Dataset Information

Highly pathogenic avian influenza H5N1 virus outbreak among Cape cormorants (Phalacrocorax capensis) in Namibia, 2022.

ABSTRACT: In January 2022, significant mortality was observed among Cape cormorants (Phalacrocorax capensis) on the west coast of Namibia. Samples collected were shown to be positive for H5N1 avian influenza by multiplex RT-qPCR. Full genome analysis and phylogenetic analysis identified the viruses as belonging to clade 2.3.4.4b and that it clustered with similar viruses identified in Lesotho and Botswana in 2021. This is the first genomic characterization of H5N1 viruses in Namibia and has important implications for poultry disease management and wildlife conservation in the region.

SUBMITTER: Molini U

PROVIDER: S-EPMC9980411 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

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Highly pathogenic avian influenza H5N1 virus outbreak among Cape cormorants (<i>Phalacrocorax capensis</i>) in Namibia, 2022.

Molini Umberto U Yabe John J Meki Irene K IK Ouled Ahmed Ben Ali Hatem H Settypalli Tirumala B K TBK Datta Sneha S Coetzee Lauren Michelle LM Hamunyela Ellini E Khaiseb Siegfried S Cattoli Giovanni G Lamien Charles E CE Dundon William G WG

Emerging microbes & infections 20231201 1

In January 2022, significant mortality was observed among Cape cormorants (<i>Phalacrocorax capensis</i>) on the west coast of Namibia. Samples collected were shown to be positive for H5N1 avian influenza by multiplex RT-qPCR. Full genome analysis and phylogenetic analysis identified the viruses as belonging to clade 2.3.4.4b and that it clustered with similar viruses identified in Lesotho and Botswana in 2021. This is the first genomic characterization of H5N1 viruses in Namibia and has importa ...[more]

PMID: 36632773

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Project description:Managing wildlife populations for conservation, control or harvesting involves uncertainty. Nevertheless, decisions need to be made based on the available evidence. The two main sources of uncertainty in population modelling are parameter estimates and structural uncertainty. Structural uncertainty in models is not included as often as parameter uncertainty.We present an approach where parameter and structural uncertainty (strength of density dependence) is included within a model, using the over-wintering English population of cormorants Phalacrocorax carbo L. Because of the damage caused to inland fishery interests by cormorants, there was a change in UK government policy in autumn 2004, increasing the numbers of birds that can be shot under licence.A stochastic Monte Carlo annual population model was produced to examine the effect of changes to the numbers of birds shot each year. Indices of annual population size were converted to population estimates and used to determine annual growth rates and strength of density dependence.There is strong evidence for density dependence in the data, which suggests the population is currently slightly above carrying capacity, with a mean growth rate of 4-6% per annum. The 1300 birds shot under licence in 2004/05 represent about 4.5% of the English population, and if this level of culling continues, the population would be expected to decline by 9% by 2007, compared to the long-term average. The a priori preferred model, which included all uncertainty, gave predictions for 2004/05 and 2005/06 in close agreement with field data.The model was used to produce short-term population projections, with the understanding that Adaptive Resource Management (ARM) will be adopted to iteratively update the parameters and model each year, feeding back into the numbers of available licences.Synthesis and applications. We recommend the approach used in this study of including parameter and structural uncertainty within a single model, where possible, with the proportion of iterations that utilize a particular structure dependent on the weight of evidence for that structure. This will produce results with wider confidence intervals, but ensures that the evidence for any particular model is not over-interpreted.

Dataset Information

Highly pathogenic avian influenza H5N1 virus outbreak among Cape cormorants (Phalacrocorax capensis) in Namibia, 2022.

Publications

Highly pathogenic avian influenza H5N1 virus outbreak among Cape cormorants (<i>Phalacrocorax capensis</i>) in Namibia, 2022.

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