Epidemiology of Deltacoronaviruses (δ-CoV) and Gammacoronaviruses (γ-CoV) in Wild Birds in the United States

Abstract

Porcine deltacoronavirus (δ-CoV) is the object of extensive research in several countries including the United States. In contrast, the epidemiology of δ-CoVs in wild birds in the US is largely unknown. Our aim was to comparatively assess the prevalence of δ- and γ-CoVs in wild migratory terrestrial and aquatic birds in Arkansas, Illinois, Indiana, Maryland, Mississippi, Missouri, Ohio, Tennessee and Wisconsin. A total of 1236 cloacal/fecal swabs collected during the period 2015-2018 were tested for γ- and δ-CoVs using genus-specific reverse transcription-PCR assays. A total of 61 (4.99%) samples were γ-CoV positive, with up to 29 positive samples per state. In contrast, only 14 samples were positive for δ-CoV (1.14%) with only 1-4 originating from the same state. Thus, unlike previous reports from Asia, γ-CoVs are more prevalent than δ-CoVs in the US, suggesting that δ-CoVs may spread in birds with lower efficiency. This may indicate δ-CoV emerging status and incomplete adaptation to new host species limiting its spread. Phylogenetic analysis of the partial N gene revealed that the newly identified δ-CoV strains were most closely related to the HKU20 (wigeon) strain. Further studies are necessary to investigate the role of aquatic bird δ-CoVs in the epidemiology of δ-CoVs in swine and terrestrial birds.

Keywords: United States; coronaviruses; epidemiology; wild birds; δ-coronavirus.

Figure 1

Gammacoronavirus (A) and Deltacoronavirus (B) detection in different states of the Mississippi Flyway (blue contour) and Atlantic Flyway (red contour).

Figure 2

Phylogenetic trees based on partial sequences (generated using NGS) of the N (A), S (B) and M (C) genes of Blue Winged Teal coronavirus/USA/Illinois2562/2017.

Figure 3

Phylogenetic trees based on partial sequences (generated using HKU20-specific primers) of the N gene of blue-winged teal coronavirus/USA/Illinois2615/2017; blue-winged teal coronavirus/USA/Illinois2662/2017 and blue-winged teal coronavirus/USA/Missouri3230/2017.

Figure 4

Porcine deltacoronavirus was detected in at least 18 US states (shaded in blue) along or adjacent to the Mississippi Flyway (blue contour). Orange circles mark states with the highest pig inventory [28]. Black duck icons identify the states where avian δ-CoVs were found (this study).