Genomic representation predicts an asymptotic host adaptation of bat coronaviruses using deep learning

Frontiers in Microbiology

Microbiology

Wei Lin¹  Zhongyi Lei¹  Jun-Qing Wei¹  Fengjuan Tian¹  Yigang Tong¹  Sen Zhang²  Ya-Dan Li²  Ye Feng²  Shun-Shuai Liu²  Tao Jiang²  Xiao-Ping Kang²  Jia-Fu Jiang²  Jing Li² 

[1] Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China;State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China;

关键词: bat coronavirus;    asymptotic adaptation;    deep learning;    dinucleotide composition representation (DCR);    convolutional neural networks;   

DOI  :  10.3389/fmicb.2023.1157608

 received in 2023-02-02, accepted in 2023-04-03,  发布年份 2023

来源: Frontiers

【 摘 要 】

IntroductionCoronaviruses (CoVs) are naturally found in bats and can occasionally cause infection and transmission in humans and other mammals. Our study aimed to build a deep learning (DL) method to predict the adaptation of bat CoVs to other mammals.MethodsThe CoV genome was represented with a method of dinucleotide composition representation (DCR) for the two main viral genes, ORF1ab and Spike. DCR features were first analyzed for their distribution among adaptive hosts and then trained with a DL classifier of convolutional neural networks (CNN) to predict the adaptation of bat CoVs.Results and discussionThe results demonstrated inter-host separation and intra-host clustering of DCR-represented CoVs for six host types: Artiodactyla, Carnivora, Chiroptera, Primates, Rodentia/Lagomorpha, and Suiformes. The DCR-based CNN with five host labels (without Chiroptera) predicted a dominant adaptation of bat CoVs to Artiodactyla hosts, then to Carnivora and Rodentia/Lagomorpha mammals, and later to primates. Moreover, a linear asymptotic adaptation of all CoVs (except Suiformes) from Artiodactyla to Carnivora and Rodentia/Lagomorpha and then to Primates indicates an asymptotic bats-other mammals-human adaptation.ConclusionGenomic dinucleotides represented as DCR indicate a host-specific separation, and clustering predicts a linear asymptotic adaptation shift of bat CoVs from other mammals to humans via deep learning.

【 授权许可】

Unknown   
Copyright © 2023 Li, Tian, Zhang, Liu, Kang, Li, Wei, Lin, Lei, Feng, Jiang, Jiang and Tong.