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

Abstract

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.

Risk Assessment of the Possible Intermediate Host Role of Pigs for Coronaviruses with a Deep Learning Predictor

“…In particular, domestic pigs and probably other species in Suiformes played a key intermediate host role for all six historic influenza pandemics [ 6 , 16 , 17 , 18 , 19 , 20 ]. Suiformes are also one main family of mammalian hosts for CoVs [ 21 , 22 , 23 , 24 , 25 , 26 ]. Swine CoVs have been implied to replicate efficiently in human primary cells [ 27 ] and, more worryingly, cause infection in malnourished Haitian children [ 28 ] or calves and chickens [ 29 ].…”

“…Phylogenetic analysis and other traditional methods in bioinformatics have provided indicative clues to infer the homology to other mammalian CoVs and the potential infection/transmission risk to these hosts of Suiformes CoVs. Phylogenetic trees have indicated that swine CoVs, such as swine acute diarrhea syndrome CoV (SADS-CoV) [ 21 ] and porcine epidemic diarrhea virus (PEDV) [ 25 ] may originate from bats [ 26 ]. Swine transmissible gastroenteritis virus (TGEV) has very high homology to canine CoVs [ 36 ].…”

“…In particular, domestic pigs and probably other species in Suiformes played a key intermediate host role for all six historic influenza pandemics [6,[16][17][18][19][20]. Suiformes are also one main family of mammalian hosts for CoVs [21][22][23][24][25][26].…”