf
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, Allschwil, 4123, Switzerland
- Faculty of Science, University of Basel, Klingelbergstrasse 50, Basel, 4056, Switzerland
| | - Kennedy Kwasi Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG 581, Accra, Ghana
| | - Gloria Ivy Mensah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG 581, Accra, Ghana
| | - Günther Fink
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, Allschwil, 4123, Switzerland
- Faculty of Science, University of Basel, Klingelbergstrasse 50, Basel, 4056, Switzerland
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, Allschwil, 4123, Switzerland
- Faculty of Science, University of Basel, Klingelbergstrasse 50, Basel, 4056, Switzerland
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, BP, 1303, Côte d'Ivoire
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Lushasi K, Brunker K, Rajeev M, Ferguson EA, Jaswant G, Baker LL, Biek R, Changalucha J, Cleaveland S, Czupryna A, Fooks AR, Govella NJ, Haydon DT, Johnson PCD, Kazwala R, Lembo T, Marston D, Masoud M, Maziku M, Mbunda E, Mchau G, Mohamed AZ, Mpolya E, Ngeleja C, Ng'habi K, Nonga H, Omar K, Rysava K, Sambo M, Sikana L, Steenson R, Hampson K. Integrating contact tracing and whole-genome sequencing to track the elimination of dog-mediated rabies: an observational and genomic study. eLife 2023; 12:85262. [PMID: 37227428 DOI: 10.7554/elife.85262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/24/2023] [Indexed: 05/26/2023] Open
Abstract
Background Dog-mediated rabies is endemic across Africa causing thousands of human deaths annually. A One Health approach to rabies is advocated, comprising emergency post-exposure vaccination of bite victims and mass dog vaccination to break the transmission cycle. However, the impacts and cost-effectiveness of these components are difficult to disentangle. Methods We combined contact tracing with whole-genome sequencing to track rabies transmission in the animal reservoir and spillover risk to humans from 2010-2020, investigating how the components of a One Health approach reduced the disease burden and eliminated rabies from Pemba Island, Tanzania. With the resulting high-resolution spatiotemporal and genomic data we inferred transmission chains and estimated case detection. Using a decision tree model we quantified the public health burden and evaluated the impact and cost-effectiveness of interventions over a ten-year time horizon. Results We resolved five transmission chains co-circulating on Pemba from 2010 that were all eliminated by May 2014. During this period, rabid dogs, human rabies exposures and deaths all progressively declined following initiation and improved implementation of annual islandwide dog vaccination. We identified two introductions to Pemba in late 2016 that seeded re-emergence after dog vaccination had lapsed. The ensuing outbreak was eliminated in October 2018 through reinstated islandwide dog vaccination. While post-exposure vaccines were projected to be highly cost-effective ($256 per death averted), only dog vaccination interrupts transmission. A combined One Health approach of routine annual dog vaccination together with free post-exposure vaccines for bite victims, rapidly eliminates rabies, is highly cost-effective ($1657 per death averted) and by maintaining rabies freedom prevents over 30 families from suffering traumatic rabid dog bites annually on Pemba island. Conclusions A One Health approach underpinned by dog vaccination is an efficient, cost-effective, equitable and feasible approach to rabies elimination, but needs scaling up across connected populations to sustain the benefits of elimination, as seen on Pemba, and for similar progress to be achieved elsewhere. Funding Wellcome [207569/Z/17/Z, 095787/Z/11/Z, 103270/Z/13/Z], the UBS Optimus Foundation, the Department of Health and Human Services of the National Institutes of Health [R01AI141712] and the DELTAS Africa Initiative [Afrique One-ASPIRE/DEL-15-008] comprising a donor consortium of the African Academy of Sciences (AAS), Alliance for Accelerating Excellence in Science in Africa (AESA), the New Partnership for Africa's Development Planning and Coordinating (NEPAD) Agency, Wellcome [107753/A/15/Z], Royal Society of Tropical Medicine and Hygiene Small Grant 2017 [GR000892] and the UK government. The rabies elimination demonstration project from 2010-2015 was supported by the Bill & Melinda Gates Foundation [OPP49679]. Whole-genome sequencing was partially supported from APHA by funding from the UK Department for Environment, Food and Rural Affairs (Defra), Scottish government and Welsh government under projects SEV3500 & SE0421.
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Affiliation(s)
- Kennedy Lushasi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | - Kirstyn Brunker
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
| | - Malavika Rajeev
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
| | - Elaine A Ferguson
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Roman Biek
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
| | - Joel Changalucha
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | - Sarah Cleaveland
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
| | - Anna Czupryna
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
| | | | - Nicodemus J Govella
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
| | - Paul C D Johnson
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
| | - Rudovick Kazwala
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, United Republic of Tanzania
| | - Tiziana Lembo
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
| | - Denise Marston
- Department of Comparative Biomedical Sciences, University of Surrey, Guilford, United Kingdom
| | - Msanif Masoud
- Ministry of Health and Social Welfare, Zanzibar, United Republic of Tanzania
| | - Matthew Maziku
- Ministry of Livestock Development and Fisheries, Dodoma, United Republic of Tanzania
| | - Eberhard Mbunda
- Ministry of Livestock Development and Fisheries, Dodoma, United Republic of Tanzania
| | - Geofrey Mchau
- Department of Epidemiology, Ministry of Health, Community Development, Gender, Elderly and Children, Dodoma, United Republic of Tanzania
| | - Ally Z Mohamed
- Ministry of Livestock Development and Fisheries, Zanzibar, United Republic of Tanzania
| | - Emmanuel Mpolya
- Department of Global Health and Biomedical Sciences, Nelson Mandela African Institution of Science and Technology, Arusha, United Republic of Tanzania
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory Agency, Dar es Salaam, United Republic of Tanzania
| | - Kija Ng'habi
- Mbeya College of Health and Allied Sciences, University of Dar es Salaam, Dar es Salaam, United Republic of Tanzania
| | - Hezron Nonga
- Ministry of Livestock Development and Fisheries, Dodoma, United Republic of Tanzania
| | - Kassim Omar
- Ministry of Livestock Development and Fisheries, Zanzibar, United Republic of Tanzania
| | | | - Maganga Sambo
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | - Lwitiko Sikana
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | - Rachel Steenson
- Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
| | - Katie Hampson
- Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
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9
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Griffiths ME, Meza DK, Haydon DT, Streicker DG. Inferring the disruption of rabies circulation in vampire bat populations using a betaherpesvirus-vectored transmissible vaccine. Proc Natl Acad Sci U S A 2023; 120:e2216667120. [PMID: 36877838 PMCID: PMC10089182 DOI: 10.1073/pnas.2216667120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/25/2023] [Indexed: 03/08/2023] Open
Abstract
Transmissible vaccines are an emerging biotechnology that hold prospects to eliminate pathogens from wildlife populations. Such vaccines would genetically modify naturally occurring, nonpathogenic viruses ("viral vectors") to express pathogen antigens while retaining their capacity to transmit. The epidemiology of candidate viral vectors within the target wildlife population has been notoriously challenging to resolve but underpins the selection of effective vectors prior to major investments in vaccine development. Here, we used spatiotemporally replicated deep sequencing to parameterize competing epidemiological mechanistic models of Desmodus rotundus betaherpesvirus (DrBHV), a proposed vector for a transmissible vaccine targeting vampire bat-transmitted rabies. Using 36 strain- and location-specific time series of prevalence collected over 6 y, we found that lifelong infections with cycles of latency and reactivation, combined with a high R0 (6.9; CI: 4.39 to 7.85), are necessary to explain patterns of DrBHV infection observed in wild bats. These epidemiological properties suggest that DrBHV may be suited to vector a lifelong, self-boosting, and transmissible vaccine. Simulations showed that inoculating a single bat with a DrBHV-vectored rabies vaccine could immunize >80% of a bat population, reducing the size, frequency, and duration of rabies outbreaks by 50 to 95%. Gradual loss of infectious vaccine from vaccinated individuals is expected but can be countered by inoculating larger but practically achievable proportions of bat populations. Parameterizing epidemiological models using accessible genomic data brings transmissible vaccines one step closer to implementation.
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Affiliation(s)
- Megan E. Griffiths
- Medical Research Council–University of Glasgow Centre for Virus Research, GlasgowG61 1QH, United Kingdom
| | - Diana K. Meza
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, GlasgowG61 1QH, United Kingdom
| | - Daniel T. Haydon
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, GlasgowG61 1QH, United Kingdom
| | - Daniel G. Streicker
- Medical Research Council–University of Glasgow Centre for Virus Research, GlasgowG61 1QH, United Kingdom
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, GlasgowG61 1QH, United Kingdom
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10
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Bach L, Ram A, Ijaz UZ, Evans TJ, Haydon DT, Lindström J. The Effects of Smoking on Human Pharynx Microbiota Composition and Stability. Microbiol Spectr 2023; 11:e0216621. [PMID: 36786634 PMCID: PMC10101099 DOI: 10.1128/spectrum.02166-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/16/2023] [Indexed: 02/15/2023] Open
Abstract
The oral microbiota is essential to the health of the host, yet little is known about how it responds to disturbances. We examined the oropharyngeal microbiota of 30 individuals over 40 weeks. As the oropharynx is an important gateway to pathogens, and as smoking is associated with increased incidence and severity of respiratory infections, we compared the microbiota of smokers and nonsmokers to shed light on its potential for facilitating infections. We hypothesized that decreased species diversity, decreased community stability, or increased differences in community structure could facilitate invading pathogens. We found that smoking is associated with reduced alpha diversity, greater differences in community structure, and increased environmental filtering. The effects of short-term perturbations (antibiotic use and participants exhibiting cold symptoms) were also investigated. Antibiotic use had a negative effect on alpha diversity, irrespective of smoking status, and both antibiotic use and cold symptoms were associated with highly unique bacterial communities. A stability analysis of models built from the data indicated that there were no differences in local or global stability in the microbial communities of smokers, compared to nonsmokers, and that their microbiota are equally resistant to species invasions. Results from these models suggest that smoker microbiota are perturbed but characterized by alternative stable states that are as stable and invasion-resistant as are the microbiota of nonsmokers. Smoking is unlikely to increase the risk of infectious disease through the altered composition and ecological function of the microbiota; this is more likely due to the effects of smoking on the local and systemic immune system. IMPORTANCE Smoking is associated with an increased risk of respiratory infections. Hypothetically, the altered community diversity of smokers' pharyngeal microbiota, together with changes in their ecological stability properties, could facilitate their invasion by pathogens. To address this question, we analyzed longitudinal microbiota data of baseline healthy individuals who were either smokers or nonsmokers. While the results indicate reduced biodiversity and increased species turnover in the smokers' pharyngeal microbiota, their ecological stability properties were not different from those of the microbiota of nonsmokers, implying, in ecological terms, that the smokers' microbial communities are not less resistant to invasions. Therefore, the study suggests that the increased propensity of respiratory infections that is seen in smokers is more likely associated with changes in the local and systemic immune system than with ecological changes in the microbial communities.
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Affiliation(s)
- Lydia Bach
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Asha Ram
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Umer Z. Ijaz
- School of Science and Engineering, University of Glasgow, United Kingdom
| | - Thomas J. Evans
- School of Infection and Immunity, Glasgow Biomedical Research Centre, University of Glasgow, United Kingdom
| | - Daniel T. Haydon
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Jan Lindström
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
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11
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Johnson PCD, Hägglund S, Näslund K, Meyer G, Taylor G, Orton RJ, Zohari S, Haydon DT, Valarcher JF. Evaluating the potential of whole-genome sequencing for tracing transmission routes in experimental infections and natural outbreaks of bovine respiratory syncytial virus. Vet Res 2022; 53:107. [PMID: 36510312 PMCID: PMC9746130 DOI: 10.1186/s13567-022-01127-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022] Open
Abstract
Bovine respiratory syncytial virus (BRSV) is a major cause of respiratory disease in cattle. Genomic sequencing can resolve phylogenetic relationships between virus populations, which can be used to infer transmission routes and potentially inform the design of biosecurity measures. Sequencing of short (<2000 nt) segments of the 15 000-nt BRSV genome has revealed geographic and temporal clustering of BRSV populations, but insufficient variation to distinguish viruses collected from herds infected close together in space and time. This study investigated the potential for whole-genome sequencing to reveal sufficient genomic variation for inferring transmission routes between herds. Next-generation sequencing (NGS) data were generated from experimental infections and from natural outbreaks in Jämtland and Uppsala counties in Sweden. Sufficient depth of coverage for analysis of consensus and sub-consensus sequence diversity was obtained from 47 to 20 samples respectively. Few (range: 0-6 polymorphisms across the six experiments) consensus-level polymorphisms were observed along experimental transmissions. A much higher level of diversity (146 polymorphic sites) was found among the consensus sequences from the outbreak samples. The majority (144/146) of polymorphisms were between rather than within counties, suggesting that consensus whole-genome sequences show insufficient spatial resolution for inferring direct transmission routes, but might allow identification of outbreak sources at the regional scale. By contrast, within-sample diversity was generally higher in the experimental than the outbreak samples. Analyses to infer known (experimental) and suspected (outbreak) transmission links from within-sample diversity data were uninformative. In conclusion, analysis of the whole-genome sequence of BRSV from experimental samples discriminated between circulating isolates from distant areas, but insufficient diversity was observed between closely related isolates to aid local transmission route inference.
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Affiliation(s)
- Paul C D Johnson
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - Sara Hägglund
- HPIG. Unit of Ruminant Medicine. Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Katarina Näslund
- Department of Microbiology, National Veterinary Institute, SVA, Uppsala, Sweden
| | - Gilles Meyer
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Siamak Zohari
- Department of Microbiology, National Veterinary Institute, SVA, Uppsala, Sweden
| | - Daniel T Haydon
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Jean François Valarcher
- HPIG. Unit of Ruminant Medicine. Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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12
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Jarrett C, Haydon DT, Morales JM, Ferreira DF, Forzi FA, Welch AJ, Powell LL, Matthiopoulos J. Integration of mark-recapture and acoustic detections for unbiased population estimation in animal communities. Ecology 2022; 103:e3769. [PMID: 35620844 PMCID: PMC9787363 DOI: 10.1002/ecy.3769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 04/15/2022] [Accepted: 04/21/2022] [Indexed: 12/30/2022]
Abstract
Abundance estimation methods that combine several types of data are becoming increasingly common because they yield more accurate and precise parameter estimates and predictions than are possible from a single data source. These beneficial effects result from increasing sample size (through data pooling) and complementarity between different data types. Here, we test whether integrating mark-recapture data with passive acoustic detections into a joint likelihood improves estimates of population size in a multi-guild community. We compared the integrated model to a mark-recapture-only model using simulated data first and then using a data set of mist-net captures and acoustic recordings from an Afrotropical agroforest bird community. The integrated model with simulated data improved accuracy and precision of estimated population size and detection parameters. When applied to field data, the integrated model was able to produce, for each bird guild, ecologically plausible estimates of population size and detection parameters, with more precision compared with the mark-recapture model. Overall, our results show that adding acoustic data to mark-recapture analyses improves estimates of population size. With the increasing availability of acoustic recording devices, this data collection technique could readily be added to routine field protocols, leading to a cost-efficient improvement of traditional mark-recapture population estimation.
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Affiliation(s)
- Crinan Jarrett
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK,Biodiversity InitiativeBelmontMassachusettsUSA
| | - Daniel T. Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Juan M. Morales
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK,Grupo de Ecología Cuantitativa, INIBIOMA‐CONICETUniversidad Nacional del ComahueBarilocheArgentina
| | - Diogo F. Ferreira
- Biodiversity InitiativeBelmontMassachusettsUSA,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de VairãoUniversidade do PortoVairãoPortugal,BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
| | | | - Andreanna J. Welch
- Biodiversity InitiativeBelmontMassachusettsUSA,Department of BiosciencesDurham UniversityDurhamUK
| | - Luke L. Powell
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK,Biodiversity InitiativeBelmontMassachusettsUSA,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de VairãoUniversidade do PortoVairãoPortugal,BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal,Department of BiosciencesDurham UniversityDurhamUK
| | - Jason Matthiopoulos
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
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13
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Mancy R, Rajeev M, Lugelo A, Brunker K, Cleaveland S, Ferguson EA, Hotopp K, Kazwala R, Magoto M, Rysava K, Haydon DT, Hampson K. Rabies shows how scale of transmission can enable acute infections to persist at low prevalence. Science 2022; 376:512-516. [PMID: 35482879 PMCID: PMC7613728 DOI: 10.1126/science.abn0713] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
How acute pathogens persist and what curtails their epidemic growth in the absence of acquired immunity remains unknown. Canine rabies is a fatal zoonosis that circulates endemically at low prevalence among domestic dogs in low- and middle-income countries. We traced rabies transmission in a population of 50,000 dogs in Tanzania from 2002 to 2016 and applied individual-based models to these spatially resolved data to investigate the mechanisms modulating transmission and the scale over which they operate. Although rabies prevalence never exceeded 0.15%, the best-fitting models demonstrated appreciable depletion of susceptible animals that occurred at local scales because of clusters of deaths and dogs already incubating infection. Individual variation in rabid dog behavior facilitated virus dispersal and cocirculation of virus lineages, enabling metapopulation persistence. These mechanisms have important implications for prediction and control of pathogens that circulate in spatially structured populations.
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Affiliation(s)
- Rebecca Mancy
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Malavika Rajeev
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Ahmed Lugelo
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Elaine A. Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Karen Hotopp
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Rudovick Kazwala
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | - Kristyna Rysava
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Warwick, UK
| | - Daniel T. Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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14
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Lushasi K, Hayes S, Ferguson EA, Changalucha J, Cleaveland S, Govella NJ, Haydon DT, Sambo M, Mchau GJ, Mpolya EA, Mtema Z, Nonga HE, Steenson R, Nouvellet P, Donnelly CA, Hampson K. Reservoir dynamics of rabies in south-east Tanzania and the roles of cross-species transmission and domestic dog vaccination. J Appl Ecol 2021; 58:2673-2685. [PMID: 35221371 PMCID: PMC7612421 DOI: 10.1111/1365-2664.13983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/24/2021] [Indexed: 12/27/2022]
Abstract
Understanding the role of different species in the transmission of multi-host pathogens, such as rabies virus, is vital for effective control strategies. Across most of sub-Saharan Africa domestic dogs Canis familiaris are considered the reservoir for rabies, but the role of wildlife has been long debated. Here we explore the multi-host transmission dynamics of rabies across south-east Tanzania.Between January 2011 and July 2019, data on probable rabies cases were collected in the regions of Lindi and Mtwara. Hospital records of animal-bite patients presenting to healthcare facilities were used as sentinels for animal contact tracing. The timing, location and species of probable rabid animals were used to reconstruct transmission trees to infer who infected whom and the relative frequencies of within- and between-species transmission.During the study, 688 probable human rabies exposures were identified, resulting in 47 deaths. Of these exposures, 389 were from domestic dogs (56.5%) and 262 from jackals (38.1%). Over the same period, 549 probable animal rabies cases were traced: 303 in domestic dogs (55.2%) and 221 in jackals (40.3%), with the remainder in domestic cats and other wildlife species.Although dog-to-dog transmission was most commonly inferred (40.5% of transmission events), a third of inferred events involved wildlife-to-wildlife transmission (32.6%), and evidence suggested some sustained transmission chains within jackal populations.A steady decline in probable rabies cases in both humans and animals coincided with the implementation of widespread domestic dog vaccination during the first 6 years of the study. Following the lapse of this program, dog rabies cases began to increase in one of the northernmost districts. Synthesis and applications. In south-east Tanzania, despite a relatively high incidence of rabies in wildlife and evidence of wildlife-to-wildlife transmission, domestic dogs remain essential to the reservoir of infection. Continued dog vaccination alongside improved surveillance would allow a fuller understanding of the role of wildlife in maintaining transmission in this area. Nonetheless, dog vaccination clearly suppressed rabies in both domestic dog and wildlife populations, reducing both public health and conservation risks and, if sustained, has potential to eliminate rabies from this region.
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Affiliation(s)
- Kennedy Lushasi
- Ifakara Health Institute, Ifakara, Tanzania
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Sarah Hayes
- Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London
| | - Elaine A. Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | | | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Nicodem J. Govella
- Ifakara Health Institute, Ifakara, Tanzania
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Daniel T. Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | | | - Geofrey J. Mchau
- Ministry of Health, Community Development, Gender, Elderly and Children, Dodoma, Tanzania
| | - Emmanuel A. Mpolya
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | - Hezron E. Nonga
- Ministry of Livestock Development and Fisheries, Dodoma, Tanzania
| | - Rachel Steenson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | | | - Christl A. Donnelly
- Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London
- Department of Statistics, University of Oxford, Oxford, UK
| | - Katie Hampson
- Ifakara Health Institute, Ifakara, Tanzania
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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15
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Bodenham RF, Mazeri S, Cleaveland S, Crump JA, Fasina FO, de Glanville WA, Haydon DT, Kazwala RR, Kibona TJ, Maro VP, Maze MJ, Mmbaga BT, Mtui-Malamsha NJ, Shirima GM, Swai ES, Thomas KM, Bronsvoort BMD, Halliday JEB. Latent class evaluation of the performance of serological tests for exposure to Brucella spp. in cattle, sheep, and goats in Tanzania. PLoS Negl Trop Dis 2021; 15:e0009630. [PMID: 34428205 PMCID: PMC8384210 DOI: 10.1371/journal.pntd.0009630] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/06/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Brucellosis is a neglected zoonosis endemic in many countries, including regions of sub-Saharan Africa. Evaluated diagnostic tools for the detection of exposure to Brucella spp. are important for disease surveillance and guiding prevention and control activities. METHODS AND FINDINGS Bayesian latent class analysis was used to evaluate performance of the Rose Bengal plate test (RBT) and a competitive ELISA (cELISA) in detecting Brucella spp. exposure at the individual animal-level for cattle, sheep, and goats in Tanzania. Median posterior estimates of RBT sensitivity were: 0.779 (95% Bayesian credibility interval (BCI): 0.570-0.894), 0.893 (0.636-0.989), and 0.807 (0.575-0.966), and for cELISA were: 0.623 (0.443-0.790), 0.409 (0.241-0.644), and 0.561 (0.376-0.713), for cattle, sheep, and goats, respectively. Sensitivity BCIs were wide, with the widest for cELISA in sheep. RBT and cELISA median posterior estimates of specificity were high across species models: RBT ranged between 0.989 (0.980-0.998) and 0.995 (0.985-0.999), and cELISA between 0.984 (0.974-0.995) and 0.996 (0.988-1). Each species model generated seroprevalence estimates for two livestock subpopulations, pastoralist and non-pastoralist. Pastoralist seroprevalence estimates were: 0.063 (0.045-0.090), 0.033 (0.018-0.049), and 0.051 (0.034-0.076), for cattle, sheep, and goats, respectively. Non-pastoralist seroprevalence estimates were below 0.01 for all species models. Series and parallel diagnostic approaches were evaluated. Parallel outperformed a series approach. Median posterior estimates for parallel testing were ≥0.920 (0.760-0.986) for sensitivity and ≥0.973 (0.955-0.992) for specificity, for all species models. CONCLUSIONS Our findings indicate that Brucella spp. surveillance in Tanzania using RBT and cELISA in parallel at the animal-level would give high test performance. There is a need to evaluate strategies for implementing parallel testing at the herd- and flock-level. Our findings can assist in generating robust Brucella spp. exposure estimates for livestock in Tanzania and wider sub-Saharan Africa. The adoption of locally evaluated robust diagnostic tests in setting-specific surveillance is an important step towards brucellosis prevention and control.
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Affiliation(s)
- Rebecca F. Bodenham
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail: ,
| | - Stella Mazeri
- The Epidemiology, Economics and Risk Assessment (EERA) group, The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - John A. Crump
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Centre for International Health, University of Otago, Dunedin, New Zealand
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Folorunso O. Fasina
- Emergency Centre for Transboundary Animal Diseases, Food and Agriculture Organization (FAO) of the United Nations, Dar es Salaam, Tanzania
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - William A. de Glanville
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel T. Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Tito J. Kibona
- Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
| | - Venance P. Maro
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Michael J. Maze
- Centre for International Health, University of Otago, Dunedin, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Blandina T. Mmbaga
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Niwael J. Mtui-Malamsha
- Emergency Centre for Transboundary Animal Diseases, Food and Agriculture Organization (FAO) of the United Nations, Dar es Salaam, Tanzania
| | - Gabriel M. Shirima
- Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
| | - Emanuel S. Swai
- Directorate of Veterinary Services, Ministry of Livestock and Fisheries, Dodoma, Tanzania
| | - Kate M. Thomas
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Barend M. deC. Bronsvoort
- The Epidemiology, Economics and Risk Assessment (EERA) group, The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Jo E. B. Halliday
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Theonest NO, Carter RW, Kasagama E, Keyyu JD, Shirima GM, Tarimo R, Thomas KM, Wheelhouse N, Maro VP, Haydon DT, Buza JJ, Allan KJ, Halliday JE. Molecular detection of Coxiella burnetii infection in small mammals from Moshi Rural and Urban Districts, northern Tanzania. Vet Med Sci 2021; 7:960-967. [PMID: 33277971 PMCID: PMC8136964 DOI: 10.1002/vms3.401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 10/16/2020] [Accepted: 11/09/2020] [Indexed: 11/08/2022] Open
Abstract
Coxiella burnetii is an obligate intracellular bacterium that causes Q fever, a zoonotic disease of public health importance. In northern Tanzania, Q fever is a known cause of human febrile illness, but little is known about its distribution in animal hosts. We used a quantitative real-time PCR (qPCR) targeting the insertion element IS1111 to determine the presence and prevalence of C. burnetii infections in small mammals trapped in 12 villages around Moshi Rural and Moshi Urban Districts, northern Tanzania. A total of 382 trapped small mammals of seven species were included in the study; Rattus rattus (n = 317), Mus musculus (n = 44), Mastomys natalensis (n = 8), Acomys wilson (n = 6), Mus minutoides (n = 3), Paraxerus flavovottis (n = 3) and Atelerix albiventris (n = 1). Overall, 12 (3.1%) of 382 (95% CI: 1.6-5.4) small mammal spleens were positive for C. burnetii DNA. Coxiella burnetii DNA was detected in five of seven of the small mammal species trapped; R. rattus (n = 7), M. musculus (n = 1), A. wilson (n = 2), P. flavovottis (n = 1) and A. albiventris (n = 1). Eleven (91.7%) of twelve (95% CI: 61.5-99.8) C. burnetii DNA positive small mammals were trapped within Moshi Urban District. These findings demonstrate that small mammals in Moshi, northern Tanzania are hosts of C. burnetii and may act as a source of C. burnetii infection to humans and other animals. This detection of C. burnetii infections in small mammals should motivate further studies into the contribution of small mammals to the transmission of C. burnetii to humans and animals in this region.
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Affiliation(s)
- Ndyetabura O. Theonest
- School of Life Sciences and BioengineeringNelson Mandela African Institution of Science and TechnologyArushaTanzania
- Kilimanjaro Clinical Research InstituteMoshiTanzania
| | - Ryan W. Carter
- The Boyd Orr Centre for Population and Ecosystem HealthInstitute of Biodiversity Animal Health and Comparative MedicineCollege of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | | | | | - Gabriel M. Shirima
- School of Life Sciences and BioengineeringNelson Mandela African Institution of Science and TechnologyArushaTanzania
| | | | - Kate M. Thomas
- Kilimanjaro Clinical Research InstituteMoshiTanzania
- Centre for International HealthDunedin School of MedicineUniversity of OtagoDunedinNew Zealand
| | - Nick Wheelhouse
- School of Applied SciencesEdinburgh Napier UniversityEdinburghUK
| | - Venance P. Maro
- Kilimanjaro Christian Medical University CollegeMoshiTanzania
| | - Daniel T. Haydon
- The Boyd Orr Centre for Population and Ecosystem HealthInstitute of Biodiversity Animal Health and Comparative MedicineCollege of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Joram J. Buza
- School of Life Sciences and BioengineeringNelson Mandela African Institution of Science and TechnologyArushaTanzania
| | - Kathryn J. Allan
- The Boyd Orr Centre for Population and Ecosystem HealthInstitute of Biodiversity Animal Health and Comparative MedicineCollege of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Jo E.B. Halliday
- The Boyd Orr Centre for Population and Ecosystem HealthInstitute of Biodiversity Animal Health and Comparative MedicineCollege of Medical Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
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Mendes ÂJ, Haydon DT, McIntosh E, Hanley N, Halliday JEB. Socially vs. Privately Optimal Control of Livestock Diseases: A Case for Integration of Epidemiology and Economics. Front Vet Sci 2020; 7:558409. [PMID: 33324694 PMCID: PMC7723844 DOI: 10.3389/fvets.2020.558409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/19/2020] [Indexed: 12/29/2022] Open
Abstract
This paper aims to illustrate the interdependencies between key epidemiological and economic factors that influence the control of many livestock infectious diseases. The factors considered here are (i) farmer heterogeneity (i.e., differences in how farmers respond to a perceived disease risk), (ii) off-farm effects of farmers' actions to control a disease (i.e., costs and benefits borne by agents that are external to the farm), and (iii) misalignment between privately and socially optimal control efforts (i.e., privately optimal behavior not conducive to a socially optimal outcome). Endemic chronic diseases cause a wide range of adverse social and economic impacts, particularly in low-income countries. The actions taken by farmers to control livestock diseases minimize some of these impacts, and heterogeneity in those actions leads to variation in prevalence at the farm level. While some farmers respond to perceived disease risks, others free-ride on the actions of these individuals, thereby compromising the potential benefits of collective, coordinated behavior. When evaluating a plausible range of disease cost to price of control ratios and assuming that farmers choose their privately optimal control effort, we demonstrate that achievement of a socially optimal disease control target is unlikely, occurring in <25% of all price-cost combinations. To achieve a socially optimal disease control outcome (reliant on farmers' voluntary actions), control policies must consider farmer heterogeneity, off-farm effects, and the predicted uptake of control measures under the assumption of optimized behavior.
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Affiliation(s)
- Ângelo J Mendes
- College of Medical, Veterinary and Life Sciences, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Daniel T Haydon
- College of Medical, Veterinary and Life Sciences, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Emma McIntosh
- College of Medical, Veterinary and Life Sciences, Institute of Health and Wellbeing, University of Glasgow, Glasgow, United Kingdom
| | - Nick Hanley
- College of Medical, Veterinary and Life Sciences, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Jo E B Halliday
- College of Medical, Veterinary and Life Sciences, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
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Rostal MK, Cleaveland S, Cordel C, van Staden L, Matthews L, Anyamba A, Karesh WB, Paweska JT, Haydon DT, Ross N. Farm-Level Risk Factors of Increased Abortion and Mortality in Domestic Ruminants during the 2010 Rift Valley Fever Outbreak in Central South Africa. Pathogens 2020; 9:E914. [PMID: 33158214 PMCID: PMC7694248 DOI: 10.3390/pathogens9110914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/25/2020] [Accepted: 10/30/2020] [Indexed: 11/28/2022] Open
Abstract
(1) Background: Rift Valley fever (RVF) outbreaks in domestic ruminants have severe socio-economic impacts. Climate-based continental predictions providing early warnings to regions at risk for RVF outbreaks are not of a high enough resolution for ruminant owners to assess their individual risk. (2) Methods: We analyzed risk factors for RVF occurrence and severity at the farm level using the number of domestic ruminant deaths and abortions reported by farmers in central South Africa during the 2010 RVF outbreaks using a Bayesian multinomial hurdle framework. (3) Results: We found strong support that the proportion of days with precipitation, the number of water sources, and the proportion of goats in the herd were positively associated with increased severity of RVF (the numbers of deaths and abortions). We did not find an association between any risk factors and whether RVF was reported on farms. (4) Conclusions: At the farm level we identified risk factors of RVF severity; however, there was little support for risk factors of RVF occurrence. The identification of farm-level risk factors for Rift Valley fever virus (RVFV) occurrence would support and potentially improve current prediction methods and would provide animal owners with critical information needed in order to assess their herd's risk of RVFV infection.
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Affiliation(s)
- Melinda K. Rostal
- EcoHealth Alliance, New York, NY 10018, USA; (W.B.K.); (N.R.)
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (S.C.); (L.M.); (D.T.H.)
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (S.C.); (L.M.); (D.T.H.)
| | - Claudia Cordel
- ExecuVet PTY LTD., Bloemfontein 9301, Free State, South Africa; (C.C.); (L.v.S.)
| | - Lara van Staden
- ExecuVet PTY LTD., Bloemfontein 9301, Free State, South Africa; (C.C.); (L.v.S.)
| | - Louise Matthews
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (S.C.); (L.M.); (D.T.H.)
| | - Assaf Anyamba
- Universities Space Research Association, Columbia, MD 21046, USA;
- NASA Goddard Space Flight Center, Biospheric Sciences Laboratory, Greenbelt, MD 20771, USA
| | | | - Janusz T. Paweska
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa;
| | - Daniel T. Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (S.C.); (L.M.); (D.T.H.)
| | - Noam Ross
- EcoHealth Alliance, New York, NY 10018, USA; (W.B.K.); (N.R.)
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Rysava K, Mancero T, Caldas E, de Carvalho MF, Castro APB, Gutiérrez V, Haydon DT, Johnson PCD, Mancy R, Montebello LR, Rocha SM, Gonzalez Roldan JF, Vigilato MAN, Vilas VDR, Hampson K. Towards the elimination of dog-mediated rabies: development and application of an evidence-based management tool. BMC Infect Dis 2020; 20:778. [PMID: 33081712 PMCID: PMC7574347 DOI: 10.1186/s12879-020-05457-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/27/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND International organizations advocate for the elimination of dog-mediated rabies, but there is only limited guidance on interpreting surveillance data for managing elimination programmes. With the regional programme in Latin America approaching elimination of dog-mediated rabies, we aimed to develop a tool to evaluate the programme's performance and generate locally-tailored rabies control programme management guidance to overcome remaining obstacles. METHODS We developed and validated a robust algorithm to classify progress towards rabies elimination within sub-national administrative units, which we applied to surveillance data from Brazil and Mexico. The method combines criteria that are easy to understand, including logistic regression analysis of case detection time series, assessment of rabies virus variants, and of incursion risk. Subjecting the algorithm to robustness testing, we further employed simulated data sub-sampled at differing levels of case detection to assess the algorithm's performance and sensitivity to surveillance quality. RESULTS Our tool demonstrated clear epidemiological transitions in Mexico and Brazil: most states progressed rapidly towards elimination, but a few regressed due to incursions and control lapses. In 2015, dog-mediated rabies continued to circulate in the poorest states, with foci remaining in only 1 of 32 states in Mexico, and 2 of 27 in Brazil, posing incursion risks to the wider region. The classification tool was robust in determining epidemiological status irrespective of most levels of surveillance quality. In endemic settings, surveillance would need to detect less than 2.5% of all circulating cases to result in misclassification, whereas in settings where incursions become the main source of cases the threshold detection level for correct classification should not be less than 5%. CONCLUSION Our tool provides guidance on how to progress effectively towards elimination targets and tailor strategies to local epidemiological situations, while revealing insights into rabies dynamics. Post-campaign assessments of dog vaccination coverage in endemic states, and enhanced surveillance to verify and maintain freedom in states threatened by incursions were identified as priorities to catalyze progress towards elimination. Our finding suggests genomic surveillance should become increasingly valuable during the endgame for discriminating circulating variants and pinpointing sources of incursions.
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Affiliation(s)
- Kristyna Rysava
- University of Warwick, School of Life Sciences, Gibbet Hill Road, Coventry, UK
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr building, MVLS, Glasgow, G12 8QQ UK
| | - Tamara Mancero
- Pan American Health Organization (PAHO), Duque de Caxias, Rio de Janeiro, Brazil
| | - Eduardo Caldas
- Virology, Central Laboratory, State Center for Health Surveillance, State Department of Health, São Paulo, Rio Grande do Sul Brazil
| | | | | | | | - Daniel T. Haydon
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr building, MVLS, Glasgow, G12 8QQ UK
| | - Paul C. D. Johnson
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr building, MVLS, Glasgow, G12 8QQ UK
| | - Rebecca Mancy
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr building, MVLS, Glasgow, G12 8QQ UK
| | | | | | | | | | - Victor Del Rio Vilas
- Pan American Health Organization (PAHO), Duque de Caxias, Rio de Janeiro, Brazil
- University of Surrey, School of Veterinary Medicine, VSM Building, Guildford, UK
| | - Katie Hampson
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr building, MVLS, Glasgow, G12 8QQ UK
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Kabalika Z, Morrison TA, McGill RAR, Munishi LK, Ekwem D, Mahene WL, Lobora AL, Newton J, Morales JM, Haydon DT, Hopcraft GGJC. Tracking animal movements using biomarkers in tail hairs: a novel approach for animal geolocating from sulfur isoscapes. Mov Ecol 2020; 8:37. [PMID: 32968486 PMCID: PMC7501629 DOI: 10.1186/s40462-020-00222-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Current animal tracking studies are most often based on the application of external geolocators such as GPS and radio transmitters. While these technologies provide detailed movement data, they are costly to acquire and maintain, which often restricts sample sizes. Furthermore, deploying external geolocators requires physically capturing and recapturing of animals, which poses an additional welfare concern. Natural biomarkers provide an alternative, non-invasive approach for addressing a range of geolocation questions and can, because of relatively low cost, be collected from many individuals thereby broadening the scope for population-wide inference. METHODS We developed a low-cost, minimally invasive method for distinguishing between local versus non-local movements of cattle using sulfur isotope ratios (δ34S) in cattle tail hair collected in the Greater Serengeti Ecosystem, Tanzania. RESULTS We used a Generalized Additive Model to generate a predicted δ34S isoscape across the study area. This isoscape was constructed using spatial smoothers and underpinned by the positive relationship between δ34S values and lithology. We then established a strong relationship between δ34S from recent sections of cattle tail hair and the δ34S from grasses sampled in the immediate vicinity of an individual's location, suggesting δ34S in the hair reflects the δ34S in the environment. By combining uncertainty in estimation of the isoscape, with predictions of tail hair δ34S given an animal's position in the isoscape we estimated the anisotropic distribution of travel distances across the Serengeti ecosystem sufficient to detect movement using sulfur stable isotopes. CONCLUSIONS While the focus of our study was on cattle, this approach can be modified to understand movements in other mobile organisms where the sulfur isoscape is sufficiently heterogeneous relative to the spatial scale of animal movements and where tracking with traditional methods is difficult.
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Affiliation(s)
- Zabibu Kabalika
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr building, Glasgow, G12 8QQ UK
| | - Thomas A. Morrison
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr building, Glasgow, G12 8QQ UK
| | - Rona A. R. McGill
- National Environmental Isotope Facility, Scottish Universities Environmental Research Centre, University of Glasgow, Glasgow, G75 0QF UK
| | - Linus K. Munishi
- Nelson Mandela African Institution of Science and Technology (NM-AIST), P.O. Box 447, Arusha, Tanzania
| | - Divine Ekwem
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr building, Glasgow, G12 8QQ UK
| | - Wilson Leonidas Mahene
- Nelson Mandela African Institution of Science and Technology (NM-AIST), P.O. Box 447, Arusha, Tanzania
| | - Alex L. Lobora
- Tanzania Wildlife Research Institute (TAWIRI), P.O Box 661, Arusha, Tanzania
| | - Jason Newton
- National Environmental Isotope Facility, Scottish Universities Environmental Research Centre, University of Glasgow, Glasgow, G75 0QF UK
| | - Juan M. Morales
- INIBIOMA, CONICET, Universidad Nacional del Comahue, San Carlos de Bariloche, Argentina
| | - Daniel T. Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr building, Glasgow, G12 8QQ UK
| | - Grant G. J. C. Hopcraft
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr building, Glasgow, G12 8QQ UK
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Bodenham RF, Lukambagire AS, Ashford RT, Buza JJ, Cash-Goldwasser S, Crump JA, Kazwala RR, Maro VP, McGiven J, Mkenda N, Mmbaga BT, Rubach MP, Sakasaka P, Shirima GM, Swai ES, Thomas KM, Whatmore AM, Haydon DT, Halliday JEB. Prevalence and speciation of brucellosis in febrile patients from a pastoralist community of Tanzania. Sci Rep 2020; 10:7081. [PMID: 32341414 PMCID: PMC7184621 DOI: 10.1038/s41598-020-62849-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/11/2020] [Indexed: 01/18/2023] Open
Abstract
Brucellosis is an endemic zoonosis in sub-Saharan Africa. Pastoralists are at high risk of infection but data on brucellosis from these communities are scarce. The study objectives were to: estimate the prevalence of human brucellosis, identify the Brucella spp. causing illness, describe non-Brucella bloodstream infections, and identify risk factors for brucellosis in febrile patients from a pastoralist community of Tanzania. Fourteen (6.1%) of 230 participants enrolled between August 2016 and October 2017 met study criteria for confirmed (febrile illness and culture positivity or ≥four-fold rise in SAT titre) or probable (febrile illness and single SAT titre ≥160) brucellosis. Brucella spp. was the most common bloodstream infection, with B. melitensis isolated from seven participants and B. abortus from one. Enterococcus spp., Escherichia coli, Salmonella enterica, Staphylococcus aureus and Streptococcus pneumoniae were also isolated. Risk factors identified for brucellosis included age and herding, with a greater probability of brucellosis in individuals with lower age and who herded cattle, sheep or goats in the previous 12 months. Disease prevention activities targeting young herders have potential to reduce the impacts of human brucellosis in Tanzania. Livestock vaccination strategies for the region should include both B. melitensis and B. abortus.
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Affiliation(s)
- Rebecca F Bodenham
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Roland T Ashford
- OIE/FAO Brucellosis Reference Laboratory, Department of Bacteriology, Animal & Plant Health Agency, Surrey, UK
| | - Joram J Buza
- Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
| | - Shama Cash-Goldwasser
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - John A Crump
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Centre for International Health, University of Otago, Dunedin, New Zealand.,Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Division of Infectious Diseases and International Health, Duke University Medical Center, North Carolina, USA
| | | | - Venance P Maro
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - John McGiven
- OIE/FAO Brucellosis Reference Laboratory, Department of Bacteriology, Animal & Plant Health Agency, Surrey, UK
| | - Nestory Mkenda
- Endulen Hospital, Ngorongoro Conservation Area, Arusha, Tanzania
| | - Blandina T Mmbaga
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Matthew P Rubach
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Division of Infectious Diseases and International Health, Duke University Medical Center, North Carolina, USA.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | | | - Gabriel M Shirima
- Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
| | - Emanuel S Swai
- Directorate of Veterinary Services, Ministry of Livestock and Fisheries, Dodoma, Tanzania
| | - Kate M Thomas
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania.,Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Adrian M Whatmore
- OIE/FAO Brucellosis Reference Laboratory, Department of Bacteriology, Animal & Plant Health Agency, Surrey, UK
| | - Daniel T Haydon
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jo E B Halliday
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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22
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Lushasi K, Steenson R, Bernard J, Changalucha JJ, Govella NJ, Haydon DT, Hoffu H, Lankester F, Magoti F, Mpolya EA, Mtema Z, Nonga H, Hampson K. One Health in Practice: Using Integrated Bite Case Management to Increase Detection of Rabid Animals in Tanzania. Front Public Health 2020; 8:13. [PMID: 32117850 PMCID: PMC7034360 DOI: 10.3389/fpubh.2020.00013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/15/2020] [Indexed: 12/25/2022] Open
Abstract
Rabies is a neglected zoonotic disease that causes an estimated 59,000 human deaths worldwide annually, mostly in Africa and Asia. A target of zero human deaths from dog-mediated rabies has been set for 2030, and large-scale control programs are now advocated. However, in most low-income endemic countries surveillance to guide rabies control is weak and few cases of rabies are recorded. There is an urgent need to enhance surveillance to improve timely case detection and inform rabies control and prevention, by operationalizing a “One Health” approach. Here we present data from a study piloting Integrated Bite Case Management (IBCM) to support intersectoral collaboration between health and veterinary workers in Tanzania. We trained government staff to implement IBCM, comprising risk assessments of bite patients by health workers, investigations by livestock field officers to diagnose rabid animals, and use of a mobile phone application to support integration. IBCM was introduced across 20 districts in four regions of Tanzania and results reported after 1 year of implementation. Numbers of bite patient presentations to health facilities varied across regions, but following the introduction of IBCM reporting of bite patients at high-risk for rabies more than doubled in all regions. Over 800 high-risk investigations were carried out, with 49% assessed as probable dog rabies cases on the basis of clinical signs, animal outcome, and rapid diagnostic testing. The status of a further 20% of biting animals could not be determined but rabies could not be ruled out. Livestock field officers reported that use of rapid diagnostic tests (RDTs) were useful for confirming rabies occurrence. Overall, our study provides further evidence that IBCM is a practical approach that can improve rabies detection in endemic countries, and be used to monitor the impact of mass dog vaccinations, including potential to verify rabies freedom. However, the main challenges to implementation are limited training of health workers in rabies, perceived burden of real-time recording and limited resources for livestock field officers to undertake investigations. Nonetheless, IBCM dramatically improved case detection and communication between sectors and we recommend further implementation research to establish best practice and applicability to other settings.
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Affiliation(s)
- Kennedy Lushasi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania.,Boyd Orr Centre for Population and Ecosystem Health, College of Medical, Institute of Biodiversity, Animal Health and Comparative Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Rachel Steenson
- Boyd Orr Centre for Population and Ecosystem Health, College of Medical, Institute of Biodiversity, Animal Health and Comparative Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jubilate Bernard
- Department of Epidemiology, Ministry of Health, Community Development, Gender, Elderly and Children (MoHCDGEC), Dodoma, Tanzania
| | - Joel Jackson Changalucha
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania
| | - Nicodem James Govella
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, College of Medical, Institute of Biodiversity, Animal Health and Comparative Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Husna Hoffu
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania
| | - Felix Lankester
- Paul G. Allen School for Global Animal Health, Washington State University, Washington, DC, United States.,Global Animal Health Tanzania, Arusha, Tanzania
| | - Frank Magoti
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania
| | - Emmanuel Abraham Mpolya
- Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Zacharia Mtema
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania
| | - Hesron Nonga
- Director of Veterinary Services, Ministry of Livestock Development and Fisheries, Dodoma, Tanzania
| | - Katie Hampson
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania.,Boyd Orr Centre for Population and Ecosystem Health, College of Medical, Institute of Biodiversity, Animal Health and Comparative Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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23
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Orton RJ, Wright CF, King DP, Haydon DT. Estimating viral bottleneck sizes for FMDV transmission within and between hosts and implications for the rate of viral evolution. Interface Focus 2019; 10:20190066. [PMID: 31897294 DOI: 10.1098/rsfs.2019.0066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
RNA viruses exist as populations of closely related genomes, characterized by a high diversity of low-frequency variants. As viral genomes from one population disperse to establish new sites of replication, the fate of these low-frequency variants depends to a large extent on the size of the founding population. Focusing on foot-and-mouth disease virus (FMDV) we conjecture that variants are more likely to be transmitted through wide bottlenecks, but more likely to approach fixation in new populations following narrow bottlenecks; therefore, the longer-term rate of accumulation of 'nearly neutral' variants at high frequencies is likely to be inversely related to the bottleneck size. We examine this conjecture in vivo by estimating bottleneck sizes relating 'parent' and 'daughter' populations observed at different scales ranging from within host to between host (within the same herd, and in different herds) using a previously established method. Within hosts, we find bottleneck sizes to range from 5 to 20 viral genomes between populations transmitted from the pharynx to the serum, and from 4 to 54 between serum and lesion populations. Between hosts, we find bottleneck sizes to range from 2 to 39, suggesting inter-host bottlenecks are of a similar size to intra-host bottlenecks. We establish a statistically significant negative relationship between the probability of genomic consensus level change and bottleneck size, and present a simple sampling model that captures this empirical relationship. We also present a novel in vitro experiment to investigate the impact of bottleneck size on the frequency of mutations within FMDV populations, demonstrate that variant frequency in a population increases more rapidly during small population passages, and provide evidence for positive selection during the passage of large populations.
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Affiliation(s)
- Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.,MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | | | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright GU24 0NF, UK
| | - Daniel T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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24
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Kruijssen JMD, Schruba A, Chevance M, Longmore SN, Hygate APS, Haydon DT, McLeod AF, Dalcanton JJ, Tacconi LJ, van Dishoeck EF. Fast and inefficient star formation due to short-lived molecular clouds and rapid feedback. Nature 2019; 569:519-522. [PMID: 31118525 PMCID: PMC6544524 DOI: 10.1038/s41586-019-1194-3] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/12/2019] [Indexed: 11/18/2022]
Abstract
The physics of star formation and the deposition of mass, momentum, and energy into the interstellar medium by massive stars (‘feedback’) are the main uncertainties in modern cosmological simulations of galaxy formation and evolution1, 2. These processes determine the properties of galaxies3, 4, but are poorly understood on the ≲100 pc scale of individual giant molecular clouds (GMCs)5, 6 resolved in modern galaxy formation simulations7, 8. The key question is why the timescale for depleting molecular gas through star formation in galaxies (tdep ≈ 2 Gyr)9, 10 exceeds the dynamical timescale of GMCs by two orders of magnitude11. Either most of a GMC’s mass is converted into stars over many dynamical times12, or only a small fraction turns into stars before the GMC is dispersed on a dynamical timescale13, 14. Here we report our observation that molecular gas and star formation are spatially decorrelated on GMC scales in the nearby flocculent spiral galaxy NGC300, contrary to their tight correlation on galactic scales5. We demonstrate that this de-correlation implies rapid evolutionary cycling between GMCs, star formation, and feedback. We apply a novel statistical method15, 16 to quantify the evolutionary timeline and find that star formation is regulated by efficient stellar feedback, driving GMC dispersal on short timescales (~1.5 Myr) due to radiation and stellar winds, prior to supernova explosions. This feedback limits GMC lifetimes to about one dynamical timescale (~10 Myr), with integrated star formation efficiencies of only 2–3%. Our findings reveal that galaxies consist of building blocks undergoing vigorous, feedback-driven lifecycles, that vary with the galactic environment and collectively define how galaxies form stars. Systematic applications of this multi-scale analysis to large galaxy samples will provide key input for a predictive, bottom-up theory of galaxy formation and evolution.
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Affiliation(s)
- J M Diederik Kruijssen
- Astronomisches Rechen-Institut, Zentrum für Astronomie der Universität Heidelberg, Heidelberg, Germany. .,Max-Planck Institut für Astronomie, Heidelberg, Germany.
| | - Andreas Schruba
- Max-Planck Institut für Extraterrestrische Physik, Garching, Germany
| | - Mélanie Chevance
- Astronomisches Rechen-Institut, Zentrum für Astronomie der Universität Heidelberg, Heidelberg, Germany
| | - Steven N Longmore
- Astrophysics Research Institute, Liverpool John Moores University, Liverpool, UK
| | - Alexander P S Hygate
- Astronomisches Rechen-Institut, Zentrum für Astronomie der Universität Heidelberg, Heidelberg, Germany.,Max-Planck Institut für Astronomie, Heidelberg, Germany
| | - Daniel T Haydon
- Astronomisches Rechen-Institut, Zentrum für Astronomie der Universität Heidelberg, Heidelberg, Germany
| | - Anna F McLeod
- Department of Astronomy, University of California Berkeley, Berkeley, CA, USA.,Department of Physics and Astronomy, Texas Tech University, Lubbock, TX, USA
| | | | - Linda J Tacconi
- Max-Planck Institut für Extraterrestrische Physik, Garching, Germany
| | - Ewine F van Dishoeck
- Max-Planck Institut für Extraterrestrische Physik, Garching, Germany.,Leiden Observatory, Leiden University, Leiden, The Netherlands
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25
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Grillet ME, Hernández-Villena JV, Llewellyn MS, Paniz-Mondolfi AE, Tami A, Vincenti-Gonzalez MF, Marquez M, Mogollon-Mendoza AC, Hernandez-Pereira CE, Plaza-Morr JD, Blohm G, Grijalva MJ, Costales JA, Ferguson HM, Schwabl P, Hernandez-Castro LE, Lamberton PHL, Streicker DG, Haydon DT, Miles MA, Acosta-Serrano A, Acquattela H, Basañez MG, Benaim G, Colmenares LA, Conn JE, Espinoza R, Freilij H, Graterol-Gil MC, Hotez PJ, Kato H, Lednicky JA, Martinez CE, Mas-Coma S, Morris JG, Navarro JC, Ramirez JL, Rodriguez M, Urbina JA, Villegas L, Segovia MJ, Carrasco HJ, Crainey JL, Luz SLB, Moreno JD, Noya Gonzalez OO, Ramírez JD, Alarcón-de Noya B. Venezuela's humanitarian crisis, resurgence of vector-borne diseases, and implications for spillover in the region. Lancet Infect Dis 2019; 19:e149-e161. [PMID: 30799251 DOI: 10.1016/s1473-3099(18)30757-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 11/14/2018] [Accepted: 11/28/2018] [Indexed: 01/19/2023]
Abstract
In the past 5-10 years, Venezuela has faced a severe economic crisis, precipitated by political instability and declining oil revenue. Public health provision has been affected particularly. In this Review, we assess the impact of Venezuela's health-care crisis on vector-borne diseases, and the spillover into neighbouring countries. Between 2000 and 2015, Venezuela witnessed a 359% increase in malaria cases, followed by a 71% increase in 2017 (411 586 cases) compared with 2016 (240 613). Neighbouring countries, such as Brazil, have reported an escalating trend of imported malaria cases from Venezuela, from 1538 in 2014 to 3129 in 2017. In Venezuela, active Chagas disease transmission has been reported, with seroprevalence in children (<10 years), estimated to be as high as 12·5% in one community tested (n=64). Dengue incidence increased by more than four times between 1990 and 2016. The estimated incidence of chikungunya during its epidemic peak is 6975 cases per 100 000 people and that of Zika virus is 2057 cases per 100 000 people. The re-emergence of many vector-borne diseases represents a public health crisis in Venezuela and has the possibility of severely undermining regional disease elimination efforts. National, regional, and global authorities must take action to address these worsening epidemics and prevent their expansion beyond Venezuelan borders.
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Affiliation(s)
- Maria E Grillet
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | | | - Martin S Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.
| | - Alberto E Paniz-Mondolfi
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Department of Tropical Medicine and Infectious Diseases, Instituto de Investigaciones Biomédicas IDB, Clinica IDB Cabudare, Cabudare, Venezuela; Instituto de Estudios Avanzados, Caracas, Venezuela
| | - Adriana Tami
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands; Facultad de Ciencias de la Salud, Universidad de Carabobo, Valencia, Venezuela
| | - Maria F Vincenti-Gonzalez
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Marilianna Marquez
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Department of Tropical Medicine and Infectious Diseases, Instituto de Investigaciones Biomédicas IDB, Clinica IDB Cabudare, Cabudare, Venezuela; Health Sciences Department, College of Medicine, Universidad Centrooccidental Lisandro Alvarado, Barquisimeto, Lara State, Venezuela
| | - Adriana C Mogollon-Mendoza
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Department of Tropical Medicine and Infectious Diseases, Instituto de Investigaciones Biomédicas IDB, Clinica IDB Cabudare, Cabudare, Venezuela; Health Sciences Department, College of Medicine, Universidad Centrooccidental Lisandro Alvarado, Barquisimeto, Lara State, Venezuela
| | - Carlos E Hernandez-Pereira
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Department of Tropical Medicine and Infectious Diseases, Instituto de Investigaciones Biomédicas IDB, Clinica IDB Cabudare, Cabudare, Venezuela; Health Sciences Department, College of Medicine, Universidad Centrooccidental Lisandro Alvarado, Barquisimeto, Lara State, Venezuela
| | - Juan D Plaza-Morr
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Department of Tropical Medicine and Infectious Diseases, Instituto de Investigaciones Biomédicas IDB, Clinica IDB Cabudare, Cabudare, Venezuela; Health Sciences Department, College of Medicine, Universidad Nacional Experimental Francisco de Miranda, Punto Fijo, Falcón State, Venezuela
| | - Gabriella Blohm
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Department of Tropical Medicine and Infectious Diseases, Instituto de Investigaciones Biomédicas IDB, Clinica IDB Cabudare, Cabudare, Venezuela; Emerging Pathogens Institute, Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Mario J Grijalva
- Infectious and Tropical Disease Institute, Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - Jaime A Costales
- Center for Research on Health in Latin America, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Heather M Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Philipp Schwabl
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | | | - Poppy H L Lamberton
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Daniel G Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK; MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Daniel T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Michael A Miles
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Alvaro Acosta-Serrano
- Department of Vector Biology and Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Maria G Basañez
- Department of Vector Biology and Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Gustavo Benaim
- Instituto de Biología Experimental, Universidad Central de Venezuela, Caracas, Venezuela; Instituto de Estudios Avanzados, Caracas, Venezuela
| | - Luis A Colmenares
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Jan E Conn
- Griffin Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA; School of Public Health, University at Albany, NY, USA
| | - Raul Espinoza
- Hospital Miguel Pérez Carreño, Instituto Venezolano de los Seguros Sociales, Caracas, Venezuela
| | - Hector Freilij
- Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Mary C Graterol-Gil
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Peter J Hotez
- National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Hirotomo Kato
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - John A Lednicky
- Emerging Pathogens Institute, Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Clara E Martinez
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Santiago Mas-Coma
- Departamento de Parasitología, Universidad de Valencia, Valencia, Spain
| | - J Glen Morris
- Emerging Pathogens Institute, Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Juan C Navarro
- Enfermedades Emergentes y Salud Ambiental, Centro de Biodiversidad, Universidad Internacional SEK, Quito, Ecuador
| | - Jose L Ramirez
- Biotechnology Center, Instituto de Estudios Avanzados, Caracas, Venezuela
| | - Marlenes Rodriguez
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Julio A Urbina
- Venezuelan Institute for Scientific Research, Caracas, Venezuela
| | | | - Maikell J Segovia
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Hernan J Carrasco
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - James L Crainey
- Instituto Leônidas e Maria Deane ILMD/FIOCRUZ, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Manaus, Amazonas, Brazil
| | - Sergio L B Luz
- Instituto Leônidas e Maria Deane ILMD/FIOCRUZ, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Manaus, Amazonas, Brazil
| | - Juan D Moreno
- Centro de Investigaciones de Campo "Dr Francesco Vitanza", Servicio Autónomo Instituto de Altos Estudios "Dr Arnoldo Gabaldon", MPPS, Tumeremo, Venezuela
| | - Oscar O Noya Gonzalez
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela; Centro de Investigaciones de Campo "Dr Francesco Vitanza", Servicio Autónomo Instituto de Altos Estudios "Dr Arnoldo Gabaldon", MPPS, Tumeremo, Venezuela
| | - Juan D Ramírez
- Grupo de Investigaciones Microbiológicas-UR, Programa de Biología, Universidad del Rosario, Bogotá, Colombia
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26
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Behdenna A, Lembo T, Calatayud O, Cleaveland S, Halliday JEB, Packer C, Lankester F, Hampson K, Craft ME, Czupryna A, Dobson AP, Dubovi EJ, Ernest E, Fyumagwa R, Hopcraft JGC, Mentzel C, Mzimbiri I, Sutton D, Willett B, Haydon DT, Viana M. Transmission ecology of canine parvovirus in a multi-host, multi-pathogen system. Proc Biol Sci 2019; 286:20182772. [PMID: 30914008 PMCID: PMC6452066 DOI: 10.1098/rspb.2018.2772] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/27/2019] [Indexed: 12/25/2022] Open
Abstract
Understanding multi-host pathogen maintenance and transmission dynamics is critical for disease control. However, transmission dynamics remain enigmatic largely because they are difficult to observe directly, particularly in wildlife. Here, we investigate the transmission dynamics of canine parvovirus (CPV) using state-space modelling of 20 years of CPV serology data from domestic dogs and African lions in the Serengeti ecosystem. We show that, although vaccination reduces the probability of infection in dogs, and despite indirect enhancement of population seropositivity as a result of vaccine shedding, the vaccination coverage achieved has been insufficient to prevent CPV from becoming widespread. CPV is maintained by the dog population and has become endemic with approximately 3.5-year cycles and prevalence reaching approximately 80%. While the estimated prevalence in lions is lower, peaks of infection consistently follow those in dogs. Dogs exposed to CPV are also more likely to become infected with a second multi-host pathogen, canine distemper virus. However, vaccination can weaken this coupling, raising questions about the value of monovalent versus polyvalent vaccines against these two pathogens. Our findings highlight the need to consider both pathogen- and host-level community interactions when seeking to understand the dynamics of multi-host pathogens and their implications for conservation, disease surveillance and control programmes.
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Affiliation(s)
- Abdelkader Behdenna
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Tiziana Lembo
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jo E. B. Halliday
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Craig Packer
- Ecology Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Felix Lankester
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164, USA
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Meggan E. Craft
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108, USA
| | - Anna Czupryna
- Lincoln Park Zoo, Chicago, IL 60614, USA
- Department of Ecology and Evolution, University of Illinois, Chicago, IL 60607, USA
| | - Andrew P. Dobson
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Edward J. Dubovi
- Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14851, USA
| | - Eblate Ernest
- Tanzania Wildlife Research Institute, Arusha, Tanzania
| | - Robert Fyumagwa
- Conservation Areas and Species Diversity Programme, South Africa Country Office, International Union for the Conservation of Nature, Pretoria, South Africa
| | - J. Grant C. Hopcraft
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Christine Mentzel
- Conservation Areas and Species Diversity Programme, South Africa Country Office, International Union for the Conservation of Nature, Pretoria, South Africa
| | | | - David Sutton
- MSD Animal Health, Walton Manor, Walton, Milton Keynes MK7 7AJ, UK
| | - Brian Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G6 1QH, UK
| | - Daniel T. Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Mafalda Viana
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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27
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Kerfua SD, Shirima G, Kusiluka L, Ayebazibwe C, Martin E, Arinaitwe E, Cleaveland S, Haydon DT. Low topotype diversity of recent foot-and-mouth disease virus serotypes O and A from districts located along the Uganda and Tanzania border. J Vet Sci 2019; 20:e4. [PMID: 30944527 PMCID: PMC6441803 DOI: 10.4142/jvs.2019.20.e4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/20/2019] [Accepted: 01/03/2019] [Indexed: 02/03/2023] Open
Abstract
Foot-and-mouth disease (FMD) is one of the most important livestock diseases in East Africa with outbreaks reported annually that cause severe economic losses. It is possible to control disease using vaccination, but antigenic matching of the vaccine to circulating strains is critical. To determine the relationship between foot-and-mouth disease viruses circulating in districts along the Uganda and Tanzanian border between 2016 and 2017 and currently used vaccines, phylogenetic analysis of the full VP1 virus sequences was carried out on samples collected from both sides of the border. A total of 43 clinical samples were collected from animals exhibiting signs of FMD and VP1 sequences generated from 11 of them. Eight out of the 11 sequences obtained belonged to serotype O and three belonged to serotype A. The serotype O sequences obtained showed limited nucleotide divergence (average of 4.9%) and belonged to topotype East Africa-2, whereas the most common O-type vaccine strain used in the region (O/KEN/77/78) belonged to East Africa-1. The serotype A viruses belonged to topotype Africa-G1 (average nucleotide divergence 7.4%), as did vaccine strain K5/1980. However, vaccine strain K35/1980 belonged to Africa G VII with an average sequence divergence of 20.5% from the study sequences. The genetic distances between current vaccine strains and circulating field strains underscores the crucial need for regular vaccine matching and the importance of collaborative efforts for better control of FMD along this border area.
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Affiliation(s)
- Susan Diana Kerfua
- Department of Global Health and Biomedical Sciences, Nelson Mandela African Institution of Science and Technology, Arusha, P.O.Box 447, Tanzania.,Department of Microbiology, National Livestock Resources Research Institute, Wakiso, P.O.Box 5704, Uganda
| | - Gabriel Shirima
- Department of Global Health and Biomedical Sciences, Nelson Mandela African Institution of Science and Technology, Arusha, P.O.Box 447, Tanzania
| | - Lughano Kusiluka
- Department of Global Health and Biomedical Sciences, Mzumbe University, Morogoro, P.O.Box 1, Tanzania
| | - Chrisostom Ayebazibwe
- National Animal Disease Diagnostics and Epidemiological Centre, Ministry of Agriculture Animal Industry and Fisheries, Entebbe, P.O.Box 53, Uganda
| | - Esau Martin
- Department of Immunology, National Animal Disease Diagnostics and Epidemiological Centre, Ministry of Agriculture Animal Industry and Fisheries, Entebbe, P.O.Box 53, Uganda
| | - Eugene Arinaitwe
- Department of Molecular Biology, National Animal Disease Diagnostics and Epidemiological Centre, Ministry of Agriculture Animal Industry and Fisheries, Entebbe, P.O.Box 53, Uganda
| | - Sarah Cleaveland
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G128QQ, United Kingdom
| | - Daniel T Haydon
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G128QQ, United Kingdom
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Casey-Bryars M, Reeve R, Bastola U, Knowles NJ, Auty H, Bachanek-Bankowska K, Fowler VL, Fyumagwa R, Kazwala R, Kibona T, King A, King DP, Lankester F, Ludi AB, Lugelo A, Maree FF, Mshanga D, Ndhlovu G, Parekh K, Paton DJ, Perry B, Wadsworth J, Parida S, Haydon DT, Marsh TL, Cleaveland S, Lembo T. Waves of endemic foot-and-mouth disease in eastern Africa suggest feasibility of proactive vaccination approaches. Nat Ecol Evol 2018; 2:1449-1457. [PMID: 30082738 DOI: 10.1038/s41559-018-0636-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/04/2018] [Indexed: 11/09/2022]
Abstract
Livestock production in Africa is key to national economies, food security and rural livelihoods, and > 85% of livestock keepers live in extreme poverty. With poverty elimination central to the Sustainable Development Goals, livestock keepers are therefore critically important. Foot-and-mouth disease is a highly contagious livestock disease widespread in Africa that contributes to this poverty. Despite its US$2.3 billion impact, control of the disease is not prioritized: standard vaccination regimens are too costly, its impact on the poorest is underestimated, and its epidemiology is too weakly understood. Our integrated analysis in Tanzania shows that the disease is of high concern, reduces household budgets for human health, and has major impacts on milk production and draft power for crop production. Critically, foot-and-mouth disease outbreaks in cattle are driven by livestock-related factors with a pattern of changing serotype dominance over time. Contrary to findings in southern Africa, we find no evidence of frequent infection from wildlife, with outbreaks in cattle sweeping slowly across the region through a sequence of dominant serotypes. This regularity suggests that timely identification of the epidemic serotype could allow proactive vaccination ahead of the wave of infection, mitigating impacts, and our preliminary matching work has identified potential vaccine candidates. This strategy is more realistic than wildlife-livestock separation or conventional foot-and-mouth disease vaccination approaches. Overall, we provide strong evidence for the feasibility of coordinated foot-and-mouth disease control as part of livestock development policies in eastern Africa, and our integrated socioeconomic, epidemiological, laboratory and modelling approach provides a framework for the study of other disease systems.
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Affiliation(s)
- Miriam Casey-Bryars
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Department of Agriculture, Food and the Marine, Dublin, Ireland.,The Pirbright Institute, Pirbright, Surrey, UK
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Umesh Bastola
- School of Economic Sciences and Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | | | - Harriet Auty
- Epidemiology Research Unit, Scotland's Rural College (SRUC), An Lòchran, Inverness, UK
| | | | | | | | | | - Tito Kibona
- Sokoine University of Agriculture, Morogoro, Tanzania.,Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | | | - Felix Lankester
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Paul G. Allen School for Global Animal Health, Washington State University, Pullman , WA, USA
| | - Anna B Ludi
- The Pirbright Institute, Pirbright, Surrey, UK
| | - Ahmed Lugelo
- Sokoine University of Agriculture, Morogoro, Tanzania
| | - Francois F Maree
- Agricultural Research Council, Onderstepoort Veterinary Institute, Pretoria, South Africa
| | - Deogratius Mshanga
- Tanzania Veterinary Laboratory Agency, Ministry of Livestock and Fisheries, Arusha, Tanzania
| | | | | | | | - Brian Perry
- College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | | | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Thomas L Marsh
- School of Economic Sciences and Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - Sarah Cleaveland
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Tiziana Lembo
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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Checchi F, Funk S, Chandramohan D, Chappuis F, Haydon DT. The impact of passive case detection on the transmission dynamics of gambiense Human African Trypanosomiasis. PLoS Negl Trop Dis 2018; 12:e0006276. [PMID: 29624584 PMCID: PMC5906023 DOI: 10.1371/journal.pntd.0006276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 04/18/2018] [Accepted: 01/26/2018] [Indexed: 12/02/2022] Open
Abstract
Gambiense Human African Trypanosomiasis (HAT), or sleeping sickness, is a vector-borne disease affecting largely rural populations in Western and Central Africa. The main method for detecting and treating cases of gambiense HAT are active screening through mobile teams and passive detection through self-referral of patients to dedicated treatment centres or hospitals. Strategies based on active case finding and treatment have drastically reduced the global incidence of the disease over recent decades. However, little is known about the coverage and transmission impact of passive case detection. We used a mathematical model to analyse data from the period between active screening sessions in hundreds of villages that were monitored as part of three HAT control projects run by Médecins Sans Frontières in Southern Sudan and Uganda in the late 1990s and early 2000s. We found heterogeneity in incidence across villages, with a small minority of villages found to have much higher transmission rates and burdens than the majority. We further found that only a minority of prevalent cases in the first, haemo-lymphatic stage of the disease were detected passively (maximum likelihood estimate <30% in all three settings), whereas around 50% of patients in the second, meningo-encephalitic were detected. We estimated that passive case detection reduced transmission in affected areas by between 30 and 50%, suggesting that there is great potential value in improving rates of passive case detection. As gambiense HAT is driven towards elimination, it will be important to establish good systems of passive screening, and estimates such as the ones here will be of value in assessing the expected impact of moving from a primarily active to a more passive screening regime. Gambiense Human African Trypanosomiasis, or sleeping sickness, is transmitted by the tsetse fly and affects rural populations in Western and Central Africa. It is a deadly disease if untreated, and it is therefore important to find people in the early stages of disease so that appropriate care and medication can be provided. Because of this, much emphasis is put on mobile teams going from village to village and actively finding as many potential patients as possible. This does not reach all infected people, though, and some are only detected passively, that is they report themselves to a health provider, often in advanced stages of disease. It is not clear what proportion of cases of sleeping sickness are detected in this way, or how much onwards transmission is prevented. Here we used a mathematical model to analyse data from a sleeping sickness control programme in Uganda and South Sudan, in order to identify which proportion of people infected with the disease are identified through passive case detection. We found that only a minority of patients are identified in this way in the early stages of disease, but around half are identified if they are in the later stages. We further found that passive screening reduced transmission in affected areas by between 30 and 50%. This suggests that there is great potential value in improving the rates of passive case detection, and we recommend that more emphasis is put on tackling potential barriers that prevent people being detected.
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Affiliation(s)
- Francesco Checchi
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sebastian Funk
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
| | - Daniel Chandramohan
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - François Chappuis
- Division of Tropical and Humanitarian Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Daniel T. Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Viana M, Faust CL, Haydon DT, Webster JP, Lamberton PHL. The effects of subcurative praziquantel treatment on life-history traits and trade-offs in drug-resistant Schistosoma mansoni. Evol Appl 2018; 11:488-500. [PMID: 29636801 PMCID: PMC5891057 DOI: 10.1111/eva.12558] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/24/2017] [Indexed: 02/03/2023] Open
Abstract
Natural selection acts on all organisms, including parasites, to maximize reproductive fitness. Drug resistance traits are often associated with life-history costs in the absence of treatment. Schistosomiasis control programmes rely on mass drug administration to reduce human morbidity and mortality. Although hotspots of reduced drug efficacy have been reported, resistance is not widespread. Using Bayesian state-space models (SSMs) fitted to data from an in vivo laboratory system, we tested the hypothesis that the spread of resistant Schistosoma mansoni may be limited by life-history costs not present in susceptible counterparts. S. mansoni parasites from a praziquantel-susceptible (S), a praziquantel-resistant (R) or a mixed line of originally resistant and susceptible parasites (RS) were exposed to a range of praziquantel doses. Parasite numbers at each life stage were quantified in their molluscan intermediate and murine definitive hosts across four generations, and SSMs were used to estimate key life-history parameters for each experimental group over time. Model outputs illustrated that parasite adult survival and fecundity in the murine host decreased across all lines, including R, with increasing drug pressure. Trade-offs between adult survival and fecundity were observed in all untreated lines, and these remained strong in S with praziquantel pressure. In contrast, trade-offs between adult survival and fecundity were lost under praziquantel pressure in R. As expected, parasite life-history traits within the molluscan host were complex, but trade-offs were demonstrated between parasite establishment and cercarial output. The observed trade-offs between generations within hosts, which were modified by praziquantel treatment in the R line, could limit the spread of R parasites under praziquantel pressure. Whilst such complex life-history costs may be difficult to detect using standard empirical methods, we demonstrate that SSMs provide robust estimates of life-history parameters, aiding our understanding of costs and trade-offs of resistant parasites within this system and beyond.
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Affiliation(s)
- Mafalda Viana
- Institute for Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Christina L. Faust
- Institute for Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- Wellcome Centre for Molecular ParasitologyUniversity of GlasgowGlasgowUK
| | - Daniel T. Haydon
- Institute for Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Joanne P. Webster
- London Centre for Neglected Tropical Disease ResearchDepartment of Infectious Disease EpidemiologySchool of Public HealthImperial College LondonLondonUK
- Centre for Endemic, Emerging and Exotic DiseasesThe Royal Veterinary CollegeUniversity of LondonLondonUK
| | - Poppy H. L. Lamberton
- Institute for Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- London Centre for Neglected Tropical Disease ResearchDepartment of Infectious Disease EpidemiologySchool of Public HealthImperial College LondonLondonUK
- Wellcome Centre for Molecular ParasitologyUniversity of GlasgowGlasgowUK
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31
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Halliday JEB, Hampson K, Hanley N, Lembo T, Sharp JP, Haydon DT, Cleaveland S. Driving improvements in emerging disease surveillance through locally relevant capacity strengthening. Science 2018; 357:146-148. [PMID: 28706036 DOI: 10.1126/science.aam8332] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Emerging infectious diseases (EIDs) threaten the health of people, animals, and crops globally, but our ability to predict their occurrence is limited. Current public health capacity and ability to detect and respond to EIDs is typically weakest in low- and middle-income countries (LMICs). Many known drivers of EID emergence also converge in LMICs. Strengthening capacity for surveillance of diseases of relevance to local populations can provide a mechanism for building the cross-cutting and flexible capacities needed to tackle both the burden of existing diseases and EID threats. A focus on locally relevant diseases in LMICs and the economic, social, and cultural contexts of surveillance can help address existing inequalities in health systems, improve the capacity to detect and contain EIDs, and contribute to broader global goals for development.
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Affiliation(s)
- Jo E B Halliday
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Katie Hampson
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Nick Hanley
- School of Geography and Sustainable Development, University of St Andrews, St Andrews, Scotland, UK
| | - Tiziana Lembo
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Joanne P Sharp
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, UK
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sarah Cleaveland
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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32
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Logan G, Newman J, Wright CF, Lasecka-Dykes L, Haydon DT, Cottam EM, Tuthill TJ. Deep Sequencing of Foot-and-Mouth Disease Virus Reveals RNA Sequences Involved in Genome Packaging. J Virol 2018; 92:e01159-17. [PMID: 29046452 PMCID: PMC5730773 DOI: 10.1128/jvi.01159-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/25/2017] [Indexed: 01/03/2023] Open
Abstract
Nonenveloped viruses protect their genomes by packaging them into an outer shell or capsid of virus-encoded proteins. Packaging and capsid assembly in RNA viruses can involve interactions between capsid proteins and secondary structures in the viral genome, as exemplified by the RNA bacteriophage MS2 and as proposed for other RNA viruses of plants, animals, and human. In the picornavirus family of nonenveloped RNA viruses, the requirements for genome packaging remain poorly understood. Here, we show a novel and simple approach to identify predicted RNA secondary structures involved in genome packaging in the picornavirus foot-and-mouth disease virus (FMDV). By interrogating deep sequencing data generated from both packaged and unpackaged populations of RNA, we have determined multiple regions of the genome with constrained variation in the packaged population. Predicted secondary structures of these regions revealed stem-loops with conservation of structure and a common motif at the loop. Disruption of these features resulted in attenuation of virus growth in cell culture due to a reduction in assembly of mature virions. This study provides evidence for the involvement of predicted RNA structures in picornavirus packaging and offers a readily transferable methodology for identifying packaging requirements in many other viruses.IMPORTANCE In order to transmit their genetic material to a new host, nonenveloped viruses must protect their genomes by packaging them into an outer shell or capsid of virus-encoded proteins. For many nonenveloped RNA viruses the requirements for this critical part of the viral life cycle remains poorly understood. We have identified RNA sequences involved in genome packaging of the picornavirus foot-and-mouth disease virus. This virus causes an economically devastating disease of livestock affecting both the developed and developing world. The experimental methods developed to carry out this work are novel, simple, and transferable to the study of packaging signals in other RNA viruses. Improved understanding of RNA packaging may lead to novel vaccine approaches or targets for antiviral drugs with broad-spectrum activity.
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Affiliation(s)
- Grace Logan
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Joseph Newman
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | | | | | - Daniel T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Trewby H, Wright DM, Skuce RA, McCormick C, Mallon TR, Presho EL, Kao RR, Haydon DT, Biek R. Relative abundance of Mycobacterium bovis molecular types in cattle: a simulation study of potential epidemiological drivers. BMC Vet Res 2017; 13:268. [PMID: 28830547 PMCID: PMC5567634 DOI: 10.1186/s12917-017-1190-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/11/2017] [Indexed: 11/10/2022] Open
Abstract
Background The patterns of relative species abundance are commonly studied in ecology and epidemiology to provide insights into underlying dynamical processes. Molecular types (MVLA-types) of Mycobacterium bovis, the causal agent of bovine tuberculosis, are now routinely recorded in culture-confirmed bovine tuberculosis cases in Northern Ireland. In this study, we use ecological approaches and simulation modelling to investigate the distribution of relative abundances of MVLA-types and its potential drivers. We explore four biologically plausible hypotheses regarding the processes driving molecular type relative abundances: sampling and speciation; structuring of the pathogen population; historical changes in population size; and transmission heterogeneity (superspreading). Results Northern Irish herd-level MVLA-type surveillance shows a right-skewed distribution of MVLA-types, with a small number of types present at very high frequencies and the majority of types very rare. We demonstrate that this skew is too extreme to be accounted for by simple neutral ecological processes. Simulation results indicate that the process of MVLA-type speciation and the manner in which the MVLA-typing loci were chosen in Northern Ireland cannot account for the observed skew. Similarly, we find that pathogen population structure, assuming for example a reservoir of infection in a separate host, would drive the relative abundance distribution in the opposite direction to that observed, generating more even abundances of molecular types. However, we find that historical increases in bovine tuberculosis prevalence and/or transmission heterogeneity (superspreading) are both capable of generating the skewed MVLA-type distribution, consistent with findings of previous work examining the distribution of molecular types in human tuberculosis. Conclusion Although the distribution of MVLA-type abundances does not fit classical neutral predictions, our simulations show that increases in pathogen population size and/or superspreading are consistent with the pattern observed, even in the absence of selective pressures acting on the system. Electronic supplementary material The online version of this article (doi:10.1186/s12917-017-1190-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hannah Trewby
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity and Animal Health, University of Glasgow, Glasgow, UK.
| | - David M Wright
- School of Medicine, Dentistry, and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Robin A Skuce
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, UK.,School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Carl McCormick
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, UK
| | - Thomas R Mallon
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, UK
| | - Eleanor L Presho
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, UK
| | - Rowland R Kao
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity and Animal Health, University of Glasgow, Glasgow, UK
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity and Animal Health, University of Glasgow, Glasgow, UK
| | - Roman Biek
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity and Animal Health, University of Glasgow, Glasgow, UK
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Cleaveland S, Sharp J, Abela-Ridder B, Allan KJ, Buza J, Crump JA, Davis A, Del Rio Vilas VJ, de Glanville WA, Kazwala RR, Kibona T, Lankester FJ, Lugelo A, Mmbaga BT, Rubach MP, Swai ES, Waldman L, Haydon DT, Hampson K, Halliday JEB. One Health contributions towards more effective and equitable approaches to health in low- and middle-income countries. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160168. [PMID: 28584176 PMCID: PMC5468693 DOI: 10.1098/rstb.2016.0168] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2016] [Indexed: 02/06/2023] Open
Abstract
Emerging zoonoses with pandemic potential are a stated priority for the global health security agenda, but endemic zoonoses also have a major societal impact in low-resource settings. Although many endemic zoonoses can be treated, timely diagnosis and appropriate clinical management of human cases is often challenging. Preventive 'One Health' interventions, e.g. interventions in animal populations that generate human health benefits, may provide a useful approach to overcoming some of these challenges. Effective strategies, such as animal vaccination, already exist for the prevention, control and elimination of many endemic zoonoses, including rabies, and several livestock zoonoses (e.g. brucellosis, leptospirosis, Q fever) that are important causes of human febrile illness and livestock productivity losses in low- and middle-income countries. We make the case that, for these diseases, One Health interventions have the potential to be more effective and generate more equitable benefits for human health and livelihoods, particularly in rural areas, than approaches that rely exclusively on treatment of human cases. We hypothesize that applying One Health interventions to tackle these health challenges will help to build trust, community engagement and cross-sectoral collaboration, which will in turn strengthen the capacity of fragile health systems to respond to the threat of emerging zoonoses and other future health challenges. One Health interventions thus have the potential to align the ongoing needs of disadvantaged communities with the concerns of the broader global community, providing a pragmatic and equitable approach to meeting the global goals for sustainable development and supporting the global health security agenda.This article is part of the themed issue 'One Health for a changing world: zoonoses, ecosystems and human well-being'.
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Affiliation(s)
- S Cleaveland
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, and
| | - J Sharp
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - B Abela-Ridder
- Department for the Control of Neglected Tropical Diseases, World Health Organization, Avenue Appia 20, 1211 Geneva 27, Switzerland
| | - K J Allan
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, and
| | - J Buza
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, PO Box 447, Arusha, Tanzania
| | - J A Crump
- Centre for International Health, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - A Davis
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - V J Del Rio Vilas
- School of Veterinary Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - W A de Glanville
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, and
| | - R R Kazwala
- College of Veterinary Medicine and Medical Sciences, Sokoine University of Agriculture, PO Box 3105, Morogoro, Tanzania
| | - T Kibona
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, PO Box 447, Arusha, Tanzania
| | - F J Lankester
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164, USA
| | - A Lugelo
- College of Veterinary Medicine and Medical Sciences, Sokoine University of Agriculture, PO Box 3105, Morogoro, Tanzania
| | - B T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, PO Box 2236, Moshi, Tanzania
| | - M P Rubach
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
| | - E S Swai
- Ministry of Agriculture, Livestock and Fisheries, PO Box 9152, Dar es Salaam, Tanzania
| | - L Waldman
- Institute for Development Studies, Library Road, Brighton BN1 9RE, UK
| | - D T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, and
| | - K Hampson
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, and
| | - J E B Halliday
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, and
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Ladbury G, J Allan K, Cleaveland S, Davis A, A de Glanville W, L Forde T, E B Halliday J, T Haydon D, Kibiki G, Kiwelu I, Lembo T, Maro V, T Mmbaga B, Ndyetabura T, Sharp J, Thomas K, N Zadoks R. One Health Research in Northern Tanzania - Challenges and Progress. East Afr Health Res J 2017. [DOI: 10.24248/eahrj.v1i1.383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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36
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Ladbury G, Allan KJ, Cleaveland S, Davis A, de Glanville WA, Forde TL, Halliday JEB, Haydon DT, Kibiki G, Kiwelu I, Lembo T, Maro V, Mmbaga BT, Ndyetabura T, Sharp J, Thomas K, Zadoks RN. One Health Research in Northern Tanzania - Challenges and Progress. East Afr Health Res J 2017; 1:8-18. [PMID: 34308154 PMCID: PMC8279194 DOI: 10.24248/eahrj-d-16-00379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/02/2017] [Indexed: 11/20/2022] Open
Abstract
East Africa has one of the world's fastest growing human populations-many of whom are dependent on livestock-as well as some of the world's largest wildlife populations. Humans, livestock, and wildlife often interact closely, intimately linking human, animal, and environmental health. The concept of One Health captures this interconnectedness, including the social structures and beliefs driving interactions between species and their environments. East African policymakers and researchers are recognising and encouraging One Health research, with both groups increasingly playing a leading role in this subject area. One Health research requires interaction between scientists from different disciplines, such as the biological and social sciences and human and veterinary medicine. Different disciplines draw on norms, methodologies, and terminologies that have evolved within their respective institutions and that may be distinct from or in conflict with one another. These differences impact interdisciplinary research, both around theoretical and methodological approaches and during project operationalisation. We present experiential knowledge gained from numerous ongoing projects in northern Tanzania, including those dealing with bacterial zoonoses associated with febrile illness, foodborne disease, and anthrax. We use the examples to illustrate differences between and within social and biological sciences and between industrialised and traditional societies, for example, with regard to consenting procedures or the ethical treatment of animals. We describe challenges encountered in ethical approval processes, consenting procedures, and field and laboratory logistics and offer suggestions for improvement. While considerable investment of time in sensitisation, communication, and collaboration is needed to overcome interdisciplinary challenges inherent in One Health research, this can yield great rewards in paving the way for successful implementation of One Health projects. Furthermore, continued investment in African institutions and scientists will strengthen the role of East Africa as a world leader in One Health research.
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Affiliation(s)
- Georgia Ladbury
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Kathryn J Allan
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sarah Cleaveland
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Alicia Davis
- School of Geographical and Earth Sciences, College of Science and Engineering, University of Glasgow, Glasgow, UK
| | - William A de Glanville
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Taya L Forde
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jo E B Halliday
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Daniel T Haydon
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Gibson Kibiki
- Kilimanjaro Clinical Research Institute, Good Samaritan Foundation, Moshi, Tanzania.,East African Health Research Commission, Arusha, Tanzania
| | - Ireen Kiwelu
- Kilimanjaro Clinical Research Institute, Good Samaritan Foundation, Moshi, Tanzania
| | - Tiziana Lembo
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Venance Maro
- Kilimanjaro Christian Medical Centre, Good Samaritan Foundation, Moshi, Tanzania
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Good Samaritan Foundation, Moshi, Tanzania.,Kilimanjaro Christian Medical Centre, Good Samaritan Foundation, Moshi, Tanzania
| | - Theonest Ndyetabura
- Kilimanjaro Clinical Research Institute, Good Samaritan Foundation, Moshi, Tanzania
| | - Jo Sharp
- School of Geographical and Earth Sciences, College of Science and Engineering, University of Glasgow, Glasgow, UK
| | - Kate Thomas
- Kilimanjaro Clinical Research Institute, Good Samaritan Foundation, Moshi, Tanzania.,Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Ruth N Zadoks
- Kilimanjaro Clinical Research Institute, Good Samaritan Foundation, Moshi, Tanzania
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Stevenson TJ, Visser ME, Arnold W, Barrett P, Biello S, Dawson A, Denlinger DL, Dominoni D, Ebling FJ, Elton S, Evans N, Ferguson HM, Foster RG, Hau M, Haydon DT, Hazlerigg DG, Heideman P, Hopcraft JGC, Jonsson NN, Kronfeld-Schor N, Kumar V, Lincoln GA, MacLeod R, Martin SAM, Martinez-Bakker M, Nelson RJ, Reed T, Robinson JE, Rock D, Schwartz WJ, Steffan-Dewenter I, Tauber E, Thackeray SJ, Umstatter C, Yoshimura T, Helm B. Disrupted seasonal biology impacts health, food security and ecosystems. Proc Biol Sci 2016; 282:20151453. [PMID: 26468242 PMCID: PMC4633868 DOI: 10.1098/rspb.2015.1453] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The rhythm of life on earth is shaped by seasonal changes in the environment. Plants and animals show profound annual cycles in physiology, health, morphology, behaviour and demography in response to environmental cues. Seasonal biology impacts ecosystems and agriculture, with consequences for humans and biodiversity. Human populations show robust annual rhythms in health and well-being, and the birth month can have lasting effects that persist throughout life. This review emphasizes the need for a better understanding of seasonal biology against the backdrop of its rapidly progressing disruption through climate change, human lifestyles and other anthropogenic impact. Climate change is modifying annual rhythms to which numerous organisms have adapted, with potential consequences for industries relating to health, ecosystems and food security. Disconcertingly, human lifestyles under artificial conditions of eternal summer provide the most extreme example for disconnect from natural seasons, making humans vulnerable to increased morbidity and mortality. In this review, we introduce scenarios of seasonal disruption, highlight key aspects of seasonal biology and summarize from biomedical, anthropological, veterinary, agricultural and environmental perspectives the recent evidence for seasonal desynchronization between environmental factors and internal rhythms. Because annual rhythms are pervasive across biological systems, they provide a common framework for trans-disciplinary research.
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Affiliation(s)
- T J Stevenson
- Institute for Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
| | - M E Visser
- Department of Animal Ecology, Nederlands Instituut voor Ecologie, Wageningen, The Netherlands
| | - W Arnold
- Research Institute of Wildlife Ecology, University of Vienna, Vienna, Austria
| | - P Barrett
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - S Biello
- School of Psychology, University of Glasgow, Glasgow, UK
| | - A Dawson
- Centre for Ecology and Hydrology, Penicuik, Midlothian, UK
| | - D L Denlinger
- Department of Entomology, Ohio State University, Columbus, OH, USA
| | - D Dominoni
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - F J Ebling
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - S Elton
- Department of Anthropology, Durham University, Durham, UK
| | - N Evans
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - H M Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - R G Foster
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - M Hau
- Max Planck Institute for Ornithology, Seewiesen, Germany
| | - D T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - D G Hazlerigg
- Department of Arctic and Marine Biology, University of Tromso, Tromso, Norway
| | - P Heideman
- Department of Biology, The College of William and Mary, Williamsburg, VA, USA
| | - J G C Hopcraft
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - N N Jonsson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | | | - V Kumar
- Department of Zoology, University of Delhi, Delhi, India
| | - G A Lincoln
- School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - R MacLeod
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - S A M Martin
- Department of Animal Ecology, Nederlands Instituut voor Ecologie, Wageningen, The Netherlands
| | - M Martinez-Bakker
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI, USA
| | - R J Nelson
- Department of Psychology, Ohio State University, Columbus, OH, USA
| | - T Reed
- Aquaculture and Fisheries Development Centre, University of College Cork, Cork, Ireland
| | - J E Robinson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - D Rock
- School of Psychiatry and Clinical Neurosciences, University of Western Australia, Perth, Australia
| | - W J Schwartz
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - I Steffan-Dewenter
- Department of Animal Ecology and Tropical Biology, University of Wuerzburg, Wuerzburg, Germany
| | - E Tauber
- Department of Genetics, University of Leicester, Leicester, UK
| | - S J Thackeray
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - C Umstatter
- Agroscope, Tanikon, CH-8356 Ettenhausen, Switzerland
| | - T Yoshimura
- Department of Applied Molecular Biosciences, University of Nagoya, Nagoya, Japan
| | - B Helm
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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King DJ, Freimanis GL, Orton RJ, Waters RA, Haydon DT, King DP. Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus. Infect Genet Evol 2016; 44:286-292. [PMID: 27421209 PMCID: PMC5036933 DOI: 10.1016/j.meegid.2016.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 11/23/2022]
Abstract
Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT–PCR method was developed to amplify a 7.6 kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal. NGS was used to characterise FMD viruses in clinical samples from cattle. 5 consensus and 104 sub-consensus level substitutions were identified. Distinct virus swarms were found in different lesions within the same host. Only 22 sub-consensus substitutions were shared between 2 or more animals. Data suggest that FMDV evolves independently at different lesion sites.
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Affiliation(s)
- David J King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Graham L Freimanis
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK; MRC-University of Glasgow, Centre for Virus Research, University of Glasgow, 464 Bearsden Road, G61 1QH, UK
| | - Ryan A Waters
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Daniel T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
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Mather AE, Reeve R, Mellor DJ, Matthews L, Reid-Smith RJ, Dutil L, Haydon DT, Reid SWJ. Detection of Rare Antimicrobial Resistance Profiles by Active and Passive Surveillance Approaches. PLoS One 2016; 11:e0158515. [PMID: 27391966 PMCID: PMC4938605 DOI: 10.1371/journal.pone.0158515] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/16/2016] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) surveillance systems are generally not specifically designed to detect emerging resistances and usually focus primarily on resistance to individual drugs. Evaluating the diversity of resistance, using ecological metrics, allows the assessment of sampling protocols with regard to the detection of rare phenotypes, comprising combinations of resistances. Surveillance data of phenotypic AMR of Canadian poultry Salmonella Heidelberg and swine Salmonella Typhimurium var. 5- were used to contrast active (representative isolates derived from healthy animals) and passive (diagnostic isolates) surveillance and assess their suitability for detecting emerging resistance patterns. Although in both datasets the prevalences of resistance to individual antimicrobials were not significantly different between the two surveillance systems, analysis of the diversity of entire resistance phenotypes demonstrated that passive surveillance of diagnostic isolates detected more unique phenotypes. Whilst the most appropriate surveillance method will depend on the relevant objectives, under the conditions of this study, passive surveillance of diagnostic isolates was more effective for the detection of rare and therefore potentially emerging resistance phenotypes.
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Affiliation(s)
- Alison E. Mather
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
- School of Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Dominic J. Mellor
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
- School of Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Louise Matthews
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Richard J. Reid-Smith
- Public Health Agency of Canada, Guelph, Ontario, Canada
- Department of Population Medicine, University of Guelph, Guelph, Ontario, Canada
| | - Lucie Dutil
- Public Health Agency of Canada, St. Hyacinthe, Quebec, Canada
| | - Daniel T. Haydon
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Stuart W. J. Reid
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom
- School of Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
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40
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Harvey WT, Benton DJ, Gregory V, Hall JPJ, Daniels RS, Bedford T, Haydon DT, Hay AJ, McCauley JW, Reeve R. Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses. PLoS Pathog 2016; 12:e1005526. [PMID: 27057693 PMCID: PMC4825936 DOI: 10.1371/journal.ppat.1005526] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
Determining phenotype from genetic data is a fundamental challenge. Identification of emerging antigenic variants among circulating influenza viruses is critical to the vaccine virus selection process, with vaccine effectiveness maximized when constituents are antigenically similar to circulating viruses. Hemagglutination inhibition (HI) assay data are commonly used to assess influenza antigenicity. Here, sequence and 3-D structural information of hemagglutinin (HA) glycoproteins were analyzed together with corresponding HI assay data for former seasonal influenza A(H1N1) virus isolates (1997–2009) and reference viruses. The models developed identify and quantify the impact of eighteen amino acid substitutions on the antigenicity of HA, two of which were responsible for major transitions in antigenic phenotype. We used reverse genetics to demonstrate the causal effect on antigenicity for a subset of these substitutions. Information on the impact of substitutions allowed us to predict antigenic phenotypes of emerging viruses directly from HA gene sequence data and accuracy was doubled by including all substitutions causing antigenic changes over a model incorporating only the substitutions with the largest impact. The ability to quantify the phenotypic impact of specific amino acid substitutions should help refine emerging techniques that predict the evolution of virus populations from one year to the next, leading to stronger theoretical foundations for selection of candidate vaccine viruses. These techniques have great potential to be extended to other antigenically variable pathogens. Influenza A viruses are characterized by rapid antigenic drift: structural changes in B-cell epitopes that facilitate escape from pre-existing immunity. Consequently, seasonal influenza continues to impose a major burden on human health. Accurate quantification of the antigenic impact of specific amino acid substitutions is a pre-requisite for predicting the fitness and evolutionary outcome of variant viruses. Using assays to attribute antigenic variation to amino acid sequence changes we identify substitutions that contribute to antigenic drift and quantify their impact. We show that substitutions identified as low-impact are a critical component of virus antigenic evolution and by including these, as well as the high-impact substitutions often focused on, the accuracy of predicting antigenic phenotypes of emerging viruses from genotype is doubled.
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Affiliation(s)
- William T. Harvey
- Boyd Orr Centre for Population and Ecosystem Health and Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Donald J. Benton
- The Crick Worldwide Influenza Centre, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom (formerly WHO Collaborating Centre for Reference and Research on Influenza, Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom)
| | - Victoria Gregory
- The Crick Worldwide Influenza Centre, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom (formerly WHO Collaborating Centre for Reference and Research on Influenza, Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom)
| | - James P. J. Hall
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rodney S. Daniels
- The Crick Worldwide Influenza Centre, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom (formerly WHO Collaborating Centre for Reference and Research on Influenza, Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom)
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Daniel T. Haydon
- Boyd Orr Centre for Population and Ecosystem Health and Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Alan J. Hay
- The Crick Worldwide Influenza Centre, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom (formerly WHO Collaborating Centre for Reference and Research on Influenza, Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom)
| | - John W. McCauley
- The Crick Worldwide Influenza Centre, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom (formerly WHO Collaborating Centre for Reference and Research on Influenza, Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom)
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health and Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- The Pirbright Institute, Pirbright, Woking, Surrey, United Kingdom
- * E-mail:
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41
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Mtema Z, Changalucha J, Cleaveland S, Elias M, Ferguson HM, Halliday JEB, Haydon DT, Jaswant G, Kazwala R, Killeen GF, Lembo T, Lushasi K, Malishee AD, Mancy R, Maziku M, Mbunda EM, Mchau GJM, Murray-Smith R, Rysava K, Said K, Sambo M, Shayo E, Sikana L, Townsend SE, Urassa H, Hampson K. Mobile Phones As Surveillance Tools: Implementing and Evaluating a Large-Scale Intersectoral Surveillance System for Rabies in Tanzania. PLoS Med 2016; 13:e1002002. [PMID: 27070315 PMCID: PMC4829224 DOI: 10.1371/journal.pmed.1002002] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Katie Hampson and colleagues describe their experience of developing and deploying a large-scale rabies surveillance system based on mobile phones in southern Tanzania.
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Affiliation(s)
- Zacharia Mtema
- Ifakara Health Institute, Ifakara, Morogoro, Tanzania
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | | | - Sarah Cleaveland
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Martin Elias
- Ministry of Health and Social Welfare, Dar es Salaam, Tanzania
| | - Heather M. Ferguson
- Ifakara Health Institute, Ifakara, Morogoro, Tanzania
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jo E. B. Halliday
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel T. Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gurdeep Jaswant
- Sokoine University of Agriculture, Department of Preventative Veterinary Medicine, Morogoro, Tanzania
| | - Rudovick Kazwala
- Sokoine University of Agriculture, Department of Preventative Veterinary Medicine, Morogoro, Tanzania
| | - Gerry F. Killeen
- Ifakara Health Institute, Ifakara, Morogoro, Tanzania
- Liverpool School of Tropical Medicine, Department of Vector Biology, Liverpool, United Kingdom
| | - Tiziana Lembo
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kennedy Lushasi
- Ifakara Health Institute, Ifakara, Morogoro, Tanzania
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Rebecca Mancy
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - Matthew Maziku
- Ministry of Agriculture, Livestock and Fisheries, Dar es Salaam, Tanzania
- World Health Organization, Country Office, Dar es Salaam, Tanzania
| | - Eberhard M. Mbunda
- Ministry of Agriculture, Livestock and Fisheries, Dar es Salaam, Tanzania
| | | | | | - Kristyna Rysava
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Khadija Said
- Sokoine University of Agriculture, Department of Preventative Veterinary Medicine, Morogoro, Tanzania
| | - Maganga Sambo
- Ifakara Health Institute, Ifakara, Morogoro, Tanzania
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Elizabeth Shayo
- Ministry of Agriculture, Livestock and Fisheries, Dar es Salaam, Tanzania
| | | | - Sunny E Townsend
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Katie Hampson
- Ifakara Health Institute, Ifakara, Morogoro, Tanzania
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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43
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Logan N, McMonagle E, Drew AA, Takahashi E, McDonald M, Baron MD, Gilbert M, Cleaveland S, Haydon DT, Hosie MJ, Willett BJ. Efficient generation of vesicular stomatitis virus (VSV)-pseudotypes bearing morbilliviral glycoproteins and their use in quantifying virus neutralising antibodies. Vaccine 2015; 34:814-22. [PMID: 26706278 PMCID: PMC4742518 DOI: 10.1016/j.vaccine.2015.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/20/2015] [Accepted: 12/06/2015] [Indexed: 12/18/2022]
Abstract
Morbillivirus neutralising antibodies are traditionally measured using either plaque reduction neutralisation tests (PRNTs) or live virus microneutralisation tests (micro-NTs). While both test formats provide a reliable assessment of the strength and specificity of the humoral response, they are restricted by the limited number of viral strains that can be studied and often present significant biological safety concerns to the operator. In this study, we describe the adaptation of a replication-defective vesicular stomatitis virus (VSVΔG) based pseudotyping system for the measurement of morbillivirus neutralising antibodies. By expressing the haemagglutinin (H) and fusion (F) proteins of canine distemper virus (CDV) on VSVΔG pseudotypes bearing a luciferase marker gene, neutralising antibody titres could be measured rapidly and with high sensitivity. Further, by exchanging the glycoprotein expression construct, responses against distinct viral strains or species may be measured. Using this technique, we demonstrate cross neutralisation between CDV and peste des petits ruminants virus (PPRV). As an example of the value of the technique, we demonstrate that UK dogs vary in the breadth of immunity induced by CDV vaccination; in some dogs the neutralising response is CDV-specific while, in others, the neutralising response extends to the ruminant morbillivirus PPRV. This technique will facilitate a comprehensive comparison of cross-neutralisation to be conducted across the morbilliviruses.
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Affiliation(s)
- Nicola Logan
- MRC-University of Glasgow Centre for Virus Research, Garscube Estate, Glasgow G61 1QH, United Kingdom.
| | - Elizabeth McMonagle
- MRC-University of Glasgow Centre for Virus Research, Garscube Estate, Glasgow G61 1QH, United Kingdom.
| | - Angharad A Drew
- MRC-University of Glasgow Centre for Virus Research, Garscube Estate, Glasgow G61 1QH, United Kingdom.
| | - Emi Takahashi
- Royal Veterinary College, University of London, London NW1 0TU, United Kingdom.
| | - Michael McDonald
- Veterinary Diagnostic Services, University of Glasgow, Garscube Estate, Glasgow G61 1QH, United Kingdom.
| | - Michael D Baron
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, United Kingdom.
| | - Martin Gilbert
- Wildlife Conservation Society, Bronx, NY, USA; Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
| | - Sarah Cleaveland
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
| | - Margaret J Hosie
- MRC-University of Glasgow Centre for Virus Research, Garscube Estate, Glasgow G61 1QH, United Kingdom.
| | - Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, Garscube Estate, Glasgow G61 1QH, United Kingdom.
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Matthiopoulos J, Fieberg J, Aarts G, Beyer HL, Morales JM, Haydon DT. Establishing the link between habitat selection and animal population dynamics. ECOL MONOGR 2015. [DOI: 10.1890/14-2244.1] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Checchi F, Funk S, Chandramohan D, Haydon DT, Chappuis F. Updated estimate of the duration of the meningo-encephalitic stage in gambiense human African trypanosomiasis. BMC Res Notes 2015; 8:292. [PMID: 26140922 PMCID: PMC4490719 DOI: 10.1186/s13104-015-1244-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 06/17/2015] [Indexed: 11/19/2022] Open
Abstract
Background The duration of the stages of HAT is an important factor in epidemiological studies and intervention planning. Previously, we published estimates of the duration of the haemo-lymphatic stage 1 and meningo-encephalitic stage 2 of the gambiense form of human African trypanosomiasis (HAT), in the absence of treatment. Here we revise the estimate of stage 2 duration, computed based on data from Uganda and South Sudan, by adjusting observed infection prevalence for incomplete case detection coverage and diagnostic inaccuracy. Findings The revised best estimate for the mean duration of stage 2 is 252 days (95% CI 171–399), about half of our initial best estimate, giving a total mean duration of untreated gambiense HAT infection of approximately 2 years and 2 months. Conclusions Our new estimate provides improved information on the transmission dynamics of this neglected tropical disease in Uganda and South Sudan. We stress that there remains considerable variability around the estimated mean values, and that one must be cautious in applying these results to other foci.
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Affiliation(s)
- Francesco Checchi
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Sebastian Funk
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Daniel Chandramohan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Daniel T Haydon
- College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK.
| | - François Chappuis
- Operational Centre Geneva, Médecins Sans Frontières, 78 Rue de Lausanne, 1202, Geneva, Switzerland. .,Division of International and Humanitarian Medicine, Geneva University Hospitals and University of Geneva, rue Gabrielle-Perret-Gentil 4, 1211, Geneva, Switzerland.
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46
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Hopcraft JGC, Mduma SAR, Borner M, Bigurube G, Kijazi A, Haydon DT, Wakilema W, Rentsch D, Sinclair ARE, Dobson A, Lembeli JD. Conservation and economic benefits of a road around the Serengeti. Conserv Biol 2015; 29:932-936. [PMID: 25711283 DOI: 10.1111/cobi.12470] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/28/2014] [Indexed: 06/04/2023]
Affiliation(s)
- J Grant C Hopcraft
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
- Frankfurt Zoological Society, P.O. Box 14935, Arusha, Tanzania.
| | - Simon A R Mduma
- Tanzania Wildlife Research Institute, P.O. Box 661, Arusha, Tanzania
| | - Markus Borner
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
- Frankfurt Zoological Society, P.O. Box 14935, Arusha, Tanzania
| | - Gerald Bigurube
- Frankfurt Zoological Society, P.O. Box 14935, Arusha, Tanzania
| | - Alain Kijazi
- Tanzania National Parks, P.O. Box 3134, Arusha, Tanzania
| | - Daniel T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | - Dennis Rentsch
- Frankfurt Zoological Society, P.O. Box 14935, Arusha, Tanzania
| | - A R E Sinclair
- Centre for Biodiversity Research, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Andrew Dobson
- Eno Hall, Princeton University, Princeton, NJ, 08544-1003, U.S.A
| | - James Daudi Lembeli
- Parliamentary Committee on Land, Natural Resources and Environment, Tanzania, P.O. Box 1065, Kahama, Tanzania
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Bari FD, Parida S, Asfor AS, Haydon DT, Reeve R, Paton DJ, Mahapatra M. Prediction and characterization of novel epitopes of serotype A foot-and-mouth disease viruses circulating in East Africa using site-directed mutagenesis. J Gen Virol 2015; 96:1033-1041. [PMID: 25614587 PMCID: PMC4631058 DOI: 10.1099/vir.0.000051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/12/2015] [Indexed: 02/06/2023] Open
Abstract
Epitopes on the surface of the foot-and-mouth disease virus (FMDV) capsid have been identified by monoclonal antibody (mAb) escape mutant studies leading to the designation of four antigenic sites in serotype A FMDV. Previous work focused on viruses isolated mainly from Asia, Europe and Latin America. In this study we report on the prediction of epitopes in African serotype A FMDVs and testing of selected epitopes using reverse genetics. Twenty-four capsid amino acid residues were predicted to be of antigenic significance by analysing the capsid sequences (n = 56) using in silico methods, and six residues by correlating capsid sequence with serum-virus neutralization data. The predicted residues were distributed on the surface-exposed capsid regions, VP1-VP3. The significance of residue changes at eight of the predicted epitopes was tested by site-directed mutagenesis using a cDNA clone resulting in the generation of 12 mutant viruses involving seven sites. The effect of the amino acid substitutions on the antigenic nature of the virus was assessed by virus neutralization (VN) test. Mutations at four different positions, namely VP1-43, VP1-45, VP2-191 and VP3-132, led to significant reduction in VN titre (P value = 0.05, 0.05, 0.001 and 0.05, respectively). This is the first time, to our knowledge, that the antigenic regions encompassing amino acids VP1-43 to -45 (equivalent to antigenic site 3 in serotype O), VP2-191 and VP3-132 have been predicted as epitopes and evaluated serologically for serotype A FMDVs. This identifies novel capsid epitopes of recently circulating serotype A FMDVs in East Africa.
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Affiliation(s)
- Fufa Dawo Bari
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
| | - Satya Parida
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
| | - Amin S. Asfor
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
| | - Daniel T. Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
| | - Richard Reeve
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
| | - David J. Paton
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
| | - Mana Mahapatra
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
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Valdazo-González B, Kim JT, Soubeyrand S, Wadsworth J, Knowles NJ, Haydon DT, King DP. The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus. Infect Genet Evol 2015; 32:440-8. [PMID: 25861750 PMCID: PMC7106308 DOI: 10.1016/j.meegid.2015.03.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/05/2015] [Accepted: 03/26/2015] [Indexed: 11/26/2022]
Abstract
45 full FMDV genomes were analysed from farms infected in the UK during 2007. Analyses revealed intra-herd clustering consistent with virus transmission events. Inter-herd sequence differences were estimated to be 4.6 nucleotides. Random selection of 1 sequence from each herd generated similar transmission trees. These results will help to design cost-effective approaches for the control of FMD.
Full-genome sequences have been used to monitor the fine-scale dynamics of epidemics caused by RNA viruses. However, the ability of this approach to confidently reconstruct transmission trees is limited by the knowledge of the genetic diversity of viruses that exist within different epidemiological units. In order to address this question, this study investigated the variability of 45 foot-and-mouth disease virus (FMDV) genome sequences (from 33 animals) that were collected during 2007 from eight premises (10 different herds) in the United Kingdom. Bayesian and statistical parsimony analysis demonstrated that these sequences exhibited clustering which was consistent with a transmission scenario describing herd-to-herd spread of the virus. As an alternative to analysing all of the available samples in future epidemics, the impact of randomly selecting one sequence from each of these herds was used to assess cost-effective methods that might be used to infer transmission trees during FMD outbreaks. Using these approaches, 85% and 91% of the resulting topologies were either identical or differed by only one edge from a reference tree comprising all of the sequences generated within the outbreak. The sequence distances that accrued during sequential transmission events between epidemiological units was estimated to be 4.6 nucleotides, although the genetic variability between viruses recovered from chronic carrier animals was higher than between viruses from animals with acute-stage infection: an observation which poses challenges for the use of simple approaches to infer transmission trees. This study helps to develop strategies for sampling during FMD outbreaks, and provides data that will guide the development of further models to support control policies in the event of virus incursions into FMD free countries.
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Affiliation(s)
| | - Jan T Kim
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, United Kingdom
| | - Samuel Soubeyrand
- INRA, UR546 Biostatistics and Spatial Processes, F-84914 Avignon, France
| | - Jemma Wadsworth
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, United Kingdom
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, United Kingdom
| | - Daniel T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, United Kingdom.
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49
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Orton RJ, Wright CF, Morelli MJ, King DJ, Paton DJ, King DP, Haydon DT. Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data. BMC Genomics 2015; 16:229. [PMID: 25886445 PMCID: PMC4425905 DOI: 10.1186/s12864-015-1456-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 03/09/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND RNA viruses have high mutation rates and exist within their hosts as large, complex and heterogeneous populations, comprising a spectrum of related but non-identical genome sequences. Next generation sequencing is revolutionising the study of viral populations by enabling the ultra deep sequencing of their genomes, and the subsequent identification of the full spectrum of variants within the population. Identification of low frequency variants is important for our understanding of mutational dynamics, disease progression, immune pressure, and for the detection of drug resistant or pathogenic mutations. However, the current challenge is to accurately model the errors in the sequence data and distinguish real viral variants, particularly those that exist at low frequency, from errors introduced during sequencing and sample processing, which can both be substantial. RESULTS We have created a novel set of laboratory control samples that are derived from a plasmid containing a full-length viral genome with extremely limited diversity in the starting population. One sample was sequenced without PCR amplification whilst the other samples were subjected to increasing amounts of RT and PCR amplification prior to ultra-deep sequencing. This enabled the level of error introduced by the RT and PCR processes to be assessed and minimum frequency thresholds to be set for true viral variant identification. We developed a genome-scale computational model of the sample processing and NGS calling process to gain a detailed understanding of the errors at each step, which predicted that RT and PCR errors are more likely to occur at some genomic sites than others. The model can also be used to investigate whether the number of observed mutations at a given site of interest is greater than would be expected from processing errors alone in any NGS data set. After providing basic sample processing information and the site's coverage and quality scores, the model utilises the fitted RT-PCR error distributions to simulate the number of mutations that would be observed from processing errors alone. CONCLUSIONS These data sets and models provide an effective means of separating true viral mutations from those erroneously introduced during sample processing and sequencing.
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Affiliation(s)
- Richard J Orton
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
- Medical Research Council-University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
| | | | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia at the IFOM-IEO Campus, Via Adamello 16, Milano, 20139, Italy.
| | - David J King
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - David J Paton
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - Donald P King
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
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50
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Bari FD, Parida S, Tekleghiorghis T, Dekker A, Sangula A, Reeve R, Haydon DT, Paton DJ, Mahapatra M. Genetic and antigenic characterisation of serotype A FMD viruses from East Africa to select new vaccine strains. Vaccine 2014; 32:5794-800. [PMID: 25171846 PMCID: PMC4194315 DOI: 10.1016/j.vaccine.2014.08.033] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/01/2014] [Accepted: 08/15/2014] [Indexed: 11/08/2022]
Abstract
Vaccine strain selection for emerging foot-and-mouth disease virus (FMDV) outbreaks in enzootic countries can be addressed through antigenic and genetic characterisation of recently circulating viruses. A total of 56 serotype A FMDVs isolated between 1998 and 2012, from Central, East and North African countries were characterised antigenically by virus neutralisation test using antisera to three existing and four candidate vaccine strains and, genetically by characterising the full capsid sequence data. A Bayesian analysis of the capsid sequence data revealed the viruses to be of either African or Asian topotypes with subdivision of the African topotype viruses into four genotypes (Genotypes I, II, IV and VII). The existing vaccine strains were found to be least cross-reactive (good matches observed for only 5.4–46.4% of the sampled viruses). Three bovine antisera, raised against A-EA-2007, A-EA-1981 and A-EA-1984 viruses, exhibited broad cross-neutralisation, towards more than 85% of the circulating viruses. Of the three vaccines, A-EA-2007 was the best showing more than 90% in-vitro cross-protection, as well as being the most recent amongst the vaccine strains used in this study. It therefore appears antigenically suitable as a vaccine strain to be used in the region in FMD control programmes.
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Affiliation(s)
- Fufa D Bari
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
| | - Satya Parida
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
| | | | - Aldo Dekker
- Central Veterinary Institute, Part of Wageningen UR, Lelystad, The Netherlands
| | | | - Richard Reeve
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK; Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - David J Paton
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
| | - Mana Mahapatra
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK.
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