Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds

Milek, Justyna; Blicharz-Domanska, Katarzyna

Diagnosis. Information about the range of avian species infected with CoVs and the prevalence of these infections has been accumulated from the increasing number of studies based on the use of virus-specific molecular tests. However, such detection methods depend on the specificity of the primers used. The method which was applied for the first time in a systemic monitoring of coronaviruses in wild birds amplified 251 bp of the replicase gene of all coronaviruses known at that time (37) . This allowed the identification of novel coronaviruses infecting graylag geese, feral pigeons, and mallards (24) . Next, the methods targeting the conserved regions of IBV viruses, i.e. 3'UTR, 5'UTR, or even S1 gene fragments (1, 3, 5) were used for monitoring purposes. Additionally, in a molecular survey of AvCoV in ducks the viral nucleocapsid (N) gene was amplified in a reverse-transcription polymerase chain reaction (RT-PCR) (10) . The viruses identified in such way were designated IBV-like. The summary of monitoring studies of coronaviruses in wild birds is given in Table 2 . However, this approach changed after a few findings; firstly, it turned out that other gammaCoVs such as TCoV or GfCoV have genomes closely related to IBV, and the only diverged gene between them is the S gene; secondly, recombination events were discerned to be a quite common phenomenon in these groups of viruses; and the most important discovery was that of deltaCoV and determination of the criteria which enable discrimination between gamma-and deltaCoV (2, 23, 27) . More recently, primers specific to the appropriate conserved site of the replicase gene have commonly been applied (11, 33, 51) . All these primers are within a region of about 840 nt occupied by the NSP12 of ORF1ab which is instrumental in coronavirus species differentiation and contains different numbers of degenerative nucleotides to detect the broader spectrum of coronavirus strains. The position of the used primers, aimed at the replicase gene, is shown in Table 3 .