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

Milek, Justyna; Blicharz-Domanska, Katarzyna

Genomic organisation of avian coronaviruses. The Coronavirinae subfamily is characterised by an exceptionally large RNA genome (19) . The genome size among viruses, included under the taxonomic species name avian coronavirus, is about 27,500 nucleotides (nt), the smallest being the 27,231 nt of 3575/98 IBV strain (GenBank no KX266757), and the largest the 27,718 nt of CK/CH/LGD/120724 (KC119407). Duck CoV (GenBank no. KM454473), a candidate for a separate species within the Gammacoronavirus genus, has a similar size of 27,754 nt. The complete genomic sequences of 18 deltaCoV strains, identified in wild birds available in GenBank, are about 1,000 nucleotides shorter, their sizes ranging from 26,041 nt in white-eye CoV HKU (NC016991) to 26,689 nt in magpie-robin CoV HKU18 (NC016993) strains. The genomes of all coronaviruses have similar structures and organisation, but also display unique groups or even strain-specific genomic structures, including accessory genes. Generally, the genome is contained between the 5'capped end and poly(A) tail at the 3'-end, comprising short untranslated regions (UTRs). About two-thirds of the genome is occupied by two overlapping large open reading frames (ORFs), encoding replicase (RNA-dependent RNA polymerase (RdRp)) polyproteins 1a and 1 ab. These two large polyproteins are formed by a ribosomal frameshift mechanism and subsequently cleaved by viral proteases into the nonstructural proteins (nsp) (19) . The number of nsps of viral replicase in the most complex of the family of positive-strand RNA viruses and in alphaand betaCoVs is 16, whereas gamma-and deltaCoVs have 15 nsps because they lack NSP1. Part of these replicase domains, the seven most conserved, which are NSP3, NSP5, and NSP12-16, serve as species demarcation among coronaviruses (4) . The other third of the genome includes four structural protein genes organised in the following, canonical way: S, E, M, and N (19) . Among these four genes, there are a set of lowmolecular accessory proteins the presence of which could be strain-dependent, and these are 3a, 3b, 4b, 4c, 5a, 5b, and 6b, this being the most recently identified in some IBV and TCoV strains and only ORF downstream of N protein, -6b (2, 20) . It is believed that accessory proteins are not essential for virus replication, but could play a role in virus virulence as 3b protein does. In addition to these four canonical structural proteins S, E, M, and N, deltaCoVs seem to have a smaller number of nonstructural accessory proteins. They contain nonstructural protein NS6 and a number of proteins located downstream of the N protein, designated NS7a, 7b, and sometimes also 7c and 7d (53) . The functions of nonstructural proteins of gamma-and deltaCoVs are largely unknown. Viral proteins. The name "coronavirus" aptly represents their appearance of solar corona in negatively stained electron micrographs, which displays characteristic club-shaped spike (S) proteins on the envelope of the virion. In addition to protruding S proteins, the envelope is formed by the most abundant membrane (M) proteins and non-glycosylated envelope proteins (E) present in lower quantities. Such an envelope surrounds the viral genomic RNA which forms the complex with a few copies of the nucleocapsid (N) protein (7).