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Humphreys JM, Shults PT, Velazquez-Salinas L, Bertram MR, Pelzel-McCluskey AM, Pauszek SJ, Peters DPC, Rodriguez LL. Interrogating Genomes and Geography to Unravel Multiyear Vesicular Stomatitis Epizootics. Viruses 2024; 16:1118. [PMID: 39066280 PMCID: PMC11281362 DOI: 10.3390/v16071118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/07/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
We conducted an integrative analysis to elucidate the spatial epidemiological patterns of the Vesicular Stomatitis New Jersey virus (VSNJV) during the 2014-15 epizootic cycle in the United States (US). Using georeferenced VSNJV genomics data, confirmed vesicular stomatitis (VS) disease cases from surveillance, and a suite of environmental factors, our study assessed environmental and phylogenetic similarity to compare VS cases reported in 2014 and 2015. Despite uncertainties from incomplete virus sampling and cross-scale spatial processes, patterns suggested multiple independent re-invasion events concurrent with potential viral overwintering between sequential seasons. Our findings pointed to a geographically defined southern virus pool at the US-Mexico interface as the source of VSNJV invasions and overwintering sites. Phylodynamic analysis demonstrated an increase in virus diversity before a rise in case numbers and a pronounced reduction in virus diversity during the winter season, indicative of a genetic bottleneck and a significant narrowing of virus variation between the summer outbreak seasons. Environment-vector interactions underscored the central role of meta-population dynamics in driving disease spread. These insights emphasize the necessity for location- and time-specific management practices, including rapid response, movement restrictions, vector control, and other targeted interventions.
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Affiliation(s)
- John M. Humphreys
- Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Plum Island Animal Disease Center (PIADC) and National Bio Agro Defense Facility (NBAF), Manhattan Kansas, KS 66502, USA; (L.V.-S.); (M.R.B.); (L.L.R.)
| | - Phillip T. Shults
- Arthropod-Borne Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA;
| | - Lauro Velazquez-Salinas
- Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Plum Island Animal Disease Center (PIADC) and National Bio Agro Defense Facility (NBAF), Manhattan Kansas, KS 66502, USA; (L.V.-S.); (M.R.B.); (L.L.R.)
| | - Miranda R. Bertram
- Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Plum Island Animal Disease Center (PIADC) and National Bio Agro Defense Facility (NBAF), Manhattan Kansas, KS 66502, USA; (L.V.-S.); (M.R.B.); (L.L.R.)
| | - Angela M. Pelzel-McCluskey
- Veterinary Services, Animal and Plant Health Inspection Service (APHIS), U.S. Department of Agriculture, Fort Collins, CO 80526, USA;
| | - Steven J. Pauszek
- Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service (APHIS), Plum Island Animal Disease Center (PIADC), U.S. Department of Agriculture, Orient, NY 11957, USA;
| | - Debra P. C. Peters
- Office of National Programs, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA;
| | - Luis L. Rodriguez
- Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Plum Island Animal Disease Center (PIADC) and National Bio Agro Defense Facility (NBAF), Manhattan Kansas, KS 66502, USA; (L.V.-S.); (M.R.B.); (L.L.R.)
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Nielsen SS, Alvarez J, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar Schmidt C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Stahl K, Calvo AV, Viltrop A, Winckler C, De Clercq K, Sjunnesson Y, Gervelmeyer A, Roberts HC. Assessment of the control measures of the Category A diseases of the Animal Health Law: prohibitions in restricted zones and risk-mitigating treatments for products of animal origin and other materials. EFSA J 2022; 20:e07443. [PMID: 35958104 PMCID: PMC9361132 DOI: 10.2903/j.efsa.2022.7443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
EFSA received a mandate from the European Commission to assess the effectiveness of prohibitions of certain activities in restricted zones, and of certain risk mitigation treatments for products of animal origin and other materials with respect to diseases included in the Category A list in the Animal Health Law (Regulation (EU) 2016/429). This opinion belongs to a series of opinions where other disease-specific control measures have been assessed. In this opinion, EFSA and the AHAW Panel of experts review the effectiveness of (i) prohibiting the movements of certain products, notably germinal products (semen, oocytes, embryos and hatching eggs), products of animal origin and animal by-products and feed of plant origin, hay and straw, and (ii) risk mitigation treatments for products of animal origin. In terms of semen, oocytes, embryos and hatching eggs, it was agreed that there was a lack of evidence particularly for embryos and oocytes reflected in a varying degree of uncertainty, whether these commodities could potentially contain the pathogen under consideration. The scenario assessed did not consider whether the presence of pathogen would lead to infection in the recipient animal. In terms of animal products, certain animal by-products and movement of feed of plant origin and straw, the assessment considered the ability of the commodity to transmit disease to another animal if exposed. For most pathogens, products were to some degree considered a risk, but lack of field evidence contributed to the uncertainty, particularly as potential exposure of ruminants to meat products is concerned. In terms of the risk mitigating treatments, recommendations have been made for several of these treatments, because the treatment description is not complete, the evidence is poor or inconclusive, or the evidence points to the treatment being ineffective.
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Nielsen SS, Alvarez J, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Spoolder H, Ståhl K, Velarde A, Viltrop A, Winckler C, Gervelmeyer A, Van der Stede Y, Bicout DJ. Guidance on good practice in conducting scientific assessments in animal health using modelling. EFSA J 2022; 20:e07346. [PMID: 35600270 PMCID: PMC9115711 DOI: 10.2903/j.efsa.2022.7346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The EFSA asked the Panel on Animal Health and Welfare to develop a guidance document on good practice in conducting scientific assessments in animal health using modelling. In previous opinions, the AHAW Panel has responded to two‐thirds of animal health‐related mandates using some kind of modelling. These models range from simple to complex, employing a combination of scientific, economic, socio‐economic or other types of data. Hence, there is strong interest in the development of a guidance document to integrate modelling efforts into the routine process of EFSA working groups. In this document, an ‘operating procedure' (OP) for the use of modelling within an AH working group is presented. The OP provides a detailed flowchart enabling modelling to be transparently and consistently integrated in the assessment. The OP is structured into phases. These phases combine the relevant standard operating procedures and working instructions of EFSA with the modelling process. Each phase includes roles and actions to be taken, expected output and the sequence of agreements that need to be made between all partners in the scientific assessment. In conclusion, it is expected that adherence to the OP will improve transparency of models in EFSA outputs, and it is recommended to adopt it as a standard procedure when responding to AHAW mandates.
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Aerts L, Haegeman A, De Leeuw I, Philips W, Van Campe W, Behaeghel I, Mostin L, De Clercq K. Detection of Clinical and Subclinical Lumpy Skin Disease Using Ear Notch Testing and Skin Biopsies. Microorganisms 2021; 9:2171. [PMID: 34683492 PMCID: PMC8541182 DOI: 10.3390/microorganisms9102171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/28/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
Lumpy skin disease (LSD) diagnosis is primarily based on clinical surveillance complemented by PCR of lesion crusts or nodule biopsies. Since LSD can be subclinical, the sensitivity of clinical surveillance could be lower than expected. Furthermore, real-time PCR for the detection of LSD viral DNA in blood samples from subclinical animals is only intermittently positive. Therefore, this study aimed to investigate an acceptable, easily applicable and more sensitive testing method for the detection of clinical and subclinical LSD. An animal experiment was conducted to investigate ear notches and biopsies from unaffected skin taken from the neck and dorsal back as alternatives to blood samples. It was concluded that for early LSD confirmation, normal skin biopsies and ear notches are less fit for purpose, as LSDV DNA is only detectable in these samples several days after it is detectable in blood samples. On the other hand, blood samples are less advisable for the detection of subclinical animals, while ear notches and biopsies were positive for LSD viral DNA in all subclinically infected animals by 16 days post infection. In conclusion, ear notches could be used for surveillance to detect subclinical animals after removing the clinical animals from a herd, to regain trade by substantiating the freedom of disease or to support research on LSDV transmission from subclinical animals.
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Affiliation(s)
- Laetitia Aerts
- European Reference Laboratory (EURL) for Diseases Caused by Capripox Viruses, Scientific Directorate Infectious Diseases in Animals, Sciensano, Groeselenberg 99, B-1180 Brussels, Belgium; (L.A.); (W.P.)
| | - Andy Haegeman
- Unit of Exotic and Particular Diseases, Scientific Directorate Infectious Diseases in Animals, Sciensano, Groeselenberg 99, B-1180 Brussels, Belgium; (A.H.); (I.D.L.)
| | - Ilse De Leeuw
- Unit of Exotic and Particular Diseases, Scientific Directorate Infectious Diseases in Animals, Sciensano, Groeselenberg 99, B-1180 Brussels, Belgium; (A.H.); (I.D.L.)
| | - Wannes Philips
- European Reference Laboratory (EURL) for Diseases Caused by Capripox Viruses, Scientific Directorate Infectious Diseases in Animals, Sciensano, Groeselenberg 99, B-1180 Brussels, Belgium; (L.A.); (W.P.)
| | - Willem Van Campe
- Experimental Center Machelen, Scientific Directorate Infectious Diseases in Animals, Sciensano, Kerklaan 68, B-1830 Machelen, Belgium; (W.V.C.); (L.M.)
| | - Isabelle Behaeghel
- Scientific Directorate Infectious Diseases in Animals, Sciensano, Groeselenberg 99, B-1180 Brussels, Belgium;
| | - Laurent Mostin
- Experimental Center Machelen, Scientific Directorate Infectious Diseases in Animals, Sciensano, Kerklaan 68, B-1830 Machelen, Belgium; (W.V.C.); (L.M.)
| | - Kris De Clercq
- Unit of Exotic and Particular Diseases, Scientific Directorate Infectious Diseases in Animals, Sciensano, Groeselenberg 99, B-1180 Brussels, Belgium; (A.H.); (I.D.L.)
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