Avian coronavirus in wild aquatic birds

Abstract

We detected a high prevalence (12.5%) of novel avian coronaviruses in aquatic wild birds. Phylogenetic analyses of these coronaviruses suggest that there is a diversity of gammacoronaviruses and deltacoronaviruses circulating in birds. Gammacoronaviruses were found predominantly in Anseriformes birds, whereas deltacoronaviruses could be detected in Ciconiiformes, Pelecaniformes, and Anseriformes birds in this study. We observed that there are frequent interspecies transmissions of gammacoronaviruses between duck species. In contrast, deltacoronaviruses may have more stringent host specificities. Our analysis of these avian viral and host mitochondrial DNA sequences also suggests that some, but not all, coronaviruses may have coevolved with birds from the same order.

Fig. 1.

Phylogenetic analysis of alphacoronaviruses, betacoronaviruses, gammacoronaviruses, and deltacoronaviruses. Partial viral RdRp sequences (360 bp) were used in this analysis. Sequences were aligned and edited manually by ClustalW (25). The best evolution model describing an alignment was determined by MEGA5 (22). Phylogenetic trees were generated using Phyml with the best substitution model selected, and with aLRT statistics SH-like branch supports (11). The novel avian coronaviruses identified in this study are in bold. The host identities determined by DNA fingerprinting techniques are in brackets. Sample collection dates are indicated (year/month/day). aLRT statistics SH-like branch supports are indicated at the nodes. The GenBank accession numbers of the genes used are as follows: 229E (human coronavirus 229E), AF304460; AIBV (avian infectious bronchitis virus), FJ904722; Asian leopard cat CoV, EF584908; BatCoV 61, AY864196; BatCoV HKU8, DQ249228; beluga whale CoV SW1, EU111742; black-headed gull CoV CIR-66187, GU396686; Brent goose CoV KR-70, GU396676; bulbul HKU11 (Bulbul coronavirus HKU11), FJ376619; glaucous-winged gull CIR-66002, GU396682; glaucous gull CoV PBA-173, GU396674; HKU1 (human coronavirus HKU1), AY597011; MHV-A59 (mouse hepatitis virus), FJ647225; munia HKU13 (munia coronavirus HKU13), FJ376622; NL63 (human coronavirus NL63), AY567487; OC43 (human coronavirus OC43), AY903460; PEDV (porcine epidemic diarrhea coronavirus), AF353511; pintail CoV PBA-124, GU396673; pintail CoV PBA-25, GU396671; rock sandpiper CoV CIR-65828, GU396688; SARS CoV (human severe acute respiratory syndrome coronavirus), JF292915; snow goose CoV WIR-159, GU396690; TGEV (transmissible gastroenteritis coronavirus), DQ811789; thrush HKU12 (thrush coronavirus HKU12), FJ376621; turkey CoV, EU095850; western sandpiper CoV KR-28, GU396675.

Fig. 2.

Genetic distances between alphacoronaviruses, betacoronaviruses, gammacoronaviruses, and deltacoronaviruses. Partial ORF1b sequences of 10 representative viruses from each genus were analyzed (data not shown). The genetic distances were estimated by using the Jukes-Cantor model. The median genetic distances between the viruses studied are shown. An asterisk indicates that all intragenus genetic distances were found to be significantly shorter than the relevant intergenus genetic distances (P < 0.005).

Fig. 3.

Phylogenetic correlation between avian coronaviruses and their hosts. A phylogenetic tree of avian host mtDNA COX1 gene (450 bp, left) and viral RdRp gene sequences (360 bp, right) is shown. The order of each bird species studied is shown. Only viral and host sequences from selected coronavirus-positive bird dropping samples in our study were included. Lines between the 2 trees were added to help visualize virus and host sequence congruence (solid lines) or incongruence (broken lines). Accession numbers of the reference host sequences used: Brent goose, DQ433366; bulbul, FJ378536; chicken, GU261717; glaucous-winged gull, HM033523; kiwi, EU525317.1; munia, EF515788; rock sandpiper, GU571303; snow goose, DQ434538; thrush, GQ482858; turkey, EF153719; western sandpiper, AY666261.