Polish gulls harbor new coronavirus strains, spotlighting avian role in viral evolution

In a recent article published in the journal Scientific Reports, researchers characterize five strains of gammacoronaviruses (gCoV) and deltacoronaviruses (dCoV) that were detected in black-headed gulls (Chroicocephalus ridibundus) and common gulls (Larus canus) in Poland.

Study: Gulls as a host for both gamma and deltacoronaviruses. Image Credit: Nataliya Dorokhina / Shutterstock.com

Background

The Orthocoronavirinae subfamily consists of Alpha-, Beta-, Gamma-, and Deltacoronavirus genera, of which gCoVs and dCoVs infect wild birds. The gCoVs and dCoVs have three subgenera each and five and seven species, respectively.

CoVs are positive-sense single-stranded ribonucleic acid (ssRNA) viruses that mutate at a maximum possible rate due to the low fidelity of their RNA-dependent RNA polymerase (RdRp) machinery. Consequently, CoVs potentially generate several viral variants during a short infection cycle that could quickly switch hosts.

About the study

Researchers obtained whole genomic sequences (WGS) of five CoV samples. Four of the selected dCoV strains were detected in three black-headed and one common gull, whereas one gCoV strain was from a common gull.

Twenty-seven samples with the highest viral load, as determined by polymerase chain reaction (PCR) assay, were subjected to next-generation sequencing (NGS). Subsequently, the researchers de novo assembled raw reads to contigs. The BLAST algorithm was used to compare these sequences with viral genome sequences from the GenBank database.

Samples with the highest homology were selected for further analysis. More specifically, using the MAFFT method, all nucleotide sequences were aligned. All similarities in nucleotide and amino acid sequences were determined and expressed in percentages.

These alignments were subsequently incorporated into the IQ-TREE software to estimate the best evolutionary model. Any recombination events within these CoV genomes, if any, were also identified.

Study findings

The genus Charadriiformes of the Laridae species was the main reservoir of gCoVs and dCoVs, with genome lengths of over 26,000 and about 23,000 nucleotides (nt), respectively. All four Chinese black-headed gulls (BHG)dCoVs genomes identified in this study exhibited high similarity with the genomes of three bird species from the United Arab Emirates and Chinese BHGs. This observation suggests their close evolutionary relationship and interspecies transmission potential.

However, phylogenetic analysis of their WGSs revealed bifurcation within a common branch. Numerous amino acid changes were also identified within their spike (S) protein, thus indicating that these dCoVs evolved within a single gull. Notably, the Polish dCoVs did not comprise any of the mutations described as host-specific receptors for gulls.

The Polish BHGdCoV/Poland/P350/2017 was identified in December 2017, 35-40 km away from where the most recent CgdCoV/Poland/P005/2019 was identified in January 2019. Comparatively, gulls sampled in Yunnan Province of China were sampled in January-March 2021 from a single location.

Nearly identical dCoVs from the Middle Eastern birds were sampled over a period of two years. Overall, the dCoVs identified in gulls in this study were highly diverse on a genomic scale, thus raising the possibility of new serotype variants that might emerge with minimal mutations in the S protein.

The phylogenetic analysis of the structural and non-structural genes of CGgCoV/Poland/P014/2019 revealed that it closely resembled duck coronavirus 2714 (DuCoV2714), which was detected in China in 2014. However, these two viruses shared a low degree of S protein homology, which formed a separate phylogenetic branch with no relation to any gCoV identified to date. Some previous studies have identified similar gCoVs in wild birds in Australia and Canada.

The subfamily of gulls and terns can be found in many regions throughout the world, thus indicating that these birds are exceptionally ecologically diverse. Whereas some of these birds exclusively inhabit the marine environment, some live in freshwater, and others live in both.

Some of these birds frequently encounter contact with humans and domesticated animals. Most of these birds live in colonies with high densities, thus facilitating direct viral transmission and disease spread.

Conclusions

The dCoV and gCoV WGS described in this study are the first to be identified from Polish gulls. Thus, the study findings provide novel insights into the evolution and diversity of CoVs circulating in the Laridae family.

The genetic characteristics of these viruses demonstrate how these two distinct CoV genera could co-infect one organism and create conditions conducive for recombination events to occur, which, in turn, could give rise to novel CoV variants. In fact, researchers have recently reported concurrent co-infection of Pacific black ducks with gCoVs and dCoVs in Australia. 

Since porcine dCoVs, which likely evolved from avian dCoVs, could infect humans, it remains crucial to continuously study animal reservoirs of CoVs and broaden the knowledge of their increasing diversity and zoonosis potential.