Diversity of Coronaviruses in Wild Representatives of the Aves Class in Poland

Abstract

The revealed prevalence of coronaviruses in wild bird populations in Poland was 4.15% and the main reservoirs were birds from orders Anseriformes and Charadriiformes, with a prevalence of 3.51% and 5.59%, respectively. Gammacoronaviruses were detected more often than deltacoronaviruses, with detection rates of 3.5% and 0.7%, respectively. Gammacoronaviruses were detected in birds belonging to six orders, including Anseriformes, Charadriiformes, Columbiformes, Galliformes, Gruiformes, and Passeriformes, indicating a relatively wide host range. Interestingly, this was the only coronavirus detected in Anseriformes (3.51%), while in Charadriiformes, the prevalence was 3.1%. The identified gammacoronaviruses belonged to the Igacovirus and Brangacovirus subgeneras. Most of these were igacoviruses and formed a common phylogenetic group with a Duck Coronavirus 2714 and two with an Avian Coronavirus/Avian Coronavirus9203, while the viruses from the pigeons formed a distinct "pigeon-like" group, not yet officially represented. The presence of deltacoronaviruses was detected in birds belonging to three orders, Charadriiformes, Galliformes, and Suliformes indicating a narrower host range. Most identified deltacoronaviruses belonged to the Buldecovirus subgenus, while only one belonged to Herdecovirus. Interestingly, the majority of buldecoviruses were identified in gulls, and they formed a distinct phylogenetic lineage not represented by any officially ratified virus species. Another separate group of buldecoviruses, also not represented by the official species, was formed by a virus identified in a common snipe. Only one identified buldecovirus (from common pheasant) formed a group with the ratified species Coronavirus HKU15. The results obtained indicate the high diversity of detected coronaviruses, and thus also the need to update their taxonomy (establishing new representative virus species). The serological studies performed revealed antibodies against an infectious bronchitis virus in the sera of white storks and mallards.

Keywords: Poland; coronavirus; wild birds.

Figure 1

Phylogenetic analysis of gammacoronaviruses based on the replicase gene fragment. (A) The tree constructed for 108 gammacoronaviruses: 46 strains identified in wild birds in Poland (marked with a dot) and 62 from GenBank, including five reference strains (written in bold and underlined) representing ratified species of three subgenera (Brangacovirus, Igacovirus, and Cegacovirus) of the Gammacoronavirus genus. (B) Gammacoronaviruses of the Igacovirus subgenus, DuCoV2714 species. Colored font represents individual bird orders: black indicates Anseriformes, green indicates Charadriiformes, and red indicates other bird orders. The tree was constructed using MEGA 7 using the maximum likelihood method based on the T92 + G model and 1000 bootstrap replicates (bootstrap values shown on the tree).

Figure 1

Phylogenetic analysis of gammacoronaviruses based on the replicase gene fragment. (A) The tree constructed for 108 gammacoronaviruses: 46 strains identified in wild birds in Poland (marked with a dot) and 62 from GenBank, including five reference strains (written in bold and underlined) representing ratified species of three subgenera (Brangacovirus, Igacovirus, and Cegacovirus) of the Gammacoronavirus genus. (B) Gammacoronaviruses of the Igacovirus subgenus, DuCoV2714 species. Colored font represents individual bird orders: black indicates Anseriformes, green indicates Charadriiformes, and red indicates other bird orders. The tree was constructed using MEGA 7 using the maximum likelihood method based on the T92 + G model and 1000 bootstrap replicates (bootstrap values shown on the tree).

Figure 2

Phylogenetic analysis of deltacoronaviruses based on the replicase gene fragment. (A) The tree constructed for 58 deltacoronaviruses: 26 strains identified in wild birds in Poland (marked with a dot) and 32 from GenBank, including seven reference strains (written in bold and underlined) representing ratified species of three subgenera (five of Buldecovirus, and one for Ardecovirus and Herdecovirus) of the Deltacoronavirus genus. (B) Deltacoronaviruses of the Brangacovirus subgenus. Colored font for given bird orders: black indicates Anseriformes, indicates Charadriiformes, red indicates other bird orders, and blue indicates mammal species. The tree was constructed using MEGA 7 using the maximum likelihood method based on the GTR + G model and 1000 bootstrap replicates (bootstrap values shown on the tree).

Figure 2

Phylogenetic analysis of deltacoronaviruses based on the replicase gene fragment. (A) The tree constructed for 58 deltacoronaviruses: 26 strains identified in wild birds in Poland (marked with a dot) and 32 from GenBank, including seven reference strains (written in bold and underlined) representing ratified species of three subgenera (five of Buldecovirus, and one for Ardecovirus and Herdecovirus) of the Deltacoronavirus genus. (B) Deltacoronaviruses of the Brangacovirus subgenus. Colored font for given bird orders: black indicates Anseriformes, indicates Charadriiformes, red indicates other bird orders, and blue indicates mammal species. The tree was constructed using MEGA 7 using the maximum likelihood method based on the GTR + G model and 1000 bootstrap replicates (bootstrap values shown on the tree).