Arvind Varsani
Arizona State University
GenePlant virusGenomeMetagenomicsGenusVirologyEcologyPhylogenetic treeVirus classificationVirusMaize streak virusGeminiviridaeBegomovirusPopulationMastrevirusDNA sequencingGeneticsDNABotanyEvolutionary biologyBiologyPhylogeneticsZoology
Publications 335
#1Kahini WadhawanH-Index: 6
#2Payel DasH-Index: 21
Last. Kush R. VarshneyH-Index: 23
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Current methods for viral discovery target evolutionarily conserved proteins that accurately identify virus families but remain unable to distinguish the zoonotic potential of newly discovered viruses. Here, we apply an attention-enhanced long-short-term memory (LSTM) deep neural net classifier to a highly conserved viral protein target to predict zoonotic potential across betacoronaviruses. The classifier performs with a 94% accuracy. Analysis and visualization of attention at the sequence and ...
#1Temitope O C Faleye (ASU: Arizona State University)H-Index: 1
#2Deborah Adams (ASU: Arizona State University)H-Index: 2
Last. Matthew Scotch (ASU: Arizona State University)H-Index: 21
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BACKGROUND Local transmission of seasonal influenza viruses (IVs) can be difficult to resolve. Here, we study if coupling high-throughput sequencing (HTS) of hemagglutinin (HA) and neuraminidase (NA) genes with variant analysis can resolve strains from local transmission that have identical consensus genome. We analyzed 24 samples collected over four days in January 2020 at a large university in the US. We amplified complete hemagglutinin (HA) and neuraminidase (NA) genomic segments followed by ...
#1Arvind Varsani (ASU: Arizona State University)H-Index: 63
#2Tanja Opriessnig (Edin.: University of Edinburgh)H-Index: 64
Last. Simona Kraberger (ASU: Arizona State University)H-Index: 26
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Anelloviruses are small negative-sense single-stranded DNA viruses with genomes ranging in size from 1.6 to 3.9 kb. The family Anelloviridae comprised 14 genera before the present changes. However, in the last five years, a large number of diverse anelloviruses have been identified in various organisms. Here, we undertake a global analysis of mammalian anelloviruses whose full genome sequences have been determined and have an intact open reading frame 1 (ORF1). We established new criteria for th...
#1Simona Kraberger (ASU: Arizona State University)H-Index: 26
#2Tanja Opriessnig (Edin.: University of Edinburgh)H-Index: 64
Last. Arvind Varsani (ASU: Arizona State University)H-Index: 63
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The genus Gyrovirus was assigned to the family Anelloviridae in 2017 with only one recognized species, Chicken anemia virus. Over the last decade, many diverse viruses related to chicken anemia virus have been identified but not classified. Here, we provide a framework for the classification of new species in the genus Gyrovirus and communicate the establishment of nine new species. We adopted the ‘Genus + freeform epithet’ binomial system for the naming of these species.
1 CitationsSource
#1Arvind Varsani (ASU: Arizona State University)H-Index: 63
#2Mart Krupovic (Pasteur Institute)H-Index: 59
The family Genomoviridae (phylum Cressdnaviricota, class Repensiviricetes, order Geplafuvirales) includes viruses with circular single-stranded DNA genomes encoding two proteins, the capsid protein and the rolling-circle replication initiation protein. The genomes of the vast majority of members in this family have been sequenced directly from diverse environmental or animal- and plant-associated samples, but two genomoviruses have been identified infecting fungi. Since the last taxonomic update...
#1Simona Kraberger (ASU: Arizona State University)H-Index: 26
#2Laurel Ek. Serieys (UCSC: University of California, Santa Cruz)
Last. John R. Squires (USDA: United States Department of Agriculture)H-Index: 23
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Abstract null null Anellovirus infections are highly prevalent in mammals but prior to this study only a handful of anellovirus genomes had been identified in members of the Felidae family. Here characterise anelloviruses in pumas (Puma concolor), bobcats (Lynx rufus), Canada lynx (Lynx canadensis), caracals (Caracal caracal) and domestic cats (Felis catus). The complete anellovirus genomes (n = 220) recovered from 149 individuals were diverse. ORF1 protein sequence similarity network analyses c...
#1Damien Robert Finn (ASU: Arizona State University)H-Index: 1
#2Juan Maldonado (ASU: Arizona State University)H-Index: 22
Last. Gillian H. Gile (ASU: Arizona State University)H-Index: 18
view all 16 authors...
Air carries a diverse load of particulate microscopic biological matter in suspension, either aerosolized or aggregated with dust particles, the aerobiome, which is dispersed by winds from sources to sinks. The aerobiome is known to contain microbes, including pathogens, as well as debris or small-sized propagules from plants and animals, but its variability and composition has not been studied comprehensibly. To gain a dynamic insight into the aerobiome existing over a mixed-use dryland setting...
#1Ilya R. Fischhoff (Institute of Ecosystem Studies)H-Index: 15
#2Adrian A. Castellanos (Institute of Ecosystem Studies)H-Index: 2
Last. Barbara A. Han (Institute of Ecosystem Studies)H-Index: 22
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Back and forth transmission of SARS-CoV-2 between humans and animals has the potential to create wild reservoirs of virus that can endanger both long-term control of COVID-19 in people, and vulnerable animal populations that are particularly susceptible to lethal disease. In the near term, SARS-CoV-2 virus variants arising in newly established animal hosts could escape immunity conferred by current human vaccines. In the long-term, animal reservoirs of SARS-CoV-2 increase the overall risk of dis...
3 CitationsSource
#1Norsazilawati Saad (UPM: Universiti Putra Malaysia)H-Index: 2
#2James W. Olmstead (UF: University of Florida)H-Index: 15
Last. Philip F. Harmon (UF: University of Florida)H-Index: 13
view all 7 authors...
Southern highbush blueberry (interspecific hybrids of Vaccinium corymbosum L.) is cultivated near wild V. corymbosum as well as closely related species in Florida, USA. The expansion of blueberry cultivation into new areas in Florida and deployment of new cultivars containing viruses can potentially increase the diversity of viruses in wild and cultivated V. corymbosum. In this study, viral diversity in wild and cultivated blueberries (V. corymbosum) is described using a metagenomic approach. RN...
#1Pacifica Sommers (CU: University of Colorado Boulder)H-Index: 7
#2Anushila Chatterjee (CU: University of Colorado Boulder)H-Index: 5
Last. Gareth Trubl (LLNL: Lawrence Livermore National Laboratory)H-Index: 10
view all 4 authors...
Viral metagenomics has expanded our knowledge of the ecology of uncultured viruses, within both environmental (e.g., terrestrial and aquatic) and host-associated (e.g., plants and animals, including humans) contexts. Here, we emphasize the implementation of an ecological framework in viral metagenomic studies to address questions in virology rarely considered ecological, which can change our perception of viruses and how they interact with their surroundings. An ecological framework explicitly c...