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In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
Mart Krupovic; Dann Turner; Vera Morozova; Mike Dyall-Smith; Hanna M. Oksanen; Rob Edwards; Bas E. Dutilh; Susan M. Lehman; Alejandro Reyes; Diana P. Baquero; Matthew B. Sullivan; Jumpei Uchiyama; Jesca Nakavuma; Jakub Barylski; Mark J. Young; Shishen Du; Poliane Alfenas-Zerbini; Alla Kushkina; Andrew M. Kropinski; Ipek Kurtböke; J. Rodney Brister; Cédric Lood; B. L. Sarkar; Tong Yigang; Ying Liu; Li Huang; Johannes Wittmann; Nina Chanishvili; Leonardo J. van Zyl; Janis Rumnieks; Tomohiro Mochizuki; Matti Jalasvuori; Ramy K. Aziz; Małgorzata Łobocka; Kenneth M. Stedman; Andrey N. Shkoporov; Annika Gillis; Xu Peng; François Enault; Petar Knezevic; Rob Lavigne; Sung-Keun Rhee; Virginija Cvirkaite-Krupovic; Cristina Moraru; Andrea I. Moreno Switt; Minna M. Poranen; Andrew Millard; David Prangishvili; Evelien M. Adriaenssens. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021. Archives of Virology 2021, 1 -6.
AMA StyleMart Krupovic, Dann Turner, Vera Morozova, Mike Dyall-Smith, Hanna M. Oksanen, Rob Edwards, Bas E. Dutilh, Susan M. Lehman, Alejandro Reyes, Diana P. Baquero, Matthew B. Sullivan, Jumpei Uchiyama, Jesca Nakavuma, Jakub Barylski, Mark J. Young, Shishen Du, Poliane Alfenas-Zerbini, Alla Kushkina, Andrew M. Kropinski, Ipek Kurtböke, J. Rodney Brister, Cédric Lood, B. L. Sarkar, Tong Yigang, Ying Liu, Li Huang, Johannes Wittmann, Nina Chanishvili, Leonardo J. van Zyl, Janis Rumnieks, Tomohiro Mochizuki, Matti Jalasvuori, Ramy K. Aziz, Małgorzata Łobocka, Kenneth M. Stedman, Andrey N. Shkoporov, Annika Gillis, Xu Peng, François Enault, Petar Knezevic, Rob Lavigne, Sung-Keun Rhee, Virginija Cvirkaite-Krupovic, Cristina Moraru, Andrea I. Moreno Switt, Minna M. Poranen, Andrew Millard, David Prangishvili, Evelien M. Adriaenssens. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021. Archives of Virology. 2021; ():1-6.
Chicago/Turabian StyleMart Krupovic; Dann Turner; Vera Morozova; Mike Dyall-Smith; Hanna M. Oksanen; Rob Edwards; Bas E. Dutilh; Susan M. Lehman; Alejandro Reyes; Diana P. Baquero; Matthew B. Sullivan; Jumpei Uchiyama; Jesca Nakavuma; Jakub Barylski; Mark J. Young; Shishen Du; Poliane Alfenas-Zerbini; Alla Kushkina; Andrew M. Kropinski; Ipek Kurtböke; J. Rodney Brister; Cédric Lood; B. L. Sarkar; Tong Yigang; Ying Liu; Li Huang; Johannes Wittmann; Nina Chanishvili; Leonardo J. van Zyl; Janis Rumnieks; Tomohiro Mochizuki; Matti Jalasvuori; Ramy K. Aziz; Małgorzata Łobocka; Kenneth M. Stedman; Andrey N. Shkoporov; Annika Gillis; Xu Peng; François Enault; Petar Knezevic; Rob Lavigne; Sung-Keun Rhee; Virginija Cvirkaite-Krupovic; Cristina Moraru; Andrea I. Moreno Switt; Minna M. Poranen; Andrew Millard; David Prangishvili; Evelien M. Adriaenssens. 2021. "Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021." Archives of Virology , no. : 1-6.
Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy.
Dann Turner; Andrew Kropinski; Evelien Adriaenssens. A Roadmap for Genome-Based Phage Taxonomy. Viruses 2021, 13, 506 .
AMA StyleDann Turner, Andrew Kropinski, Evelien Adriaenssens. A Roadmap for Genome-Based Phage Taxonomy. Viruses. 2021; 13 (3):506.
Chicago/Turabian StyleDann Turner; Andrew Kropinski; Evelien Adriaenssens. 2021. "A Roadmap for Genome-Based Phage Taxonomy." Viruses 13, no. 3: 506.
Escherichia phage N4 was isolated in 1966 in Italy and has remained a genomic orphan for a long time. It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. In recent years, due to new and relatively inexpensive sequencing techniques the number of publicly available phage genome sequences expanded rapidly. This revealed new members of the N4-like phage group, from 33 members in 2015 to 115 N4-like viruses in 2020. Using new technologies and methods for classification, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) has moved the classification and taxonomy of bacterial viruses from mere morphological approaches to genomic and proteomic methods. The analysis of 115 N4-like genomes resulted in a huge reassessment of this group and the proposal of a new family “Schitoviridae”, including eight subfamilies and numerous new genera.
Johannes Wittmann; Dann Turner; Andrew D. Millard; Padmanabhan Mahadevan; Andrew M. Kropinski; Evelien M. Adriaenssens. From Orphan Phage to a Proposed New Family–the Diversity of N4-Like Viruses. Antibiotics 2020, 9, 663 .
AMA StyleJohannes Wittmann, Dann Turner, Andrew D. Millard, Padmanabhan Mahadevan, Andrew M. Kropinski, Evelien M. Adriaenssens. From Orphan Phage to a Proposed New Family–the Diversity of N4-Like Viruses. Antibiotics. 2020; 9 (10):663.
Chicago/Turabian StyleJohannes Wittmann; Dann Turner; Andrew D. Millard; Padmanabhan Mahadevan; Andrew M. Kropinski; Evelien M. Adriaenssens. 2020. "From Orphan Phage to a Proposed New Family–the Diversity of N4-Like Viruses." Antibiotics 9, no. 10: 663.
Carbapenem-resistant A. baumannii are prevalent in low- and middle-income countries such as Egypt, but little is known about the molecular epidemiology and mechanisms of resistance in these settings. Here we characterise carbapenem-resistant A. baumannii from Alexandria, Egypt, and place it in a regional context. 54 carbapenem-resistant isolates from Alexandria Main University Hospital, Egypt, collected between 2010 and 2015 were genome sequenced using Illumina technology. Genomes were de novo assembled and annotated. Genomes for 36 isolates from the Middle East region were downloaded from GenBank. Core gene compliment was determined using Roary, and analyses of recombination were performed in Gubbins. MLST sequence type and antibiotic resistance genes were identified. The majority of Egyptian isolates belonged to one of 3 major clades, corresponding to Pasteur MLST clonal complex (CCPAS) 1, CCPAS2 and sequence type (STPAS) 158. Strains belonging to STPAS158 have been reported almost exclusively from North Africa, the Middle East and Pakistan, and may represent a region-specific lineage. All isolates carried an oxa23 gene, six carried blaNDM-1, and one carried blaNDM-2. The oxa23 gene was located on a variety of different mobile elements, with Tn2006 predominant in CCPAS2 strains, and Tn2008 predominant in other lineages. Of particular concern, in 8 of the 11 CCPAS1 strains, the carbapenemase gene was located in a temperate bacteriophage phiOXA, previously identified only once before in a CCPAS1 clone from the US military. The carbapenem-resistant A. baumannii population in Alexandria Main University hospital is very diverse, and indicates an endemic circulating population, including a region-specific lineage. The major mechanism for oxa23 dissemination in CCPAS1 isolates appears to be a bacteriophage, presenting new concerns about the ability of these carbapenemases to spread throughout the bacterial population.
Alaa Abouelfetouh; Jennifer Mattock; Dann Turner; Erica Li; Benjamin A Evans. Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase. 2020, 1 .
AMA StyleAlaa Abouelfetouh, Jennifer Mattock, Dann Turner, Erica Li, Benjamin A Evans. Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase. . 2020; ():1.
Chicago/Turabian StyleAlaa Abouelfetouh; Jennifer Mattock; Dann Turner; Erica Li; Benjamin A Evans. 2020. "Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase." , no. : 1.
This article is a summary of the activities of the ICTV’s Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV’s ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.
Evelien M. Adriaenssens; Matthew B. Sullivan; Petar Knezevic; Leonardo J. van Zyl; B. L. Sarkar; Bas E. Dutilh; Poliane Alfenas-Zerbini; Małgorzata Łobocka; Yigang Tong; James Rodney Brister; Andrea I. Moreno Switt; Jochen Klumpp; Ramy Karam Aziz; Jakub Barylski; Jumpei Uchiyama; Rob A. Edwards; Andrew M. Kropinski; Nicola K. Petty; Martha R. J. Clokie; Alla I. Kushkina; Vera V. Morozova; Siobain Duffy; Annika Gillis; Janis Rumnieks; Ipek Kurtböke; Nina Chanishvili; Lawrence Goodridge; Johannes Wittmann; Rob Lavigne; Ho Bin Jang; David Prangishvili; Francois Enault; Dann Turner; Minna M. Poranen; Hanna M. Oksanen; Mart Krupovic. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Archives of Virology 2020, 165, 1253 -1260.
AMA StyleEvelien M. Adriaenssens, Matthew B. Sullivan, Petar Knezevic, Leonardo J. van Zyl, B. L. Sarkar, Bas E. Dutilh, Poliane Alfenas-Zerbini, Małgorzata Łobocka, Yigang Tong, James Rodney Brister, Andrea I. Moreno Switt, Jochen Klumpp, Ramy Karam Aziz, Jakub Barylski, Jumpei Uchiyama, Rob A. Edwards, Andrew M. Kropinski, Nicola K. Petty, Martha R. J. Clokie, Alla I. Kushkina, Vera V. Morozova, Siobain Duffy, Annika Gillis, Janis Rumnieks, Ipek Kurtböke, Nina Chanishvili, Lawrence Goodridge, Johannes Wittmann, Rob Lavigne, Ho Bin Jang, David Prangishvili, Francois Enault, Dann Turner, Minna M. Poranen, Hanna M. Oksanen, Mart Krupovic. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Archives of Virology. 2020; 165 (5):1253-1260.
Chicago/Turabian StyleEvelien M. Adriaenssens; Matthew B. Sullivan; Petar Knezevic; Leonardo J. van Zyl; B. L. Sarkar; Bas E. Dutilh; Poliane Alfenas-Zerbini; Małgorzata Łobocka; Yigang Tong; James Rodney Brister; Andrea I. Moreno Switt; Jochen Klumpp; Ramy Karam Aziz; Jakub Barylski; Jumpei Uchiyama; Rob A. Edwards; Andrew M. Kropinski; Nicola K. Petty; Martha R. J. Clokie; Alla I. Kushkina; Vera V. Morozova; Siobain Duffy; Annika Gillis; Janis Rumnieks; Ipek Kurtböke; Nina Chanishvili; Lawrence Goodridge; Johannes Wittmann; Rob Lavigne; Ho Bin Jang; David Prangishvili; Francois Enault; Dann Turner; Minna M. Poranen; Hanna M. Oksanen; Mart Krupovic. 2020. "Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee." Archives of Virology 165, no. 5: 1253-1260.
Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.
Ho Bin Jang; Benjamin Bolduc; Olivier Zablocki; Jens H. Kuhn; Simon Roux; Evelien M. Adriaenssens; J. Rodney Brister; Andrew M Kropinski; Mart Krupovic; Rob Lavigne; Dann Turner; Matthew B. Sullivan. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology 2019, 37, 632 -639.
AMA StyleHo Bin Jang, Benjamin Bolduc, Olivier Zablocki, Jens H. Kuhn, Simon Roux, Evelien M. Adriaenssens, J. Rodney Brister, Andrew M Kropinski, Mart Krupovic, Rob Lavigne, Dann Turner, Matthew B. Sullivan. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology. 2019; 37 (6):632-639.
Chicago/Turabian StyleHo Bin Jang; Benjamin Bolduc; Olivier Zablocki; Jens H. Kuhn; Simon Roux; Evelien M. Adriaenssens; J. Rodney Brister; Andrew M Kropinski; Mart Krupovic; Rob Lavigne; Dann Turner; Matthew B. Sullivan. 2019. "Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks." Nature Biotechnology 37, no. 6: 632-639.
The retina contains several ciliated cell types, including the retinal pigment epithelium (RPE) and photoreceptor cells. The photoreceptor cilium is one of the most highly modified sensory cilia in the human body. The outer segment of the photoreceptor is a highly elaborate primary cilium, containing stacks or folds of membrane where the photopigment molecules are located. Perhaps unsurprisingly, defects in cilia often lead to retinal phenotypes, either as part of syndromic conditions involving other organs, or in isolation in the so-called retinal ciliopathies. The study of retinal ciliopathies has been limited by a lack of retinal cell lines. RPE1 retinal pigment epithelial cell line is commonly used in such studies, but the existence of a photoreceptor cell line has largely been neglected in the retinal ciliopathy field. 661W cone photoreceptor cells, derived from mouse, have been widely used as a model for studying macular degeneration, but not described as a model for studying retinal ciliopathies such as retinitis pigmentosa. Here, we characterize the 661W cell line as a model for studying retinal ciliopathies. We fully characterize the expression profile of these cells, using whole transcriptome RNA sequencing, and provide this data on Gene Expression Omnibus for the advantage of the scientific community. We show that these cells express the majority of markers of cone cell origin. Using immunostaining and confocal microscopy, alongside scanning electron microscopy, we show that these cells grow long primary cilia, reminiscent of photoreceptor outer segments, and localize many cilium proteins to the axoneme, membrane and transition zone. We show that siRNA knockdown of cilia genes Ift88 results in loss of cilia, and that this can be assayed by high-throughput screening. We present evidence that the 661W cell line is a useful cell model for studying retinal ciliopathies.
Gabrielle Wheway; Liliya Nazlamova; Dann Turner; Stephen Cross. 661W Photoreceptor Cell Line as a Cell Model for Studying Retinal Ciliopathies. Frontiers in Genetics 2019, 10, 308 .
AMA StyleGabrielle Wheway, Liliya Nazlamova, Dann Turner, Stephen Cross. 661W Photoreceptor Cell Line as a Cell Model for Studying Retinal Ciliopathies. Frontiers in Genetics. 2019; 10 ():308.
Chicago/Turabian StyleGabrielle Wheway; Liliya Nazlamova; Dann Turner; Stephen Cross. 2019. "661W Photoreceptor Cell Line as a Cell Model for Studying Retinal Ciliopathies." Frontiers in Genetics 10, no. : 308.
The retina contains several ciliated cell types, including the retinal pigment epithelium (RPE) and photoreceptor cells. The photoreceptor cilium is one of the most highly modified sensory cilia in the human body. The outer segment of the photoreceptor is a highly elaborate primary cilium, containing stacks or folds of membrane where the photopigment molecules are located. Perhaps unsurprisingly, defects in cilia often lead to retinal phenotypes, either as part of syndromic conditions involving other organs, or in isolation in the so-called retinal ciliopathies.The study of retinal ciliopathies has been limited by a lack of retinal cell lines. RPE1 retinal pigment epithelial cell line is commonly used in such studies, but the existence of a photoreceptor cell line has largely been neglected in the retinal ciliopathy field. 661W cone photoreceptor cells, derived from mouse, have been widely used as a model for studying macular degeneration, but not described as a model for studying retinal ciliopathies such as retinitis pigmentosa.Here, we characterise the 661W cell line as a model for studying retinal ciliopathies. We fully characterise the expression profile of these cells over many passages, using whole transcriptome RNA sequencing, and provide this data on Gene Expression Omnibus (GEO) for the advantage of the scientific community. We show that these cells robustly express the majority of markers of cone cell origin, including short wave and medium wave opsin. Western blotting confirms expression of selected markers.Using immunostaining and confocal microscopy, alongside scanning electron microscopy, we show that these cells grow long primary cilia, reminiscent of photoreceptor outer segments, and localise many cilium proteins to the axoneme, membrane and transition zone. Immunostaining shows that opsins are localised to the base of this primary cilium. We show that siRNA knockdown of cilia genes Ift88 results in loss of cilia, and that this can be assayed by high-throughput screening. We present evidence that the 661W cell line is a useful cell model for studying retinal ciliopathies.
Gabrielle Wheway; Liliya Nazlamova; Dann Turner; Stephen Cross. 661W photoreceptor cell line as a cell model for studying retinal ciliopathies. 2018, 479212 .
AMA StyleGabrielle Wheway, Liliya Nazlamova, Dann Turner, Stephen Cross. 661W photoreceptor cell line as a cell model for studying retinal ciliopathies. . 2018; ():479212.
Chicago/Turabian StyleGabrielle Wheway; Liliya Nazlamova; Dann Turner; Stephen Cross. 2018. "661W photoreceptor cell line as a cell model for studying retinal ciliopathies." , no. : 479212.
Pectobacterium atrosepticum is a phytopathogen of economic importance as it is the causative agent of potato blackleg and soft rot. Here we describe the Pectobacterium phage vB_PatP_CB5 (abbreviated as CB5), which specifically infects the bacterium. The bacteriophage is characterized in detail and TEM micrographs indicate that it belongs to the Podoviridae family. CB5 shares significant pairwise nucleotide identity (≥80%) with P. atrosepticum phages φM1, Peat1, and PP90 and also shares common genome organization. Phylograms constructed using conserved proteins and whole-genome comparison-based amino acid sequences show that these phages form a distinct clade within the Autographivirinae. They also possess conserved RNA polymerase recognition and specificity loop sequences. Their lysis cassette resembles that of KP34virus, containing in sequential order a U-spanin, a holin, and a signal–arrest–release (SAR) endolysin. However, they share low pairwise nucleotide identity with the type phage of the KP34virus genus, Klebsiella phage KP34. In addition, phage KP34 does not possess several conserved proteins associated with these P. atrosepticum phages. As such, we propose the allocation of phages CB5, Peat1, φM1, and PP90 to a separate new genus designated Phimunavirus.
Colin Buttimer; Alan Lucid; Horst Neve; Charles M. A. P. Franz; Jim O’Mahony; Dann Turner; Rob Lavigne; Aidan Coffey. Pectobacterium atrosepticum Phage vB_PatP_CB5: A Member of the Proposed Genus ‘Phimunavirus’. Viruses 2018, 10, 394 .
AMA StyleColin Buttimer, Alan Lucid, Horst Neve, Charles M. A. P. Franz, Jim O’Mahony, Dann Turner, Rob Lavigne, Aidan Coffey. Pectobacterium atrosepticum Phage vB_PatP_CB5: A Member of the Proposed Genus ‘Phimunavirus’. Viruses. 2018; 10 (8):394.
Chicago/Turabian StyleColin Buttimer; Alan Lucid; Horst Neve; Charles M. A. P. Franz; Jim O’Mahony; Dann Turner; Rob Lavigne; Aidan Coffey. 2018. "Pectobacterium atrosepticum Phage vB_PatP_CB5: A Member of the Proposed Genus ‘Phimunavirus’." Viruses 10, no. 8: 394.
Bacteriophages SP-15 and ΦW-14 are members of the Myoviridae infecting Bacillus subtilis and Delftia (formerly Pseudomonas) acidovorans, respectively. What links them is that in both cases, approximately 50% of the thymine residues are replaced by hypermodified bases. The consequence of this is that the physico-chemical properties of the DNA are radically altered (melting temperature (Tm), buoyant density and susceptibility to restriction endonucleases). Using 454 pyrosequencing technology, we sequenced the genomes of both viruses. Phage ΦW-14 possesses a 157-kb genome (56.3% GC) specifying 236 proteins, while SP-15 is larger at 222 kb (38.6 mol % G + C) and encodes 318 proteins. In both cases, the phages can be considered genomic singletons since they do not possess BLASTn homologs. While no obvious genes were identified as being responsible for the modified base in ΦW-14, SP-15 contains a cluster of genes obviously involved in carbohydrate metabolism.
Andrew M. Kropinski; Dann Turner; John H. E. Nash; Hans-Wolfgang Ackermann; Erika J. Lingohr; Richard A. Warren; Kenneth C. Ehrlich; Melanie Ehrlich. The Sequence of Two Bacteriophages with Hypermodified Bases Reveals Novel Phage-Host Interactions. Viruses 2018, 10, 217 .
AMA StyleAndrew M. Kropinski, Dann Turner, John H. E. Nash, Hans-Wolfgang Ackermann, Erika J. Lingohr, Richard A. Warren, Kenneth C. Ehrlich, Melanie Ehrlich. The Sequence of Two Bacteriophages with Hypermodified Bases Reveals Novel Phage-Host Interactions. Viruses. 2018; 10 (5):217.
Chicago/Turabian StyleAndrew M. Kropinski; Dann Turner; John H. E. Nash; Hans-Wolfgang Ackermann; Erika J. Lingohr; Richard A. Warren; Kenneth C. Ehrlich; Melanie Ehrlich. 2018. "The Sequence of Two Bacteriophages with Hypermodified Bases Reveals Novel Phage-Host Interactions." Viruses 10, no. 5: 217.
Evelien M. Adriaenssens; Johannes Wittmann; Jens H. Kuhn; Dann Turner; Matthew B. Sullivan; Bas E. Dutilh; Ho Bin Jang; Leonardo J. Van Zyl; Jochen Klumpp; Malgorzata Lobocka; Andrea I. Moreno Switt; Jānis Rūmnieks; Robert A. Edwards; Jumpei Uchiyama; Poliane Alfenas-Zerbini; Nicola K. Petty; Andrew M. Kropinski; Jakub Barylski; Annika Gillis; Martha R. C. Clokie; David Prangishvili; Rob Lavigne; Ramy Karam Aziz; Siobain Duffy; Mart Krupovic; Minna M. Poranen; Petar Knezevic; Francois Enault; Yigang Tong; Hanna M. Oksanen; J. Rodney Brister. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Archives of Virology 2018, 163, 1125 -1129.
AMA StyleEvelien M. Adriaenssens, Johannes Wittmann, Jens H. Kuhn, Dann Turner, Matthew B. Sullivan, Bas E. Dutilh, Ho Bin Jang, Leonardo J. Van Zyl, Jochen Klumpp, Malgorzata Lobocka, Andrea I. Moreno Switt, Jānis Rūmnieks, Robert A. Edwards, Jumpei Uchiyama, Poliane Alfenas-Zerbini, Nicola K. Petty, Andrew M. Kropinski, Jakub Barylski, Annika Gillis, Martha R. C. Clokie, David Prangishvili, Rob Lavigne, Ramy Karam Aziz, Siobain Duffy, Mart Krupovic, Minna M. Poranen, Petar Knezevic, Francois Enault, Yigang Tong, Hanna M. Oksanen, J. Rodney Brister. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Archives of Virology. 2018; 163 (4):1125-1129.
Chicago/Turabian StyleEvelien M. Adriaenssens; Johannes Wittmann; Jens H. Kuhn; Dann Turner; Matthew B. Sullivan; Bas E. Dutilh; Ho Bin Jang; Leonardo J. Van Zyl; Jochen Klumpp; Malgorzata Lobocka; Andrea I. Moreno Switt; Jānis Rūmnieks; Robert A. Edwards; Jumpei Uchiyama; Poliane Alfenas-Zerbini; Nicola K. Petty; Andrew M. Kropinski; Jakub Barylski; Annika Gillis; Martha R. C. Clokie; David Prangishvili; Rob Lavigne; Ramy Karam Aziz; Siobain Duffy; Mart Krupovic; Minna M. Poranen; Petar Knezevic; Francois Enault; Yigang Tong; Hanna M. Oksanen; J. Rodney Brister. 2018. "Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee." Archives of Virology 163, no. 4: 1125-1129.
Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A comparative bioinformatics analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades.
Dann Turner; Hans-Wolfgang Ackermann; Andrew M. Kropinski; Rob Lavigne; J. Mark Sutton; Darren M. Reynolds. Comparative Analysis of 37 Acinetobacter Bacteriophages. Viruses 2017, 10, 5 .
AMA StyleDann Turner, Hans-Wolfgang Ackermann, Andrew M. Kropinski, Rob Lavigne, J. Mark Sutton, Darren M. Reynolds. Comparative Analysis of 37 Acinetobacter Bacteriophages. Viruses. 2017; 10 (1):5.
Chicago/Turabian StyleDann Turner; Hans-Wolfgang Ackermann; Andrew M. Kropinski; Rob Lavigne; J. Mark Sutton; Darren M. Reynolds. 2017. "Comparative Analysis of 37 Acinetobacter Bacteriophages." Viruses 10, no. 1: 5.
The presentation of bacteriophage genomes as diagrams allows the location and organization of features to be communicated in a clear and effective manner. A wide range of software applications are available for the clear and accurate visualization of genomic data. Several of these applications incorporate comparative analysis tools, allowing for insertions, deletions, rearrangements and variations in syntenic regions to be visualized. In this chapter, freely available software and resources for the generation of high-quality graphical maps of bacteriophage genomes are listed and discussed.
Dann Turner; J. Mark Sutton; Darren M. Reynolds; Eby M. Sim; Nicola K. Petty. Visualization of Phage Genomic Data: Comparative Genomics and Publication-Quality Diagrams. Advanced Structural Safety Studies 2017, 1681, 239 -260.
AMA StyleDann Turner, J. Mark Sutton, Darren M. Reynolds, Eby M. Sim, Nicola K. Petty. Visualization of Phage Genomic Data: Comparative Genomics and Publication-Quality Diagrams. Advanced Structural Safety Studies. 2017; 1681 ():239-260.
Chicago/Turabian StyleDann Turner; J. Mark Sutton; Darren M. Reynolds; Eby M. Sim; Nicola K. Petty. 2017. "Visualization of Phage Genomic Data: Comparative Genomics and Publication-Quality Diagrams." Advanced Structural Safety Studies 1681, no. : 239-260.
Acinetobacter baumannii has emerged as an important nosocomial pathogen in healthcare and community settings. While over 100 of Acinetobacter phages have been described in the literature, relatively few have been sequenced. This work describes the characterisation and genome annotation of a new lytic Acinetobacter siphovirus, vB_AbaS_Loki, isolated from activated sewage sludge. Sequencing revealed that Loki encapsulates a 41,308 bp genome, encoding 51 predicted open reading frames. Loki is most closely related to Acinetobacter phage IME_AB3 and more distantly related to Burkholderia phage KL1, Paracoccus phage vB_PmaS_IMEP1 and Pseudomonas phages vB_Pae_Kakheti25, vB_PaeS_SCH_Ab26 and PA73. Loki is characterised by a narrow host range, among the 40 Acinetobacter isolates tested, productive infection was only observed for the propagating host, A. baumannii ATCC 17978. Plaque formation was found to be dependent upon the presence of Ca2+ ions and adsorption to host cells was abolished upon incubation with a mutant of ATCC 17978 encoding a premature stop codon in lpxA. The complete genome sequence of vB_AbaS_Loki was deposited in the European Nucleotide Archive (ENA) under the accession number LN890663.
Dann Turner; Matthew Wand; Yves Briers; Rob Lavigne; J. Mark Sutton; Darren M. Reynolds. Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki. PLOS ONE 2017, 12, e0172303 .
AMA StyleDann Turner, Matthew Wand, Yves Briers, Rob Lavigne, J. Mark Sutton, Darren M. Reynolds. Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki. PLOS ONE. 2017; 12 (2):e0172303.
Chicago/Turabian StyleDann Turner; Matthew Wand; Yves Briers; Rob Lavigne; J. Mark Sutton; Darren M. Reynolds. 2017. "Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki." PLOS ONE 12, no. 2: e0172303.
A novel temperate phage, vB_AbaS_TRS1, was isolated from cultures of Acinetobacter baumannii strain A118 that had been exposed to mitomycin C. Phage TRS1 belongs to the Siphoviridae family of bacteriophages and encapsulates a 40,749-bp genome encoding 70 coding sequences and a single tRNA.
Dann Turner; Matthew Wand; J. Mark Sutton; Daniela Centron; Andrew M. Kropinski; Darren M. Reynolds. Genome Sequence of vB_AbaS_TRS1, a Viable Prophage Isolated from Acinetobacter baumannii Strain A118. Genome Announcements 2016, 4, e01051-16 .
AMA StyleDann Turner, Matthew Wand, J. Mark Sutton, Daniela Centron, Andrew M. Kropinski, Darren M. Reynolds. Genome Sequence of vB_AbaS_TRS1, a Viable Prophage Isolated from Acinetobacter baumannii Strain A118. Genome Announcements. 2016; 4 (5):e01051-16.
Chicago/Turabian StyleDann Turner; Matthew Wand; J. Mark Sutton; Daniela Centron; Andrew M. Kropinski; Darren M. Reynolds. 2016. "Genome Sequence of vB_AbaS_TRS1, a Viable Prophage Isolated from Acinetobacter baumannii Strain A118." Genome Announcements 4, no. 5: e01051-16.
Mannheimia haemolytica is a commensal bacterium that resides in the upper respiratory tract of cattle that can play a role in bovine respiratory disease. Prophages are common in the M. haemolytica genome and contribute significantly to host diversity. The objective of this research was to undertake comparative genomic analysis of phages induced from strains of M. haemolytica serotype A1 (535A and 2256A), A2 (587A and 1127A) and A6 (1152A and 3927A). Overall, four P2-like (535AP1, 587AP1, 1127AP1 and 2256AP1; genomes: 34.9–35.7 kb; G+C content: 41.5–42.1 %; genes: 51–53 coding sequences, CDSs), four λ-like (535AP2, 587AP2, 1152AP2 and 3927AP1; genomes: 48.6–52.1 kb; 41.1–41.4 % mol G+C; genes: 77–83 CDSs and 2 tRNAs) and one Mu-like (3927AP2; genome: 33.8 kb; 43.1 % mol G+C; encoding 50 CDSs) phages were identified. All P2-like phages are collinear with the temperate phage φMhaA1-PHL101 with 535AP1, 2256AP1 and 1152AP1 being most closely related, followed by 587AP1 and 1127AP1. Lambdoid phages are not collinear with any other known λ-type phages, with 587AP2 being distinct from 535AP2, 3927AP1 and 1152AP2. All λ-like phages contain genes encoding a toxin-antitoxin (TA) system and cell-associated haemolysin XhlA. The Mu-like phage induced from 3927A is closely related to the phage remnant φMhaMu2 from M. haemolytica PHL21, with similar Mu-like phages existing in the genomes of M. haemolytica 535A and 587A. This is among the first reports of both λ- and Mu-type phages being induced from M. haemolytica. Compared to phages induced from commensal strains of M. haemolytica serotype A2, those induced from the more virulent A1 and A6 serotypes are more closely related. Moreover, when P2-, λ- and Mu-like phages co-existed in the M. haemolytica genome, only P2- and λ-like phages were detected upon induction, suggesting that Mu-type phages may be more resistant to induction. Toxin-antitoxin gene cassettes in λ-like phages may contribute to their genomic persistence or the establishment of persister subpopulations of M. haemolytica. Further work is required to determine if the cell-associated haemolysin XhlA encoded by λ-like phages contributes to the pathogenicity and ecological fitness of M. haemolytica.
Yan D. Niu; Shaun R. Cook; Jiaying Wang; Cassidy Klima; Yu-Hung Hsu; Andrew M. Kropinski; Dann Turner; Tim A. McAllister. Comparative analysis of multiple inducible phages from Mannheimia haemolytica. BMC Microbiology 2015, 15, 1 -15.
AMA StyleYan D. Niu, Shaun R. Cook, Jiaying Wang, Cassidy Klima, Yu-Hung Hsu, Andrew M. Kropinski, Dann Turner, Tim A. McAllister. Comparative analysis of multiple inducible phages from Mannheimia haemolytica. BMC Microbiology. 2015; 15 (1):1-15.
Chicago/Turabian StyleYan D. Niu; Shaun R. Cook; Jiaying Wang; Cassidy Klima; Yu-Hung Hsu; Andrew M. Kropinski; Dann Turner; Tim A. McAllister. 2015. "Comparative analysis of multiple inducible phages from Mannheimia haemolytica." BMC Microbiology 15, no. 1: 1-15.
Based on morphology and comparative nucleotide and protein sequence analysis, a new subfamily of the family Siphoviridae is proposed, named “Jerseyvirinae” and consisting of three genera, “Jerseylikevirus”, “Sp3unalikevirus” and “K1glikevirus”. To date, this subfamily consists of 18 phages for which the genomes have been sequenced. Salmonella phages Jersey, vB_SenS_AG11, vB_SenS-Ent1, vB_SenS-Ent2, vB_SenS-Ent3, FSL SP-101, SETP3, SETP7, SETP13, SE2, SS3e and wksl3 form the proposed genus “Jerseylikevirus”. The proposed genus “K1glikevirus” consists of Escherichia phages K1G, K1H, K1ind1, K1ind2 and K1ind3. The proposed genus “Sp3unalikevirus” contains one member so far. Jersey-like phages appear to be widely distributed, as the above phages were isolated in the UK, Canada, the USA and South Korea between 1970 and the present day. The distinguishing features of this subfamily include a distinct siphovirus morphotype, genomes of 40.7-43.6 kb (49.6-51.4 mol % G+C), a syntenic genome organisation, and a high degree of nucleotide sequence identity and shared proteins. All known members of the proposed subfamily are strictly lytic.
Hany Anany; Andrea I. Moreno Switt; Niall De Lappe; Hans-Wolfgang Ackermann; Darren M Reynolds; Andrew M. Kropinski; Martin Wiedmann; Mansel W. Griffiths; Denise Tremblay; Sylvain Moineau; John H. E. Nash; Dann Turner. A proposed new bacteriophage subfamily: “Jerseyvirinae”. Archives of Virology 2015, 160, 1021 -1033.
AMA StyleHany Anany, Andrea I. Moreno Switt, Niall De Lappe, Hans-Wolfgang Ackermann, Darren M Reynolds, Andrew M. Kropinski, Martin Wiedmann, Mansel W. Griffiths, Denise Tremblay, Sylvain Moineau, John H. E. Nash, Dann Turner. A proposed new bacteriophage subfamily: “Jerseyvirinae”. Archives of Virology. 2015; 160 (4):1021-1033.
Chicago/Turabian StyleHany Anany; Andrea I. Moreno Switt; Niall De Lappe; Hans-Wolfgang Ackermann; Darren M Reynolds; Andrew M. Kropinski; Martin Wiedmann; Mansel W. Griffiths; Denise Tremblay; Sylvain Moineau; John H. E. Nash; Dann Turner. 2015. "A proposed new bacteriophage subfamily: “Jerseyvirinae”." Archives of Virology 160, no. 4: 1021-1033.
CoreGenes3.5 is a webserver that determines sets of core genes from viral and small bacterial genomes as an automated batch process. Previous versions of CoreGenes have been used to classify bacteriophage genomes and mine data from pathogen genomes.
Dann Turner; Darren M Reynolds; Nald Seto; Padmanabhan Mahadevan. CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes. BMC Research Notes 2013, 6, 140 -140.
AMA StyleDann Turner, Darren M Reynolds, Nald Seto, Padmanabhan Mahadevan. CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes. BMC Research Notes. 2013; 6 (1):140-140.
Chicago/Turabian StyleDann Turner; Darren M Reynolds; Nald Seto; Padmanabhan Mahadevan. 2013. "CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes." BMC Research Notes 6, no. 1: 140-140.
The bacteriophage vB_SenS-Ent1 (Ent1) is a member of the family Siphoviridae of tailed bacteriophages and infects a broad range of serovars of the enteric pathogen Salmonella enterica. The virion particle is composed of an icosahedral head 64 nm in diameter and a flexible, non-contractile tail of 116 × 8.5 nm possessing terminal fibres. The adsorption rate constant at 37 °C is 6.73 × 10−9 ml min−1. Latent and eclipse periods are 25 and 20 min, respectively, and the burst size is 35 progeny particles per cell after 35 min at 37 °C. Sequencing revealed a circularly permuted, 42 391 bp dsDNA genome containing 58 ORFs organized into four major transcriptional units. Comparisons with the genome sequences of other bacteriophages revealed a high level of nucleotide sequence identity and shared orthologous proteins with the Salmonella phages SETP3, SE2 and KS7 (SS3e) and the Escherichia phages K1G, K1H, K1ind1 and K1ind3.
Dann Turner; Mohammed Hezwani; Shona Nelson; Vyv Salisbury; Darren M Reynolds. Characterization of the Salmonella bacteriophage vB_SenS-Ent1. Journal of General Virology 2012, 93, 2046 -2056.
AMA StyleDann Turner, Mohammed Hezwani, Shona Nelson, Vyv Salisbury, Darren M Reynolds. Characterization of the Salmonella bacteriophage vB_SenS-Ent1. Journal of General Virology. 2012; 93 (9):2046-2056.
Chicago/Turabian StyleDann Turner; Mohammed Hezwani; Shona Nelson; Vyv Salisbury; Darren M Reynolds. 2012. "Characterization of the Salmonella bacteriophage vB_SenS-Ent1." Journal of General Virology 93, no. 9: 2046-2056.