Coronaviruses in avian species – review with focus on epidemiology and diagnosis in wild birds
and | Oct 23, 2018
About this article
Article Category: Review Article
Published Online: Oct 23, 2018
Page range: 249 - 255
Received: May 02, 2018
Accepted: Sep 19, 2018
DOI: https://doi.org/10.2478/jvetres-2018-0035
Keywords
© 2018 J. Miłek and K. Blicharz-Domańska published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.
Summary of monitoring studies on coronavirus prevalence in wild birds
| Method | Primers location | Product size (bp) | Method source | Used by | Obtained results | Place | ||
|---|---|---|---|---|---|---|---|---|
| Order | Positives (%) | CoV detected | ||||||
| RT-PCR | RdRp | 250 | (37) | (24) | Anseriformes | 24.4 | AvCoV | Norway |
| Columbiformes | 2.0 | |||||||
| (25) | Charadriiformes | - | gammaCoV | USA | ||||
| Hemi-nested RT-PCR | 3 ’UTR | 214 | (5) | (22) | Anseriformes | 1.6 | IBV-like | Northern England |
| Charadriiformes | ||||||||
| RT-PCRB | RdRp | 440 | (51) | ( | Passeriformes | 1.8 | deltaCoV | Hong Kong |
| (53) | Unknown | 1.1 | deltaCoV | Hong Kong | ||||
| Passeriformes | ||||||||
| Nested RT-PCRB | RdRd | 440 | (11) | (11) | Anseriformes | 15.0 | gammaCoV deltaCoV | Hong Kong Cambodia |
| Ciconiiformes | ||||||||
| Pelecaniformes | ||||||||
| ( | Anseriformes | 0.95 | gammaCoV | Korea | ||||
| (15) | Psittaciformes | - | deltaCoV | Brazil | ||||
| various | - | betaCoV | ||||||
| ( | Gruiformes | 7.8 | gammaCoV | Madagascar | ||||
| Passeriformes | ||||||||
| Ciconiiformes | ||||||||
| Anseriformes | ||||||||
| Charadriiformes | ||||||||
| SybrGreen RT-PCRC | RdRp | 179 | (33) | (33) | Anseriformes | - | IBV-like | Sweden |
| ( | Anseriformes | 6.4 | gammaCoV | Beringia | ||||
| Charadriiformes | ||||||||
| Pelecaniformes | ||||||||
| ( | Anseriformes | 12.0 | gammaCoV | Sweden | ||||
| ( | Anseriformes | 18.7 | gammaCoV | Sweden | ||||
| Charadriiformes | ||||||||
| ( | Anseriformes | 0.3 | gammaCoV | Sweden | ||||
| Nested RT-PCR | S1 | 572 | (1) | (16) | Columbiformes | 50.0 | IBV (Mass, Conn) | Brazil |
| Real time RT-PCR | 5 ’UTR | 143 | (3) | (13) | Anseriformes | 3.5 | IBV-like | Poland |
| Charadriiformes | 2.3 | |||||||
| Galliformes | 17.6 | |||||||
| Pyrosequencing/RT-PCR | RdRp | 508 | ( | - | Charadriiformes | - | deltaCoV | USA (Delaware Bay) |
Primers aimed at the replicase gene used in monitoring studies of coronaviruses in wild birds
| Method | Primer | Genome position primer positions refer to the sequences of the gammacoronavirus representative, IBV M41 strain (GenBank accession no.: DQ834384) | Amplicon (bp) | Reference |
|---|---|---|---|---|
| 1 | 2Bp | 13960–13982 | ||
| 4Bm | 14189–14210 | 251 | (37) | |
| Pol1 | 14188–14210 | |||
| 2 | Pol2 | 14604–14627 | 440 | (51) |
| Pol1 | 14188–14207 | |||
| Pol2 | 14770–14789 | 600 | ||
| 3 | Pol3 | 14188–14210 | (11) | |
| Pol4 | 14605–14627 | 440 | ||
| 11-FW | 14619–14642 | |||
| 4 | 13-RW | 14773–14797 | 179 | (33) |
List of all identified coronavirus species within individual genera according to virus taxonomy released in 2016
| Genus | Species Bat coronavirus CDPHE15 |
|---|---|
| Bat coronavirus HKU10 | |
| Human coronavirus 229E | |
| Human coronavirus NL63 | |
| Miniopterus bat coronavirus 1 | |
| Miniopterus bat coronavirus HKU8 | |
| Mink coronavirus 1 | |
| Porcine epidemic diarrhoea virus | |
| Rhinolophus bat coronavirus HKU2 | |
| Scotophilus bat coronavirus 512 | |
| Betacoronavirus 1 | |
| Hedgehog coronavirus 1 | |
| Human coronavirus HKU1 | |
| Middle East respiratory syndrome-related coronavirus | |
| Murine coronavirus | |
| Pipistrellus bat coronavirus HKU5 | |
| Rousettus bat coronavirus HKU9 | |
| Severe acute respiratory syndrome-related coronavirus | |
| Tylonycteris bat coronavirus HKU4 | |
| Bulbul coronavirus HKU11 | |
| Common moorhen coronavirus HKU21 | |
| Coronavirus HKU15 | |
| Munia coronavirus HKU13 | |
| Night heron coronavirus HKU19 | |
| Thrush coronavirus HKU12 | |
| White-eye coronavirus HKU16 | |
| Wigeon coronavirus HKU20 | |
| Avian coronavirus | |
| Beluga whale coronavirus SW1 | |