Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK.
Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK.
J Gen Virol. 2023 Aug;104(8). doi: 10.1099/jgv.0.001883.
Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans () and the diverse species that they interact with. We discovered and characterised the full genome of a divergent gammacoronavirus belonging to the species. We investigated the genetic diversity and dynamics of this gammacoronavirus using untargeted metagenomic sequencing of 223 faecal samples from swans of known age and sex, and RT-PCR screening of 1632 additional bird samples. The virus circulated persistently within the bird community; virus prevalence in mute swans exhibited seasonal variations, but did not change with swan age-class or epidemiological year. One whole genome was fully characterised, and revealed that the virus originated from a recombination event involving an undescribed gammacoronavirus species. Multiple lineages of this gammacoronavirus co-circulated within our study population. Viruses from this species have recently been detected in aquatic birds from both the Anatidae and Rallidae families, implying that host species habitat sharing may be important in shaping virus host range. As the host range of the species is not limited to geese, we propose that this species name should be updated to ''. Non-invasive sampling of bird coronaviruses may provide a tractable model system for understanding the evolutionary and cross-species dynamics of coronaviruses.
从野生动物中出现的病毒会导致人类和家养动物爆发疾病。预测未来病原体的出现并减轻其影响，需要了解是什么塑造了野生动物宿主中病毒的多样性和动态。为了更好地了解野生动物中冠状病毒的生态学，我们在 5 年内对沿海淡水泻湖生境中的鸟类进行了采样，重点关注了一个大型的默西鹅种群（）及其与之相互作用的多种物种。我们发现并鉴定了一种属于 种的新型γ冠状病毒的全基因组。我们使用针对已知年龄和性别的天鹅的 223 份粪便样本进行了非靶向宏基因组测序，并对 1632 份额外的鸟类样本进行了 RT-PCR 筛查，从而研究了这种γ冠状病毒的遗传多样性和动态。该病毒在鸟类群体中持续循环；默西鹅中的病毒流行率存在季节性变化，但不会随天鹅年龄或流行病学年份而改变。一个完整的基因组被完全鉴定，结果表明该病毒源自涉及一种未描述的γ冠状病毒物种的重组事件。该γ冠状病毒的多个谱系在我们的研究种群中共同循环。该物种的病毒最近在来自鸭科和秧鸡科的水禽中被检测到，这意味着宿主物种栖息地共享可能在塑造病毒宿主范围方面很重要。由于 种的宿主范围不仅限于鹅，因此我们建议更新该物种名称为“”。对鸟类冠状病毒的非侵入性采样可能为了解冠状病毒的进化和跨物种动态提供一个可行的模型系统。
