Genetic Diversity and Phylodynamics of Avian Coronaviruses in Egyptian Wild Birds

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.

Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses

“…Finally, there appears to be a bias towards the detection of deltacoronaviruses in herons and egrets; no gammacoronaviruses have been detected to date in these host species with the exception of AvCoV spill-over events (Rohaim et al . 2019 ; Table 1 ).…”

“… 2017 ; Rohaim et al . 2019 ). House sparrows are known to frequent poultry barns and therefore are important spill-over hosts for notifiable avian viruses such as influenza A virus (Brown et al .…”

“…Wild ducks seem to be competent hosts for AvCoV without signs of disease, with the identification of endemic AvCoV strains in wild ducks in Egypt (Rohaim et al . 2017 , 2019 ), Poland (Domanska-Blicharz et al . 2014 ) and the UK (Hughes et al .…”

Evolutionary Analysis of Infectious Bronchitis Virus Reveals Marked Genetic Diversity and Recombination Events

“…Therefore, further studies are required to clearly determine the clinicopathobiological features of these viruses in a chicken model. Interestingly, the GI-23 genotype plays a two-faced role in these recombinant events in the Saudi Arabian poultry flocks, not only providing fragments for other strains but also receiving fragments during infection, which has been reported previously in neighboring countries [ 31 , 32 ].…”

“…Our results indicated that Saudi Arabian IBV viruses in this study were diversified into three distinct genotypes, i.e., GI-1, GI-13, and GI-23 ( Figure 1 and Figure 2 ) according to Valsastro et al [ 17 ]. Multiple reports have demonstrated the emergence of variant strains related to 4/91, IS/1494, and IS/885 (IS/720/99) within the Middle East [ 31 , 32 ]. A Bayesian consensus phylogenetic analysis, which was verified using the neighbor-joining method, clearly divided isolated IBV strains in this study into three lineages.…”