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Eric Delwart - One of the best experts on this subject based on the ideXlab platform.
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Rights Creative Commons: Attribution 3.0 Hong Kong License The Viruses of Wild Pigeon Droppings
2016Co-Authors: Tung Gia Phan, Xutao Deng, Chunling Wang, Leo L. M. Poon, Eric DelwartAbstract:Birds are frequent sources of emerging human infectious diseases. Viral particles were enriched from the feces of 51 wild urban pigeons (Columba livia) from Hong Kong and Hungary, their nucleic acids randomly amplified and then sequenced. We identified sequences from known and novel species from the viral families Circoviridae, Parvoviridae, Picornaviridae, Reoviridae, Adenovirus, Astroviridae, and Caliciviridae (listed in decreasing number of reads), as well as plant and insect viruses likely originating from consumed food. The near full genome of a new species of a proposed parvovirus genus provisionally called Aviparvovirus contained an unusually long middle ORF showing weak similarity to an ORF of unknown function from a fowl adenovirus. Picornaviruses found in both Asia and Europe that are distantly related to the turkey megrivirus and contained a highly divergent 2A1 region were named mesiviruses. All eleven segments of a novel rotavirus subgroup related to a chicken rotavirus in group G were sequenced and phylogenetically analyzed. This study provides an initia
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The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses.
PloS one, 2015Co-Authors: Piyada Linsuwanon, Xutao Deng, Yong Poovorawan, Sompong Vongpunsawad, Eric DelwartAbstract:Hand, foot, and mouth disease (HFMD) affects infant and young children. A viral metagenomic approach was used to identify the eukaryotic viruses in fecal samples from 29 Thai children with clinical diagnosis of HFMD collected during the 2012 outbreak. These children had previously tested negative by PCR for enterovirus 71 and coxsackievirus A16 and A6. Deep sequencing revealed nine virus families: Picornaviridae, Astroviridae, Parvoviridae, Caliciviridae, Paramyxoviridae, Adenoviridae, Reoviridae, Picobirnaviridae, and Polyomaviridae. The highest number of viral sequences belonged to human rhinovirus C, astrovirus-MLB2, and coxsackievirus A21. Our study provides an overview of virus community and highlights a broad diversity of viruses found in feces from children with HFMD.
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Faecal virome of cats in an animal shelter.
The Journal of general virology, 2014Co-Authors: Wen Zhang, Beatrix Kapusinszky, Patricia A Pesavento, Linlin Li, Xutao Deng, Eric DelwartAbstract:We describe the metagenomics-derived feline enteric virome in the faeces of 25 cats from a single shelter in California. More than 90 % of the recognizable viral reads were related to mammalian viruses and the rest to bacterial viruses. Eight viral families were detected: Astroviridae, Coronaviridae, Parvoviridae, Circoviridae, Herpesviridae, Anelloviridae, Caliciviridae and Picobirnaviridae. Six previously known viruses were also identified: feline coronavirus type 1, felid herpes 1, feline calicivirus, feline norovirus, feline panleukopenia virus and picobirnavirus. Novel species of astroviruses and bocaviruses, and the first genome of a cyclovirus in a feline were characterized. The RNA-dependent RNA polymerase region from four highly divergent partial viral genomes in the order Picornavirales were sequenced. The detection of such a diverse collection of viruses shed within a single shelter suggested that such animals experience robust viral exposures. This study increases our understanding of the viral diversity in cats, facilitating future evaluation of their pathogenic and zoonotic potentials.
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The Viruses of Wild Pigeon Droppings
PloS one, 2013Co-Authors: Tung Gia Phan, Akos Boros, Gábor Reuter, Péter Pankovics, Xutao Deng, Chunling Wang, Leo L. M. Poon, Eric DelwartAbstract:Birds are frequent sources of emerging human infectious diseases. Viral particles were enriched from the feces of 51 wild urban pigeons (Columba livia) from Hong Kong and Hungary, their nucleic acids randomly amplified and then sequenced. We identified sequences from known and novel species from the viral families Circoviridae, Parvoviridae, Picornaviridae, Reoviridae, Adenovirus, Astroviridae, and Caliciviridae (listed in decreasing number of reads), as well as plant and insect viruses likely originating from consumed food. The near full genome of a new species of a proposed parvovirus genus provisionally called Aviparvovirus contained an unusually long middle ORF showing weak similarity to an ORF of unknown function from a fowl adenovirus. Picornaviruses found in both Asia and Europe that are distantly related to the turkey megrivirus and contained a highly divergent 2A1 region were named mesiviruses. All eleven segments of a novel rotavirus subgroup related to a chicken rotavirus in group G were sequenced and phylogenetically analyzed. This study provides an initial assessment of the enteric virome in the droppings of pigeons, a feral urban species with frequent human contact.
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The Viruses of Wild Pigeon Droppings
2013Co-Authors: Tung Gia Phan, Xutao Deng, Chunling Wang, Leo L. M. Poon, Eric DelwartAbstract:Birds are frequent sources of emerging human infectious diseases. Viral particles were enriched from the feces of 51 wild urban pigeons (Columba livia) from Hong Kong and Hungary, their nucleic acids randomly amplified and then sequenced. We identified sequences from known and novel species from the viral families Circoviridae, Parvoviridae, Picornaviridae, Reoviridae, Adenovirus, Astroviridae, and Caliciviridae (listed in decreasing number of reads), as well as plant and insect viruses likely originating from consumed food. The near full genome of a new species of a proposed parvovirus genus provisionally called Aviparvovirus contained an unusually long middle ORF showing weak similarity to an ORF of unknown function from a fowl adenovirus. Picornaviruses found in both Asia and Europe that are distantly related to the turkey megrivirus and contained a highly divergent 2A1 region were named mesiviruses. All eleven segments of a novel rotavirus subgroup related to a chicken rotavirus in group G were sequenced and phylogenetically analyzed. This study provides an initia
Xutao Deng - One of the best experts on this subject based on the ideXlab platform.
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Viral metagenomics reveals significant viruses in the genital tract of apparently healthy dairy cows.
Archives of virology, 2019Co-Authors: Yu Ling, Xiaodan Zhang, Shixing Yang, Li Jingjiao, Quan Shen, Xiaochun Wang, Li Cui, Xiuguo Hua, Xutao DengAbstract:The virome in genital tract secretion samples collected from 80 dairy cattle in Shanghai, China, was characterized. Viruses detected included members of the families Papillomaviridae, Polyomaviridae, Hepeviridae, Parvoviridae, Astroviridae, Picornaviridae, and Picobirnaviridae. A member of a new species within the genus Dyoxipapillomavirus and six circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viral genomes were fully sequenced and phylogenetically analyzed. The prevalence of bovine polyomaviruses 1 and 2 was measured by PCR to be 10% (8/80) and 6.25% (5/80), respectively. PCR screening also indicated that the novel papillomavirus ujs-21015 and bovine herpesvirus 6 were present in three and two out of the 80 samples, respectively.
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Rights Creative Commons: Attribution 3.0 Hong Kong License The Viruses of Wild Pigeon Droppings
2016Co-Authors: Tung Gia Phan, Xutao Deng, Chunling Wang, Leo L. M. Poon, Eric DelwartAbstract:Birds are frequent sources of emerging human infectious diseases. Viral particles were enriched from the feces of 51 wild urban pigeons (Columba livia) from Hong Kong and Hungary, their nucleic acids randomly amplified and then sequenced. We identified sequences from known and novel species from the viral families Circoviridae, Parvoviridae, Picornaviridae, Reoviridae, Adenovirus, Astroviridae, and Caliciviridae (listed in decreasing number of reads), as well as plant and insect viruses likely originating from consumed food. The near full genome of a new species of a proposed parvovirus genus provisionally called Aviparvovirus contained an unusually long middle ORF showing weak similarity to an ORF of unknown function from a fowl adenovirus. Picornaviruses found in both Asia and Europe that are distantly related to the turkey megrivirus and contained a highly divergent 2A1 region were named mesiviruses. All eleven segments of a novel rotavirus subgroup related to a chicken rotavirus in group G were sequenced and phylogenetically analyzed. This study provides an initia
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RESEARCH ARTICLE The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for
2016Co-Authors: Pathogenic Enteroviruses, Xutao Deng, Piyada Linsuwanon, Yong Poovorawan, Sompong Vongpunsawad EricAbstract:Hand, foot, and mouth disease (HFMD) affects infant and young children. A viral metage-nomic approach was used to identify the eukaryotic viruses in fecal samples from 29 Thai children with clinical diagnosis of HFMD collected during the 2012 outbreak. These children had previously tested negative by PCR for enterovirus 71 and coxsackievirus A16 and A6. Deep sequencing revealed nine virus families: Picornaviridae, Astroviridae, Parvoviridae, Caliciviridae, Paramyxoviridae, Adenoviridae, Reoviridae, Picobirnaviridae, and Polyomavir-idae. The highest number of viral sequences belonged to human rhinovirus C, astrovirus-MLB2, and coxsackievirus A21. Our study provides an overview of virus community and highlights a broad diversity of viruses found in feces from children with HFMD
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The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses.
PloS one, 2015Co-Authors: Piyada Linsuwanon, Xutao Deng, Yong Poovorawan, Sompong Vongpunsawad, Eric DelwartAbstract:Hand, foot, and mouth disease (HFMD) affects infant and young children. A viral metagenomic approach was used to identify the eukaryotic viruses in fecal samples from 29 Thai children with clinical diagnosis of HFMD collected during the 2012 outbreak. These children had previously tested negative by PCR for enterovirus 71 and coxsackievirus A16 and A6. Deep sequencing revealed nine virus families: Picornaviridae, Astroviridae, Parvoviridae, Caliciviridae, Paramyxoviridae, Adenoviridae, Reoviridae, Picobirnaviridae, and Polyomaviridae. The highest number of viral sequences belonged to human rhinovirus C, astrovirus-MLB2, and coxsackievirus A21. Our study provides an overview of virus community and highlights a broad diversity of viruses found in feces from children with HFMD.
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Faecal virome of cats in an animal shelter.
The Journal of general virology, 2014Co-Authors: Wen Zhang, Beatrix Kapusinszky, Patricia A Pesavento, Linlin Li, Xutao Deng, Eric DelwartAbstract:We describe the metagenomics-derived feline enteric virome in the faeces of 25 cats from a single shelter in California. More than 90 % of the recognizable viral reads were related to mammalian viruses and the rest to bacterial viruses. Eight viral families were detected: Astroviridae, Coronaviridae, Parvoviridae, Circoviridae, Herpesviridae, Anelloviridae, Caliciviridae and Picobirnaviridae. Six previously known viruses were also identified: feline coronavirus type 1, felid herpes 1, feline calicivirus, feline norovirus, feline panleukopenia virus and picobirnavirus. Novel species of astroviruses and bocaviruses, and the first genome of a cyclovirus in a feline were characterized. The RNA-dependent RNA polymerase region from four highly divergent partial viral genomes in the order Picornavirales were sequenced. The detection of such a diverse collection of viruses shed within a single shelter suggested that such animals experience robust viral exposures. This study increases our understanding of the viral diversity in cats, facilitating future evaluation of their pathogenic and zoonotic potentials.
Xiuguo Hua - One of the best experts on this subject based on the ideXlab platform.
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Viral metagenomics reveals significant viruses in the genital tract of apparently healthy dairy cows.
Archives of virology, 2019Co-Authors: Yu Ling, Xiaodan Zhang, Shixing Yang, Li Jingjiao, Quan Shen, Xiaochun Wang, Li Cui, Xiuguo Hua, Xutao DengAbstract:The virome in genital tract secretion samples collected from 80 dairy cattle in Shanghai, China, was characterized. Viruses detected included members of the families Papillomaviridae, Polyomaviridae, Hepeviridae, Parvoviridae, Astroviridae, Picornaviridae, and Picobirnaviridae. A member of a new species within the genus Dyoxipapillomavirus and six circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viral genomes were fully sequenced and phylogenetically analyzed. The prevalence of bovine polyomaviruses 1 and 2 was measured by PCR to be 10% (8/80) and 6.25% (5/80), respectively. PCR screening also indicated that the novel papillomavirus ujs-21015 and bovine herpesvirus 6 were present in three and two out of the 80 samples, respectively.
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Molecular characterization of a porcine astrovirus strain in China
Archives of virology, 2011Co-Authors: Daoliang Lan, Li Cui, Congli Yuan, Tongling Shan, Zhibiao Yang, Xiuguo HuaAbstract:Pigs are increasingly recognized to harbor a wide range of viruses that apparently establish long-term persistence in these animals. They serve as reservoirs for a number of human zoonotic diseases. In this study, a porcine astrovirus (PAstV) strain, designated as PAstV JWH-1, is identified from a diarrheal pig in China, and it is partially characterized genetically. Sequence analysis shows that the PAstV JWH-1 strain contains divergent nucleotide sequences in both the open reading frame (ORF)1b/ORF2 consensus and the 3′-UTR regions (s2m motif), which are usually highly conserved among members of the family Astroviridae. Phylogenetic analysis indicates that the JWH-1 strain clusters closely with newly identified strains PAstV 12-4 and 14-4 and forms a group of mamastroviruses with the proposed novel deer astrovirus. Further recombination analysis shows that two possible interspecies recombination events between porcine and deer astroviruses occurred in the genome of the JWH-1 strain. This study further confirms that multiple lineages are present among PAstVs, and each lineage likely represents an independent origin. Additionally, the possibility of interspecies transmission among PAstVs is also suggested.
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Complete sequence and genetic characterization of pigeon avian nephritis virus, a member of the family Astroviridae.
Archives of virology, 2011Co-Authors: W. Zhao, Li Cui, A. L. Zhu, Congli Yuan, Caixia Zhu, Z. B. Yang, Xiuguo HuaAbstract:In the current study, the complete genome sequence of a member of the family Astroviridae isolated from pigeons was determined through genetic characterization and phylogeny analysis. The isolated genome sequence was proposed to be that of pigeon avian nephritis virus (ANV), whose genome structure and characteristics were similar to previously reported avian astroviruses. The sequenced ssRNA genome comprises 6928 nucleotides, excluding the poly(A) tail, and contains three open reading frames. Phylogenetic analysis using a partial nucleotide sequence of the polymerase gene and the entire amino acid sequence of the full-length capsid protein revealed that pigeon avian nephritis virus is closely related to the previously published ANV, especially to the Japanese G-4260 and Chinese strains. This investigation provides information on the sequence and genetic characteristics of this virus and contributes to a better understanding of pigeon ANV and the possible occurrence of astrovirus transmission between chickens and pigeons.
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Sequence Analyses of the Representative Chinese-Prevalent Strain of Avian Nephritis Virus in Healthy Chicken Flocks
Avian diseases, 2011Co-Authors: W. Zhao, Li Cui, Xiuguo Hua, A. L. Zhu, Congli Yuan, Caixia Zhu, Tongling Shan, Xiaoyan Dai, Z. B. YangAbstract:SUMMARY. Avian nephritis virus (ANV), which belongs to the Astroviridae family, has been associated with acute nephritis in chickens. Cases of ANV infection have been recorded in Japan and in several European countries. However, related studies have never been performed in China. Thus, this study isolated ANV in Chinese chicken flocks. ANV RNA was detected by reverse transcription–PCR in stool samples collected from healthy layer chickens in the Sichuan Province of China in 2009. Of the 192 stool specimens collected, 32.3% (62/192) were positive for ANV infection. The whole genome of ANV-Sichuan54, the first representative Chinese strain, was 6941 nucleotides in length, including the 5′ untranslated region, three open reading frames (ORFs), a 3′ UTR, and a poly-(A) tail. Comparative and phylogenetic analyses based on partial RNA-dependent RNA polymerase (ORF1b) demonstrated that the majority of ANV investigations were more closely related to the U.S. ANV strain (DQ324827–324836) than to the G-4260 (AB033998).
Ben Berkhout - One of the best experts on this subject based on the ideXlab platform.
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Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function
Virology journal, 2007Co-Authors: Formijn J. Van Hemert, Vladimir V Lukashov, Ben BerkhoutAbstract:Background Complete genome sequences of the Astroviridae include human, non-human mammalian and avian species. A consensus topology of astroviruses has been derived from nucleotide substitutions in the full-length genomes and from non-synonymous nucleotide substitutions in each of the three ORFs. Analyses of synonymous substitutions displayed a loss of tree structure, suggesting either saturation of the substitution model or a deviant pattern of synonymous substitutions in certain virus species.
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Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function
Virology Journal, 2007Co-Authors: Formijn J. Van Hemert, Vladimir V Lukashov, Ben BerkhoutAbstract:Background Complete genome sequences of the Astroviridae include human, non-human mammalian and avian species. A consensus topology of astroviruses has been derived from nucleotide substitutions in the full-length genomes and from non-synonymous nucleotide substitutions in each of the three ORFs. Analyses of synonymous substitutions displayed a loss of tree structure, suggesting either saturation of the substitution model or a deviant pattern of synonymous substitutions in certain virus species. Results We analyzed the complete Astroviridae family for the inference of adaptive molecular evolution at sites and in branches. High rates of synonymous mutations are observed among the non-human virus species. Deviant patterns of synonymous substitutions are found in the capsid structural genes. Purifying selection is a dominant force among all astrovirus genes and only few codon sites showed values for the dN/dS ratio that may indicate site-specific molecular adaptation during virus evolution. One of these sites is the glycine residue of a RGD motif in ORF2 of human astrovirus serotype 1. RGD or similar integrin recognition motifs are present in nearly all astrovirus species. Conclusion Phylogenetic analysis directed by maximum likelihood approximation allows the inclusion of significantly more evolutionary history and thereby, improves the estimation of dN and dS. Sites with enhanced values for dN/dS are prominent at domains in charge of environmental communication (f.i. VP27 and domain 4 in ORF1a) more than at domains dedicated to intrinsic virus functions (f.i. VP34 and ORF1b (the virus polymerase)). Integrin recognition may play a key role in astrovirus to target cell attachment.
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Host-related nucleotide composition and codon usage as driving forces in the recent evolution of the Astroviridae
Virology, 2006Co-Authors: Formijn J. Van Hemert, Ben Berkhout, Vladimir V LukashovAbstract:The evolutionary history of the Astroviridae comprises the ancient separation between avian and mammalian astrovirus lineages followed by diversification among mammalian astroviruses. The latter process included several cross-species transmissions. We found that the recent, but not the ancient, evolution of astroviruses was associated with a switch in nucleotide composition and codon usage among non-human mammalian versus human/avian astroviruses. Virus and hosts phylogenies based on codon usage agreed with each other and matched the hosts' evolutionary emergence order. This recent switch in driving forces acting at the synonymous level points to the adaptation of codon usage by viruses to that of their hosts after cross-species transmissions. This is the first demonstration of nucleotide composition and codon usage being active driving forces during the recent evolutionary history of a virus group in the host-parasite system.
Edward C. Holmes - One of the best experts on this subject based on the ideXlab platform.
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Virome heterogeneity and connectivity in waterfowl and shorebird communities
The ISME Journal, 2019Co-Authors: Michelle Wille, Marcel Klaassen, Aeron C. Hurt, Edward C. HolmesAbstract:Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses ( Picobirnaviridae and Reoviridae ), single-stranded RNA viruses ( Astroviridae , Caliciviridae , Picornaviridae ), a retro-transcribing DNA virus ( Hepadnaviridae ), and a single-stranded DNA virus ( Parvoviridae ). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity (host sharing) and heterogeneity (host specificity). Virome connectivity was apparent in two well described multi-host virus species -avian coronavirus and influenza A virus- and a novel Rotavirus species that were shared among some Anseriform species, while virome heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes, as well as differences in viral abundance and alpha diversity among species. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.
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Virome heterogeneity and connectivity in waterfowl and shorebird communities
2019Co-Authors: Michelle Wille, Marcel Klaassen, Aeron C. Hurt, Mang Shi, Edward C. HolmesAbstract:Abstract Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses (Picobirnaviridae and Reoviridae), single-stranded RNA viruses (Astroviridae, Caliciviridae, Picornaviridae), a retro-transcribing DNA virus (Hepadnaviridae), and a single-stranded DNA virus (Parvoviridae). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity and heterogeneity. Virome connectivity was apparent in two well described multi-host virus species (avian coronavirus and influenza A virus) and a novel Rotavirus species that were shared among some Anseriform species, while heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes. Notably, within avian host families there was no significant relationship between either host taxonomy or foraging ecology and virome composition, although Anseriform species positive for influenza A virus harboured more additional viruses than those negative for influenza virus. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.
