Genetic diversity and phylodynamics of avian coronaviruses in Egyptian wild birds

Rohaim, M.A. and El Naggar, R.F. and Helal, A.M. and Bayoumi, M.M. and El-Saied, M.A. and Ahmed, K.A. and Shabbir, M.Z. and Munir, M. (2019) Genetic diversity and phylodynamics of avian coronaviruses in Egyptian wild birds. Viruses, 11 (1). ISSN 1999-4915

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Abstract

Avian coronaviruses (ACoVs) are continuously evolving and causing serious economic consequences in the poultry industry and around the globe. Owing to their extensive genetic diversity and high mutation rates, controlling ACoVs has become a challenge. In this context, the potential contribution of wild birds in the disease dynamics, especially in domesticated birds, remains largely unknown. In the present study, five hundred fifty-seven (n = 557) cloacal/fecal swabs were collected from four different wild bird species from eight Egyptian governorates during 2016 and a total of fourteen positive isolates were used for phylodynamics and evolutionary analysis. Genetic relatedness based on spike (S1) gene demonstrated the clustering of majority of these isolates where nine isolates grouped within Egy/variant 2 (IS/885 genotype) and five isolates clustered within Egy/variant 1 (IS/1494/06 genotype). Interestingly, these isolates showed noticeable genetic diversity and were clustered distal to the previously characterized Egy/variant 1 and Egy/variant 2 in Egyptian commercial poultry. The S1 gene based comparison of nucleotide identity percentages revealed that all fourteen isolates reported in this study were genetically related to the variant GI-23 lineage with 92–100% identity. Taken together, our results demonstrate that ACoVs are circulating in Egyptian wild birds and highlight their possible contributions in the disease dynamics. The study also proposes that regular monitoring of the ACoVs in wild birds is required to effectively assess the role of wild birds in disease spread, and the emergence of ACoVs strains in the country. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.

Item Type: Journal Article
Journal or Publication Title: Viruses
Uncontrolled Keywords: /dk/atira/pure/subjectarea/asjc/2700/2725
Subjects:
Departments: Faculty of Health and Medicine > Biomedical & Life Sciences
ID Code: 131044
Deposited By: ep_importer_pure
Deposited On: 04 Feb 2019 13:35
Refereed?: Yes
Published?: Published
Last Modified: 15 Sep 2019 03:26
URI: https://eprints.lancs.ac.uk/id/eprint/131044

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