Molecular Study of Gamma Coronaviruses in Birds from the Southern Caspian Sea Coast of Iran

Zoleikha  Tatari; Arash Ghalyanchi Langeroudi; Hossein Hosseini; Mohammad Malekan; Zahra Ziafati Kafi; Rima Morshed; Hamideh Najafi; Soroush Sasrmadi; Naser Sadri; Nazanin Sarvian; Safoura Tatari

Authors

Zoleikha Tatari Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran

Arash Ghalyanchi Langeroudi * Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran ghalyana@ut.ac.ir

Hossein Hosseini Faculty of Veterinary Medicine, Karaj Branch, Islamic Azad University, Karaj, Alborz

Mohammad Malekan Department of Veterinary Service, SAVAPARS (Ceva Sante Animale Exclusive Distributor in Iran), Tehran, Iran

Zahra Ziafati Kafi Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran

Rima Morshed Faculty of Encyclopedia, IHCS, Tehran, Iran

Hamideh Najafi Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran

Soroush Sasrmadi Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran

Naser Sadri Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran

Nazanin Sarvian Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran

Safoura Tatari Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran

Keywords:

Gamma Coronavirus; Infectious Bronchitis Virus; Wild Birds; Rural Chickens; White headed Duck

Abstract

Gammacoronaviruses (γ-CoVs), including infectious bronchitis virus (IBV), cause economically important diseases in poultry and may act as reservoirs or bridges for viral dissemination. This study aimed to determine the frequency and genetic relationships of γ‑CoVs in asymptomatic wild and free-ranging birds of northern Iran. From February to December 2020, 60 cloacal swabs were collected from 11 bird species (n=3–10 per species); RNA was extracted and a one‑step RT‑PCR targeting a 266‑bp fragment of the 3’ untranslated region (3’ UTR) was performed, positive amplicons were Sanger‑sequenced, sequences were aligned with reference γ‑CoV sequences, and phylogenetic analysis was carried out. Six of 60 samples (10.0%) were RT‑PCR positive—4/10 rural chickens (40.0%) and 2/10 white‑headed ducks (20.0%)—while all other sampled species were negative. Sequence analysis of six isolates placed chicken‑derived viruses in a cluster with known chicken IBV strains (one isolate clustering closely with the H120 vaccine sequence and two forming a separate subcluster), whereas the two duck-derived sequences were identical to each other and formed a distinct cluster with reference γCoV sequences from wild birds (e.g., duck, pigeon, and other avian hosts), indicating a shared lineage but not necessarily genetic identity with those reference strains. These findings indicate that asymptomatic free-ranging chickens and white-headed ducks in Golestan Province harbor γ-CoV RNA, suggesting local viral circulation and potential interactions at the wild–domestic interface

Downloads

Download data is not yet available.

References

Miłek J, Blicharz-Domańska K. Coronaviruses in avian species – review with focus on epidemiology and diagnosis in wild birds. J Vet Res. 2018;62(3):249–55.

Su S, Wong G, Shi W, Liu J, Lai AC, Zhou J, Gao GF. Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends Microbiol. 2016;24(6):490–502.

Abolnik C. Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus. Infect Genet Evol. 2015; 32:416–24.

Rezaee H, Ghalyanchilangeroudi A, Karimi V, Fallah Mehrabadi M, Motamed Chaboki P, Shayganmehr A, Esmaeelzadeh Dizaji R. Molecular detection of avian infectious bronchitis viruses in live bird markets, Gilan Province. Arch Razi Inst. 2020;75(2):155–62.

Jonassen CM, Kofstad T, Larsen IL, Løvland A, Handeland K, Follestad A, Lillehaug A. Molecular identification and characterization of novel coronaviruses infecting graylag geese (Anser anser), feral pigeons (Columba livia) and mallards (Anas platyrhynchos). J Gen Virol. 2005;86(6):1597–607.

Takiuchi E, Stipp DT, Alfieri AF, Alfieri AA. Improved detection of bovine coronavirus N gene in faeces of calves infected naturally by a semi-nested PCR assay and an internal control. J Virol Methods. 2006;131(2):148–54.

Sheikh A, Al Taher A, Al Nazawi M, Al Mubarak AI, Kandeel M. Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design. J Virol Methods. 2020; 277:113806.

Stern DF, Soften BM. Coronavirus proteins: biogenesis of avian infectious bronchitis virus virion proteins. J Virol. 1982;44(3):794–803.

Woo PCY, Lau SKP, Lam CSF, Lau CCC, Tsang AKL, Lau JHN, Wang M. Discovery of seven novel mammalian and avian coronaviruses in the genus Deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol. 2012;86(7):3995–4008.

Berg M, Johansson M, Montell H, Berg AL. Wild birds as a possible natural reservoir of Borna disease virus. Epidemiol Infect. 2001;127(1):173–8.

Snoeck CJ, Marinelli M, Charpentier E, Sausy A, Conzemius T, Losch S, Muller CP. Characterization of Newcastle disease viruses in wild and domestic birds in Luxembourg from 2006 to 2008. Appl Environ Microbiol. 2013;79(2):639–45.

Yaghoubi H, Ghalyanchilangeroudi A, Karimi V, Ghafouri S, Hashemzadeh M, Hosseini H, Najafi H. Molecular detection of gamma coronaviruses in bird parks of Iran. Arch Razi Inst. 2019;74(4):349–55.

Cavanagh D, Mawditt K, Welchman DB, Britton P, Gough R. Coronaviruses from pheasants (Phasianus colchicus) are genetically closely related to coronaviruses of domestic fowl (infectious bronchitis virus) and turkeys. Avian Pathol. 2002;31(1):81–93.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547–49.

Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4(4):406–25.

Rahman MM, Talukder A, Chowdhury MMH, Talukder R, Akter R. Coronaviruses in wild birds – a potential and suitable vector for global distribution. Vet Med Sci. 2021;7(1):264–72.

De Sales Lima FE, Gil P, Pedrono M, Minet C, Kwiatek O, Campos FS, Maminiaina OF. Diverse gammacoronaviruses detected in wild birds from Madagascar. Eur J Wildl Res. 2015;61(4):635–39.

Rohaim MA, El Naggar RF, Clayton E, Munir M. Structural and functional insights into non-structural proteins of coronaviruses. Microb Pathog. 2021; 150:104641.

Domanska-Blicharz K, Jacukowicz A, Lisowska A, Wyrostek K, Minta Z. Detection and molecular characterization of infectious bronchitis-like viruses in wild bird populations. Avian Pathol. 2014;43(5):406–13.

Wille M, Muradrasoli S, Nilsson A, Järhult JD. High prevalence and putative lineage maintenance of avian coronaviruses in Scandinavian waterfowl. PLoS One. 2016;11(3):e0150198.

Chu DKW, Leung CYH, Gilbert M, Joyner PH, Ng EM, Tsemay MT, Poon LLM. Avian coronavirus in wild aquatic birds. J Virol. 2011;85(23):12815–20.

Paim FC, Bowman AS, Miller L, Feehan BJ, Marthaler D, Saif LJ, Vlasova AN. Epidemiology of deltacoronaviruses (δ CoV) and gammacoronaviruses (γ CoV) in wild birds in the United States. Viruses. 2019;11(10):897.

Hepojoki S, Lindh E, Vapalahti O, Huovilainen A. Prevalence and genetic diversity of coronaviruses in wild birds, Finland. Infect Ecol Epidemiol. 2017;7(1):1408360.

Traavik T, Mehl R, Kjeldsberg E. “Runde” virus, a coronavirus-like agent associated with seabirds and ticks. Arch Virol. 1977;55(1):25–38.

Liu S, Chen J, Chen J, Kong X, Shao Y, Han Z, Liu M. Isolation of avian infectious bronchitis coronavirus from domestic peafowl (Pavo cristatus) and teal (Anas). J Gen Virol. 2005;86(3):719–

Woo PCY, Lau SKP, Lam CSF, Lai KKC, Huang Y, Lee P, Yuen KY. Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus. J Virol. 2009;83(2):908–17.

Pauly M, Snoeck CJ, Phoutana V, Keosengthong A, Sausy A, Khenkha L, Vilivong K. Cross-species transmission of poultry pathogens in backyard farms: ducks as carriers of chicken viruses. Avian Pathol. 2019;48(6):503–11.