Evaluation of the risk of neighbourhood infection of H7N1 Highly Pathogenic Avian Influenza in Italy using Q statistic

Mulatti, Paolo; Kitron, Uriel; Jacquez, Geoffrey M.; Mannelli, Alessandro; Marangon, Stefano

doi:10.1016/j.prevetmed.2010.04.005

Cited by 7 publications

(10 citation statements)

References 16 publications

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“…Indeed, limited dissemination of the virus toward other provinces was observed from Verona. These findings are in agreement with previous epidemiological studies (39,40,44) and possibly are explained by differences among the provinces in the control strategies employed at the time. In Veneto, a ban of restocking and a preemptive culling strategy were started 20 days earlier and on a greater number of farms than in Lombardia, reducing virus transmission within and outside the Veneto area.…”

Section: Discussionsupporting

confidence: 92%

“…In contrast, HPAI viruses exhibited little structuring by province, reflecting their rapid spread among all of the affected provinces, even those separated by large distances. Although the risk of infection has been found to be associated with proximity to an infected farm (39,41,44), the movement of contaminated people, trucks, equipment, and products can rapidly drive viral transmission between distant flocks during an HPAI outbreak (39,42). Nevertheless, it is possible that we have missed the direct link between infected farms located in distant areas, as several outbreaks were identified only on the basis of results of serological, epidemiological, and clinical investigations (such that viruses and related genetic data were not available for these cases).…”

Section: Discussionmentioning

confidence: 99%

“…The Italian HPAI H7N1 outbreak has been well characterized epidemiologically, including identifying risk factors and withinflock viral transmission dynamics (39)(40)(41)(42)(43)(44). However, few pieces of genetic data have been published from this epidemic (12).…”

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confidence: 99%

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Emergence of a Highly Pathogenic Avian Influenza Virus from a Low-Pathogenic Progenitor

Monne

Fusaro

Nelson

et al. 2014

J Virol

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128

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Avian influenza (AI) viruses of the H7 subtype have the potential to evolve into highly pathogenic (HP) viruses that represent a major economic problem for the poultry industry and a threat to global health. However, the emergence of HPAI viruses from low-pathogenic (LPAI) progenitor viruses currently is poorly understood. To investigate the origin and evolution of one of the most important avian influenza epidemics described in Europe, we investigated the evolutionary and spatial dynamics of the entire genome of 109 H7N1 (46 LPAI and 63 HPAI) viruses collected during Italian H7N1 outbreaks between March 1999 and February 2001. Phylogenetic analysis revealed that the LPAI and HPAI epidemics shared a single ancestor, that the HPAI strains evolved from the LPAI viruses in the absence of reassortment, and that there was a parallel emergence of mutations among HPAI and later LPAI lineages. Notably, an ultradeep-sequencing analysis demonstrated that some of the amino acid changes characterizing the HPAI virus cluster were already present with low frequency within several individual viral populations from the beginning of the LPAI H7N1 epidemic. A Bayesian phylogeographic analysis revealed stronger spatial structure during the LPAI outbreak, reflecting the more rapid spread of the virus following the emergence of HPAI. The data generated in this study provide the most complete evolutionary and phylogeographic analysis of epidemiologically intertwined high-and low-pathogenicity viruses undertaken to date and highlight the importance of implementing prompt eradication measures against LPAI to prevent the appearance of viruses with fitness advantages and unpredictable pathogenic properties. IMPORTANCEThe Italian H7 AI epidemic of 1999 to 2001 was one of the most important AI outbreaks described in Europe. H7 viruses have the ability to evolve into HP forms from LP precursors, although the mechanisms underlying this evolutionary transition are only poorly understood. We combined epidemiological information, whole-genome sequence data, and ultradeep sequencing approaches to provide the most complete characterization of the evolution of HPAI from LPAI viruses undertaken to date. Our analysis revealed that the LPAI viruses were the direct ancestors of the HPAI strains and identified low-frequency minority variants with HPAI mutations that were present in the LPAI samples. Spatial analysis provided key information for the design of effective control strategies for AI at both local and global scales. Overall, this work highlights the importance of implementing rapid eradication measures to prevent the emergence of novel influenza viruses with severe pathogenic properties.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Emergence of a Highly Pathogenic Avian Influenza Virus from a Low-Pathogenic Progenitor

Monne

Fusaro

Nelson

et al. 2014

J Virol

Self Cite

128

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“…Following the second level of screening, a total of 29 manuscripts were selected for data extraction. Excluded manuscripts (n = 116) were manuscripts describing (hereafter only a few references are given as examples, for a full overview see file "SR datasets.xlsx"): simulation models evaluating control measures (Backer et al, 2015;Dent et al, 2011;Dorigatti et al, 2010;Gonzales et al, 2014;Nickbakhsh et al, 2013;Nickbakhsh et al, 2014;Smith and Dunipace, 2011;te Beest et al, 2011), theoretical risk assessments (Edmunds et al, 2013;Hop and Saatkamp, 2010;Malladi et al, 2015;Martinez et al, 2009;Sanchez-Vizcaino et al, 2010), evaluation of control measures during epidemics (Busani et al, 2007a;Busani et al, 2007b;Mulatti et al, 2010a), quantifying or studying between or within farm transmission during epidemics (Bos et al, 2009), descriptive reviews (Artois et al, 2009;Brown et al, 2007;de Jong et al, 2009;van den Berg, 2009), quantifying risk factors for transmission or infection during epidemics (Busani et al, 2009a;Busani et al, 2009b;Mulatti et al, 2010b;Thomas et al, 2005;Ward et al, 2009a;Ypma et al, 2012), economic analysis of control measures (Boni et al, 2013;Longworth et al, 2014a, b), evaluation of surveillance data or design of surveillance programmes where some of the key features identified for selection and data collection were not provided (Comin et al, 2011;Gonzales et al, 2010;Welby et al, 2010), manuscripts describing the same outbreak as other manuscripts which were considered better suited for this study (Bouwstra et al, 2015a;Ward et al, 2008b), news releases or letters on peer-reviewed journa...…”

Section: Assessment/resultsmentioning

confidence: 99%

Risk factors of primary introduction of highly pathogenic and low pathogenic avian influenza virus into European poultry holdings, considering at least material contaminated by wild birds and contact with wild birds

Gonzáles¹,

Elbers²,

Beerens³

2017

EFS3

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Avian influenza (AI) is a constant threat to the poultry industry in Europe. Up to date assessments of the factors influencing the probability of introduction of infection into poultry holdings are required for the implementation of informed prevention and control measures. We carried out a systematic literature review to identify and synthesise the evidence on risk factors of AI introduction into European poultry holdings. A review protocol was built, which considered the electronic search strategy, criteria for relevance screening, quality assessment and data collection. A total of 941 abstracts were evaluated and 145 relevant manuscripts were selected for evaluation of the full text. This assessment resulted in the selection of 29 manuscripts for data collection and analyses. These manuscripts provided information on 54 AI introductions (outbreaks) in poultry, with 25 of those being caused by highly pathogenic AI viruses and 29 caused by low pathogenic AI viruses.

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“…Also geographical representativeness may represent an issue, and some results may be difficultly transferrable to areas or Countries different than those accounted for in the article (Martínez et al, 2007;Milanko et al, 2009;Mulatti et al, 2010;Muzinic et al, 2010;Muzyka et al, 2012;Pannwitz et al, 2009). Similarly in a study performed on data derived from surveillance in Europe, 5 Member States contributed for 70% of the whole samples considered, and 2 of these represented the 30% of the total samples (Breed et al, 2010).…”

Section: Risk Of Biasmentioning

confidence: 99%

Effect of biosecurity measures and early detection systems, mitigation measures and surveillance strategies on the spread of HPAI and LPAI between farms

Mulatti

Dorotea

Vieira

et al. 2017

EFSA Supporting Publications

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An extensive literature review was performed to provide insights on the effect of biosecurity and control measures on the risk of introduction and spread of avian influenza in the domestic poultry sector, whether there are gaps in surveillance on wild birds, and to investigate the trigger thresholds for early detection activities through passive surveillance. A total of 1390 articles were retrieved from on-line databases, including Thomson-Reuters Web of Knowledge, PubMed, Ovid and Medline. After removing duplicates 788 studies were screened, and 194 papers were fully read to evaluate whether they could provide reliable information. Twenty-seven papers were considered relevant for assessing the effect of biosecurity and control measures, 7 were included in the assessment of early detection thresholds, and 66 provided information on surveillance gaps in wild birds. Due to the different types of studies included in the review, it resulted impossible to make direct comparison between the results obtained in the articles, as many of them did not report quantitative assessments of the effects of interest. Instead of a formal comparison between studies, the results were reported to provide recommendations on the research questions, also supplying evidences obtained through quantitative analysis and mathematical modeling. Nevertheless it was possible to assess the likely effects of control measures such as pre-emptive culling of farms nearby infected premises, ring vaccination and compartmentalization. Insights on early detection measures provided useful information to reconsider the passive surveillance thresholds to be accounted for to avoid the undetected circulation of avian influenza. The reporting of surveillance on wild birds allowed to identify species to be integrated within the commonly considered target species, and procedures to optimize activities by focusing on defined areas and temporal periods, in the context of a fine tuned Risk Based Surveillance plan. © IZSVe, 2016Key words: avian influenza, biosecurity, surveillance, early detection, introduction, spread Disclaimer: The present document has been produced and adopted by the bodies identified above as authors. This task has been carried out exclusively by the authors in the context of a contract between the European Food Safety Authority and the authors, awarded following a tender procedure. The present document is published complying with the transparency principle to which the Authority is subject. It may not be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the authors.Suggested citation: Mulatti P, Dorotea T, Vieira JT, Bonfanti Lebana, Marangon S, 2016. Effect of biosecurity measures and early detection systems, mitigation measures and surveillance strategies on the spread of HPAI and LPAI between farms. EFSA supporting publication 2016:EN-1142....

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Evaluation of the risk of neighbourhood infection of H7N1 Highly Pathogenic Avian Influenza in Italy using Q statistic

Cited by 7 publications

References 16 publications

Emergence of a Highly Pathogenic Avian Influenza Virus from a Low-Pathogenic Progenitor

Emergence of a Highly Pathogenic Avian Influenza Virus from a Low-Pathogenic Progenitor

Risk factors of primary introduction of highly pathogenic and low pathogenic avian influenza virus into European poultry holdings, considering at least material contaminated by wild birds and contact with wild birds

Effect of biosecurity measures and early detection systems, mitigation measures and surveillance strategies on the spread of HPAI and LPAI between farms

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