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Six foals with interstitial pneumonia of undetermined etiology from Southern California were analyzed by viral metagenomics. Spleen, lung, and colon content samples obtained during necropsy from each animal were pooled, and nucleic acids from virus-like particles enriched for deep sequencing. The recently described equine copiparvovirus named eqcopivirus, as well as three previously uncharacterized viruses, were identified. The complete ORFs genomes of two closely related protoparvoviruses, and of a bocaparvovirus, plus the partial genome of a picornavirus were assembled. The parvoviruses were classified as members of new ungulate protoparvovirus and bocaparvovirus species in the Parvoviridae family. The picornavirus was classified as a new species in the Salivirus genus of the Picornaviridae family. Spleen, lung, and colon content samples from each foal were then tested for these viral genomes by nested PCR and RT-PCR. When present, parvoviruses were detected in both feces and spleen. The picornavirus, protoparvovirus, and eqcopivirus genomes were detected in the lungs of one animal each. Three foals were co-infected with the picornavirus and either a protoparvovirus, bocaparvovirus, or eqcopivirus. Two other foals were infected with a protoparvovirus only. No viral infection was detected in one animal. The complete ORFs of the first equine protoparvoviruses and bocaparvovirus, the partial ORF of the third equine picornavirus, and their detection in tissues of foals with interstitial pneumonia are described here. Testing the involvement of these viruses in fatal interstitial pneumonia or other equine diseases will require larger epidemiological and/or inoculation studies.
Eda Altan; Alvin Hui; Yanpeng Li; Patricia Pesavento; Javier Asín; Beate Crossley; Xutao Deng; Francisco A. Uzal; Eric Delwart. New Parvoviruses and Picornavirus in Tissues and Feces of Foals with Interstitial Pneumonia. Viruses 2021, 13, 1612 .
AMA StyleEda Altan, Alvin Hui, Yanpeng Li, Patricia Pesavento, Javier Asín, Beate Crossley, Xutao Deng, Francisco A. Uzal, Eric Delwart. New Parvoviruses and Picornavirus in Tissues and Feces of Foals with Interstitial Pneumonia. Viruses. 2021; 13 (8):1612.
Chicago/Turabian StyleEda Altan; Alvin Hui; Yanpeng Li; Patricia Pesavento; Javier Asín; Beate Crossley; Xutao Deng; Francisco A. Uzal; Eric Delwart. 2021. "New Parvoviruses and Picornavirus in Tissues and Feces of Foals with Interstitial Pneumonia." Viruses 13, no. 8: 1612.
While recent changes in treatment have reduced the lethality of idiopathic chronic diarrhea (ICD), this condition remains one of the most common causes of rhesus macaque deaths in non-human primate research centers. We compared the eukaryotic viromes in fecal swabs from 52 animals with ICD and 41 healthy animals. Viral metagenomics targeting virus-like particles was used to identify viruses shed by each animal. Five viruses belonging to the Picornaviridae, one to the Caliciviridae, one to the Parvoviridae, and one to the Adenoviridae families were identified. The fraction of reads matching each viral species was then used to estimate and compare viral loads in ICD cases versus healthy controls. None of the eukaryotic viruses detected in fecal swabs were strongly associated with ICD. Other potential causes of ICD are discussed.
Eric Delwart; Michael J. Tisza; Eda Altan; Yanpeng Li; Xutao Deng; J. Dennis Hartigan-O'Connor; Amir Ardeshir. Idiopathic chronic diarrhea in rhesus macaques is not associated with enteric viral infections. 2021, 1 .
AMA StyleEric Delwart, Michael J. Tisza, Eda Altan, Yanpeng Li, Xutao Deng, J. Dennis Hartigan-O'Connor, Amir Ardeshir. Idiopathic chronic diarrhea in rhesus macaques is not associated with enteric viral infections. . 2021; ():1.
Chicago/Turabian StyleEric Delwart; Michael J. Tisza; Eda Altan; Yanpeng Li; Xutao Deng; J. Dennis Hartigan-O'Connor; Amir Ardeshir. 2021. "Idiopathic chronic diarrhea in rhesus macaques is not associated with enteric viral infections." , no. : 1.
Idiopathic chronic diarrhea (ICD) is a common clinical condition in captive rhesus macaques, claiming 33% of medical culls (i.e. deaths unrelated to research). Using viral metagenomics we characterized the eukaryotic virome in digestive tract tissues collected at necropsy from nine animals with ICD. We show the presence of multiple viruses in the Parvoviridae and Picornaviridae family. We then compared the distribution of viral reads in the stomach, duodenum, jejunum, ileum, and the proximal, transverse, and distal colons. Tissues and mucosal scraping from the same locations showed closely related results while different gut tissues from the same animal varied widely. Picornavirus reads were generally more abundant in the lower digestive tract, particularly in the descending (distal) colon. Parvoviruses were more abundant in the upper reach particularly in the stomach. In situ hydridization (ISH) of fixed tissues showed punctuated staining for both these RNA and DNA viruses in the distal colon. Parvovirus ISH staining was also detected in the stomach/duodenum/jejunum in distinct oval-shaped structures. Therefore, the location of enteric viral nucleic acid differed widely between different viral families and along the length of the digestive tract.
Eric Delwart; David Merriam; Amir Ardeshir; Eda Altan; Yanpeng Li; Xutao Deng; J. Dennis Hartigan-O’Connor. Enteric viruses nucleic acids distribution along the digestive tract of rhesus macaques with idiopathic chronic diarrhea. 2021, 1 .
AMA StyleEric Delwart, David Merriam, Amir Ardeshir, Eda Altan, Yanpeng Li, Xutao Deng, J. Dennis Hartigan-O’Connor. Enteric viruses nucleic acids distribution along the digestive tract of rhesus macaques with idiopathic chronic diarrhea. . 2021; ():1.
Chicago/Turabian StyleEric Delwart; David Merriam; Amir Ardeshir; Eda Altan; Yanpeng Li; Xutao Deng; J. Dennis Hartigan-O’Connor. 2021. "Enteric viruses nucleic acids distribution along the digestive tract of rhesus macaques with idiopathic chronic diarrhea." , no. : 1.
Squash mosaic virus (SqMV) is a phytovirus that infects great diversity of plants worldwide. In Brazil, the SqMV has been identified in the states of Ceará, Maranhão, Piauí, Rio Grande do Norte, and Tocantins. The presence of non-pathogenic viruses in animals, such as phytoviruses, may not be completely risk-free. Similarities in gene repertories between these viruses and viruses that affect animal species have been reported. The present study describes the fully sequenced genomes of SqMV found in human feces, collected in Tocantins, and analyzes the viral profile by metagenomics in the context of diarrhea symptomatology. The complete SqMV genome was obtained in 39 of 253 analyzed samples (15.5%); 97.4% of them belonged to children under 5 years old. There was no evidence that the observed symptoms were related to the presence of SqMV. Of the different virus species detected in these fecal samples, at least 4 (rotavirus, sapovirus, norovirus, parechovirus) are widely known to cause gastrointestinal symptoms. The presence of SqMV nucleic acid in fecal samples is likely due to recent dietary consumption and it is not evidence of viral replication in the human intestinal cells. Identifying the presence of SqMV in human feces and characterization of its genome is a relevant precursor to determining whether and how plant viruses interact with host cells or microorganisms in the human gastrointestinal tract.
Fabiola Villanova; Roberta Marcatti; Mayara Bertanhe; Vanessa Morais; Flavio Milagres; Rafael Brustulin; Emerson Araújo; Roozbeh Tahmasebi; Steven Witkin; Xutao Deng; Eric Delwart; Ester Sabino; Cassio Abreu-Junior; Élcio Leal; Antonio Costa. New Variants of Squash Mosaic Viruses Detected in Human Fecal Samples. Microorganisms 2021, 9, 1349 .
AMA StyleFabiola Villanova, Roberta Marcatti, Mayara Bertanhe, Vanessa Morais, Flavio Milagres, Rafael Brustulin, Emerson Araújo, Roozbeh Tahmasebi, Steven Witkin, Xutao Deng, Eric Delwart, Ester Sabino, Cassio Abreu-Junior, Élcio Leal, Antonio Costa. New Variants of Squash Mosaic Viruses Detected in Human Fecal Samples. Microorganisms. 2021; 9 (7):1349.
Chicago/Turabian StyleFabiola Villanova; Roberta Marcatti; Mayara Bertanhe; Vanessa Morais; Flavio Milagres; Rafael Brustulin; Emerson Araújo; Roozbeh Tahmasebi; Steven Witkin; Xutao Deng; Eric Delwart; Ester Sabino; Cassio Abreu-Junior; Élcio Leal; Antonio Costa. 2021. "New Variants of Squash Mosaic Viruses Detected in Human Fecal Samples." Microorganisms 9, no. 7: 1349.
Circoviruses infect vertebrates where they can result in a wide range of disease signs or in asymptomatic infections. Using viral metagenomics we analyzed a pool of five sera from four healthy and one sick horse. Sequences from parvovirus-H, equus anellovirus, and distantly related to mammalian circoviruses were recognized. PCR identified the circovirus reads as originating from a pregnant mare with fever and hepatitis. That horse’s serum was also positive by real time PCR for equine parvovirus H and negative for the flavivirus equine hepacivirus. The complete circular genome of equine circovirus 1 strain Charaf (EqCV1-Charaf) was completed using PCR and Sanger sequencing. EqCV1 replicase showed 73–74% identity to those of their closest relatives, pig circoviruses 1/2, and elk circovirus. The closest capsid proteins were from the same ungulate circoviruses with 62–63% identity. The overall nucleotide identity of 72% to its closest relative indicates that EqCV1 is a new species in the Circovirus genus, the first reported in genus Equus. Whether EqCV1 alone or in co-infections can result in disease and its prevalence in different equine populations will require further studies now facilitated using EqCV1′s genome sequence.
Alvin Hui; Eda Altan; Nathan Slovis; Caitlin Fletcher; Xutao Deng; Eric Delwart. Circovirus in Blood of a Febrile Horse with Hepatitis. Viruses 2021, 13, 944 .
AMA StyleAlvin Hui, Eda Altan, Nathan Slovis, Caitlin Fletcher, Xutao Deng, Eric Delwart. Circovirus in Blood of a Febrile Horse with Hepatitis. Viruses. 2021; 13 (5):944.
Chicago/Turabian StyleAlvin Hui; Eda Altan; Nathan Slovis; Caitlin Fletcher; Xutao Deng; Eric Delwart. 2021. "Circovirus in Blood of a Febrile Horse with Hepatitis." Viruses 13, no. 5: 944.
Dengue virus (DENV) is a mosquito-borne viral pathogen that plagues many tropical-climate nations around the world, including Brazil. Molecular epidemiology is a growing and increasingly invaluable tool for understanding the dispersal, persistence, and diversity of this impactful virus. In this study, plasma samples (n = 824) from individuals with symptoms consistent with an arboviral febrile illness were analyzed to identity the molecular epidemiological dynamics of DENV circulating in the Brazilian state of Amapá. Twelve DENV type 1 (DENV-1) genomes were identified, which were phylogenetically related to the BR4 lineage of genotype V. Phylodynamics analysis suggested that DENV-1 BR-4 was introduced into Amapá around early 2010, possibly from other states in northern Brazil. We also found unique amino acids substitutions in the DENV-1 envelope and NS5 protein sequences in the Amapá isolates. Characterization of the DENV-1 BR-4 sequences highlights the potential of this new lineage to drive outbreaks of dengue in the Amazon region.
Geovani Ribeiro; Danielle Gill; Edcelha Ribeiro; Fred Monteiro; Vanessa Morais; Roberta Marcatti; Marlisson Rego; Emerson Araújo; Steven Witkin; Fabiola Villanova; Xutao Deng; Ester Sabino; Eric Delwart; Élcio Leal; Antonio da Costa. Adaptive Evolution of New Variants of Dengue Virus Serotype 1 Genotype V Circulating in the Brazilian Amazon. Viruses 2021, 13, 689 .
AMA StyleGeovani Ribeiro, Danielle Gill, Edcelha Ribeiro, Fred Monteiro, Vanessa Morais, Roberta Marcatti, Marlisson Rego, Emerson Araújo, Steven Witkin, Fabiola Villanova, Xutao Deng, Ester Sabino, Eric Delwart, Élcio Leal, Antonio da Costa. Adaptive Evolution of New Variants of Dengue Virus Serotype 1 Genotype V Circulating in the Brazilian Amazon. Viruses. 2021; 13 (4):689.
Chicago/Turabian StyleGeovani Ribeiro; Danielle Gill; Edcelha Ribeiro; Fred Monteiro; Vanessa Morais; Roberta Marcatti; Marlisson Rego; Emerson Araújo; Steven Witkin; Fabiola Villanova; Xutao Deng; Ester Sabino; Eric Delwart; Élcio Leal; Antonio da Costa. 2021. "Adaptive Evolution of New Variants of Dengue Virus Serotype 1 Genotype V Circulating in the Brazilian Amazon." Viruses 13, no. 4: 689.
Echoviruses (E) are a diverse group of viruses responsible for various pathological conditions in humans including aseptic meningitis, myocarditis, and acute flaccid paralysis. The detection and identification of echovirus genotypes in clinical samples is challenging due to its high genetic diversity. Here, we report the complete genome sequences of nine echoviruses, obtained by next-generation sequencing of 238 fecal samples from individuals with gastroenteritis in regions of Brazil. Detected viruses were classified into six genotypes: Three E1 sequences (BRA/TO-028, BRA/TO-069 and BRA/TO-236), one E3 (BRA/TO-018), one E11 (BRA/TO-086), one E20 (BRA/TO-016), two E29 (BRA/TO-030 and BRA/TO-193), and one E30 sequence (BRA/TO-032). Phylogenetic analysis indicated that the echoviruses E1 and E29 circulating in Brazil are divergent from strains circulating worldwide. The genotype diversity identified in our study may under-represent the total echovirus diversity in Brazil because of the small sample size and the restricted geographical distribution covered by the survey.
Endrya Do Socorro Fôro Ramos; Ulisses Rosa; Geovani De Oliveira Ribeiro; Fabiola Villanova; Flávio de Pádua Milagres; Rafael Brustulin; Vanessa Dos Santos Morais; Mayara Bertanhe; Roberta Marcatti; Emerson Araújo; Steven Witkin; Eric Delwart; Adriana Luchs; Antonio da Costa; Élcio Leal. High Heterogeneity of Echoviruses in Brazilian Children with Acute Gastroenteritis. Viruses 2021, 13, 595 .
AMA StyleEndrya Do Socorro Fôro Ramos, Ulisses Rosa, Geovani De Oliveira Ribeiro, Fabiola Villanova, Flávio de Pádua Milagres, Rafael Brustulin, Vanessa Dos Santos Morais, Mayara Bertanhe, Roberta Marcatti, Emerson Araújo, Steven Witkin, Eric Delwart, Adriana Luchs, Antonio da Costa, Élcio Leal. High Heterogeneity of Echoviruses in Brazilian Children with Acute Gastroenteritis. Viruses. 2021; 13 (4):595.
Chicago/Turabian StyleEndrya Do Socorro Fôro Ramos; Ulisses Rosa; Geovani De Oliveira Ribeiro; Fabiola Villanova; Flávio de Pádua Milagres; Rafael Brustulin; Vanessa Dos Santos Morais; Mayara Bertanhe; Roberta Marcatti; Emerson Araújo; Steven Witkin; Eric Delwart; Adriana Luchs; Antonio da Costa; Élcio Leal. 2021. "High Heterogeneity of Echoviruses in Brazilian Children with Acute Gastroenteritis." Viruses 13, no. 4: 595.
Redondoviridae is a recently discovered DNA virus family consisting of two species, vientovirus and brisavirus. Here we used PCR amplification and sequencing to characterize redondoviruses in nasal/throat swabs collected longitudinally from a cohort of 58 individuals working with animals in Vietnam. We additionally analyzed samples from animals to which redondovirus DNA-positive participants were exposed. Redondoviruses were detected in approximately 60% of study participants, including 33% (30/91) of samples collected during episodes of acute respiratory disease and in 50% (29/58) of baseline samples (with no respiratory symptoms). Vientovirus (73%; 24/33) was detected more frequently in samples than brisaviruses (27%; 9/33). In the 23 participants with at least 2 redondovirus-positive samples among their longitudinal samples, 10 (43.5%) had identical redondovirus replication-gene sequences detected (sampling duration: 35–132 days). We found no identical redondovirus replication genes in samples from different participants, and no redondoviruses were detected in 53 pooled nasal/throat swabs collected from domestic animals. Phylogenetic analysis described no large-scale geographical clustering between viruses from Vietnam, the US, Spain, and China, indicating that redondoviruses are highly genetically diverse and have a wide geographical distribution. Collectively, our study provides novel insights into the Redondoviridae family in humans, describing a high prevalence, potentially associated with chronic shedding in the respiratory tract with lack of evidence of zoonotic transmission from close animal contacts. The tropism and potential pathogenicity of this viral family remain to be determined.
Nguyen Tu; Xutao Deng; Nguyen Hong; Nguyen Ny; Tran Phuc; Pham Tam; Duong Han; Luu Ha; Guy Thwaites; H. Doorn; Anna-Maija Virtala; Eric Delwart; Stephen Baker; Olli Vapalahti; Le Tan; on behalf of the VIZIONS Consortium. Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission. Viruses 2021, 13, 533 .
AMA StyleNguyen Tu, Xutao Deng, Nguyen Hong, Nguyen Ny, Tran Phuc, Pham Tam, Duong Han, Luu Ha, Guy Thwaites, H. Doorn, Anna-Maija Virtala, Eric Delwart, Stephen Baker, Olli Vapalahti, Le Tan, on behalf of the VIZIONS Consortium. Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission. Viruses. 2021; 13 (4):533.
Chicago/Turabian StyleNguyen Tu; Xutao Deng; Nguyen Hong; Nguyen Ny; Tran Phuc; Pham Tam; Duong Han; Luu Ha; Guy Thwaites; H. Doorn; Anna-Maija Virtala; Eric Delwart; Stephen Baker; Olli Vapalahti; Le Tan; on behalf of the VIZIONS Consortium. 2021. "Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission." Viruses 13, no. 4: 533.
Background Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in which longer contigs, ideally whole chromosomes/genomes, are formed from shorter NGS reads. However, the contigs generated from the de novo assembly are often very fragmented and rarely longer than a few kilo base pairs (kb). Therefore, a time-consuming extension process is routinely performed on the de novo assembled contigs. Results To facilitate this process, we propose a new tool for metagenome contig extension after de novo assembly. ContigExtender employs a novel recursive extending strategy that explores multiple extending paths to achieve highly accurate longer contigs. We demonstrate that ContigExtender outperforms existing tools in synthetic, animal, and human metagenomics datasets. Conclusions A novel software tool ContigExtender has been developed to assist and enhance the performance of metagenome de novo assembly. ContigExtender effectively extends contigs from a variety of sources and can be incorporated in most viral metagenomics analysis pipelines for a wide variety of applications, including pathogen detection and viral discovery.
Zachary Deng; Eric Delwart. ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data. BMC Bioinformatics 2021, 22, 1 -19.
AMA StyleZachary Deng, Eric Delwart. ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data. BMC Bioinformatics. 2021; 22 (1):1-19.
Chicago/Turabian StyleZachary Deng; Eric Delwart. 2021. "ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data." BMC Bioinformatics 22, no. 1: 1-19.
Classical insect-flaviviruses (cISFVs) and dual host-related insect-specific flavivirus (dISFV) are within the major group of insect-specific flavivirus. Remarkably dISFV are evolutionarily related to some of the pathogenic flavivirus, such as Zika and dengue viruses. The Evolutionary relatedness of dISFV to flavivirus allowed us to investigate the evolutionary principle of host adaptation. Additionally, dISFV can be used for the development of flavivirus vaccines and to explore underlying principles of mammalian pathogenicity. Here we describe the genetic characterization of a novel putative dISFV, termed Guapiaçu virus (GUAPV). Distinct strains of GUAPV were isolated from pools of Aedes terrens and Aedes scapularis mosquitoes. Additionally, we also detected viral GUAPV RNA in a plasma sample of an individual febrile from the Amazon region (North of Brazil). Although GUAPV did not replicate in tested mammalian cells, 3′UTR secondary structures duplication and codon usage index were similar to pathogenic flavivirus.
Geovani De Oliveira Ribeiro; Antonio Charlys da Costa; Danielle Elise Gill; Edcelha Soares D’Athaide Ribeiro; Marlisson Octavio da S. Rego; Fred Julio Costa Monteiro; Fabiola Villanova; Juliana Silva Nogueira; Adriana Yurika Maeda; Renato Pereira de Souza; Roozbeh Tahmasebi; Vanessa S. Morais; Ramendra Pati Pandey; V. Samuel Raj; Sirle Abdo Salloum Scandar; Fernanda Gisele da Silva Vasami; Leandro Guaraglia D’Agostino; Paulo César Maiorka; Xutao Deng; Maurício Lacerda Nogueira; Ester Cerdeira Sabino; Eric Delwart; Élcio Leal; Mariana Sequetin Cunha. Guapiaçu virus, a new insect-specific flavivirus isolated from two species of Aedes mosquitoes from Brazil. Scientific Reports 2021, 11, 1 -13.
AMA StyleGeovani De Oliveira Ribeiro, Antonio Charlys da Costa, Danielle Elise Gill, Edcelha Soares D’Athaide Ribeiro, Marlisson Octavio da S. Rego, Fred Julio Costa Monteiro, Fabiola Villanova, Juliana Silva Nogueira, Adriana Yurika Maeda, Renato Pereira de Souza, Roozbeh Tahmasebi, Vanessa S. Morais, Ramendra Pati Pandey, V. Samuel Raj, Sirle Abdo Salloum Scandar, Fernanda Gisele da Silva Vasami, Leandro Guaraglia D’Agostino, Paulo César Maiorka, Xutao Deng, Maurício Lacerda Nogueira, Ester Cerdeira Sabino, Eric Delwart, Élcio Leal, Mariana Sequetin Cunha. Guapiaçu virus, a new insect-specific flavivirus isolated from two species of Aedes mosquitoes from Brazil. Scientific Reports. 2021; 11 (1):1-13.
Chicago/Turabian StyleGeovani De Oliveira Ribeiro; Antonio Charlys da Costa; Danielle Elise Gill; Edcelha Soares D’Athaide Ribeiro; Marlisson Octavio da S. Rego; Fred Julio Costa Monteiro; Fabiola Villanova; Juliana Silva Nogueira; Adriana Yurika Maeda; Renato Pereira de Souza; Roozbeh Tahmasebi; Vanessa S. Morais; Ramendra Pati Pandey; V. Samuel Raj; Sirle Abdo Salloum Scandar; Fernanda Gisele da Silva Vasami; Leandro Guaraglia D’Agostino; Paulo César Maiorka; Xutao Deng; Maurício Lacerda Nogueira; Ester Cerdeira Sabino; Eric Delwart; Élcio Leal; Mariana Sequetin Cunha. 2021. "Guapiaçu virus, a new insect-specific flavivirus isolated from two species of Aedes mosquitoes from Brazil." Scientific Reports 11, no. 1: 1-13.
An outbreak of cat vomiting was observed in an animal shelter. Testing for known enteric feline pathogens did not identify a causative agent. Viral metagenomics on four mini pools of feces from cases and controls housed in the same area revealed the presence of feline astrovirus in all pools. Also found with fewer reads in one pool each were rotavirus I, carnivore bocaparvovirus 3, norovirus (NoV) GVI, and a novel dependovirus. The genome of the highly prevalent astrovirus was sequenced and classified into mamastrovirus species two, also known as feline astrovirus. Real-time RT-PCR on longitudinally acquired fecal samples from 11 sick cases showed 10 (91%) to be shedding astrovirus for as long as 19 days. Affected cats were sick for an average of 9.8 days, with a median of 2.5 days (range = 1–31 days). Unaffected control cats housed in the same areas during the outbreak showed five out of nine (56%) to also be shedding astrovirus. Feline fecal samples collected from the same animal shelter ~1 year before (n = 8) and after (n = 10) showed none to be shedding astrovirus, indicating that this virus was temporarily associated with the vomiting outbreak and is not part of the commensal virome for cats in this shelter. Together with the absence of highly prevalent known pathogens, our results support a role for feline astrovirus infection, as well as significant asymptomatic shedding, in an outbreak of contagious feline vomiting.
Yanpeng Li; Emilia Gordon; Amanda Idle; Alvin Hui; Roxanne Chan; M. Alexis Seguin; Eric Delwart. Astrovirus Outbreak in an Animal Shelter Associated With Feline Vomiting. Frontiers in Veterinary Science 2021, 8, 1 .
AMA StyleYanpeng Li, Emilia Gordon, Amanda Idle, Alvin Hui, Roxanne Chan, M. Alexis Seguin, Eric Delwart. Astrovirus Outbreak in an Animal Shelter Associated With Feline Vomiting. Frontiers in Veterinary Science. 2021; 8 ():1.
Chicago/Turabian StyleYanpeng Li; Emilia Gordon; Amanda Idle; Alvin Hui; Roxanne Chan; M. Alexis Seguin; Eric Delwart. 2021. "Astrovirus Outbreak in an Animal Shelter Associated With Feline Vomiting." Frontiers in Veterinary Science 8, no. : 1.
Characterizing the bat virome is important for understanding viral diversity and detecting viral spillover between animal species. Using an unbiased metagenomics method, we characterize the virome in guano collected from multiple roosts of common Northern California bat species. We describe several novel viral genomes and report the detection of viruses with close relatives reported in other bat species, likely reflecting cross-species transmissions. Viral sequences from well-known carnivore and rodent parvoviruses were also detected, whose presence are likely the result of contamination from defecation and urination atop guano and which reflect the close interaction of these mammals in the wild.
Yanpeng Li; Eda Altan; Gabriel Reyes; Brian Halstead; Xutao Deng; Eric Delwart. Virome of Bat Guano from Nine Northern California Roosts. Journal of Virology 2021, 95, 1 .
AMA StyleYanpeng Li, Eda Altan, Gabriel Reyes, Brian Halstead, Xutao Deng, Eric Delwart. Virome of Bat Guano from Nine Northern California Roosts. Journal of Virology. 2021; 95 (3):1.
Chicago/Turabian StyleYanpeng Li; Eda Altan; Gabriel Reyes; Brian Halstead; Xutao Deng; Eric Delwart. 2021. "Virome of Bat Guano from Nine Northern California Roosts." Journal of Virology 95, no. 3: 1.
CrAssphages are a diverse group of related phages detected in human feces where they are the most prevalent and abundant prokaryotic virus. CrAssphages’ cellular host has been identified as the anaerobic Bacteroides intestinalis. CrAssphage has also been reported in non-human primates and environmental samples and has been proposed as a marker of human fecal contamination. Here we describe crAssphage DNA in a feline fecal sample. 95% of the ~ 100 Kb genome could be assembled and classified in genus 1 of the recently proposed Alphacrassvirinae subfamily. The cat origin of the fecal sample was confirmed by partial mitochondrial DNA sequencing. High levels of Bacteroides intestinalis DNA could also be detected in this cat’s feces. Fecal samples longitudinally collected over a 4-week period showed the continuous shedding of crAssphage DNA. We therefore report the first genome sequence-confirmed detection of crAssphage in fecal samples of a non-primate mammal.
Yanpeng Li; Emilia Gordon; Ryan C. Shean; Amanda Idle; Xutao Deng; Alexander L. Greninger; Eric Delwart. CrAssphage and its bacterial host in cat feces. Scientific Reports 2021, 11, 1 -6.
AMA StyleYanpeng Li, Emilia Gordon, Ryan C. Shean, Amanda Idle, Xutao Deng, Alexander L. Greninger, Eric Delwart. CrAssphage and its bacterial host in cat feces. Scientific Reports. 2021; 11 (1):1-6.
Chicago/Turabian StyleYanpeng Li; Emilia Gordon; Ryan C. Shean; Amanda Idle; Xutao Deng; Alexander L. Greninger; Eric Delwart. 2021. "CrAssphage and its bacterial host in cat feces." Scientific Reports 11, no. 1: 1-6.
The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.
Tu Thi Kha Nguyen; Hong Thi Thu Nguyen; Ny Thi Han Nguyen; Phuc My Tran; Tam Thi Thanh Pham; H. Rogier Van Doorn; Nghia Dang Trung Ho; Huong Thao Dang; Han An Duong; Ha Thi Thu Luu; Xutao Deng; Guy Thwaites; Eric Delwart; Anna-Maija K. Virtala; Olli Vapalahti; Stephen Baker; Tan Van Le. The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections. Viruses 2020, 12, 960 .
AMA StyleTu Thi Kha Nguyen, Hong Thi Thu Nguyen, Ny Thi Han Nguyen, Phuc My Tran, Tam Thi Thanh Pham, H. Rogier Van Doorn, Nghia Dang Trung Ho, Huong Thao Dang, Han An Duong, Ha Thi Thu Luu, Xutao Deng, Guy Thwaites, Eric Delwart, Anna-Maija K. Virtala, Olli Vapalahti, Stephen Baker, Tan Van Le. The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections. Viruses. 2020; 12 (9):960.
Chicago/Turabian StyleTu Thi Kha Nguyen; Hong Thi Thu Nguyen; Ny Thi Han Nguyen; Phuc My Tran; Tam Thi Thanh Pham; H. Rogier Van Doorn; Nghia Dang Trung Ho; Huong Thao Dang; Han An Duong; Ha Thi Thu Luu; Xutao Deng; Guy Thwaites; Eric Delwart; Anna-Maija K. Virtala; Olli Vapalahti; Stephen Baker; Tan Van Le. 2020. "The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections." Viruses 12, no. 9: 960.
Viruses are the most diverse and abundant microorganisms on earth, highly adaptive to a wide range of hosts. Viral diversity within invertebrate hosts has gained notoriety in recent years in public health as several such viruses have been of medical importance. Aedes aegypti serves as a vector for several viruses that have caused epidemics within the last year throughout Brazil; including Dengue, Zika and Chikungunya. This study aimed to identify new viral agents within Aedes aegypti mosquito in a city of the Amazonian region, where it is highly endemic. Metagenomic investigation was performed on 60 mosquito pools and viral RNA sequences present in their microbiota were characterized using genomic and phylogenetic tools. In total, we identified five putative novel virus species related to the Sobemovirus genus, Iflavirus genus and Permutatetraviridae family. These findings indicate a diverse taxonomy of viruses present in the mosquito microbiota of the Amazon, the region with the greatest invertebrate diversity in the world.
Geovani De Oliveira Ribeiro; Vanessa S. Morais; Fred Julio Costa Monteiro; Edcelha Soares D’Athaide Ribeiro; Marlisson Octavio Da S Rego; Raimundo Nonato Picanço Souto; Fabiola Villanova; Roozbeh Tahmasebi; Philip Michael Hefford; Xutao Deng; Eric Delwart; Ester Cerdeira Sabino; Licia Natal Fernandes; Antonio Charlys Da Costa; Élcio Leal. Aedes aegypti from Amazon Basin Harbor High Diversity of Novel Viral Species. Viruses 2020, 12, 866 .
AMA StyleGeovani De Oliveira Ribeiro, Vanessa S. Morais, Fred Julio Costa Monteiro, Edcelha Soares D’Athaide Ribeiro, Marlisson Octavio Da S Rego, Raimundo Nonato Picanço Souto, Fabiola Villanova, Roozbeh Tahmasebi, Philip Michael Hefford, Xutao Deng, Eric Delwart, Ester Cerdeira Sabino, Licia Natal Fernandes, Antonio Charlys Da Costa, Élcio Leal. Aedes aegypti from Amazon Basin Harbor High Diversity of Novel Viral Species. Viruses. 2020; 12 (8):866.
Chicago/Turabian StyleGeovani De Oliveira Ribeiro; Vanessa S. Morais; Fred Julio Costa Monteiro; Edcelha Soares D’Athaide Ribeiro; Marlisson Octavio Da S Rego; Raimundo Nonato Picanço Souto; Fabiola Villanova; Roozbeh Tahmasebi; Philip Michael Hefford; Xutao Deng; Eric Delwart; Ester Cerdeira Sabino; Licia Natal Fernandes; Antonio Charlys Da Costa; Élcio Leal. 2020. "Aedes aegypti from Amazon Basin Harbor High Diversity of Novel Viral Species." Viruses 12, no. 8: 866.
An emaciated subadult free-ranging California sea lion (Csl or Zalophus californianus) died following stranding with lesions similar to 11 other stranded animals characterized by chronic disseminated granulomatous inflammation with necrotizing steatitis and vasculitis, involving visceral adipose tissues in the thoracic and peritoneal cavities. Histologically, affected tissues had extensive accumulations of macrophages with perivascular lymphocytes, plasma cells, and fewer neutrophils. Using viral metagenomics on a mesenteric lymph node six mammalian viruses were identified consisting of novel parvovirus, polyomavirus, rotavirus, anellovirus, and previously described Csl adenovirus 1 and Csl bocavirus 4. The causal or contributory role of these viruses to the gross and histologic lesions of this sea lion remains to be determined.
Eda Altan; Martha A. Delaney; Kathleen M. Colegrove; Terry R. Spraker; Elizabeth A. Wheeler; Xutao Deng; Yanpeng Li; Frances M. D. Gulland; Eric Delwart. Complex Virome in a Mesenteric Lymph Node from a Californian Sea Lion (Zalophus Californianus) with Polyserositis and Steatitis. Viruses 2020, 12, 793 .
AMA StyleEda Altan, Martha A. Delaney, Kathleen M. Colegrove, Terry R. Spraker, Elizabeth A. Wheeler, Xutao Deng, Yanpeng Li, Frances M. D. Gulland, Eric Delwart. Complex Virome in a Mesenteric Lymph Node from a Californian Sea Lion (Zalophus Californianus) with Polyserositis and Steatitis. Viruses. 2020; 12 (8):793.
Chicago/Turabian StyleEda Altan; Martha A. Delaney; Kathleen M. Colegrove; Terry R. Spraker; Elizabeth A. Wheeler; Xutao Deng; Yanpeng Li; Frances M. D. Gulland; Eric Delwart. 2020. "Complex Virome in a Mesenteric Lymph Node from a Californian Sea Lion (Zalophus Californianus) with Polyserositis and Steatitis." Viruses 12, no. 8: 793.
Eukaryotic single-stranded (ss) DNA viruses are classified into ten families (Table 1) but many remain 38 unclassified (1, 2).…
Mart Krupovic; Arvind Varsani; Darius Kazlauskas; Mya Breitbart; Eric Delwart; Karyna Rosario; Natalya Yutin; Yuri I. Wolf; Balázs Harrach; F. Murilo Zerbini; Valerian V. Dolja; Jens H. Kuhn; Eugene V. Koonin. Cressdnaviricota : a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes. Journal of Virology 2020, 94, 1 .
AMA StyleMart Krupovic, Arvind Varsani, Darius Kazlauskas, Mya Breitbart, Eric Delwart, Karyna Rosario, Natalya Yutin, Yuri I. Wolf, Balázs Harrach, F. Murilo Zerbini, Valerian V. Dolja, Jens H. Kuhn, Eugene V. Koonin. Cressdnaviricota : a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes. Journal of Virology. 2020; 94 (12):1.
Chicago/Turabian StyleMart Krupovic; Arvind Varsani; Darius Kazlauskas; Mya Breitbart; Eric Delwart; Karyna Rosario; Natalya Yutin; Yuri I. Wolf; Balázs Harrach; F. Murilo Zerbini; Valerian V. Dolja; Jens H. Kuhn; Eugene V. Koonin. 2020. "Cressdnaviricota : a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes." Journal of Virology 94, no. 12: 1.
All of the known porcine sapeloviruses (PSVs) currently belong to a single genotype in the genus Sapelovirus (family Picornaviridae). Here, the complete genome of a second, possibly recombinant, genotype of PSV strain SZ1M-F/PSV/HUN2013 (MN807752) from a faecal sample of a paraplegic pig in Hungary was characterized using viral metagenomics and RT-PCR. This sapelovirus strain showed only 64 % nucleotide identity in the VP1 region to its closest PSV-1 relative. Complete VP1 sequence-based epidemiological investigations of PSVs circulating in Hungary showed the presence of diverse strains found in high prevalence in enteric and respiratory samples collected from both asymptomatic and paraplegic pigs from 12 swine farms. Virus isolation attempts using PK-15 cell cultures were successful in 3/8 cases for the classic but not the novel PSV genotype. Sequence comparisons of faeces and isolate strains derived VP1 showed that cultured PSV strains not always represent the dominant PSVs found in vivo.
Ákos Boros; Zoltán László; Péter Pankovics; András Marosi; Mihály Albert; Attila Cságola; Hunor Bíró; Elizabeth Fahsbender; Eric Delwart; Gábor Reuter. High prevalence, genetic diversity and a potentially novel genotype of Sapelovirus A (Picornaviridae) in enteric and respiratory samples in Hungarian swine farms. Journal of General Virology 2020, 101, 609 -621.
AMA StyleÁkos Boros, Zoltán László, Péter Pankovics, András Marosi, Mihály Albert, Attila Cságola, Hunor Bíró, Elizabeth Fahsbender, Eric Delwart, Gábor Reuter. High prevalence, genetic diversity and a potentially novel genotype of Sapelovirus A (Picornaviridae) in enteric and respiratory samples in Hungarian swine farms. Journal of General Virology. 2020; 101 (6):609-621.
Chicago/Turabian StyleÁkos Boros; Zoltán László; Péter Pankovics; András Marosi; Mihály Albert; Attila Cságola; Hunor Bíró; Elizabeth Fahsbender; Eric Delwart; Gábor Reuter. 2020. "High prevalence, genetic diversity and a potentially novel genotype of Sapelovirus A (Picornaviridae) in enteric and respiratory samples in Hungarian swine farms." Journal of General Virology 101, no. 6: 609-621.
Human Adenovirus species C (HAdV-C) is the most common etiologic agent of respiratory disease. In the present study, we characterized the nearly full-length genome of one potential new HAdV-C recombinant strain constituted by Penton and Fiber proteins belonging to type 89 and a chimeric Hexon protein of types 1 and 89. By using viral metagenomics techniques, we screened out, in the states of Tocantins and Pará, Northern and North regions of Brazil, from 2010 to 2016, 251 fecal samples of children between 0.5 to 2.5 years old. These children were presenting acute diarrhea not associated with common pathogens (i.e., rotavirus, norovirus). We identified two HAdV-C strains in two distinct patients. Phylogenetic analysis performed using all complete genomes available at GenBank database indicated that one strain (HAdV-C BR-245) belonged to type 1. The phylogenetic analysis also indicated that the second strain (HAdV-C BR-211) was located at the base of the clade formed by the newly HAdV-C strains type 89. Recombination analysis revealed that strain HAdV-C BR-211 is a chimera in which the variable regions of Hexon gene combined HAdV-C1 and HAdV-C89 sequences. Therefore, HAdV-C BR-211 strain possesses a genomic backbone of type HAdV-C89 and a unique insertion of HAdV-C1 in the Hexon sequence. Recombination may play an important driving force in HAdV-C diversity and evolution. Studies employing complete genomic sequencing on circulating HAdV-C strains in Brazil are needed to understand the clinical significance of the presented data.
Roozbeh Tahmasebi; Antonio Charlys Da Costa; Kaelan Tardy; Rory J. Tinker; Flavio Augusto De Padua Milagres; Rafael Brustulin; Maria Da Aparecida Rodrigues Teles; Rogério Togisaki Das Chagas; Cassia Vitória De Deus Alves Soares; Aripuana Sakurada Aranha Watanabe; Cecilia Salete Alencar; Fabiola Villanova; Xutao Deng; Eric Delwart; Adriana Luchs; Élcio Leal; Ester Cerdeira Sabino. Genomic Analyses of Potential Novel Recombinant Human Adenovirus C in Brazil. Viruses 2020, 12, 508 .
AMA StyleRoozbeh Tahmasebi, Antonio Charlys Da Costa, Kaelan Tardy, Rory J. Tinker, Flavio Augusto De Padua Milagres, Rafael Brustulin, Maria Da Aparecida Rodrigues Teles, Rogério Togisaki Das Chagas, Cassia Vitória De Deus Alves Soares, Aripuana Sakurada Aranha Watanabe, Cecilia Salete Alencar, Fabiola Villanova, Xutao Deng, Eric Delwart, Adriana Luchs, Élcio Leal, Ester Cerdeira Sabino. Genomic Analyses of Potential Novel Recombinant Human Adenovirus C in Brazil. Viruses. 2020; 12 (5):508.
Chicago/Turabian StyleRoozbeh Tahmasebi; Antonio Charlys Da Costa; Kaelan Tardy; Rory J. Tinker; Flavio Augusto De Padua Milagres; Rafael Brustulin; Maria Da Aparecida Rodrigues Teles; Rogério Togisaki Das Chagas; Cassia Vitória De Deus Alves Soares; Aripuana Sakurada Aranha Watanabe; Cecilia Salete Alencar; Fabiola Villanova; Xutao Deng; Eric Delwart; Adriana Luchs; Élcio Leal; Ester Cerdeira Sabino. 2020. "Genomic Analyses of Potential Novel Recombinant Human Adenovirus C in Brazil." Viruses 12, no. 5: 508.
An unexplained outbreak of feline diarrhea and vomiting, negative for common enteric viral and bacterial pathogens, was subjected to viral metagenomics and PCR. We characterized from fecal samples the genome of a novel chapparvovirus we named fechavirus that was shed by 8/17 affected cats and identified three different feline bocaviruses shed by 9/17 cats. Also detected were nucleic acids from attenuated vaccine viruses, members of the normal feline virome, viruses found in only one or two cases, and viruses likely derived from ingested food products. Epidemiological investigation of disease signs, time of onset, and transfers of affected cats between three facilities support a possible role for this new chapparvovirus in a highly contagious feline diarrhea and vomiting disease.
Yanpeng Li; Emilia Gordon; Amanda Idle; Eda Altan; M. Alexis Seguin; Marko Estrada; Xutao Deng; Eric Delwart. Virome of a Feline Outbreak of Diarrhea and Vomiting Includes Bocaviruses and a Novel Chapparvovirus. Viruses 2020, 12, 506 .
AMA StyleYanpeng Li, Emilia Gordon, Amanda Idle, Eda Altan, M. Alexis Seguin, Marko Estrada, Xutao Deng, Eric Delwart. Virome of a Feline Outbreak of Diarrhea and Vomiting Includes Bocaviruses and a Novel Chapparvovirus. Viruses. 2020; 12 (5):506.
Chicago/Turabian StyleYanpeng Li; Emilia Gordon; Amanda Idle; Eda Altan; M. Alexis Seguin; Marko Estrada; Xutao Deng; Eric Delwart. 2020. "Virome of a Feline Outbreak of Diarrhea and Vomiting Includes Bocaviruses and a Novel Chapparvovirus." Viruses 12, no. 5: 506.