Alphacoronaviruses from bats captured in European Russia in 2015 and 2021 are closely related to those of Northern Europe

IF 2.4 3区环境科学与生态学 Q2 ECOLOGY

Frontiers in Ecology and Evolution Pub Date : 2024-07-09 DOI:10.3389/fevo.2024.1324605

Elena V. Korneenko, Andrei E. Samoilov, Ivan K. Chudinov, Ivan O. Butenko, Ignat V. Sonets, Ilya V. Artyushin, Alexander P. Yusefovich, Sergei V. Kruskop, Sergei O. Sinitsyn, Ekaterina O. Klyuchnikova, Anna S. Gladkikh, Vladimir G. Dedkov, Marina V. Safonova, Peter Daszak, Anna S. Speranskaya

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引用次数: 0

Abstract

IntroductionBats are considered the natural reservoirs of several viruses including coronaviruses (CoVs), two genera of which, alpha- and betacoronaviruses, infect humans. Despite widespread screening of bat samples for novel viruses, information on the diversity of coronaviruses in bats inhabiting Russian territory remains scarce. Here, we analyzed the presence and diversity of alphacoronaviruses (Alpha-CoVs) in bats from European Russia.MethodsFourty three fecal samples from bats of 8 species: P. nathusii, P. kuhlii, M. brandtii, M. daubentonii, N. noctula, V. murinus, M. dasycneme, and P. auritus were taken to study.Results and discussionWe detected Alpha-CoV RdRp gene fragments in 30% (13/43) of samples examined in 75% (6/8) of species sampled. Phylogenetic analysis of RdRp showed that most of the identified Alpha-CoV sequences fall into clades within the Pedacovirus subgenus, with minor clusters of nyctacoviruses or myotacoviruses. We assert that closely related pedacoviruses have been circulating for a long time (from 2015 to 2021) in a large region from European Russia to Northern Europe. We propose that closely related pedacoviruses collected from common areas represent a separate species, which we name NE-Alpha coronavirus, with its host being bats of the genus Pipistrellus that inhabit a region from the European part of Russia to Northern Europe. Among the animals sampled, 4.6% (2/43) carried two Alpha-CoVs related to different subgenera (pedacovirus/myotacovirus or pedacovirus/nyctacovirus) simultaneously. We confirmed the presence of two different Alpha-CoV subgenera related to pedacovirus and nyctacovirus in P. kuhlii captured in 2021 and kept in captivity using whole genome sequencing of these viruses. The presence of two or more coronaviruses in one individual animal host is an essential prerequisite for recombination to occur. We also obtained two Alpha-CoV whole genomes from two specimens of P. nathusii captured in 2015. The genomic organization of BatCoV/MOW15-21 and BatCoV/MOW15-23 was similar to other Alpha-CoVs, but the assembled genomes contained a long insertion in the ORF1ab gene which has not been described in other Alpha-CoVs, except for a single sequence from P. nathusii captured in the Netherlands. We propose that the insertion encodes a previously undescribed domain of unknown function, probably related to the SEA domain superfamily.

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2015年和2021年在俄罗斯欧洲捕获的蝙蝠中的阿法克龙病毒与北欧的蝙蝠密切相关

导言蝙蝠被认为是包括冠状病毒（CoVs）在内的多种病毒的天然贮库，其中有两个属，即α-冠状病毒和β-冠状病毒会感染人类。尽管对蝙蝠样本进行了广泛的新型病毒筛查，但有关栖息在俄罗斯境内的蝙蝠冠状病毒多样性的信息仍然很少。在这里，我们分析了俄罗斯欧洲蝙蝠中阿尔法冠状病毒（Alpha-CoVs）的存在和多样性：结果与讨论我们在 75%（6/8）的抽样物种中的 30%（13/43）样本中检测到了 Alpha-CoV RdRp 基因片段。RdRp的系统进化分析表明，大部分已鉴定的阿尔法-CoV序列都属于小袋鼠病毒亚属中的支系，小群的小袋鼠病毒或肌小袋鼠病毒。我们断言，在从欧洲俄罗斯到北欧的广大地区，密切相关的有脚病毒已经流行了很长时间（从 2015 年到 2021 年）。我们提出，从常见地区收集到的密切相关的小尾寒羊病毒代表了一个独立的物种，我们将其命名为东北-阿尔法冠状病毒，其宿主是栖息在从俄罗斯欧洲部分到北欧地区的蝙蝠属（Pipistrellus）。在采样的动物中，有4.6%（2/43）的动物同时携带两种不同亚属的阿尔法冠状病毒（脚气病毒/贻贝病毒或脚气病毒/贻贝病毒）。通过对这些病毒进行全基因组测序，我们证实了在 2021 年捕获并人工饲养的 P. kuhlii 中存在与 pedacovirus 和 nyctacovirus 相关的两个不同 Alpha-CoV 亚属。在一个动物宿主个体中存在两种或两种以上冠状病毒是发生重组的必要前提。我们还从2015年捕获的两只P. nathusii标本中获得了两个Alpha-CoV全基因组。BatCoV/MOW15-21和BatCoV/MOW15-23的基因组结构与其他阿尔法-CoV相似，但组装后的基因组在ORF1ab基因中含有一个长插入片段，除了在荷兰捕获的P. nathusii的单一序列外，其他阿尔法-CoV中还没有描述过这一插入片段。我们认为，该插入物编码了一个以前未曾描述过的未知功能域，可能与 SEA 功能域超家族有关。

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来源期刊

Frontiers in Ecology and Evolution Environmental Science-Ecology

CiteScore

4.00

自引率

6.70%

发文量

1143

审稿时长

12 weeks

期刊介绍： Frontiers in Ecology and Evolution publishes rigorously peer-reviewed research across fundamental and applied sciences, to provide ecological and evolutionary insights into our natural and anthropogenic world, and how it should best be managed. Field Chief Editor Mark A. Elgar at the University of Melbourne is supported by an outstanding Editorial Board of international researchers. This multidisciplinary open-access journal is at the forefront of disseminating and communicating scientific knowledge and impactful discoveries to researchers, academics and the public worldwide. Eminent biologist and theist Theodosius Dobzhansky’s astute observation that “Nothing in biology makes sense except in the light of evolution” has arguably even broader relevance now than when it was first penned in The American Biology Teacher in 1973. One could similarly argue that not much in evolution makes sense without recourse to ecological concepts: understanding diversity — from microbial adaptations to species assemblages — requires insights from both ecological and evolutionary disciplines. Nowadays, technological developments from other fields allow us to address unprecedented ecological and evolutionary questions of astonishing detail, impressive breadth and compelling inference. The specialty sections of Frontiers in Ecology and Evolution will publish, under a single platform, contemporary, rigorous research, reviews, opinions, and commentaries that cover the spectrum of ecological and evolutionary inquiry, both fundamental and applied. Articles are peer-reviewed according to the Frontiers review guidelines, which evaluate manuscripts on objective editorial criteria. Through this unique, Frontiers platform for open-access publishing and research networking, Frontiers in Ecology and Evolution aims to provide colleagues and the broader community with ecological and evolutionary insights into our natural and anthropogenic world, and how it might best be managed.