A complex system is inherently high-dimensional.Recent studies indicate that,even without complete knowledge of its evolutionary dynamics,the future behavior of such a system can be predicted using time-series data(da...A complex system is inherently high-dimensional.Recent studies indicate that,even without complete knowledge of its evolutionary dynamics,the future behavior of such a system can be predicted using time-series data(data-driven prediction).This suggests that the essential dynamics of a complex system can be captured through a low-dimensional representation.Virus evolution and climate change are two examples of complex,time-varying systems.In this article,we show that mutations in the spike protein provide valuable data for predicting SARS-CoV-2 variants,forecasting the possible emergence of the new macro-lineage Q in the near future.Our analysis also demonstrates that carbon dioxide concentration is a reliable indicator for predicting the evolution of the climate system,extending global surface air temperature(GSAT)forecasts through 2500.展开更多
Mammals are critical reservoirs of human infectious diseases and the spillover of viruses is related to climate conditions.We conducted meta-transcriptomic sequencing of 226 mammals(bats,rodents,hedgehogs,and shrews)r...Mammals are critical reservoirs of human infectious diseases and the spillover of viruses is related to climate conditions.We conducted meta-transcriptomic sequencing of 226 mammals(bats,rodents,hedgehogs,and shrews)representing 20 species collected across eight cities in south China between 2018 and 2024.Samples included internal organs,oropharyngeal and anal swabs,and feces.We identified 63 vertebrate-associated viruses,including 34 novel viruses.Phylogenetic analysis revealed six viruses with potential infection risks to humans or domestic animals due to their close phylogenetic relationships with known pathogens.Cross-species transmission was observed in 14.3%(9/63)of viruses,shared by at least two host species,with bats,particularly Rhinolophus and Hipposideros,serving as key hubs for viral circulation and zoonotic spillover.Virome composition varied substantially among mammalian species and geographic regions(adonis test,R^(2)=0.50,P=0.001).Generalized linear models quantified the roles of host taxonomy,ecotypes,and meteorological factors in shaping viral diversity,demonstrating host taxonomy(at the order level)as a predominant role(25.70%deviance explained),followed by ecotypes(10.27%deviance explained).Phylogenetic analysis conducted using our betacoronavirus sequences,as well as betacoronavirus sequences derived from 2.0×10^(4) bats sampled in China between July 2013 and March 2024,revealed that no betacoronaviruses exhibited closer phylogenetic relationships to SARS-CoV-2 than the known strains(e.g.,RaTG13).These findings provide critical insights into virus evolution,transmission,and ecological determinants,which are essential for the prevention of emerging infectious diseases.展开更多
AIM： To investigate the hoLspoLs, direction, and the time course of evolution of hepatitis A virus in the process of consecutive cell culture passage in human KMB17 diploid cells.METHODS： Wild type hepatitis A virus...AIM： To investigate the hoLspoLs, direction, and the time course of evolution of hepatitis A virus in the process of consecutive cell culture passage in human KMB17 diploid cells.METHODS： Wild type hepatitis A virus H2w was serially propagated in KMB17 cells until passage 30, and the fulllength genomes of H2w and its six chosen progenies were determined by directly sequencing RT-PCR products amplified from viral genomic RNA. Alignment comparison of sequences from H2w with its six progenies and phylogenetic analysis of the whole VP1 region from H2w, progenies of H2w, and other cell culture adapted hepatitis A virus were then carried out to obtain data on the molecular evolution of hepatitis A virus in the process of consecutive passage in KMB17 cells.RESULTS： Most of the mutations occurred by passage 5 and several hotspots related to adaptation of the virus during cell growth were observed. After that stage, few additional mutations occurred through the remaining duration of passage in KMB17 cells except for mutation in the virulence determinants, which occurred in the vicinity of passage 15. The phylogenetic analysis of the whole VP1 region suggested that the progenies of H2w evolved closely to other cell culture adapted hepatitis A virus, i.e. MBB, L-A-l, other than its progenitor H2w.CONCLUSION： Hepatitis A virus served as a useful model for studying molecular evolution of viruses in a given environment. The information obtained in this study may provide assistance in cultivating the next generation of a seed virus for live hepatitis A vaccine production.展开更多
The H7 subtype avian influenza viruses, including H7N2, HTN3 and HTN7, have posed a public health threat worldwide. Except one H7N7 fatal case in the Netherlands in 2003, the other H7 human cases have resulted in self...The H7 subtype avian influenza viruses, including H7N2, HTN3 and HTN7, have posed a public health threat worldwide. Except one H7N7 fatal case in the Netherlands in 2003, the other H7 human cases have resulted in self-limiting conjunc- tivitis or mild upper respiratory illness.展开更多
In order to reveal variation and revolution of NP genes of human avian H5 N1 influenza virus strains, the NP gene of a human avian H5 N1 influenza virus strain in Guangdong was sequenced and the global NP genes of str...In order to reveal variation and revolution of NP genes of human avian H5 N1 influenza virus strains, the NP gene of a human avian H5 N1 influenza virus strain in Guangdong was sequenced and the global NP genes of strains were retrieved. The sequences were analyzed by DNAStar 5.0, and the evolutionary speed was studied with reference to the epidemiological data. It was found that NP genes of 45 strains during 1997-2006 were homologically classified into three groups： strains in 1997-1998, strains in 2004-2005 and strains from 2003 to 2006. There were 35 substitutions in NPs in all strains accounting for a ratio of 7.03% （35/498）. An additional glycoprotein domain （NGT430-432） was found in NP genes in the strains of 2003-2006, the mutation of N370S in GD-01-06 resulted in occurrence of one more glycoprotein domain （NES368-370）. In the synonymous variation, Ks values in NP were 2.03 × 10^-5-2.55 × 10^-5 Nt/d and K. values in NP were 1.58 × 10^-6-3.10 × 10^-6 Nt/d. There didn＇t exist obviously selective pressure. An additional glycoprotein domain in every strain of 2003-2006 and one more in strain GD-01-06 might change the antigenicity of human avian H5 N1 influenza virus. The variation on human avian H5 N1 influenza strains occurred frequently in the natural world, which would result in high probability of human-human transmission along with the natural evolution of the virus.展开更多
Diarrhea is the third leading cause of death in developing countries in children under the age of five.About half a million children die of diarrhea every year,most of which in developing countries.Viruses are the mai...Diarrhea is the third leading cause of death in developing countries in children under the age of five.About half a million children die of diarrhea every year,most of which in developing countries.Viruses are the main pathogen of diarrhea.In China,the fecal virome of children with diarrhea has been rarely studied.Using an unbiased viral metagenomics approach,we analyzed the fecal virome in children with diarrhea.Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae,Astroviridae,Caliciviridae,Parvoviridae,Picornaviridae,and Reoviridae.Among them,the family of Caliciviridae accounts for the largest proportion of 78.42%,following with Adenoviridae(8.94%)and Picornaviridae(8.36%).In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea,the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus.This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area.展开更多
Mink enteritis virus(MEV),a member of the Protoparvovirus genus within the Parvovirinae subfamily,causes severe hemorrhagic enteritis and leukopenia in minks,thus representing a serious economic threat to mink farming...Mink enteritis virus(MEV),a member of the Protoparvovirus genus within the Parvovirinae subfamily,causes severe hemorrhagic enteritis and leukopenia in minks,thus representing a serious economic threat to mink farming.MEV,feline panleukopenia virus(FPV),and canine parvovirus(CPV)are closely related Protoparvovirus members;CPV and FPV infect hosts via binding to transferrin receptor 1(TfR1).However,the structural mechanism of MEV entry remains poorly understood.This study used cryo-electron microscopy(cryo-EM)and structural bioinformatics to determine the structure of MEV virus-like particles at 2.5 A resolution.The analysis revealed that MEV shares a highly conserved capsid architecture with CPV and FPV,particularly in theβ-barrel core and three-fold protrusions.We predict that MEV utilizes mink TfR1 for host entry,similar to CPV and FPV.Structural superposition and sequence alignment identified key residues in the MEV VP2 protein that are critical for mink TfR1 interaction.These findings provide structural and evolutionary insights into MEV host tropism,offering valuable information for efforts to mitigate the zoonotic risks of mammalian parvoviruses.展开更多
Hand,foot,and mouth disease(HFMD)is one of the most common class C infectious diseases,posing a seri-ous threat to public health worldwide.Enterovirus A71(EV-A71)and coxsackievirus A16(CV-A16)have been regarded as the...Hand,foot,and mouth disease(HFMD)is one of the most common class C infectious diseases,posing a seri-ous threat to public health worldwide.Enterovirus A71(EV-A71)and coxsackievirus A16(CV-A16)have been regarded as the major pathogenic agents of HFMD;however,since an outbreak caused by coxsackievirus A6(CV-A6)in France in 2008,CV-A6 has gradually become the predominant pathogen in many regions.CV-A6 infects not only children but also adults,and causes atypical clinical symptoms such as a more generalized rash,eczema herpeticum,high fever,and onychomadesis,which are different from the symptoms associated with EV-A71 and CV-A16.Importantly,the rate of genetic recombination of CV-A6 is high,which can lead to changes in virulence and the rapid evolution of other characteristics,thus posing a serious threat to public health.To date,no specific vaccines or therapeutics have been approved for CV-A6 prevention or treatment,hence it is essential to fully understand the relationship between recombination and evolution of this virus.Here,we systematically review the genetic recombination events of CV-A6 that have occurred worldwide and explore how these events have promoted virus evolution,thus providing important information regarding future HFMD surveillance and prevention.展开更多
Circular single-stranded DNA(ssDNA)viruses have been rarely found in fungi,and the evolutionary and ecological relationships among ssDNA viruses infecting fungi and other organisms remain unclear.In this study,a novel...Circular single-stranded DNA(ssDNA)viruses have been rarely found in fungi,and the evolutionary and ecological relationships among ssDNA viruses infecting fungi and other organisms remain unclear.In this study,a novel circular ssDNA virus,tentatively named Diaporthe sojae circular DNA virus 1(DsCDV1),was identified in the phytopathogenic fungus Diaporthe sojae isolated from pear trees.DsCDV1 has a monopartite genome(3185 nt in size)encapsidated in isometric virions(21-26 nm in diameter).The genome comprises seven putative open reading frames encoding a discrete replicase(Rep)split by an intergenic region,a putative capsid protein(CP),several proteins of unknown function(P1-P4),and a long intergenic region.Notably,the two split parts of DsCDV1 Rep share high identities with the Reps of Geminiviridae and Genomoviridae,respectively,indicating an evolutionary linkage with both families.Phylogenetic analysis based on Rep or CP sequences placed DsCDV1 in a unique cluster,supporting the establishment of a new family,tentatively named Gegemycoviridae,intermediate to both families.DsCDV1 significantly attenuates fungal growth and nearly erases fungal virulence when transfected into the host fungus.Remarkably,DsCDV1 can systematically infect tobacco and pear seedlings,providing broad-spectrum resistance to fungal diseases.Subcellular localization analysis revealed that DsCDV1 P3 is systematically localized in the plasmodesmata,while its expression in trans-complementation experiments could restore systematic infection of a movement-deficient plant virus,suggesting that P3 is a movement protein.DsCDV1 exhibits unique molecular and biological traits not observed in other ssDNA viruses,serving as a link between fungal and plant ssDNA viruses and presenting an evolutionary connection between ssDNA viruses and fungi.These findings contribute to expanding our understanding of ssDNA virus diversity and evolution,offering potential biocontrol applications for managing crucial plant diseases.展开更多
Plant Dicer-like(DCL)and Argonaute(AGO)are the key enzymes involved in anti-virus post-transcriptional gene silencing(AV-PTGS).Here we show that AV-PTGS exhibited nucleotide preference by calculating a relative AV-PTG...Plant Dicer-like(DCL)and Argonaute(AGO)are the key enzymes involved in anti-virus post-transcriptional gene silencing(AV-PTGS).Here we show that AV-PTGS exhibited nucleotide preference by calculating a relative AV-PTGS efficiency on processing viral RNA substrates.In comparison with genome sequences of dicot-infecting Turnip mosaic virus(TuMV)and monocot-infecting Cocksfoot streak virus(CSV),viral-derived small interfering RNAs(vsiRNAs)displayed positive correlations between AV-PTGS efficiency and G+C content(GC%).Further investigations on nucleotide contents revealed that the vsiRNA populations had G-biases.This finding was further supported by our analyses of previously reported vsiRNA populations in diverse plant-virus associations,and AGO associated Arabidopsis endogenous siRNA populations,indicating that plant AGOs operated with G-preference.We further propose a hypothesis that AV-PTGS imposes selection pressure(s)on the evolution of plant viruses.This hypothesis was supported when potyvirus genomes were analysed for evidence of GC elimination,suggesting that plant virus evolution to have low GC%genomes would have a unique function,which is to reduce the host AV-PTGS attack during infections.展开更多
基金Natural science foundation of Inner Mongolia(2024LHMS06018)The basic scientific research funding for directly affiliated universities in the Inner Mongolia(JY20250094)。
文摘A complex system is inherently high-dimensional.Recent studies indicate that,even without complete knowledge of its evolutionary dynamics,the future behavior of such a system can be predicted using time-series data(data-driven prediction).This suggests that the essential dynamics of a complex system can be captured through a low-dimensional representation.Virus evolution and climate change are two examples of complex,time-varying systems.In this article,we show that mutations in the spike protein provide valuable data for predicting SARS-CoV-2 variants,forecasting the possible emergence of the new macro-lineage Q in the near future.Our analysis also demonstrates that carbon dioxide concentration is a reliable indicator for predicting the evolution of the climate system,extending global surface air temperature(GSAT)forecasts through 2500.
基金supported by the 3-year Public Health Program of the Shanghai Municipal Health Commission[grant number GWVI-11.1-10(GC)]the National Key Research and Development Program of China[grant number 2022YFC2602900(GC)]the Shanghai Municipal Health Commission[grant number 2022JC033(GC)].
文摘Mammals are critical reservoirs of human infectious diseases and the spillover of viruses is related to climate conditions.We conducted meta-transcriptomic sequencing of 226 mammals(bats,rodents,hedgehogs,and shrews)representing 20 species collected across eight cities in south China between 2018 and 2024.Samples included internal organs,oropharyngeal and anal swabs,and feces.We identified 63 vertebrate-associated viruses,including 34 novel viruses.Phylogenetic analysis revealed six viruses with potential infection risks to humans or domestic animals due to their close phylogenetic relationships with known pathogens.Cross-species transmission was observed in 14.3%(9/63)of viruses,shared by at least two host species,with bats,particularly Rhinolophus and Hipposideros,serving as key hubs for viral circulation and zoonotic spillover.Virome composition varied substantially among mammalian species and geographic regions(adonis test,R^(2)=0.50,P=0.001).Generalized linear models quantified the roles of host taxonomy,ecotypes,and meteorological factors in shaping viral diversity,demonstrating host taxonomy(at the order level)as a predominant role(25.70%deviance explained),followed by ecotypes(10.27%deviance explained).Phylogenetic analysis conducted using our betacoronavirus sequences,as well as betacoronavirus sequences derived from 2.0×10^(4) bats sampled in China between July 2013 and March 2024,revealed that no betacoronaviruses exhibited closer phylogenetic relationships to SARS-CoV-2 than the known strains(e.g.,RaTG13).These findings provide critical insights into virus evolution,transmission,and ecological determinants,which are essential for the prevention of emerging infectious diseases.
文摘AIM： To investigate the hoLspoLs, direction, and the time course of evolution of hepatitis A virus in the process of consecutive cell culture passage in human KMB17 diploid cells.METHODS： Wild type hepatitis A virus H2w was serially propagated in KMB17 cells until passage 30, and the fulllength genomes of H2w and its six chosen progenies were determined by directly sequencing RT-PCR products amplified from viral genomic RNA. Alignment comparison of sequences from H2w with its six progenies and phylogenetic analysis of the whole VP1 region from H2w, progenies of H2w, and other cell culture adapted hepatitis A virus were then carried out to obtain data on the molecular evolution of hepatitis A virus in the process of consecutive passage in KMB17 cells.RESULTS： Most of the mutations occurred by passage 5 and several hotspots related to adaptation of the virus during cell growth were observed. After that stage, few additional mutations occurred through the remaining duration of passage in KMB17 cells except for mutation in the virulence determinants, which occurred in the vicinity of passage 15. The phylogenetic analysis of the whole VP1 region suggested that the progenies of H2w evolved closely to other cell culture adapted hepatitis A virus, i.e. MBB, L-A-l, other than its progenitor H2w.CONCLUSION： Hepatitis A virus served as a useful model for studying molecular evolution of viruses in a given environment. The information obtained in this study may provide assistance in cultivating the next generation of a seed virus for live hepatitis A vaccine production.
基金supported by a Combination Project of Guangdong Province from Guangdong Provincial Department of Science and Technology, China (Grant No. 2010B091000018)Emergency Response Project of Ministry of Science and Technology of China (Grant No. KJYJ-2013-01-05)+1 种基金the National Science and Technology Major Project of the Ministry of Science and Technology of China (Grant Nos. 2014ZX10004006, 2013ZX09201021 and 2013ZX09304102)the National Key Technology R&D Program of the 12th National Five-year Development Plan (Grant No. 2012BAI05B01)
文摘The H7 subtype avian influenza viruses, including H7N2, HTN3 and HTN7, have posed a public health threat worldwide. Except one H7N7 fatal case in the Netherlands in 2003, the other H7 human cases have resulted in self-limiting conjunc- tivitis or mild upper respiratory illness.
文摘In order to reveal variation and revolution of NP genes of human avian H5 N1 influenza virus strains, the NP gene of a human avian H5 N1 influenza virus strain in Guangdong was sequenced and the global NP genes of strains were retrieved. The sequences were analyzed by DNAStar 5.0, and the evolutionary speed was studied with reference to the epidemiological data. It was found that NP genes of 45 strains during 1997-2006 were homologically classified into three groups： strains in 1997-1998, strains in 2004-2005 and strains from 2003 to 2006. There were 35 substitutions in NPs in all strains accounting for a ratio of 7.03% （35/498）. An additional glycoprotein domain （NGT430-432） was found in NP genes in the strains of 2003-2006, the mutation of N370S in GD-01-06 resulted in occurrence of one more glycoprotein domain （NES368-370）. In the synonymous variation, Ks values in NP were 2.03 × 10^-5-2.55 × 10^-5 Nt/d and K. values in NP were 1.58 × 10^-6-3.10 × 10^-6 Nt/d. There didn＇t exist obviously selective pressure. An additional glycoprotein domain in every strain of 2003-2006 and one more in strain GD-01-06 might change the antigenicity of human avian H5 N1 influenza virus. The variation on human avian H5 N1 influenza strains occurred frequently in the natural world, which would result in high probability of human-human transmission along with the natural evolution of the virus.
基金supported by Jiangsu Provincial Key Research and Development Projects No.BE2017693National Natural Science Foundation of China No.81741062
文摘Diarrhea is the third leading cause of death in developing countries in children under the age of five.About half a million children die of diarrhea every year,most of which in developing countries.Viruses are the main pathogen of diarrhea.In China,the fecal virome of children with diarrhea has been rarely studied.Using an unbiased viral metagenomics approach,we analyzed the fecal virome in children with diarrhea.Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae,Astroviridae,Caliciviridae,Parvoviridae,Picornaviridae,and Reoviridae.Among them,the family of Caliciviridae accounts for the largest proportion of 78.42%,following with Adenoviridae(8.94%)and Picornaviridae(8.36%).In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea,the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus.This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area.
基金supported by the National Key Research and Development Program of China(Grant No.2019YFC1604602-1)the Natural Science Foundation of Hebei Province(Grant No.19226631D).
文摘Mink enteritis virus(MEV),a member of the Protoparvovirus genus within the Parvovirinae subfamily,causes severe hemorrhagic enteritis and leukopenia in minks,thus representing a serious economic threat to mink farming.MEV,feline panleukopenia virus(FPV),and canine parvovirus(CPV)are closely related Protoparvovirus members;CPV and FPV infect hosts via binding to transferrin receptor 1(TfR1).However,the structural mechanism of MEV entry remains poorly understood.This study used cryo-electron microscopy(cryo-EM)and structural bioinformatics to determine the structure of MEV virus-like particles at 2.5 A resolution.The analysis revealed that MEV shares a highly conserved capsid architecture with CPV and FPV,particularly in theβ-barrel core and three-fold protrusions.We predict that MEV utilizes mink TfR1 for host entry,similar to CPV and FPV.Structural superposition and sequence alignment identified key residues in the MEV VP2 protein that are critical for mink TfR1 interaction.These findings provide structural and evolutionary insights into MEV host tropism,offering valuable information for efforts to mitigate the zoonotic risks of mammalian parvoviruses.
文摘Hand,foot,and mouth disease(HFMD)is one of the most common class C infectious diseases,posing a seri-ous threat to public health worldwide.Enterovirus A71(EV-A71)and coxsackievirus A16(CV-A16)have been regarded as the major pathogenic agents of HFMD;however,since an outbreak caused by coxsackievirus A6(CV-A6)in France in 2008,CV-A6 has gradually become the predominant pathogen in many regions.CV-A6 infects not only children but also adults,and causes atypical clinical symptoms such as a more generalized rash,eczema herpeticum,high fever,and onychomadesis,which are different from the symptoms associated with EV-A71 and CV-A16.Importantly,the rate of genetic recombination of CV-A6 is high,which can lead to changes in virulence and the rapid evolution of other characteristics,thus posing a serious threat to public health.To date,no specific vaccines or therapeutics have been approved for CV-A6 prevention or treatment,hence it is essential to fully understand the relationship between recombination and evolution of this virus.Here,we systematically review the genetic recombination events of CV-A6 that have occurred worldwide and explore how these events have promoted virus evolution,thus providing important information regarding future HFMD surveillance and prevention.
基金supported by Earmarked Fund for China Agricultural Research System(grant number CARS-28)to G.W.and W.X.the National Natural Science Foundation of China(grant number 32172475)to W.X.
文摘Circular single-stranded DNA(ssDNA)viruses have been rarely found in fungi,and the evolutionary and ecological relationships among ssDNA viruses infecting fungi and other organisms remain unclear.In this study,a novel circular ssDNA virus,tentatively named Diaporthe sojae circular DNA virus 1(DsCDV1),was identified in the phytopathogenic fungus Diaporthe sojae isolated from pear trees.DsCDV1 has a monopartite genome(3185 nt in size)encapsidated in isometric virions(21-26 nm in diameter).The genome comprises seven putative open reading frames encoding a discrete replicase(Rep)split by an intergenic region,a putative capsid protein(CP),several proteins of unknown function(P1-P4),and a long intergenic region.Notably,the two split parts of DsCDV1 Rep share high identities with the Reps of Geminiviridae and Genomoviridae,respectively,indicating an evolutionary linkage with both families.Phylogenetic analysis based on Rep or CP sequences placed DsCDV1 in a unique cluster,supporting the establishment of a new family,tentatively named Gegemycoviridae,intermediate to both families.DsCDV1 significantly attenuates fungal growth and nearly erases fungal virulence when transfected into the host fungus.Remarkably,DsCDV1 can systematically infect tobacco and pear seedlings,providing broad-spectrum resistance to fungal diseases.Subcellular localization analysis revealed that DsCDV1 P3 is systematically localized in the plasmodesmata,while its expression in trans-complementation experiments could restore systematic infection of a movement-deficient plant virus,suggesting that P3 is a movement protein.DsCDV1 exhibits unique molecular and biological traits not observed in other ssDNA viruses,serving as a link between fungal and plant ssDNA viruses and presenting an evolutionary connection between ssDNA viruses and fungi.These findings contribute to expanding our understanding of ssDNA virus diversity and evolution,offering potential biocontrol applications for managing crucial plant diseases.
基金supported by the Vietnamese Studentship to TH(Ministry of Education and Training,Decision No 322/QD-TTg)NERC(UK)grants to TD(NER/A/S/2003/00547)+1 种基金HW(NER/A/S/2003/00548,NE/E008933/1)CEH Biodiversity research fund to HW(C02875).
文摘Plant Dicer-like(DCL)and Argonaute(AGO)are the key enzymes involved in anti-virus post-transcriptional gene silencing(AV-PTGS).Here we show that AV-PTGS exhibited nucleotide preference by calculating a relative AV-PTGS efficiency on processing viral RNA substrates.In comparison with genome sequences of dicot-infecting Turnip mosaic virus(TuMV)and monocot-infecting Cocksfoot streak virus(CSV),viral-derived small interfering RNAs(vsiRNAs)displayed positive correlations between AV-PTGS efficiency and G+C content(GC%).Further investigations on nucleotide contents revealed that the vsiRNA populations had G-biases.This finding was further supported by our analyses of previously reported vsiRNA populations in diverse plant-virus associations,and AGO associated Arabidopsis endogenous siRNA populations,indicating that plant AGOs operated with G-preference.We further propose a hypothesis that AV-PTGS imposes selection pressure(s)on the evolution of plant viruses.This hypothesis was supported when potyvirus genomes were analysed for evidence of GC elimination,suggesting that plant virus evolution to have low GC%genomes would have a unique function,which is to reduce the host AV-PTGS attack during infections.
