期刊
FRONTIERS IN MICROBIOLOGY
卷 14, 期 -, 页码 -出版社
FRONTIERS MEDIA SA
DOI: 10.3389/fmicb.2023.1157608
关键词
bat coronavirus; asymptotic adaptation; deep learning; dinucleotide composition representation (DCR); convolutional neural networks
类别
This study aimed to predict the adaptation of bat coronaviruses to other mammals using a deep learning method. The distribution and clustering analysis of dinucleotide composition represented coronaviruses showed inter-host separation and intra-host clustering. The deep learning model based on dinucleotide composition predicted the sequential adaptation of bat coronaviruses to different types of mammals and revealed a linear asymptotic adaptation shift to humans.
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.
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