Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses

Abstract

Wild birds interconnect all parts of the globe through annual cycles of migration with little respect for country or continental borders. Although wild birds are reservoir hosts for a high diversity of gamma- and deltacoronaviruses, we have little understanding of the ecology or evolution of any of these viruses. In this review we use genome sequence and ecological data to disentangle the evolution of coronaviruses in wild birds. Specifically, we explore host range at the levels of viral genus and species, and reveal the multi-host nature of many viral species, albeit with biases to certain types of avian host. We conclude that it is currently challenging to infer viral ecology due to major sampling and technical limitations, and suggest that improved assay performance across the breadth of gamma- and deltacoronaviruses, assay standardization, as well as better sequencing approaches, will improve both the repeatability and interpretation of results. Finally, we discuss cross-species virus transmission across both the wild bird—poultry interface as well as from birds to mammals. Clarifying the ecology and diversity in the wild bird reservoir has important ramifications for our ability to respond to the likely future emergence of coronaviruses in socioeconomically important animal species or human populations.

Deltacoronavirus Evolution and Transmission: Current Scenario and Evolutionary Perspectives

“…Previously, avian DCoVs were suggested to have more stringent host specificities than GCoVs ( 13 ); however, emerging evidence provides numerous examples of the ability of DCoV to efficiently cross interspecies barriers under field or experimental conditions. These examples include: (1) evidence of circulation of “novel” avian DCoVs in a broad range of host species, such as gulls, shorebirds, penguins, passerines, and even bustards ( 26 ); (2) emergence of FalCoV UAE-HKU27, HouCoV UAE-HKU28, and PiCoV UAE-HKU29 through recombination between WECoV HKU16 and MRCoV HKU18; (3) emergence of QuaCoV UAE-HKU30 through recombination between PDCoV HKU15/SpCoV HKU17 and MunCoV HKU13; and (4) emergence of PDCoV HKU15 from recombination between SpCoV HKU17 and BuCoV HKU11 ( 10 ) ( Figure 1 ). Additionally, it was demonstrated that PDCoV can infect chicks and turkey poults and gnotobiotic calves under experimental conditions ( 48 – 50 ) ( Figure 1 ).…”

“…Of interest, PDCoV HKU15, SpCoV HKU17, and QuaCoV HKU30 share more than 90% amino acid identity, indicating that these three CoVs may be subspecies of the same species ( 9 , 10 ). While DCoVs were also detected in Asian leopard cats, Chinese ferret-badgers, green-cheeked Amazon parrot, and several other avian species, the complete genomes could not be recovered, which warrants further studies to determine whether DCoVs can replicate in these species ( 9 , 11 , 12 , 26 ).…”

Investigating the Diversity and Host Range of Novel Parvoviruses from North American Ducks Using Epidemiology, Phylogenetics, Genome Structure, and Codon Usage Analysis

“…This viral promiscuity is likely linked to the capability of these viruses to infect different bird species when the opportunity for cross-species infections occurs, for example when different birds share the same ecological niche. These epidemiological characteristics of high viral prevalence, frequent co-infection, and relaxed host-specificity are characteristics shared with other avian viruses from other families [ 21 , 45 , 46 ].…”

Drawing Comparisons between SARS-CoV-2 and the Animal Coronaviruses

“…Furthermore, BCoVs, thought to be descendants of the rodent CoVs, were hypothesized to be involved in the evolution of non-bovine CoVs, such as canine respiratory CoVs (CRCoV), porcine hemagglutinating encephalomyelitis virus (PHEV), and equine CoVs [ 13 , 88 , 92 ]. On the other hand, birds are considered as reservoirs of the ancestors of gammacoronaviruses and deltacoronaviruses [ 13 , 93 ].…”

“…More recently, another porcine alphacoronavirus, swine enteric alphacoronavirus (SeACoV), also referred to as swine acute diarrhea syndrome coronavirus (SADS-CoV) or porcine enteric alphacoronavirus (PEAV), which emerged in Guangdong province in China in 2016, was derived from Rhinolophus bat CoV-HKU2-like strains [ 24 , 35 , 110 ]. The ancestor of porcine deltacoronavirus (PDCoV) was proposed to have originated through recombination events involving sparrow CoV HKU15 and bulbul CoV HKU11 [ 13 , 93 ].…”