Persistent minimal sequences of SARS-CoV-2
Persistent minimal sequences of SARS-CoV-2
复制标题
SARS-CoV-2 的持久最小序列
DOI：
10.1093/bioinformatics/btaa686
复制
发表时间：
2020
期刊：
影响因子：
5.8
通讯作者：
J. M. Silva
中科院分区：
文献类型：
--
作者：
Diogo Pratas;J. M. Silva
抽象动机严重的急性呼吸综合症冠状病毒2（SARS-COV-2）导致超过1400万例病例和超过50万人死亡。鉴于没有实施疗法，新的分析，诊断和治疗疗法非常重要。对当前爆发的SARS-COV-2基因组的结果分析揭示了人类基因组和转录组（PMRAWS）不存在的短持续DNA/RNA序列的存在。对于长度为12的PMRAWS，在所有SARS-COV-2中，在同一位置只有四个。在基因水平上，我们在尖峰糖蛋白编码序列下发现了一个尺寸13的PMRAW。该蛋白是在人ACE2中结合的基础，并进一步用作入侵靶细胞的入口受体。采用蛋白质结构预测，我们将此PMRAW定位在峰值蛋白的表面，为诊断和治疗剂提供了潜在的靶向载体。此外，根据病毒和宿主基因组分布，我们显示出一种相对缺失单词（RAW）的新模式，其特征是GC含量（鸟嘌呤和胞嘧啶）的逐渐增加。新分析显示了在埃博拉病毒爆发期间具有相同的特性。在计算水平上，我们改进了无对解的方法，以识别与GC测量平衡的病原体特异性特异性特异性签名，并消除了先前的尺寸限制。可用性和实现https://github.com/cobilab/eagle。补充信息BTAA686_SUPPENTRY-DATA单击此处以获取其他数据文件。补充数据可在线生物信息学上获得。
Abstract Motivation Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 14 million cases and more than half million deaths. Given the absence of implemented therapies, new analysis, diagnosis, and therapeutics are of great importance. Results Analysis of SARS-CoV-2 genomes from the current outbreak reveals the presence of short persistent DNA/RNA sequences that are absent from the human genome and transcriptome (PmRAWs). For the PmRAWs with length 12, only four exist at the same location in all SARS-CoV-2. At the gene level, we found one PmRAW of size 13 at the Spike glycoprotein coding sequence. This protein is fundamental for binding in human ACE2 and further use as an entry receptor to invade target cells. Applying protein structural prediction, we localized this PmRAW at the surface of the Spike protein, providing a potential targeted vector for diagnostics and therapeutics. Additionally, we show a new pattern of relative absent words (RAWs), characterized by the progressive increase of GC content (Guanine and Cytosine) according to the decrease of RAWs length, contrarily to the virus and host genome distributions. New analysis shows the same property during the Ebola virus outbreak. At a computational level, we improved the alignment-free method to identify pathogen-specific signatures in balance with GC measures and removed previous size limitations. Availability and Implementation https://github.com/cobilab/eagle. Supplementary informationbtaa686_Supplementary-data Click here for additional data file. Supplementary data are available at Bioinformatics online.
DOI：
10.1016/j.ijantimicag.2020.105924
发表时间：
2020-03-01
影响因子：
10.8
作者：
Lai, Chih-Cheng;Shih, Tzu-Ping;Hsueh, Po-Ren
通讯作者：
Hsueh, Po-Ren