VanAcker Meredith C, Ergunay Koray, Webala Paul W, Kamau Maureen, Mutura Janerose, Lebunge Rashid, Ochola Griphin Ochieng, Bourke Brian P, McDermott Emily G, Achee Nicole L, Jiang Le, Grieco John P, Keter Erick, Musanga Audrey, Murray Suzan, Stabach Jared A, Craft Meggan E, Fèvre Eric M, Linton Yvonne-Marie, Hassell James
Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA.
Global Health Program, Smithsonian Institution, National Zoo and Conservation Biology Institute, Washington, DC 20008, USA.
Viruses. 2025 Apr 12;17(4):557. doi: 10.3390/v17040557.
Most human emerging infectious diseases are zoonotic, originating in animal hosts prior to spillover to humans. Prioritizing the surveillance of wildlife that overlaps with humans and human activities can increase the likelihood of detecting viruses with a high potential for human infection. Here, we obtained fecal swabs from two fruit bat species- ( = 6) and ( = 43) (family Pteropodidae)-in peridomestic habitats in Nairobi, Kenya, and used metagenome sequencing to detect microorganisms. A near-complete genome of a novel virus assigned taxonomically to the family genus and subclade was characterized from . Phylogenetic analysis indicates this unique clade shares a common ancestor with Eidolon/Rousettus Nobecovirus subclades isolated from Madagascar, Kenya, and Cameroon. Recombination was detected across open reading frames, except the spike protein, in all BOOTSCAN analyses, indicating intra-host coinfection and genetic exchange between genome regions. Although Nobecoviruses are currently bat-specific and are not known to be zoonotic, the propensity of coronaviruses to undergo frequent recombination events and the location of the virus alongside high human and livestock densities in one of East Africa's most rapidly developing cities justifies continued surveillance of animal viruses in high-risk urban landscapes.
大多数新出现的人类传染病是人畜共患病，在传播给人类之前起源于动物宿主。优先监测与人类和人类活动重叠的野生动物，可增加检测到具有高人类感染潜力病毒的可能性。在这里，我们从肯尼亚内罗毕周边栖息地的两种果蝠物种（锤头果蝠，n = 6；埃及果蝠，n = 43）（狐蝠科）获取粪便拭子，并使用宏基因组测序来检测微生物。从埃及果蝠中鉴定出一种新型病毒的近乎完整的基因组，该病毒在分类学上属于冠状病毒科、正冠状病毒属和A亚分支。系统发育分析表明，这个独特的A冠状病毒分支与从马达加斯加、肯尼亚和喀麦隆分离出的锤头果蝠属/埃及果蝠属诺贝病毒亚分支有共同的祖先。在所有BOOTSCAN分析中，除了刺突蛋白外，在开放阅读框中均检测到重组，这表明宿主内共感染以及基因组区域之间的基因交换。尽管诺贝病毒目前是蝙蝠特有的，并且未知是人畜共患病，但冠状病毒频繁发生重组事件的倾向以及该病毒在东非发展最快的城市之一中与高人口和高牲畜密度并存的情况，证明在高风险城市环境中持续监测动物病毒是合理的。
