越南及其邻国马蹄蝠沙棘病毒的系统地理学。对 SARS-CoV 和 SARS-CoV-2 起源的影响。

IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Molecular Ecology Pub Date : 2024-08-19 DOI:10.1111/mec.17486
Alexandre Hassanin, Vuong Tan Tu, Tamás Görföl, Lam Quang Ngon, Phu Van Pham, Chu Thi Hang, Tran Anh Tuan, Mathieu Prot, Etienne Simon-Lorière, Gábor Kemenesi, Gábor Endre Tóth, Laurent Moulin, Sébastien Wurtzer
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引用次数: 0

摘要

以往关于马蹄蝠(Rhinolophus spp.)的研究描述了中国许多与SARS-CoV(SARSCoVr)相关的冠状病毒,而在云南(中国南部)、柬埔寨、老挝和泰国仅有少数与SARS-CoV-2(SARSCoV2r)相关的冠状病毒。在此,我们报告了 2017 年、2021 年和 2022 年在越南进行的几次实地考察的结果,考察期间在 19 个地点对 1218 只马蹄蝠进行了采样。在 11% 的粪便 RNA 提取物中检测到了沙棘病毒,其中马蹄蝠的阳性率更高(46%)。我们组装了 38 个沙棘病毒基因组,包括 32 个 SARSCoVr、4 个 SARSCoV2r 和两个 SARSCoVr 和 SARSCoV2r 的重组体(RecSar),其中一个重组体显示出与 SARS-CoV-2 非常相似的尖峰蛋白。我们发现一只蝙蝠同时感染了四种冠状病毒,其中包括两种沙棘病毒。我们的分析表明,沙棘病毒基因组在越南的进化受到了强烈的地理和宿主限制。首先,我们发现了越南北部病毒与越南中部和南部病毒之间存在深度分离的证据。其次,我们只在 Rhinolophus thomasi 中检测到了 SARSCoVr,在 Rhinolophus affinis 中检测到了 SARSCoVr 和 SARSCoV2r,而在靠近中国边境的 Rhinolophus pusillus 中只检测到了 RecSar。第三,在从 R. thomasi 提取的 SARSCoVr 中,同义第三密码子位置的 Uracil 偏向与纬度呈负相关。我们的研究结果还支持了云南北部马蹄蝠出现 SARS-CoV 和印度支那北部亚热带森林(云南南部、老挝北部和越南西北部)马蹄蝠出现 SARS-CoV-2 的观点。
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Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. Implications for the origins of SARS-CoV and SARS-CoV-2

Previous studies on horseshoe bats (Rhinolophus spp.) have described many coronaviruses related to SARS-CoV (SARSCoVr) in China and only a few coronaviruses related to SARS-CoV-2 (SARSCoV2r) in Yunnan (southern China), Cambodia, Laos and Thailand. Here, we report the results of several field missions carried out in 2017, 2021 and 2022 across Vietnam during which 1218 horseshoe bats were sampled from 19 locations. Sarbecoviruses were detected in 11% of faecal RNA extracts, with much more positives among Rhinolophus thomasi (46%). We assembled 38 Sarbecovirus genomes, including 32 SARSCoVr, four SARSCoV2r, and two recombinants of SARSCoVr and SARSCoV2r (RecSar), one showing a Spike protein very similar to SARS-CoV-2. We detected a bat co-infected with four coronaviruses, including two sarbecoviruses. Our analyses revealed that Sarbecovirus genomes evolve in Vietnam under strong geographical and host constraints. First, we found evidence for a deep separation between viruses from northern Vietnam and those from central and southern Vietnam. Second, we detected only SARSCoVr in Rhinolophus thomasi, both SARSCoVr and SARSCoV2r in Rhinolophus affinis, and only RecSar in Rhinolophus pusillus captured close to the border with China. Third, the bias in favour of Uracil in synonymous third codon positions of SARSCoVr extracted from R. thomasi showed a negative correlation with latitudes. Our results also provided support for an emergence of SARS-CoV in horseshoe bats from northern Yunnan and emergence of SARS-CoV-2 in horseshoe bats from northern Indochina subtropical forests (southern Yunnan, northern Laos and north-western Vietnam).

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来源期刊
Molecular Ecology
Molecular Ecology 生物-进化生物学
CiteScore
8.40
自引率
10.20%
发文量
472
审稿时长
1 months
期刊介绍: Molecular Ecology publishes papers that utilize molecular genetic techniques to address consequential questions in ecology, evolution, behaviour and conservation. Studies may employ neutral markers for inference about ecological and evolutionary processes or examine ecologically important genes and their products directly. We discourage papers that are primarily descriptive and are relevant only to the taxon being studied. Papers reporting on molecular marker development, molecular diagnostics, barcoding, or DNA taxonomy, or technical methods should be re-directed to our sister journal, Molecular Ecology Resources. Likewise, papers with a strongly applied focus should be submitted to Evolutionary Applications. Research areas of interest to Molecular Ecology include: * population structure and phylogeography * reproductive strategies * relatedness and kin selection * sex allocation * population genetic theory * analytical methods development * conservation genetics * speciation genetics * microbial biodiversity * evolutionary dynamics of QTLs * ecological interactions * molecular adaptation and environmental genomics * impact of genetically modified organisms
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