Discovery, phylogenetic, and comparative genomic analysis of novel avian gammacoronaviruses identified in feral pigeons (Columba livia domestica).

IF 3.8 2区 医学 Q2 VIROLOGY
Journal of Virology Pub Date : 2025-09-23 Epub Date: 2025-08-20 DOI:10.1128/jvi.01112-25
Mohamed E El Zowalaty, Louis J Taylor, Yongwoo Son, Heesu Lee, Adam M Rubrum, Richard J Webby, Stephen A Bustin, Sean G Young, Sun-Hak Lee, Dong-Hun Lee, Matthew B Frieman
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引用次数: 0

Abstract

The COVID-19 pandemic caused by SARS-CoV-2 has intensified efforts to identify emerging coronaviruses (CoVs) across diverse hosts. Spillover events, where CoVs transition from wildlife reservoirs to other species, can lead to infections with varying clinical outcomes, emphasizing the need for continued surveillance. Understanding the diversity and distribution of both known and novel CoVs in wildlife reservoirs is crucial for predicting and preventing future spillover events. In this study, we employed Illumina's Pan-CoV library panel and next-generation sequencing (NGS) to identify five novel avian-associated gammacoronavirus genomes from cloacal and oropharyngeal swabs of clinically healthy feral pigeons captured in Durban, KwaZulu-Natal Province, South Africa, in 2018. The genome sequences, ranging from 27,582 to 27,611 nucleotides, clustered with gammacoronaviruses in phylogenetic analyses but formed a distinct clade. Comparative analysis of the five conserved domains in the ORF1ab coding sequence with other gammacoronaviruses revealed Pairwise Patristic Distances (PPD) that exceeded both species and subgenus demarcation cutoffs. These findings highlight the critical need for ongoing surveillance to enhance understanding of CoV diversity, host range, and potential for cross-species transmission, aligning with One Health principles. Based on these results, we propose Gammacoronavirus columbae as a new species for these pigeon gammacoronaviruses that clusters with the recently reported duck gammacoronaviruses to form a novel subgenus within Gammacoronavirus.IMPORTANCEAlthough coronaviruses are significant pathogens affecting a wide range of hosts, surveillance efforts have predominantly focused on wild mammals, leaving the diversity of avian coronaviruses largely underexplored. Here, we report the detection of novel gammacoronaviruses from feral pigeons in South Africa and propose revisions to the current taxonomic classification of Gammacoronavirus based on genetic distance analyses. These findings highlight the potential role of wild birds in the dissemination of novel coronaviruses, analogous to their established involvement in the transmission of avian influenza viruses. Our study also highlights the utility of next-generation sequencing (NGS) technologies in uncovering the hidden diversity of viruses in wildlife populations. Finally, this study reinforces the need for ongoing surveillance, continued vigilance, and further research into avian coronaviruses. The ongoing highly pathogenic avian influenza (HPAI) outbreaks in the USA have demonstrated the devastating impact of emerging avian viruses on wildlife, agriculture, and public health. Given the unpredictability of coronavirus evolution, failing to monitor their diversity and potential for cross-species transmission risks leaving us unprepared for future outbreaks. This study reinforces the urgent need for proactive, large-scale genomic surveillance of wildlife reservoirs to identify emerging CoVs before they become significant threats to animal and human populations.

在野鸽(Columba livia domestica)中发现的新型禽γ冠状病毒的发现、系统发育和比较基因组分析。
由SARS-CoV-2引起的COVID-19大流行加强了在不同宿主中识别新发冠状病毒(cov)的努力。外溢事件,即冠状病毒从野生宿主转移到其他物种,可导致具有不同临床结果的感染,强调需要继续监测。了解野生水库中已知和新型冠状病毒的多样性和分布对于预测和预防未来的溢出事件至关重要。在这项研究中,我们利用Illumina的Pan-CoV文库面板和下一代测序(NGS)技术,从2018年在南非夸祖鲁-纳塔尔省德班捕获的临床健康野鸽的粪腔和口咽拭子中鉴定了五种新型鸟类相关的伽玛冠状病毒基因组。基因组序列从27,582到27,611个核苷酸不等,在系统发育分析中与γ冠状病毒聚集在一起,但形成了一个独特的进化支。ORF1ab编码序列的5个保守结构域与其他伽玛冠状病毒的比较分析显示,Pairwise Patristic距离(PPD)超过了种和亚属的界限。这些发现突出了持续监测的迫切需要,以加强对冠状病毒多样性、宿主范围和跨物种传播可能性的了解,并与“同一个健康”原则保持一致。基于这些结果,我们提出了伽玛冠状病毒柱状病毒作为鸽子伽玛冠状病毒的一个新种,它与最近报道的鸭伽玛冠状病毒聚集在一起,在伽玛冠状病毒中形成一个新的亚属。尽管冠状病毒是影响广泛宿主的重要病原体,但监测工作主要集中在野生哺乳动物身上,因此对禽冠状病毒的多样性的探索在很大程度上不足。在这里,我们报告了在南非野鸽中检测到的新型伽玛冠状病毒,并提出了基于遗传距离分析对目前伽玛冠状病毒分类的修订。这些发现强调了野生鸟类在新型冠状病毒传播中的潜在作用,类似于它们在禽流感病毒传播中的已知参与。我们的研究还强调了下一代测序(NGS)技术在揭示野生动物种群中隐藏的病毒多样性方面的实用性。最后,这项研究强调了持续监测、持续警惕和进一步研究禽流感冠状病毒的必要性。美国正在爆发的高致病性禽流感(HPAI)已经证明了新出现的禽流感病毒对野生动物、农业和公共卫生的破坏性影响。鉴于冠状病毒进化的不可预测性,如果不能监测其多样性和跨物种传播的可能性,我们可能会对未来的疫情毫无准备。这项研究强调,迫切需要对野生动物宿主进行主动、大规模的基因组监测,以便在新出现的冠状病毒对动物和人类构成重大威胁之前识别它们。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of Virology
Journal of Virology 医学-病毒学
CiteScore
10.10
自引率
7.40%
发文量
906
审稿时长
1 months
期刊介绍: Journal of Virology (JVI) explores the nature of the viruses of animals, archaea, bacteria, fungi, plants, and protozoa. We welcome papers on virion structure and assembly, viral genome replication and regulation of gene expression, genetic diversity and evolution, virus-cell interactions, cellular responses to infection, transformation and oncogenesis, gene delivery, viral pathogenesis and immunity, and vaccines and antiviral agents.
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