Discovery and Characterization of Novel RNA Viruses in Aquatic North American Wild Birds

Abstract

Wild birds are recognized viral reservoirs but our understanding about avian viral diversity is limited. We describe here three novel RNA viruses that we identified in oropharyngeal/cloacal swabs collected from wild birds. The complete genome of a novel gull metapneumovirus (GuMPV B29) was determined. Phylogenetic analyses indicated that this virus could represent a novel avian metapneumovirus (AMPV) sub-group, intermediate between AMPV-C and the subgroup of the other AMPVs. This virus was detected in an American herring (1/24, 4.2%) and great black-backed (4/26, 15.4%) gulls. A novel gull coronavirus (GuCoV B29) was detected in great black-backed (3/26, 11.5%) and American herring (2/24, 8.3%) gulls. Phylogenetic analyses of GuCoV B29 suggested that this virus could represent a novel species within the genus Gammacoronavirus, close to other recently identified potential novel avian coronaviral species. One GuMPV–GuCoV co-infection was detected. A novel duck calicivirus (DuCV-2 B6) was identified in mallards (2/5, 40%) and American black ducks (7/26, 26.9%). This virus, of which we identified two different types, was fully sequenced and was genetically closest to other caliciviruses identified in Anatidae, but more distant to other caliciviruses from birds in the genus Anas. These discoveries increase our knowledge about avian virus diversity and host distributions.

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

“… 2018, 2019, 2020 ; Canuti et al . 2019 ) and these cluster with the sequences from wild birds, forming a clade that is distinct from AvCoV (Fig. 1 ).…”

“… 2018 , 2019 , 2020 ; Canuti et al . 2019 ). This is creating a new narrative in which disease-causing viruses are the exception rather the rule.…”

Coronaviruses in wild birds – A potential and suitable vector for global distribution

“…Canuti et al. (2019) reported that a novel GuCoV (B29) was identified in great black‐backed gulls ( L. marinus ) (3/26, 11.5%) and American herring gulls ( Larus argentatus smithsonianus ) (2/24, 8.3%) belonging to the Charadriiformes order. GuCoV B29’s phylogenetic analysis indicated that this virus may represent a novel species within the gamma‐CoV family, similar to other novel CoV species described recently (Canuti et al., 2019).…”

Coronaviruses in the Sea

“…Wild birds are known viral reservoirs, and birds which live mainly in the marine environment are also known to harbor coronaviruses. For instance, a novel coronavirus within the Gammacoronaviruses was identified in American herring and great black backed gulls (Canuti et al, 2019). Interestingly, these sea bird coronaviruses are within the same clade as marine mammal coronaviruses (Figure 1), suggesting that in the past, transmission between these animals has occurred.…”