Evolution Analysis Of Deltacoronavirus Cross-species Transmission And PDCoV

In the RNA virus,CoVs contains the largest known genome which makes it genetically more plasticity in genome modification.Through mutations and recombinations,CoVs increased the probability for interspecies host jump and novel CoVs emerged under specific conditions.Deltacoronavirus is a new identified genus in the subfamily Coronaviridae.Different from other genus of coronaviruses(CoVs)which infected only birds or mammals,deltacoronaviruses(?-CoVs)were reported to infect both birds and mammals.As a new identified genus in the subfamily Coronavirinae,deltacoronaviruses(?-CoVs)were first detected from wild Asian leopard cats and Chinese ferret badgers in 2006 during virological surveillance in southern China.Subsequently three avian ?-CoV species were reported in 2009 and seven ?-CoV species were identified in birds or pigs between 2009 and 2012.In 2014,an emerging swine enteropathogenic coronavirus(CoV),porcine deltacoronavirus(PDCoV),was detected in the United States.To date,it was widely reported in North America and Asia and caused huge economic losses.The recent research showed that ?-CoVs were present in birds in Saudi Arabia,the Sparrow-CoVs were detected in the USA and Poland.These evidences showed the active existence and potential threat of ?-CoVs.However,the evolutionary history of ?-CoVs is poorly understood.Therefore,the zoonotic spread of new viruses poses a significant threat to global public health.Here,we investigated the origin and evolution of ?-CoVs.These data will help prepare countermeasures against the potential risk in future.Together,our analyses provided valuable insights into the diversification,evolution,and interspecies transmission of ?-CoVs and the origin of PDCoV,providing a model to explore the relationship of ?-CoVs between birds and mammals.The mian research contents are as follows: Phylogenetic analyses of ?-CoVsThe sequences 18 avian deltacoronaviruses(ADCoVs)and 100 PDCoVs were obtained from the NCBI for for phylogenetic and host-virus evolutionary relationships analysis.The maximum?likelihood(ML)phylogenetic trees were constructed based on the genome and the primary genes(Orf1ab-S-E-M-N,Orf1 ab,S,E-M-N)of ?-CoVs.Based on the phylogenetic tree topologies and viral hosts,?-CoVs were divided into three groups: PDCoVs,Sparrow-CoVs(Sp-CoVs)and other birds-CoVs.The intra-and inter-group genetic distances(p-distance)analyze presented that the genetic diversity of ADCoV exceeds that of PDCoV,suggesting a long evolution of ?-CoVs in avian.Interestingly,ML-trees and p-distance analyses shows that Sp-CoV is the closest to PDCoV on all genes,which implies that there is a strong correlation between these two viruses.Previous researches have been reported that cross-species transmission of coronavirus is closely related to Spike(S)protein,nsp3(papain-like protease,PLpro)and accessory protein..Thus,the sequence divergence of Orf1ab-S-E-M-N was performed and the intra-and inter-group of the p-distance and the synonymous & non-synonymous p-distance were calculated.The results showed that the PLpro,S gene and accessory protein of ?-CoVs owned a high level of molecular variability.Moreover,the ranges of fluctuation in synonymous and non-synonymous mutation rate showed that the S gene of Sp-CoVs had a large span through all ?-CoVs,which may promoted the virus to spill over into new hosts.Cross-species transmission of ?-CoVsTo further figure out the spread of ?-CoVs among different hosts,we performed event-based co-phylogenetic reconstructions using the Jane program version 4 that can analyze five types of events of host-virus phylogeny(cospeciation,duplication,duplication &host switching,loss and failure to diverge).The results showed that there are large amounts of duplication and host switch in ?-CoVs,suggesting that the Sp-CoV may switched the host from sparrow to swine and generated PDCoV.During the cross-species transmission,the virus usually takes various strategies,such as the change of codon preference,to adapt to the new host and support the proliferation itself.The genomic GC content is one of the most reliable signals which relate to cross-species codon usage variation,and the wobble of the third position of the codons,GC3 s may be related to the evolution of the virus.Our analysis showed that the change of the total GC content is mainly caused by GC3 s,and there is a strong correlation between different kinds of ?-CoVs in the change of GC content with GC12s(R2=0.9321)and GC3s(R2=0.9906),which confirmed that the ?-CoVs had undergone long-term evolution and the PDCoV might come from ADCoV.The result of heatmap showed high similarity in the codon usage of PDCoVs and Sp-CoVs.While the codon usage of PDCoVs and Sp-CoVs was different from that of other avian-CoVs,suggesting that PDCoVs still maintained the previous codon preference and did not yet fully adapt to the new host.The analysis of close genetic similarity,codon usage and GC bias implied that PDCoVs maybe originated from ADCoVs,especially the Sp-CoVs.The origin and evolution of PDCoVsTo identify the relationship between Sp-CoVs and PDCoVs,the viral origin time was explored through time-scaled phylogenetic tree constructed in the program BEAST 2.The origin time of PDCoVs was around 1990 s,while the origin time of Sp-CoVs was much earlier,supporting the speculation that the PDCoVs may originated from Sp-CoVs.To further compare the origin time of different genotyping of PDCoV isolates,the Bayesian time?scaled and phylogeographic tree of the PDCoVs,PDCoV might originate around 1993 from the SEA.