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Fontenele RS, Yang Y, Driver EM, Magge A, Kraberger S, Custer JM, Dufault-Thompson K, Cox E, Newell ME, Varsani A, Halden RU, Scotch M, Jiang X. Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA. Sci Total Environ 2023; 877:162862. [PMID: 36933724 PMCID: PMC10017378 DOI: 10.1016/j.scitotenv.2023.162862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 05/06/2023]
Abstract
Wastewater-based epidemiology (WBE) is a non-invasive and cost-effective approach for monitoring the spread of a pathogen within a community. WBE has been adopted as one of the methods to monitor the spread and population dynamics of the SARS-CoV-2 virus, but significant challenges remain in the bioinformatic analysis of WBE-derived data. Here, we have developed a new distance metric, CoVdist, and an associated analysis tool that facilitates the application of ordination analysis to WBE data and the identification of viral population changes based on nucleotide variants. We applied these new approaches to a large-scale dataset from 18 cities in nine states of the USA using wastewater collected from July 2021 to June 2022. We found that the trends in the shift between the Delta and Omicron SARS-CoV-2 lineages were largely consistent with what was seen in clinical data, but that wastewater analysis offered the added benefit of revealing significant differences in viral population dynamics at the state, city, and even neighborhood scales. We also were able to observe the early spread of variants of concern and the presence of recombinant lineages during the transitions between variants, both of which are challenging to analyze based on clinically-derived viral genomes. The methods outlined here will be beneficial for future applications of WBE to monitor SARS-CoV-2, particularly as clinical monitoring becomes less prevalent. Additionally, these approaches are generalizable, allowing them to be applied for the monitoring and analysis of future viral outbreaks.
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Affiliation(s)
- Rafaela S Fontenele
- National Library of Medicine, National Institute of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Yiyan Yang
- National Library of Medicine, National Institute of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Erin M Driver
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Arjun Magge
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | - Keith Dufault-Thompson
- National Library of Medicine, National Institute of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Erin Cox
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Melanie Engstrom Newell
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Center of Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
| | - Rolf U Halden
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85281, USA; OneWaterOneHealth, Nonprofit Project of the Arizona State University Foundation, Tempe, AZ 85287, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA; College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institute of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
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Butkovic A, Kraberger S, Smeele Z, Martin DP, Schmidlin K, Fontenele RS, Shero MR, Beltran RS, Kirkham AL, Aleamotu’a M, Burns JM, Koonin EV, Varsani A, Krupovic M. Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein. Virus Evol 2023; 9:vead035. [PMID: 37325085 PMCID: PMC10266747 DOI: 10.1093/ve/vead035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the 'healthy virome'. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm Monodnaviria. To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal (Leptonychotes weddellii) from Antarctica and a fecal sample of grizzly bear (Ursus arctos horribilis) from the USA and performed a comprehensive family-wide analysis of the signature anellovirus protein ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all Anelloviridae genera adopt a jelly-roll fold typical of viral capsid proteins (CPs), establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike CPs of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between β-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus-host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll CPs through gradual augmentation of the projection domain. We suggest assigning Anelloviridae to a new phylum, 'Commensaviricota', and including it into the kingdom Shotokuvirae (realm Monodnaviria), alongside Cressdnaviricota and Cossaviricota.
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Affiliation(s)
- Anamarija Butkovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Zoe Smeele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | | | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Michelle R Shero
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Roxanne S Beltran
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Amy L Kirkham
- U.S. Fish and Wildlife Service, Marine Mammals Management, 1011 E, Tudor Road, Anchorage, AK 99503, USA
| | - Maketalena Aleamotu’a
- School of Environmental and Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Jennifer M Burns
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
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Payne N, Combrink L, Kraberger S, Fontenele RS, Schmidlin K, Cassaigne I, Culver M, Varsani A, Van Doorslaer K. DNA virome composition of two sympatric wild felids, bobcat (Lynx rufus) and puma (Puma concolor) in Sonora, Mexico. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1126149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
With viruses often having devastating effects on wildlife population fitness and wild mammals serving as pathogen reservoirs for potentially zoonotic diseases, determining the viral diversity present in wild mammals is both a conservation and One Health priority. Additionally, transmission from more abundant hosts could increase the extinction risk of threatened sympatric species. We leveraged an existing circular DNA enriched metagenomic dataset generated from bobcat (Lynx rufus, n = 9) and puma (Puma concolor, n = 13) scat samples non-invasively collected from Sonora, Mexico, to characterize fecal DNA viromes of each species and determine the extent that viruses are shared between them. Using the metaWRAP pipeline to co-assemble viral genomes for comparative metagenomic analysis, we observed diverse circular DNA viruses in both species, including circoviruses, genomoviruses, and anelloviruses. We found that differences in DNA virome composition were partly attributed to host species, although there was overlap between viruses in bobcats and pumas. Pumas exhibited greater levels of alpha diversity, possibly due to bioaccumulation of pathogens in apex predators. Shared viral taxa may reflect dietary overlap, shared environmental resources, or transmission through host interactions, although we cannot rule out species-specific host-virus coevolution for the taxa detected through co-assembly. However, our detection of integrated feline foamy virus (FFV) suggests Sonoran pumas may interact with domestic cats. Our results contribute to the growing baseline knowledge of wild felid viral diversity. Future research including samples from additional sources (e.g., prey items, tissues) may help to clarify host associations and determine the pathogenicity of detected viruses.
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Bowes DA, Driver EM, Kraberger S, Fontenele RS, Holland LA, Wright J, Johnston B, Savic S, Engstrom Newell M, Adhikari S, Kumar R, Goetz H, Binsfeld A, Nessi K, Watkins P, Mahant A, Zevitz J, Deitrick S, Brown P, Dalton R, Garcia C, Inchausti R, Holmes W, Tian XJ, Varsani A, Lim ES, Scotch M, Halden RU. Leveraging an established neighbourhood-level, open access wastewater monitoring network to address public health priorities: a population-based study. Lancet Microbe 2023; 4:e29-e37. [PMID: 36493788 PMCID: PMC9725778 DOI: 10.1016/s2666-5247(22)00289-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Before the COVID-19 pandemic, the US opioid epidemic triggered a collaborative municipal and academic effort in Tempe, Arizona, which resulted in the world's first open access dashboard featuring neighbourhood-level trends informed by wastewater-based epidemiology (WBE). This study aimed to showcase how wastewater monitoring, once established and accepted by a community, could readily be adapted to respond to newly emerging public health priorities. METHODS In this population-based study in Greater Tempe, Arizona, an existing opioid monitoring WBE network was modified to track SARS-CoV-2 transmission through the analysis of 11 contiguous wastewater catchments. Flow-weighted and time-weighted 24 h composite samples of untreated wastewater were collected at each sampling location within the wastewater collection system for 3 days each week (Tuesday, Thursday, and Saturday) from April 1, 2020, to March 31, 2021 (Area 7 and Tempe St Luke's Hospital were added in July, 2020). Reverse transcription quantitative PCR targeting the E gene of SARS-CoV-2 isolated from the wastewater samples was used to determine the number of genome copies in each catchment. Newly detected clinical cases of COVID-19 by zip code within the City of Tempe, Arizona were reported daily by the Arizona Department of Health Services from May 23, 2020. Maricopa County-level new positive cases, COVID-19-related hospitalisations, deaths, and long-term care facility deaths per day are publicly available and were collected from the Maricopa County Epidemic Curve Dashboard. Viral loads of SARS-CoV-2 (genome copies per day) measured in wastewater from each catchment were aggregated at the zip code level and city level and compared with the clinically reported data using root mean square error to investigate early warning capability of WBE. FINDINGS Between April 1, 2020, and March 31, 2021, 1556 wastewater samples were analysed. Most locations showed two waves in viral levels peaking in June, 2020, and December, 2020-January, 2021. An additional wave of viral load was seen in catchments close to Arizona State University (Areas 6 and 7) at the beginning of the fall (autumn) semester in late August, 2020. Additionally, an early infection hotspot was detected in the Town of Guadalupe, Arizona, starting the week of May 4, 2020, that was successfully mitigated through targeted interventions. A shift in early warning potential of WBE was seen, from a leading (mean of 8·5 days [SD 2·1], June, 2020) to a lagging (-2·0 days [1·4], January, 2021) indicator compared with newly reported clinical cases. INTERPRETATION Lessons learned from leveraging an existing neighbourhood-level WBE reporting dashboard include: (1) community buy-in is key, (2) public data sharing is effective, and (3) sub-ZIP-code (postal code) data can help to pinpoint populations at risk, track intervention success in real time, and reveal the effect of local clinical testing capacity on WBE's early warning capability. This successful demonstration of transitioning WBE efforts from opioids to COVID-19 encourages an expansion of WBE to tackle newly emerging and re-emerging threats (eg, mpox and polio). FUNDING National Institutes of Health's RADx-rad initiative, National Science Foundation, Virginia G Piper Charitable Trust, J M Kaplan Fund, and The Flinn Foundation.
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Affiliation(s)
- Devin A Bowes
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA; School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA; OneWaterOneHealth, The Arizona State University Foundation, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Erin M Driver
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA; School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| | - Simona Kraberger
- The Biodesign Institute Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Rafaela S Fontenele
- The Biodesign Institute Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - LaRinda A Holland
- The Biodesign Institute Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Jillian Wright
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA; OneWaterOneHealth, The Arizona State University Foundation, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Bridger Johnston
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | - Sonja Savic
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | - Melanie Engstrom Newell
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA; School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA
| | - Sangeet Adhikari
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA; School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| | - Rahul Kumar
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | - Hanah Goetz
- School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA
| | - Allison Binsfeld
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA; OneWaterOneHealth, The Arizona State University Foundation, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Kaxandra Nessi
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | - Payton Watkins
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | - Akhil Mahant
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | - Jacob Zevitz
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | | | | | | | | | - Rosa Inchausti
- Strategic Management and Diversity Office, Tempe, AZ, USA
| | - Wydale Holmes
- Strategic Management and Diversity Office, Tempe, AZ, USA
| | - Xiao-Jun Tian
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Arvind Varsani
- The Biodesign Institute Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Efrem S Lim
- The Biodesign Institute Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Matthew Scotch
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA; College of Health Solutions, Arizona State University, Tempe, AZ, USA
| | - Rolf U Halden
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA; School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA; Global Futures Laboratory, Arizona State University, Tempe, AZ, USA; OneWaterOneHealth, The Arizona State University Foundation, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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5
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Ketsela D, Oyeniran KA, Feyissa B, Fontenele RS, Kraberger S, Varsani A. Molecular identification and phylogenetic characterization of A-strain isolates of maize streak virus from western Ethiopia. Arch Virol 2022; 167:2753-2759. [PMID: 36169719 DOI: 10.1007/s00705-022-05614-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
Abstract
The A-strain of maize streak virus (MSV) causes maize streak disease (MSD), which is a major biotic threat to maize production in sub-Saharan Africa. Previous studies have described different MSV strains of economic importance from southern and eastern African countries and how eastern African regions are hubs for MSV diversification. Despite these efforts, due to a lack of extensive sampling, there is limited knowledge about the MSV-A diversity in Ethiopia. Here, field sampling of maize plants and wild grasses with visible MSD symptoms was carried out in the western Ethiopian regions of Gambela, Oromia, and Benishangul-Gumuz during the maize-growing season of 2019. The complete genomes of MSV isolates (n = 60) were cloned and sequenced by the Sanger method. We used a model-based phylogenetic approach to analyse 725 full MSV genome sequences available in the GenBank database together with newly determined genome sequences from Ethiopia to determine their subtypes and identify recombinant lineages. Of the 127 fields accessed, MSD prevalence was highest, at 96%, in the Gambela region and lowest in Oromia, at 66%. The highest mean symptom severity of 4/5 (where 5 is the highest and 1 the lowest) was observed in Gambela and Benishangul-Gumuz. Our results show that these newly determined MSV isolates belong to recombinant lineage V of the A1 subtype, with the widest dissemination and greatest economic significance in sub-Saharan Africa and the adjacent Indian Ocean islands.
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Affiliation(s)
- Daniel Ketsela
- Virology Research Laboratory, Ambo Agricultural Research Centre, Ethiopian Institute of Agricultural Research, P.O. Box 37, Ambo, Ethiopia
| | - Kehinde A Oyeniran
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa.
- Department of Biological Sciences, Bamidele Olumilua University of Education, Science and Technology, Ikere-Ekiti, Nigeria.
| | - Berhanu Feyissa
- Virology Research Laboratory, Ambo Agricultural Research Centre, Ethiopian Institute of Agricultural Research, P.O. Box 37, Ambo, Ethiopia
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
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6
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Moubset O, François S, Maclot F, Palanga E, Julian C, Claude L, Fernandez E, Rott P, Daugrois JH, Antoine-Lorquin A, Bernardo P, Blouin AG, Temple C, Kraberger S, Fontenele RS, Harkins GW, Ma Y, Marais A, Candresse T, Chéhida SB, Lefeuvre P, Lett JM, Varsani A, Massart S, Ogliastro M, Martin DP, Filloux D, Roumagnac P. Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses. Phytopathology 2022; 112:2253-2272. [PMID: 35722889 DOI: 10.1094/phyto-03-22-0096-rvw] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Oumaima Moubset
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - François Maclot
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Essowè Palanga
- Institut Togolais de Recherche Agronomique (ITRA-CRASS), B.P. 129, Kara, Togo
| | - Charlotte Julian
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Lisa Claude
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Rott
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jean-Heinrich Daugrois
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | | | - Arnaud G Blouin
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Plant Protection Department, Agroscope, 1260, Nyon, Switzerland
| | - Coline Temple
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics, Institute, University of the Western Cape, South Africa
| | - Yuxin Ma
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | | | | | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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7
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Desvignes T, Lauridsen H, Valdivieso A, Fontenele RS, Kraberger S, Murray KN, Le François NR, Detrich HW, Kent ML, Varsani A, Postlethwait JH. A parasite outbreak in notothenioid fish in an Antarctic fjord. iScience 2022; 25:104588. [PMID: 35800770 PMCID: PMC9253362 DOI: 10.1016/j.isci.2022.104588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/25/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Climate changes can promote disease outbreaks, but their nature and potential impacts in remote areas have received little attention. In a hot spot of biodiversity on the West Antarctic Peninsula, which faces among the fastest changing climates on Earth, we captured specimens of two notothenioid fish species affected by large skin tumors at an incidence never before observed in the Southern Ocean. Molecular and histopathological analyses revealed that X-cell parasitic alveolates, members of a genus we call Notoxcellia, are the etiological agent of these tumors. Parasite-specific molecular probes showed that xenomas remained within the skin but largely outgrew host cells in the dermis. We further observed that tumors induced neovascularization in underlying tissue and detrimentally affected host growth and condition. Although many knowledge gaps persist about X-cell disease, including its mode of transmission and life cycle, these findings reveal potentially active biotic threats to vulnerable Antarctic ecosystems.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Henrik Lauridsen
- Department of Clinical Medicine, Aarhus University; Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Alejandro Valdivieso
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona Spain
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Katrina N Murray
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Nathalie R Le François
- Laboratoire Physiologie, Aquaculture et Conservation, Biodôme de Montréal/Espace pour la vie, 4777 Avenue Pierre-De Coubertin, Montreal, QC H1V 1B3, Canada
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd, Nahant, MA 01908, USA
| | - Michael L Kent
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925 Cape Town, South Africa
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8
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Kraberger S, Austin C, Farkas K, Desvignes T, Postlethwait JH, Fontenele RS, Schmidlin K, Bradley RW, Warzybok P, Van Doorslaer K, Davison W, Buck CB, Varsani A. Discovery of novel fish papillomaviruses: From the Antarctic to the commercial fish market. Virology 2022; 565:65-72. [PMID: 34739918 PMCID: PMC8713439 DOI: 10.1016/j.virol.2021.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023]
Abstract
Fish papillomaviruses form a newly discovered group broadly recognized as the Secondpapillomavirinae subfamily. This study expands the documented genomes of the fish papillomaviruses from six to 16, including one from the Antarctic emerald notothen, seven from commercial market fishes, one from data mining of sea bream sequence data, and one from a western gull cloacal swab that is likely diet derived. The genomes of secondpapillomaviruses are ∼6 kilobasepairs (kb), which is substantially smaller than the ∼8 kb of terrestrial vertebrate papillomaviruses. Each genome encodes a clear homolog of the four canonical papillomavirus genes, E1, E2, L1, and L2. In addition, we identified open reading frames (ORFs) with short linear peptide motifs reminiscent of E6/E7 oncoproteins. Fish papillomaviruses are extremely diverse and phylogenetically distant from other papillomaviruses suggesting a model in which terrestrial vertebrate-infecting papillomaviruses arose after an evolutionary bottleneck event, possibly during the water-to-land transition.
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Charlotte Austin
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
| | | | - Rafaela S. Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Russell W. Bradley
- Santa Rosa Island Research Station, California State University Channel Islands, Camarillo CA 93012, USA
| | - Pete Warzybok
- Point Blue Conservation Science, Petaluma, California, CA 94954, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute; Department of Immunobiology; Cancer Biology Graduate Interdisciplinary Program; UA Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - William Davison
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Christopher B. Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA,corresponding authors Christopher B. Buck, Arvind Varsani
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925, Cape Town, South Africa,corresponding authors Christopher B. Buck, Arvind Varsani
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9
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Finn DR, Maldonado J, de Martini F, Yu J, Penton CR, Fontenele RS, Schmidlin K, Kraberger S, Varsani A, Gile GH, Barker B, Kollath DR, Muenich RL, Herckes P, Fraser M, Garcia-Pichel F. Agricultural practices drive biological loads, seasonal patterns and potential pathogens in the aerobiome of a mixed-land-use dryland. Sci Total Environ 2021; 798:149239. [PMID: 34325138 DOI: 10.1016/j.scitotenv.2021.149239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
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, we conducted a biologically comprehensive, year-long survey of its composition and dynamics for particles less than 10 μm in diameter based on quantitative analyses of DNA content coupled to genomic sequencing. Airborne biological loads were more dependent on seasonal events than on meteorological conditions and only weakly correlated with dust loads. Core aerobiome species could be understood as a mixture of high elevation (e.g. Microbacteriaceae, Micrococcaceae, Deinococci), and local plant and soil sources (e.g. Sphingomonas, Streptomyces, Acinetobacter). Despite the mixed used of the land surrounding the sampling site, taxa that contributed to high load events were largely traceable to proximal agricultural practices like cotton and livestock farming. This included not only the predominance of specific crop plant signals over those of native vegetation, but also that of their pathogens (bacterial, viral and eukaryotic). Faecal bacterial loads were also seasonally important, possibly sourced in intensive animal husbandry or manure fertilization activity, and this microbial load was enriched in tetracycline resistance genes. The presence of the native opportunistic pathogen, Coccidioides spp., by contrast, was detected only with highly sensitive techniques, and only rarely. We conclude that agricultural activity exerts a much stronger influence that the native vegetation as a mass loss factor to the land system and as an input to dryland aerobiomes, including in the dispersal of plant, animal and human pathogens and their genetic resistance characteristics.
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Affiliation(s)
- Damien R Finn
- Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Braunschweig 38116, Germany; The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA
| | - Juan Maldonado
- Knowledge Enterprise Genomics Core, Arizona State University, Tempe 85287-5001, AZ, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA
| | - Francesca de Martini
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Julian Yu
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - C Ryan Penton
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Kara Schmidlin
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Simona Kraberger
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA; Center for Evolution and Medicine, Arizona State University, Tempe 85287-5001, AZ, USA
| | - Gillian H Gile
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Bridget Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff 86011-4073, AZ, USA
| | - Daniel R Kollath
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff 86011-4073, AZ, USA
| | - Rebecca L Muenich
- School of Sustainable Engineering, Arizona State University, Tempe 85287-3005, AZ, USA
| | - Pierre Herckes
- School of Molecular Sciences, Arizona State University, Tempe 85287-1604, AZ, USA
| | - Matthew Fraser
- School of Sustainable Engineering, Arizona State University, Tempe 85287-3005, AZ, USA
| | - Ferran Garcia-Pichel
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
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10
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Fontenele RS, Köhler M, Majure LC, Avalos-Calleros JA, Argüello-Astorga GR, Font F, Vidal AH, Roumagnac P, Kraberger S, Martin DP, Lefeuvre P, Varsani A. Novel circular DNA virus identified in Opuntia discolor ( Cactaceae) that codes for proteins with similarity to those of geminiviruses. J Gen Virol 2021; 102. [PMID: 34726588 DOI: 10.1099/jgv.0.001671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Viral metagenomic studies have enabled the discovery of many unknown viruses and revealed that viral communities are much more diverse and ubiquitous than previously thought. Some viruses have multiple genome components that are encapsidated either in separate virions (multipartite viruses) or in the same virion (segmented viruses). In this study, we identify what is possibly a novel bipartite plant-associated circular single-stranded DNA virus in a wild prickly pear cactus, Opuntia discolor, that is endemic to the Chaco ecoregion in South America. Two ~1.8 kb virus-like circular DNA components were recovered, one encoding a replication-associated protein (Rep) and the other a capsid protein (CP). Both of the inferred protein sequences of the Rep and CP are homologous to those encoded by members of the family Geminiviridae. These two putatively cognate components each have a nonanucleotide sequence within a likely hairpin structure that is homologous to the origins of rolling-circle replication (RCR), found in diverse circular single-stranded DNA viruses. In addition, the two components share similar putative replication-associated iterative sequences (iterons), which in circular single-stranded DNA viruses are important for Rep binding during the initiation of RCR. Such molecular features provide support for the possible bipartite nature of this virus, which we named utkilio virus (common name of the Opuntia discolor in South America) components A and B. In the infectivity assays conducted in Nicotiana benthamiana plants, only the A component of utkilio virus, which encodes the Rep protein, was found to move and replicate systemically in N. benthamiana. This was not true for component B, for which we did not detect replication, which may have been due to this being a defective molecule or because of the model plants (N. benthamiana) used for the infection assays. Future experiments need to be conducted with other plants, including O. discolor, to understand more about the biology of these viral components.
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Affiliation(s)
- Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, 85287, USA
| | - Matias Köhler
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lucas C Majure
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Jesús A Avalos-Calleros
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, Mexico
| | - Gerardo R Argüello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, Mexico
| | - Fabián Font
- Herbario Museo de Farmacobotánica 'Juan A. Domínguez' (BAF), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andreza H Vidal
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, Brazil
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, 85287, USA
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, 85287, USA.,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925, Cape Town, South Africa
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11
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Fontenele RS, Kraberger S, Hadfield J, Driver EM, Bowes D, Holland LA, Faleye TOC, Adhikari S, Kumar R, Inchausti R, Holmes WK, Deitrick S, Brown P, Duty D, Smith T, Bhatnagar A, Yeager RA, Holm RH, von Reitzenstein NH, Wheeler E, Dixon K, Constantine T, Wilson MA, Lim ES, Jiang X, Halden RU, Scotch M, Varsani A. High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. Water Res 2021. [PMID: 34607084 DOI: 10.1101/2021.01.22.21250320%j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) likely emerged from a zoonotic spill-over event and has led to a global pandemic. The public health response has been predominantly informed by surveillance of symptomatic individuals and contact tracing, with quarantine, and other preventive measures have then been applied to mitigate further spread. Non-traditional methods of surveillance such as genomic epidemiology and wastewater-based epidemiology (WBE) have also been leveraged during this pandemic. Genomic epidemiology uses high-throughput sequencing of SARS-CoV-2 genomes to inform local and international transmission events, as well as the diversity of circulating variants. WBE uses wastewater to analyse community spread, as it is known that SARS-CoV-2 is shed through bodily excretions. Since both symptomatic and asymptomatic individuals contribute to wastewater inputs, we hypothesized that the resultant pooled sample of population-wide excreta can provide a more comprehensive picture of SARS-CoV-2 genomic diversity circulating in a community than clinical testing and sequencing alone. In this study, we analysed 91 wastewater samples from 11 states in the USA, where the majority of samples represent Maricopa County, Arizona (USA). With the objective of assessing the viral diversity at a population scale, we undertook a single-nucleotide variant (SNV) analysis on data from 52 samples with >90% SARS-CoV-2 genome coverage of sequence reads, and compared these SNVs with those detected in genomes sequenced from clinical patients. We identified 7973 SNVs, of which 548 were "novel" SNVs that had not yet been identified in the global clinical-derived data as of 17th June 2020 (the day after our last wastewater sampling date). However, between 17th of June 2020 and 20th November 2020, almost half of the novel SNVs have since been detected in clinical-derived data. Using the combination of SNVs present in each sample, we identified the more probable lineages present in that sample and compared them to lineages observed in North America prior to our sampling dates. The wastewater-derived SARS-CoV-2 sequence data indicates there were more lineages circulating across the sampled communities than represented in the clinical-derived data. Principal coordinate analyses identified patterns in population structure based on genetic variation within the sequenced samples, with clear trends associated with increased diversity likely due to a higher number of infected individuals relative to the sampling dates. We demonstrate that genetic correlation analysis combined with SNVs analysis using wastewater sampling can provide a comprehensive snapshot of the SARS-CoV-2 genetic population structure circulating within a community, which might not be observed if relying solely on clinical cases.
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Affiliation(s)
- Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Erin M Driver
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Devin Bowes
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - LaRinda A Holland
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Temitope O C Faleye
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ USA
| | - Rahul Kumar
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Rosa Inchausti
- Strategic Management and Diversity Office, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Wydale K Holmes
- Strategic Management and Diversity Office, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Stephanie Deitrick
- Enterprise GIS & Data Analytics, Information Technology, 31 E Fifth Street, City of Tempe, Tempe, AZ 85281, USA
| | - Philip Brown
- Municipal Utilities, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Darrell Duty
- Tempe Fire Medical Rescue, 31 E Fifth Street, City of Tempe, Tempe, AZ 85281, USA
| | - Ted Smith
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Aruni Bhatnagar
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Ray A Yeager
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Rochelle H Holm
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | | | - Elliott Wheeler
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Kevin Dixon
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Tim Constantine
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA
| | - Efrem S Lim
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institute of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Rolf U Halden
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; OneWaterOneHealth, Nonprofit Project of the Arizona State University Foundation, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; College of Health Solutions, Arizona State University, 550 N. 3rd St, Phoenix, AZ 85004, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA.
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12
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Fontenele RS, Kraberger S, Hadfield J, Driver EM, Bowes D, Holland LA, Faleye TOC, Adhikari S, Kumar R, Inchausti R, Holmes WK, Deitrick S, Brown P, Duty D, Smith T, Bhatnagar A, Yeager RA, Holm RH, von Reitzenstein NH, Wheeler E, Dixon K, Constantine T, Wilson MA, Lim ES, Jiang X, Halden RU, Scotch M, Varsani A. High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. Water Res 2021; 205:117710. [PMID: 34607084 PMCID: PMC8464352 DOI: 10.1016/j.watres.2021.117710] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 09/15/2021] [Accepted: 09/22/2021] [Indexed: 05/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) likely emerged from a zoonotic spill-over event and has led to a global pandemic. The public health response has been predominantly informed by surveillance of symptomatic individuals and contact tracing, with quarantine, and other preventive measures have then been applied to mitigate further spread. Non-traditional methods of surveillance such as genomic epidemiology and wastewater-based epidemiology (WBE) have also been leveraged during this pandemic. Genomic epidemiology uses high-throughput sequencing of SARS-CoV-2 genomes to inform local and international transmission events, as well as the diversity of circulating variants. WBE uses wastewater to analyse community spread, as it is known that SARS-CoV-2 is shed through bodily excretions. Since both symptomatic and asymptomatic individuals contribute to wastewater inputs, we hypothesized that the resultant pooled sample of population-wide excreta can provide a more comprehensive picture of SARS-CoV-2 genomic diversity circulating in a community than clinical testing and sequencing alone. In this study, we analysed 91 wastewater samples from 11 states in the USA, where the majority of samples represent Maricopa County, Arizona (USA). With the objective of assessing the viral diversity at a population scale, we undertook a single-nucleotide variant (SNV) analysis on data from 52 samples with >90% SARS-CoV-2 genome coverage of sequence reads, and compared these SNVs with those detected in genomes sequenced from clinical patients. We identified 7973 SNVs, of which 548 were "novel" SNVs that had not yet been identified in the global clinical-derived data as of 17th June 2020 (the day after our last wastewater sampling date). However, between 17th of June 2020 and 20th November 2020, almost half of the novel SNVs have since been detected in clinical-derived data. Using the combination of SNVs present in each sample, we identified the more probable lineages present in that sample and compared them to lineages observed in North America prior to our sampling dates. The wastewater-derived SARS-CoV-2 sequence data indicates there were more lineages circulating across the sampled communities than represented in the clinical-derived data. Principal coordinate analyses identified patterns in population structure based on genetic variation within the sequenced samples, with clear trends associated with increased diversity likely due to a higher number of infected individuals relative to the sampling dates. We demonstrate that genetic correlation analysis combined with SNVs analysis using wastewater sampling can provide a comprehensive snapshot of the SARS-CoV-2 genetic population structure circulating within a community, which might not be observed if relying solely on clinical cases.
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Affiliation(s)
- Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Erin M Driver
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Devin Bowes
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - LaRinda A Holland
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Temitope O C Faleye
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ USA
| | - Rahul Kumar
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Rosa Inchausti
- Strategic Management and Diversity Office, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Wydale K Holmes
- Strategic Management and Diversity Office, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Stephanie Deitrick
- Enterprise GIS & Data Analytics, Information Technology, 31 E Fifth Street, City of Tempe, Tempe, AZ 85281, USA
| | - Philip Brown
- Municipal Utilities, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Darrell Duty
- Tempe Fire Medical Rescue, 31 E Fifth Street, City of Tempe, Tempe, AZ 85281, USA
| | - Ted Smith
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Aruni Bhatnagar
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Ray A Yeager
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Rochelle H Holm
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | | | - Elliott Wheeler
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Kevin Dixon
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Tim Constantine
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA
| | - Efrem S Lim
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institute of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Rolf U Halden
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; OneWaterOneHealth, Nonprofit Project of the Arizona State University Foundation, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; College of Health Solutions, Arizona State University, 550 N. 3rd St, Phoenix, AZ 85004, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA.
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13
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Schmidlin K, Kraberger S, Cook C, DeNardo DF, Fontenele RS, Van Doorslaer K, Martin DP, Buck CB, Varsani A. A novel lineage of polyomaviruses identified in bark scorpions. Virology 2021; 563:58-63. [PMID: 34425496 DOI: 10.1016/j.virol.2021.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/15/2021] [Accepted: 08/15/2021] [Indexed: 11/30/2022]
Abstract
Polyomaviruses are non-enveloped viruses with circular double-stranded DNA genomes (~4-7 kb). Initially identified in mammals, polyomaviruses have now been identified in birds and a few fish species. Although fragmentary polyomavirus-like sequences have been detected as apparent 'hitchhikers' in shotgun genomics datasets of various arthropods, the possible diversity of these viruses in invertebrates remains unclear. Scorpions are predatory arachnids that are among the oldest terrestrial animals. Using high-throughput sequencing and traditional molecular techniques we determine the genome sequences of eight novel polyomaviruses in scorpions (Centruroides sculpturatus) from the greater Phoenix area, Arizona, USA. Analysis of Centruroides transcriptomic datasets elucidated the splicing of the viral late gene array, which is more complex than that of vertebrate polyomaviruses. Phylogenetic analysis provides further evidence of co-divergence of polyomaviruses with their hosts, suggesting that at least one ancestral species of polyomaviruses was circulating amongst the primitive common ancestors of arthropods and chordates.
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Affiliation(s)
- Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Chelsea Cook
- Department of Biological Sciences, Marquette University, 11428 W. Clybourn St, Milwaukee, WI, 53233, USA
| | - Dale F DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Koenraad Van Doorslaer
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85719, USA; School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, Tucson, AZ, 85724, USA
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, 7925, Cape Town, South Africa.
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14
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Hasanvand V, Heydanejad J, Massumi H, Kleinow T, Jeske H, Fontenele RS, Kraberger S, Varsani A. Genome characterization of parsley severe stunt-associated virus in Iran. Virus Genes 2021; 57:293-301. [PMID: 33881682 DOI: 10.1007/s11262-021-01835-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
Parsley severe stunt-associated virus (PSSaV) is a recently identified nanovirus first reported in Germany. During a survey for identification of nanoviruses infecting apiaceous plants in south-eastern Iran, PSSaV was identified and characterized using a combination of rolling circle amplification (RCA) and high-throughput sequencing. Parsley plant samples were collected from vegetable production farms in Kerman province. From two symptomatic samples (39Ba and 40Ba), seven PSSaV components (DNA-C, -S, -M, -R, -N, -U1 and -U2) with two phylogenetically distinct variants of DNA-R (R1 and R2) were identified. In common with the German isolate of PSSaV, no DNA-U4 component was identified. In addition, associated alphasatellite molecules were identified in samples 39Ba [n = 6] and 40Ba [n = 5]. Sequence analyses showed that concatenated component sequences of the two Iranian PSSaVs share 97.2% nucleotide identity with each other and 82% to the German isolate. The coat proteins (CPs) of the PSSaV Iranian sequences share 97.2% amino acid identity and ~ 84% identity with that of the German isolate. Sequence and phylogenetic analyses of a total of 11 recovered alphasatellites from the two samples can be classified into the genera Fabenesatellite [n = 2], Milvetsatellite [n = 1], Mivedwarsatellite [n = 2], Subclovsatellite [n = 2], Sophoyesatellite [n = 4] in the family Alphasatellitidae. Identification of PSSaV and other nanoviruses in wild and cultivated plants in Iran reveals that nanoviruses could be causing yield reduction in crops plants in this country.
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Affiliation(s)
- Vahid Hasanvand
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran
| | - Jahangir Heydanejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran. .,Research and Technology Institute of Plant Production (RTIPP), Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran.
| | - Hossain Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran
| | - Tatjana Kleinow
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Holger Jeske
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Rafaela S Fontenele
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA
| | - Simona Kraberger
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
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15
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Smith K, Fielding R, Schiavone K, Hall KR, Reid VS, Boyea D, Smith EL, Schmidlin K, Fontenele RS, Kraberger S, Varsani A. Circular DNA viruses identified in short-finned pilot whale and orca tissue samples. Virology 2021; 559:156-164. [PMID: 33892449 DOI: 10.1016/j.virol.2021.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 12/15/2022]
Abstract
Members of the Delphinidae family are widely distributed across the world's oceans. We used a viral metagenomic approach to identify viruses in orca (Orcinus orca) and short-finned pilot whale (Globicephala macrorhynchus) muscle, kidney, and liver samples from deceased animals. From orca tissue samples (muscle, kidney, and liver), we identified a novel polyomavirus (Polyomaviridae), three cressdnaviruses, and two genomoviruses (Genomoviridae). In the short-finned pilot whale we were able to identify one genomovirus in a kidney sample. The presence of unclassified cressdnavirus within two samples (muscle and kidney) of the same animal supports the possibility these viruses might be widespread within the animal. The orca polyomavirus identified here is the first of its species and is not closely related to the only other dolphin polyomavirus previously discovered. The identification and verification of these viruses expands the current knowledge of viruses that are associated with the Delphinidae family.
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Affiliation(s)
- Kendal Smith
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Russell Fielding
- HTC Honors College, Coastal Carolina University, Conway, SC, 29528, USA.
| | - Kelsie Schiavone
- Department of Earth and Environmental Systems, The University of the South, Sewanee, TN, 37383, USA
| | - Katharine R Hall
- Department of Earth and Environmental Systems, The University of the South, Sewanee, TN, 37383, USA
| | - Vincent S Reid
- Barrouallie Whaler's Project, Saint Vincent and the Grenadines
| | | | - Emma L Smith
- Department of Chemical & Biological Sciences, University of the West Indies-Cave Hill, Barbados
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, 7700, Cape Town, South Africa.
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16
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Fontenele RS, Kraberger S, Hadfield J, Driver EM, Bowes D, Holland LA, Faleye TO, Adhikari S, Kumar R, Inchausti R, Holmes WK, Deitrick S, Brown P, Duty D, Smith T, Bhatnagar A, Yeager RA, Holm RH, von Reitzenstein NH, Wheeler E, Dixon K, Constantine T, Wilson MA, Lim ES, Jiang X, Halden RU, Scotch M, Varsani A. High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. medRxiv 2021:2021.01.22.21250320. [PMID: 33501452 PMCID: PMC7836124 DOI: 10.1101/2021.01.22.21250320] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged from a zoonotic spill-over event and has led to a global pandemic. The public health response has been predominantly informed by surveillance of symptomatic individuals and contact tracing, with quarantine, and other preventive measures have then been applied to mitigate further spread. Non-traditional methods of surveillance such as genomic epidemiology and wastewater-based epidemiology (WBE) have also been leveraged during this pandemic. Genomic epidemiology uses high-throughput sequencing of SARS-CoV-2 genomes to inform local and international transmission events, as well as the diversity of circulating variants. WBE uses wastewater to analyse community spread, as it is known that SARS-CoV-2 is shed through bodily excretions. Since both symptomatic and asymptomatic individuals contribute to wastewater inputs, we hypothesized that the resultant pooled sample of population-wide excreta can provide a more comprehensive picture of SARS-CoV-2 genomic diversity circulating in a community than clinical testing and sequencing alone. In this study, we analysed 91 wastewater samples from 11 states in the USA, where the majority of samples represent Maricopa County, Arizona (USA). With the objective of assessing the viral diversity at a population scale, we undertook a single-nucleotide variant (SNV) analysis on data from 52 samples with >90% SARS-CoV-2 genome coverage of sequence reads, and compared these SNVs with those detected in genomes sequenced from clinical patients. We identified 7973 SNVs, of which 5680 were novel SNVs that had not yet been identified in the global clinical-derived data as of 17th June 2020 (the day after our last wastewater sampling date). However, between 17th of June 2020 and 20th November 2020, almost half of the SNVs have since been detected in clinical-derived data. Using the combination of SNVs present in each sample, we identified the more probable lineages present in that sample and compared them to lineages observed in North America prior to our sampling dates. The wastewater-derived SARS-CoV-2 sequence data indicates there were more lineages circulating across the sampled communities than represented in the clinical-derived data. Principal coordinate analyses identified patterns in population structure based on genetic variation within the sequenced samples, with clear trends associated with increased diversity likely due to a higher number of infected individuals relative to the sampling dates. We demonstrate that genetic correlation analysis combined with SNVs analysis using wastewater sampling can provide a comprehensive snapshot of the SARS-CoV-2 genetic population structure circulating within a community, which might not be observed if relying solely on clinical cases.
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Affiliation(s)
- Rafaela S. Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, Arizona, AZ 85281, USA
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, Arizona, AZ 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, Arizona, AZ 85281, USA
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Erin M. Driver
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Devin Bowes
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - LaRinda A. Holland
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, Arizona, AZ 85281, USA
| | - Temitope O.C. Faleye
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ USA
| | - Rahul Kumar
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Rosa Inchausti
- Strategic Management and Diversity Office, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Wydale K. Holmes
- Strategic Management and Diversity Office, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Stephanie Deitrick
- Enterprise GIS & Data Analytics, Information Technology, 31 E Fifth Street, City of Tempe, Tempe, AZ 85281, USA
| | - Philip Brown
- Municipal Utilities, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Darrell Duty
- Tempe Fire Medical Rescue, 31 E Fifth Street, City of Tempe, Tempe, AZ 85281, USA
| | - Ted Smith
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Aruni Bhatnagar
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Ray A. Yeager
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Rochelle H. Holm
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | | | - Elliott Wheeler
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Kevin Dixon
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Tim Constantine
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, Arizona, AZ 85287, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, 401 E. Tyler Mall, Tempe, AZ 85287, USA
| | - Efrem S. Lim
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, Arizona, AZ 85281, USA
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, Arizona, AZ 85287, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institute of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Rolf U. Halden
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
- OneWaterOneHealth, Nonprofit Project of the Arizona State University Foundation, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
- College of Health Solutions, Arizona State University, 550 N. 3 St, Phoenix, AZ 85004, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, Arizona, AZ 85281, USA
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, Arizona, AZ 85287, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, 401 E. Tyler Mall, Tempe, AZ 85287, USA
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17
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Khalifeh A, Blumstein DT, Fontenele RS, Schmidlin K, Richet C, Kraberger S, Varsani A. Diverse cressdnaviruses and an anellovirus identified in the fecal samples of yellow-bellied marmots. Virology 2020; 554:89-96. [PMID: 33388542 DOI: 10.1016/j.virol.2020.12.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
Over that last decade, coupling multiple strand displacement approaches with high throughput sequencing have resulted in the identification of genomes of diverse groups of small circular DNA viruses. Using a similar approach but with recovery of complete genomes by PCR, we identified a diverse group of single-stranded viruses in yellow-bellied marmot (Marmota flaviventer) fecal samples. From 13 fecal samples we identified viruses in the family Genomoviridae (n = 7) and Anelloviridae (n = 1), and several others that ware part of the larger Cressdnaviricota phylum but not within established families (n = 19). There were also circular DNA molecules identified (n = 4) that appear to encode one viral-like gene and have genomes of <1545 nts. This study gives a snapshot of viruses associated with marmots based on fecal sampling.
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Affiliation(s)
- Anthony Khalifeh
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Daniel T Blumstein
- Department of Ecology & Evolutionary Biology, Institute of the Environment & Sustainability, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Cécile Richet
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, 7925, Cape Town, South Africa.
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18
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Payne N, Kraberger S, Fontenele RS, Schmidlin K, Bergeman MH, Cassaigne I, Culver M, Varsani A, Van Doorslaer K. Novel Circoviruses Detected in Feces of Sonoran Felids. Viruses 2020; 12:v12091027. [PMID: 32942563 PMCID: PMC7551060 DOI: 10.3390/v12091027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 01/22/2023] Open
Abstract
Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small felid populations with lower genetic diversity are likely to be most threatened with extinction by emerging diseases, as with other selective pressures, due to having less adaptive potential. We used a metagenomic approach to identify novel circoviruses, which may have a negative impact on the population viability, from confirmed bobcat (Lynx rufus) and puma (Puma concolor) scats collected in Sonora, Mexico. Given some circoviruses are known to cause disease in their hosts, such as porcine and avian circoviruses, we took a non-invasive approach using scat to identify circoviruses in free-roaming bobcats and puma. Three circovirus genomes were determined, and, based on the current species demarcation, they represent two novel species. Phylogenetic analyses reveal that one circovirus species is more closely related to rodent associated circoviruses and the other to bat associated circoviruses, sharing highest genome-wide pairwise identity of approximately 70% and 63%, respectively. At this time, it is unknown whether these scat-derived circoviruses infect felids, their prey, or another organism that might have had contact with the scat in the environment. Further studies should be conducted to elucidate the host of these viruses and assess health impacts in felids.
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Affiliation(s)
- Natalie Payne
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85719, USA;
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA; (S.K.); (R.S.F.); (K.S.)
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA; (S.K.); (R.S.F.); (K.S.)
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA; (S.K.); (R.S.F.); (K.S.)
| | - Melissa H Bergeman
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA;
| | | | - Melanie Culver
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85719, USA;
- U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, University of Arizona, Tucson, AZ 85721, USA;
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA; (S.K.); (R.S.F.); (K.S.)
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7701, South Africa
- Correspondence: (A.V.); (K.V.D.)
| | - Koenraad Van Doorslaer
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85719, USA;
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA;
- The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, Tucson, AZ 85724, USA
- Correspondence: (A.V.); (K.V.D.)
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19
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Pinheiro-Lima B, Pereira-Carvalho RC, Alves-Freitas DMT, Kitajima EW, Vidal AH, Lacorte C, Godinho MT, Fontenele RS, Faria JC, Abreu EFM, Varsani A, Ribeiro SG, Melo FL. Transmission of the Bean-Associated Cytorhabdovirus by the Whitefly Bemisia tabaci MEAM1. Viruses 2020; 12:v12091028. [PMID: 32942623 PMCID: PMC7551397 DOI: 10.3390/v12091028] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/04/2020] [Accepted: 09/11/2020] [Indexed: 01/09/2023] Open
Abstract
The knowledge of genomic data of new plant viruses is increasing exponentially; however, some aspects of their biology, such as vectors and host range, remain mostly unknown. This information is crucial for the understanding of virus–plant interactions, control strategies, and mechanisms to prevent outbreaks. Typically, rhabdoviruses infect monocot and dicot plants and are vectored in nature by hemipteran sap-sucking insects, including aphids, leafhoppers, and planthoppers. However, several strains of a potentially whitefly-transmitted virus, papaya cytorhabdovirus, were recently described: (i) bean-associated cytorhabdovirus (BaCV) in Brazil, (ii) papaya virus E (PpVE) in Ecuador, and (iii) citrus-associated rhabdovirus (CiaRV) in China. Here, we examine the potential of the Bemisia tabaci Middle East-Asia Minor 1 (MEAM1) to transmit BaCV, its morphological and cytopathological characteristics, and assess the incidence of BaCV across bean producing areas in Brazil. Our results show that BaCV is efficiently transmitted, in experimental conditions, by B. tabaci MEAM1 to bean cultivars, and with lower efficiency to cowpea and soybean. Moreover, we detected BaCV RNA in viruliferous whiteflies but we were unable to visualize viral particles or viroplasm in the whitefly tissues. BaCV could not be singly isolated for pathogenicity tests, identification of the induced symptoms, and the transmission assay. BaCV was detected in five out of the seven states in Brazil included in our study, suggesting that it is widely distributed throughout bean producing areas in the country. This is the first report of a whitefly-transmitted rhabdovirus.
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Affiliation(s)
- Bruna Pinheiro-Lima
- Embrapa Recursos Genéticos e Biotecnologia, Brasília DF 70770-017, Brazil; (B.P.-L.); (D.M.T.A.-F.); (A.H.V.); (C.L.); (M.T.G.); (E.F.M.A.)
- Departamento de Fitopatologia, Instituto de Biologia, Universidade de Brasília, Brasília DF 70275-970, Brazil;
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília DF 70275-970, Brazil
| | - Rita C. Pereira-Carvalho
- Departamento de Fitopatologia, Instituto de Biologia, Universidade de Brasília, Brasília DF 70275-970, Brazil;
| | - Dione M. T. Alves-Freitas
- Embrapa Recursos Genéticos e Biotecnologia, Brasília DF 70770-017, Brazil; (B.P.-L.); (D.M.T.A.-F.); (A.H.V.); (C.L.); (M.T.G.); (E.F.M.A.)
| | - Elliot W. Kitajima
- Departamento de Fitopatologia, Escola Superior de Agricultura Luiz de Queiroz, Piracicaba SP 13418-900, Brazil;
| | - Andreza H. Vidal
- Embrapa Recursos Genéticos e Biotecnologia, Brasília DF 70770-017, Brazil; (B.P.-L.); (D.M.T.A.-F.); (A.H.V.); (C.L.); (M.T.G.); (E.F.M.A.)
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília DF 70275-970, Brazil
| | - Cristiano Lacorte
- Embrapa Recursos Genéticos e Biotecnologia, Brasília DF 70770-017, Brazil; (B.P.-L.); (D.M.T.A.-F.); (A.H.V.); (C.L.); (M.T.G.); (E.F.M.A.)
| | - Marcio T. Godinho
- Embrapa Recursos Genéticos e Biotecnologia, Brasília DF 70770-017, Brazil; (B.P.-L.); (D.M.T.A.-F.); (A.H.V.); (C.L.); (M.T.G.); (E.F.M.A.)
| | - Rafaela S. Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA; (R.S.F.); (A.V.)
| | | | - Emanuel F. M. Abreu
- Embrapa Recursos Genéticos e Biotecnologia, Brasília DF 70770-017, Brazil; (B.P.-L.); (D.M.T.A.-F.); (A.H.V.); (C.L.); (M.T.G.); (E.F.M.A.)
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA; (R.S.F.); (A.V.)
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7701, South Africa
| | - Simone G. Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília DF 70770-017, Brazil; (B.P.-L.); (D.M.T.A.-F.); (A.H.V.); (C.L.); (M.T.G.); (E.F.M.A.)
- Correspondence: (S.G.R.); (F.L.M.)
| | - Fernando L. Melo
- Departamento de Fitopatologia, Instituto de Biologia, Universidade de Brasília, Brasília DF 70275-970, Brazil;
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília DF 70275-970, Brazil
- Correspondence: (S.G.R.); (F.L.M.)
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20
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Fontenele RS, Roumagnac P, Richet C, Kraberger S, Stainton D, Aleamotu'a M, Filloux D, Bernardo P, Harkins GW, McCarthy J, Charles LS, Lamas NS, Abreu EFM, Abreu RA, Batista GB, Lacerda ALM, Salywon A, Wojciechowski MF, Majure LC, Martin DP, Ribeiro SG, Lefeuvre P, Varsani A. Diverse genomoviruses representing twenty-nine species identified associated with plants. Arch Virol 2020; 165:2891-2901. [PMID: 32893316 DOI: 10.1007/s00705-020-04801-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/09/2020] [Indexed: 02/06/2023]
Abstract
Genomoviruses (family Genomoviridae) are circular single-stranded DNA viruses that have been mainly identified through metagenomics studies in a wide variety of samples from various environments. Here, we describe 98 genomes of genomoviruses found associated with members of 19 plant families from Australia, Brazil, France, South Africa and the USA. These 98 genomoviruses represent 29 species, 26 of which are new, in the genera Gemykolovirus (n = 37), Gemyduguivirus (n = 9), Gemygorvirus (n = 8), Gemykroznavirus (n = 6), Gemycircularvirus (n = 21) and Gemykibivirus (n = 17).
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Affiliation(s)
- Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics and Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Life sciences, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Philippe Roumagnac
- CIRAD, BGPI, 34398, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, 34398, Montpellier, France
| | - Cécile Richet
- CIRAD, BGPI, 34398, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, 34398, Montpellier, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics and Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, 72701, USA
| | - Maketalena Aleamotu'a
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Denis Filloux
- CIRAD, BGPI, 34398, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, 34398, Montpellier, France
| | - Pauline Bernardo
- CIRAD, BGPI, 34398, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, 34398, Montpellier, France.,Enza Zaden, Haling 1-E, 1602 DB, Enkhuizen, The Netherlands
| | - Gordon W Harkins
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - James McCarthy
- Manaaki Whenua, Landcare Research, Lincoln, 7640, New Zealand
| | - Lachlan S Charles
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Natalia S Lamas
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | | | - Rayane A Abreu
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.,PPG Ciências Naturais e Biotecnologia, Universidade Federal de Campina Grande, Cuité, PB, Brazil
| | - Graciete B Batista
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.,PPG Ciências Naturais e Biotecnologia, Universidade Federal de Campina Grande, Cuité, PB, Brazil
| | - Ana L M Lacerda
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | | | | | - Lucas C Majure
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, 7925, South Africa
| | - Simone G Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.,PPG Ciências Naturais e Biotecnologia, Universidade Federal de Campina Grande, Cuité, PB, Brazil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics and Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-5001, USA. .,School of Life sciences, Arizona State University, Tempe, AZ, 85287-5001, USA. .,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa.
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21
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Fontenele RS, Salywon AM, Majure LC, Cobb IN, Bhaskara A, Avalos-Calleros JA, Argüello-Astorga GR, Schmidlin K, Khalifeh A, Smith K, Schreck J, Lund MC, Köhler M, Wojciechowski MF, Hodgson WC, Puente-Martinez R, Van Doorslaer K, Kumari S, Vernière C, Filloux D, Roumagnac P, Lefeuvre P, Ribeiro SG, Kraberger S, Martin DP, Varsani A. A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants. Viruses 2020; 12:E398. [PMID: 32260283 PMCID: PMC7232249 DOI: 10.3390/v12040398] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022] Open
Abstract
Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share > 78.4% nucleotide identity with one another and < 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe.
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Affiliation(s)
- Rafaela S. Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Andrew M. Salywon
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Lucas C. Majure
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Ilaria N. Cobb
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Amulya Bhaskara
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- Center for Research in Engineering, Science and Technology, Paradise Valley High School, 3950 E Bell Rd, Phoenix, AZ 85032, USA
| | - Jesús A. Avalos-Calleros
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., Mexico; (J.A.A.-C.); (G.R.A.-A.)
| | - Gerardo R. Argüello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., Mexico; (J.A.A.-C.); (G.R.A.-A.)
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Anthony Khalifeh
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Kendal Smith
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Joshua Schreck
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Michael C. Lund
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Matias Köhler
- Departamento de BotânicaPrograma de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501970, Brazil;
| | | | - Wendy C. Hodgson
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Raul Puente-Martinez
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and UA Cancer Center, University of Arizona, Tucson, AZ 85721, USA;
| | - Safaa Kumari
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol Station, Beqa’a, Zahle, Lebanon;
| | - Christian Vernière
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | - Denis Filloux
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | - Philippe Roumagnac
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | | | - Simone G. Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, Brazil;
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
| | - Darren P. Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa;
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7925, South Africa
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22
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Chabi-Jesus C, Najar A, Fontenele RS, Kumari SG, Ramos-González PL, Freitas-Astúa J, Kraberger S, Varsani A. Viruses representing two new genomovirus species identified in citrus from Tunisia. Arch Virol 2020; 165:1225-1229. [PMID: 32146505 DOI: 10.1007/s00705-020-04569-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/31/2020] [Indexed: 11/26/2022]
Abstract
Using a high-throughput sequencing approach, we identified four genomoviruses (family Genomoviridae) associated with a sweet orange (Citrus sinensis) plant collected in Tunisia. The ssDNA genomes of these genomoviruses, which were amplified, cloned and Sanger sequenced, range in size from 2156 to 2191 nt. Three of these viruses share > 99% full-genome pairwise sequence identity and are referred to as citrus Tunisia genomovirus 1 (CTNGmV-1). The CTNGmV-1 isolates share < 62% genome-wide pairwise nucleotide sequence identity with other genomoviruses and belong to the genus Gemykolovirus. The genome of the fourth virus, which was called CTNGmV-2, shares < 68% nucleotide sequence identity with other genomoviruses and belongs to the genus Gemycircularvirus. Based on the species demarcation criteria for members of the family Genomoviridae, CTNGmV-1 and -2 would each represent a new species. Although found associated with Citrus sp. plants, it is likely that these viruses infect fungi or other organisms associated with the plants.
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Affiliation(s)
- Camila Chabi-Jesus
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Escola Superior de Agricultura Luiz de Queiroz/Esalq/USP, Piracicaba, SP, Brazil
- Instituto Biológico/IB, São Paulo, SP, Brazil
| | - Asma Najar
- Laboratory of Plant Protection, National Institute of Agronomic Research of Tunisia, Rue Hédi Karray, El Menzah, Tunisia.
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Safaa G Kumari
- Virology Laboratory, International Centre for Agricultural Research in the Dry Areas (ICARDA), Tunis, Tunisia
- International Centre for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | | | - Juliana Freitas-Astúa
- Instituto Biológico/IB, São Paulo, SP, Brazil
- Embrapa Mandioca e Fruticultura/CNPMF, Cruz das Almas, BA, Brazil
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
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23
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Orton JP, Morales M, Fontenele RS, Schmidlin K, Kraberger S, Leavitt DJ, Webster TH, Wilson MA, Kusumi K, Dolby GA, Varsani A. Virus Discovery in Desert Tortoise Fecal Samples: Novel Circular Single-Stranded DNA Viruses. Viruses 2020; 12:v12020143. [PMID: 31991902 PMCID: PMC7077246 DOI: 10.3390/v12020143] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 12/25/2022] Open
Abstract
The Sonoran Desert tortoise Gopherus morafkai is adapted to the desert, and plays an important ecological role in this environment. There is limited information on the viral diversity associated with tortoises (family Testudinidae), and to date no DNA virus has been identified associated with these animals. This study aimed to assess the diversity of DNA viruses associated with the Sonoran Desert tortoise by sampling their fecal matter. A viral metagenomics approach was used to identify the DNA viruses in fecal samples from wild Sonoran Desert tortoises in Arizona, USA. In total, 156 novel single-stranded DNA viruses were identified from 40 fecal samples. Those belonged to two known viral families, the Genomoviridae (n = 27) and Microviridae (n = 119). In addition, 10 genomes were recovered that belong to the unclassified group of circular-replication associated protein encoding single-stranded (CRESS) DNA virus and five circular molecules encoding viral-like proteins.
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Affiliation(s)
- Joseph P. Orton
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
| | - Rafaela S. Fontenele
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
| | - Kara Schmidlin
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
| | - Daniel J. Leavitt
- Natural Resources Program, Naval Facilities Engineering Command-Navy Region Southwest, San Diego, CA 92101, USA, USA;
| | - Timothy H. Webster
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
| | - Greer A. Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- Correspondence: (G.A.D.); (A.V.); Tel.: +1-480-965-7456 (G.A.D.); +1-480-727-2093 (A.V.)
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7925, South Africa
- Correspondence: (G.A.D.); (A.V.); Tel.: +1-480-965-7456 (G.A.D.); +1-480-727-2093 (A.V.)
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Sommers P, Fontenele RS, Kringen T, Kraberger S, Porazinska DL, Darcy JL, Schmidt SK, Varsani A. Single-Stranded DNA Viruses in Antarctic Cryoconite Holes. Viruses 2019; 11:E1022. [PMID: 31689942 PMCID: PMC6893807 DOI: 10.3390/v11111022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/28/2022] Open
Abstract
Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.
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Affiliation(s)
- Pacifica Sommers
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Tayele Kringen
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Dorota L Porazinska
- Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, USA.
| | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Steven K Schmidt
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7701, South Africa.
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25
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Fontenele RS, Lacorte C, Lamas NS, Schmidlin K, Varsani A, Ribeiro SG. Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil. Viruses 2019; 11:E710. [PMID: 31382446 PMCID: PMC6723397 DOI: 10.3390/v11080710] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 12/27/2022] Open
Abstract
Capybaras (Hydrochoerus hydrochaeris), the world's largest rodents, are distributed throughout South America. These wild herbivores are commonly found near water bodies and are well adapted to rural and urban areas. There is limited information on the viruses circulating through capybaras. This study aimed to expand the knowledge on the viral diversity associated with capybaras by sampling their faeces. Using a viral metagenomics approach, we identified diverse single-stranded DNA viruses in the capybara faeces sampled in the Distrito Federal, Brazil. A total of 148 complete genomes of viruses in the Microviridae family were identified. In addition, 14 genomoviruses (family Genomoviridae), a novel cyclovirus (family Circoviridae), and a smacovirus (family Smacoviridae) were identified. Also, 37 diverse viruses that cannot be assigned to known families and more broadly referred to as unclassified circular replication associated protein encoding single-stranded (CRESS) DNA viruses were identified. This study provides a snapshot of the viral diversity associated with capybaras that may be infectious to these animals or associated with their microbiota or diet.
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Affiliation(s)
- Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF 70770-017, Brazil
| | - Cristiano Lacorte
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF 70770-017, Brazil
| | - Natalia S Lamas
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF 70770-017, Brazil
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa.
| | - Simone G Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF 70770-017, Brazil.
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26
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Kraberger S, Schmidlin K, Fontenele RS, Walters M, Varsani A. Unravelling the Single-Stranded DNA Virome of the New Zealand Blackfly. Viruses 2019; 11:E532. [PMID: 31181730 PMCID: PMC6630596 DOI: 10.3390/v11060532] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/01/2019] [Accepted: 06/04/2019] [Indexed: 01/23/2023] Open
Abstract
Over the last decade, arthropods have been shown to harbour a rich diversity of viruses. Through viral metagenomics a large diversity of single-stranded (ss) DNA viruses have been identified. Here we examine the ssDNA virome of the hematophagous New Zealand blackfly using viral metagenomics. Our investigation reveals a plethora of novel ssDNA viral genomes, some of which cluster in the viral families Genomoviridae (n = 9), Circoviridae (n = 1), and Microviridae (n = 108), others in putative families that, at present, remain unclassified (n = 20) and one DNA molecule that only encodes a replication associated protein. Among these novel viruses, two putative multi-component virus genomes were recovered, and these are most closely related to a Tongan flying fox faeces-associated multi-component virus. Given that the only other known multi-component circular replication-associated (Rep) protein encoding single-stranded (CRESS) DNA viruses infecting plants are in the families Geminiviridae (members of the genus Begomovirus) and Nanoviridae, it appears these are likely a new multi-component virus group which may be associated with animals. This study reiterates the diversity of ssDNA viruses in nature and in particular with the New Zealand blackflies.
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Matthew Walters
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa.
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27
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Kraberger S, Cook CN, Schmidlin K, Fontenele RS, Bautista J, Smith B, Varsani A. Diverse single-stranded DNA viruses associated with honey bees (Apis mellifera). Infect Genet Evol 2019; 71:179-188. [PMID: 30928605 DOI: 10.1016/j.meegid.2019.03.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/28/2019] [Accepted: 03/25/2019] [Indexed: 11/26/2022]
Abstract
Honey bees (Apis mellifera) research has increased in light of their progressive global decline over the last decade and the important role they play in pollination. One expanding area of honey bee research is analysis of their microbial community including viruses. Several RNA viruses have been characterized but little is known about DNA viruses associated with bees. Here, using a metagenomics based approach, we reveal the presence of a broad range of novel single-stranded DNA viruses from the hemolymph and brain of nurse and forager (worker divisions of labour) bees belonging to two honey bees subspecies, Italian (Apis mellifera linguistica) and New World Carniolan (Apis mellifera carnica). Genomes of 100 diverse viruses were identified, designated into three groupings; genomoviruses (family Genomoviridae) (n = 4), unclassified replication associated protein encoding single-stranded DNA viruses (n = 28), and microviruses (family Microviridae; subfamily Gokushovirinae) (n = 70). Amongst the viruses identified, it appears that nurses harbour a higher diversity of these viruses comparative to the foragers. Between subspecies, the most striking outcome was the extremely high number of diverse microviruses identified in the Italian bees comparative to the New World Carniolan, likely indicating an association to the diversity of the bacterial community associated with these subspecies.
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA.
| | - Chelsea N Cook
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joshua Bautista
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | - Brian Smith
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, 7925 Cape Town, South Africa.
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28
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Fontenele RS, Ribeiro GC, Lamas NS, Ribeiro SG, Costa AF, Boiteux LS, Fonseca MEN. First Report of Sida micrantha mosaic virus Infecting Oxalis Species in Brazil. Plant Dis 2018; 102:1862. [PMID: 30125166 DOI: 10.1094/pdis-01-18-0149-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- R S Fontenele
- Embrapa Recursos Genéticos e Biotecnologia, Brasília - DF, Brazil
| | - G C Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília - DF, Brazil
| | - N S Lamas
- Embrapa Recursos Genéticos e Biotecnologia, Brasília - DF, Brazil
| | - S G Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília - DF, Brazil
| | - A F Costa
- Embrapa Hortaliças, Brasília - DF, Brazil
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29
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Smeele ZE, Burns JM, Van Doorsaler K, Fontenele RS, Waits K, Stainton D, Shero MR, Beltran RS, Kirkham AL, Berngartt R, Kraberger S, Varsani A. Diverse papillomaviruses identified in Weddell seals. J Gen Virol 2018; 99:549-557. [PMID: 29469687 DOI: 10.1099/jgv.0.001028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Papillomaviridae is a diverse family of circular, double-stranded DNA (dsDNA) viruses that infect a broad range of mammalian, avian and fish hosts. While papillomaviruses have been characterized most extensively in humans, the study of non-human papillomaviruses has contributed greatly to our understanding of their pathogenicity and evolution. Using high-throughput sequencing approaches, we identified 7 novel papillomaviruses from vaginal swabs collected from 81 adult female Weddell seals (Leptonychotes weddellii) in the Ross Sea of Antarctica between 2014-2017. These seven papillomavirus genomes were amplified from seven individual seals, and six of the seven genomes represented novel species with distinct evolutionary lineages. This highlights the diversity of papillomaviruses among the relatively small number of Weddell seal samples tested. Viruses associated with large vertebrates are poorly studied in Antarctica, and this study adds information about papillomaviruses associated with Weddell seals and contributes to our understanding of the evolutionary history of papillomaviruses.
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Affiliation(s)
- Zoe E Smeele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.,School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Jennifer M Burns
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
| | - Koenraad Van Doorsaler
- School of Animal and Comparative Biomedical Sciences, Cancer Biology Graduate Interdisciplinary Program, Genetics Graduate Interdisciplinary Program, and Bio5, University of Arizona, 1657 E Helen St., Tucson, AZ 85721, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Kara Waits
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Daisy Stainton
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Michelle R Shero
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
| | - Roxanne S Beltran
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA.,Department of Biology and Wildlife, University of Alaska Fairbanks, PO Box 756100, Fairbanks, AK 99775, USA
| | - Amy L Kirkham
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA.,College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Rd Juneau, Alaska 99801, USA
| | | | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.,The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
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30
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Fontenele RS, Alves-Freitas DMT, Silva PIT, Foresti J, Silva PR, Godinho MT, Varsani A, Ribeiro SG. Discovery of the first maize-infecting mastrevirus in the Americas using a vector-enabled metagenomics approach. Arch Virol 2017; 163:263-267. [PMID: 28956174 DOI: 10.1007/s00705-017-3571-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 09/04/2017] [Indexed: 01/18/2023]
Abstract
The genus Mastrevirus (family Geminiviridae) is composed of single-stranded DNA viruses that infect mono- and dicotyledonous plants and are transmitted by leafhoppers. In South America, there have been only two previous reports of mastreviruses, both identified in sweet potatoes (from Peru and Uruguay). As part of a general viral surveillance program, we used a vector-enabled metagenomics (VEM) approach and sampled leafhoppers (Dalbulus maidis) in Itumbiara (State of Goiás), Brazil. High-throughput sequencing of viral DNA purified from the leafhopper sample revealed mastrevirus-like contigs. Using a set of abutting primers, a 2746-nt circular genome was recovered. The circular genome has a typical mastrevirus genome organization and shares <63% pairwise identity with other mastrevirus isolates from around the world. Therefore, the new mastrevirus was tentatively named "maize striate mosaic virus". Seventeen maize leaf samples were collected in the same field as the leafhoppers, and ten samples were found to be positive for this mastrevirus. Furthermore, the ten genomes recovered from the maize samples share >99% pairwise identity with the one from the leafhopper. This is the first report of a maize-infecting mastrevirus in the Americas, the first identified in a non-vegetatively propagated mastrevirus host in South America, and the first mastrevirus to be identified in Brazil.
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Affiliation(s)
- Rafaela S Fontenele
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil.,The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA, 85287
| | | | - Pedro I T Silva
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | - Josemar Foresti
- Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Universidade de Brasília, Brasília, DF, Brasil
| | - Paulo R Silva
- Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Universidade de Brasília, Brasília, DF, Brasil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA, 85287. .,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa.
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31
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Fontenele RS, Lamas NS, Lacorte C, Lacerda ALM, Varsani A, Ribeiro SG. A novel geminivirus identified in tomato and cleome plants sampled in Brazil. Virus Res 2017; 240:175-179. [PMID: 28843502 DOI: 10.1016/j.virusres.2017.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/11/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022]
Abstract
Viruses in the family Geminiviridae have single-stranded DNA genomes encapsulated in geminate icosahedral particles. High throughput sequencing (HTS) for metagenomic approaches are being extensively used for the identification of known and novel viruses. Using a HTS approach, we identified a novel geminivirus in a tomato (Solanum lycopersicum) sample and a Cleome sp. sample collected in the midwest region of Brazil. The genomes from the two samples share 99.96% identity and ∼61-63% to genomes in the genus Capulavirus. The novel virus has been tentatively named tomato associated geminivirus 1 (TaGV1). No visual symptoms were observed in the field tomato plant or in the inoculated Nicotiana benthamiana where the virus established a systemic infection. The replication associated protein of TaGV1 is most similar to that encoded by capulaviruses (sharing 62-70% identity), whereas the CP is most similar to that of tomato pseudo curly top virus (sharing ∼31% identity). In the TaGV1 positive Cleome sp. sample, begomovirus DNA A and B components were also detected sharing 96% and 90% sequence identity to cleome leaf crumple virus DNA A and B components, respectively. Using a HTS approach, we identified TaGV1 in tomato and Cleome sp. samples and this is the first report of a geminivirus that is non-begomovirus in Brazil.
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Affiliation(s)
- Rafaela S Fontenele
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Natalia S Lamas
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa.
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32
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Blawid R, Fontenele RS, Lacorte C, Ribeiro SG. Molecular and biological characterization of corchorus mottle virus, a new begomovirus from Brazil. Arch Virol 2013; 158:2603-9. [PMID: 23812656 DOI: 10.1007/s00705-013-1764-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/05/2013] [Indexed: 10/26/2022]
Abstract
A begomovirus infecting Orinoco jute (Corchorus hirtus) from Brazil was characterized. Molecular analysis revealed a bipartite genomic organization, which is typical of the New World begomoviruses. Sequence analysis and phylogenetic data showed that both genomic components have the closest relationship with abutilon mosaic Brazil virus, with an identity of 87.3 % for DNA-A, indicating that this virus is a member of a new begomovirus species for which the name "Corchorus mottle virus" (CoMoV) is proposed. Sida rhombifolia plants inoculated by biolistics with an infectious clone of CoMoV showed systemic vein chlorosis, mottling and leaf deformation symptoms, while Nicotiana benthamiana and tomato plants had symptomless infection. CoMoV is the first corchorus-infecting begomovirus reported in Brazil.
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Affiliation(s)
- Rosana Blawid
- Laboratório de Interação Planta-Praga III, Embrapa Recursos Genéticos e Biotecnologia, Pq. Estação Biológica, Brasília, DF, 70770-917, Brazil
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33
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Diniz JR, Correa JR, Moreira DDA, Fontenele RS, de Oliveira AL, Abdelnur PV, Dutra JDL, Freire RO, Rodrigues MO, Neto BAD. Water-Soluble Tb3+ and Eu3+ Complexes with Ionophilic (Ionically Tagged) Ligands as Fluorescence Imaging Probes. Inorg Chem 2013; 52:10199-205. [DOI: 10.1021/ic4017678] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | | | | | | | | | - Patrícia V. Abdelnur
- National Center for Agroenergy Research, Brazilian Enterprise for Agricultural Research, EMBRAPA Agroenergy, 3448-4246
Brasília-DF, Brazil
| | - José D. L. Dutra
- Pople Computational Chemistry Laboratory, Universidade Federal de Sergipe, 49100-000, São Cristóvão,
Sergipe, Brazil
| | - Ricardo O. Freire
- Pople Computational Chemistry Laboratory, Universidade Federal de Sergipe, 49100-000, São Cristóvão,
Sergipe, Brazil
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34
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Fernandes-Acioli NAN, Pereira-Carvalho RC, Fontenele RS, Lacorte C, Ribeiro SG, Fonseca MEN, Boiteux LS. First Report of Sida micrantha mosaic virus in Phaseolus vulgaris in Brazil. Plant Dis 2011; 95:1196. [PMID: 30732032 DOI: 10.1094/pdis-05-10-0343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Snap and common beans (Phaseolus vulgaris L.) are severely affected by Bean golden mosaic virus (BGMV) infection, so far the only begomovirus reported on these crops in Brazil (1). Samples of snap and common beans colonized by the whitefly Bemisia tabaci biotype B and displaying golden mosaic, chlorotic spots, and leaf distortion were collected in three production regions in Goiás State (Goianápolis, Luziânia, and Itaberaí) between 2003 and 2007. Total DNA extracted from leaf samples was used as template in PCR assays using universal primers targeting conserved regions of the DNA-A and DNA-B genomes (3). Begomovirus-specific amplicons were observed only with DNA template from symptomatic plants. Two single amplicons were observed for both genomic segments, indicating the presence of bipartite species in all samples. Sequence analysis of four isolates (named as GO-176, GO-260, GO-354, and GO-368) obtained from common bean samples indicated identity levels of approximately 95% with the DNA-A segment of BGMV (GenBank Accession No. FJ665283). However, the complete DNA-A sequence (GenBank Accession No. HM357459.1) of the GO-060 isolate (from a symptomatic snap bean plant collected in Goianápolis) displayed 76% identity with BGMV (GenBank Accession No. FJ665283) and 95% identity with the DNA-A of a Sida micrantha mosaic virus (SimMV) isolate (GenBank Accession No. EU908733.1) reported to be infecting okra (Abelmoschus esculentus L.) and 94.8% with a SimMV isolate reported to be infecting soybean (GenBank Accession No. FJ686693) in Brazil (2). Koch's postulates were fulfilled for the isolate GO-060 by inoculating a set of soybean and bean accessions via a biolistic approach. The ratio of positive PCR amplicons per total of inoculated plants were 15 of 16 for snap bean cv. Trepador, 9 of 10 for snap bean cv. Fartura, 18 of 24 for common bean cv. Olate Pinto, and 19 of 25 for common bean cv. Carioca. The isolate was also able to infect eight of nine soybean 'Doko' plants. Sequence analysis using symptomatic leaf samples (15 days after inoculation) confirmed SimMV as the causal agent. To our knowledge, this is the first report of a SimMV isolate infecting P. vulgaris. This virus is apparently fast expanding its host range from Malvaceae to Solanaceae species and leguminous hosts after the introduction of B. tabaci biotype B (2). More extensive surveys are necessary to access the current epidemiological importance of SimMV in both snap and common beans in Brazil. References: (1) J.C. Faria and D. P. Maxwell. Phytopathology 89:262, 1999. (2) F. R. Fernandes et al. Arch. Virol. 154:1567, 2009. (3) M. R. Rojas et al. Plant Dis. 77:340, 1993.
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Affiliation(s)
- N A N Fernandes-Acioli
- Universidade de Brasília (UnB), Departamento de Fitopatologia, 70910-900, Brasília-DF, Brazil
| | - R C Pereira-Carvalho
- Universidade de Brasília (UnB), Departamento de Fitopatologia, 70910-900, Brasília-DF, Brazil
| | - R S Fontenele
- Embrapa Recursos Genéticos and Biotecnologia, CP 2372, 70770-900, Brasília-DF, Brazil
| | - C Lacorte
- Embrapa Recursos Genéticos and Biotecnologia, CP 2372, 70770-900, Brasília-DF, Brazil
| | - S G Ribeiro
- Embrapa Recursos Genéticos and Biotecnologia, CP 2372, 70770-900, Brasília-DF, Brazil
| | - M E N Fonseca
- Embrapa Hortaliças, CP 218, 70359-970, Brasília-DF, Brazil
| | - L S Boiteux
- Embrapa Hortaliças, CP 218, 70359-970, Brasília-DF, Brazil
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