The Genomes of Sheeppox and Goatpox Viruses

ABSTRACT Sheeppox virus (SPPV) and goatpox virus (GTPV), members of the Capripoxvirus genus of the Poxviridae, are etiologic agents of important diseases of sheep and goats in northern and central Africa, southwest and central Asia, and the Indian subcontinent. Here we report the genomic sequence and comparative analysis of five SPPV and GTPV isolates, including three pathogenic field isolates and two attenuated vaccine viruses. SPPV and GTPV genomes are approximately 150 kbp and are strikingly similar to each other, exhibiting 96% nucleotide identity over their entire length. Wild-type genomes share at least 147 putative genes, including conserved poxvirus replicative and structural genes and genes likely involved in virulence and host range. SPPV and GTPV genomes are very similar to that of lumpy skin disease virus (LSDV), sharing 97% nucleotide identity. All SPPV and GTPV genes are present in LSDV. Notably in both SPPV and GTPV genomes, nine LSDV genes with likely virulence and host range functions are disrupted, including a gene unique to LSDV (LSDV132) and genes similar to those coding for interleukin-1 receptor, myxoma virus M003.2 and M004.1 genes (two copies each), and vaccinia virus F11L, N2L, and K7L genes. The absence of these genes in SPPV and GTPV suggests a significant role for them in the bovine host range. SPPV and GTPV genomes contain specific nucleotide differences, suggesting they are phylogenetically distinct. Relatively few genomic changes in SPPV and GTPV vaccine viruses account for viral attenuation, because they contain 71 and 7 genomic changes compared to their respective field strains. Notable genetic changes include mutation or disruption of genes with predicted functions involving virulence and host range, including two ankyrin repeat proteins in SPPV and three kelch-like proteins in GTPV. These comparative genomic data indicate the close genetic relationship among capripoxviruses, and they suggest that SPPV and GTPV are distinct and likely derived from an LSDV-like ancestor.

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Genome of Deerpox Virus

Journal of Virology ◽

10.1128/jvi.79.2.966-977.2005 ◽

2005 ◽

Vol 79 (2) ◽

pp. 966-977 ◽

Cited By ~ 42

Author(s):

C. L. Afonso ◽

G. Delhon ◽

E. R. Tulman ◽

Z. Lu ◽

A. Zsak ◽

...

Keyword(s):

Host Range ◽

Chemokine Receptors ◽

Transforming Growth Factor ◽

Genomic Sequence ◽

Core Protein ◽

Interleukin 1 ◽

Transforming Growth Factor Β1 ◽

Open Reading Frames ◽

Host Responses ◽

Tgf Β1

ABSTRACT Deerpox virus (DPV), an uncharacterized and unclassified member of the Poxviridae, has been isolated from North American free-ranging mule deer (Odocoileus hemionus) exhibiting mucocutaneous disease. Here we report the genomic sequence and comparative analysis of two pathogenic DPV isolates, W-848-83 (W83) and W-1170-84 (W84). The W83 and W84 genomes are 166 and 170 kbp, containing 169 and 170 putative genes, respectively. Nucleotide identity between DPVs is 95% over the central 157 kbp. W83 and W84 share similar gene orders and code for similar replicative, structural, virulence, and host range functions. DPV open reading frames (ORFs) with putative virulence and host range functions include those similar to cytokine receptors (R), including gamma interferon receptor (IFN-γR), interleukin 1 receptor (IL-1R), and type 8 CC-chemokine receptors; cytokine binding proteins (BP), including IL-18BP, IFN-α/βBP, and tumor necrosis factor binding protein (TNFBP); serpins; and homologues of vaccinia virus (VACV) E3L, K3L, and A52R proteins. DPVs also encode distinct forms of major histocompatibility complex class I, C-type lectin-like protein, and transforming growth factor β1 (TGF-β1), a protein not previously described in a mammalian chordopoxvirus. Notably, DPV encodes homologues of cellular endothelin 2 and IL-1R antagonist, novel poxviral genes also likely involved in the manipulation of host responses. W83 and W84 differ from each other by the presence or absence of five ORFs. Specifically, homologues of a CD30 TNFR family protein, swinepox virus SPV019, and VACV E11L core protein are absent in W83, and homologues of TGF-β1 and lumpy skin disease virus LSDV023 are absent in W84. Phylogenetic analysis indicates that DPVs are genetically distinct from viruses of other characterized poxviral genera and that they likely comprise a new genus within the subfamily Chordopoxvirinae.

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Diversity and Host Specificity Revealed by Biological Characterization and Whole Genome Sequencing of Bacteriophages Infecting Salmonella enterica

Viruses ◽

10.3390/v11090854 ◽

2019 ◽

Vol 11 (9) ◽

pp. 854 ◽

Cited By ~ 7

Author(s):

Fong ◽

Tremblay ◽

Delaquis ◽

Goodridge ◽

Levesque ◽

...

Keyword(s):

Host Range ◽

Salmonella Enterica ◽

Nucleotide Identity ◽

Comparative Genomic ◽

Broad Host Range ◽

Natural Environments ◽

Host Interactions ◽

Knowledge Framework ◽

Isolation And Characterization ◽

Opportunistic Human Pathogen

Phages infecting members of the opportunistic human pathogen, Salmonella enterica, are widespread in natural environments and offer a potential source of agents that could be used for controlling populations of this bacterium; yet, relatively little is known about these phages. Here we describe the isolation and characterization of 45 phages of Salmonella enterica from disparate geographic locations within British Columbia, Canada. Host-range profiling revealed host-specific patterns of susceptibility and resistance, with several phages identified that have a broad-host range (i.e., able to lyse >40% of bacterial hosts tested). One phage in particular, SE13, is able to lyse 51 out of the 61 Salmonella strains tested. Comparative genomic analyses also revealed an abundance of sequence diversity in the sequenced phages. Alignment of the genomes grouped the phages into 12 clusters with three singletons. Phages within certain clusters exhibited extraordinarily high genome homology (>98% nucleotide identity), yet between clusters, genomes exhibited a span of diversity (<50% nucleotide identity). Alignment of the major capsid protein also supported the clustering pattern observed with alignment of the whole genomes. We further observed associations between genomic relatedness and the site of isolation, as well as genetic elements related to DNA metabolism and host virulence. Our data support the knowledge framework for phage diversity and phage–host interactions that are required for developing phage-based applications for various sectors, including biocontrol, detection and typing.

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Revealing genomic changes responsible for cannabinoid receptor loss in parrots: mechanism and functional effects

10.1101/2022.01.03.474805 ◽

2022 ◽

Author(s):

Daniel Divin ◽

Mercedes Gomez Samblas ◽

Nithya Kuttiyarthu Veetil ◽

Eleni Voukali ◽

Zuzana Swiderska ◽

...

Keyword(s):

Cannabinoid Receptors ◽

Cannabinoid Receptor ◽

Inflammatory Marker ◽

Interleukin 1 ◽

Expression Patterns ◽

Genomic Analysis ◽

Sterile Inflammation ◽

Comparative Genomic ◽

Genomic Changes ◽

The Brain

In vertebrates, an ancient duplication in the genes for cannabinoid receptors (CNRs) allowed the evolution of specialised endocannabinoid receptors expressed in the brain (CNR1) and the periphery (CNR2). While dominantly conserved throughout vertebrate phylogeny, our comparative genomic analysis suggests that certain taxa may have lost either the CNR1 regulator of neural processes or, more frequently, the CNR2 involved in immune regulation. Focussing on conspicuous CNR2 pseudogenization in parrots (Psittaciformes), a diversified crown lineage of cognitively-advanced birds, we highlight possible functional effects of such a loss. Parrots appear to have lost the CNR2 gene at at least two separate occasions due to chromosomal rearrangement. Using gene expression data from the brain and periphery of birds with experimentally-induced sterile inflammation, we compare CNR and inflammatory marker (interleukin 1 beta, IL1B) expression patterns in CNR2-deficient parrots (represented by the budgerigar, Melopsittacus undulatus and five other parrot species) with CNR2-intact passerines (represented by the zebra finch, Taeniopygia guttata). Though no significant changes in CNR expression were observed in either parrots or passerines during inflammation of the brain or periphery, we detected a significant up-regulation of IL1B expression in the brain after stimulation with lipopolysaccharide (LPS) only in parrots. As our analysis failed to show evidence for selection on altered CNR1 functionality in parrots, compared to other birds, CNR1 is unlikely to be involved in compensation for CNR2 loss in modulation of the neuroimmune interaction. Thus, our results provide evidence for the functional importance of CNR2 pseudogenization for regulation of neuroinflammation.

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Comparative Genomic Analyses of Attenuated Strains of Mycoplasma gallisepticum

Infection and Immunity ◽

10.1128/iai.01172-09 ◽

2010 ◽

Vol 78 (4) ◽

pp. 1760-1771 ◽

Cited By ~ 37

Author(s):

S. M. Szczepanek ◽

E. R. Tulman ◽

T. S. Gorton ◽

X. Liao ◽

Z. Lu ◽

...

Keyword(s):

Genomic Sequence ◽

Sugar Metabolism ◽

Mycoplasma Gallisepticum ◽

Comparative Genomic ◽

Genomic Variability ◽

Genomic Changes ◽

Genomic Analyses ◽

Low Passage ◽

Related Proteins ◽

Complete Genomic

ABSTRACT Mycoplasma gallisepticum is a significant respiratory and reproductive pathogen of domestic poultry. While the complete genomic sequence of the virulent, low-passage M. gallisepticum strain R (Rlow) has been reported, genomic determinants responsible for differences in virulence and host range remain to be completely identified. Here, we utilize genome sequencing and microarray-based comparative genomic data to identify these genomic determinants of virulence and to elucidate genomic variability among strains of M. gallisepticum. Analysis of the high-passage, attenuated derivative of Rlow, Rhigh, indicated that relatively few total genomic changes (64 loci) occurred, yet they are potentially responsible for the observed attenuation of this strain. In addition to previously characterized mutations in cytadherence-related proteins, changes included those in coding sequences of genes involved in sugar metabolism. Analyses of the genome of the M. gallisepticum vaccine strain F revealed numerous differences relative to strain R, including a highly divergent complement of vlhA surface lipoprotein genes, and at least 16 genes absent or significantly fragmented relative to strain R. Notably, an Rlow isogenic mutant in one of these genes (MGA_1107) caused significantly fewer severe tracheal lesions in the natural host compared to virulent M. gallisepticum Rlow. Comparative genomic hybridizations indicated few genetic loci commonly affected in F and vaccine strains ts-11 and 6/85, which would correlate with proteins affecting strain R virulence. Together, these data provide novel insights into inter- and intrastrain M. gallisepticum genomic variability and the genetic basis of M. gallisepticum virulence.

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Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

Tropical Animal Health and Production ◽

10.1007/s11250-021-02877-y ◽

2021 ◽

Vol 53 (4) ◽

Author(s):

Jean N. Hakizimana ◽

Jean B. Ntirandekura ◽

Clara Yona ◽

Lionel Nyabongo ◽

Gladson Kamwendo ◽

...

Keyword(s):

Complete Genome ◽

African Swine Fever Virus ◽

Gc Content ◽

Genomic Analysis ◽

African Swine Fever ◽

Eastern Africa ◽

Nucleotide Identity ◽

Comparative Genomic ◽

Genome Sequences ◽

Domestic Pigs

AbstractSeveral African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

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Zucchini yellow mosaic virus Genomic Sequences from Papua New Guinea: Lack of Genetic Connectivity with Northern Australian or East Timorese Genomes, and New Recombination Findings

Plant Disease ◽

10.1094/pdis-09-18-1666-re ◽

2019 ◽

Vol 103 (6) ◽

pp. 1326-1336 ◽

Cited By ~ 1

Author(s):

Solomon Maina ◽

Martin J. Barbetti ◽

Owain R. Edwards ◽

David Minemba ◽

Michael W. Areke ◽

...

Keyword(s):

Mosaic Virus ◽

Papua New Guinea ◽

High Throughput Sequencing ◽

Genomic Sequence ◽

Zucchini Yellow Mosaic Virus ◽

New Guinea ◽

Yellow Mosaic Virus ◽

Genetic Connectivity ◽

Genomic Sequences ◽

Nucleotide Identity

Zucchini yellow mosaic virus (ZYMV) isolates were obtained in Papua New Guinea (PNG) from cucumber (Cucumis sativus) or pumpkin (Cucurbita spp.) plants showing mosaic symptoms growing at Kongop in the Mount Hagen District, Western Highlands Province, or Zage in the Goroka District, Eastern Highlands Province. The samples were blotted onto FTA cards, which were sent to Australia, where they were subjected to high-throughput sequencing. When the coding regions of the nine new ZYMV genomic sequences found were compared with those of 64 other ZYMV sequences from elsewhere, they grouped together, forming new minor phylogroup VII within ZYMV’s major phylogroup A. Genetic connectivity was lacking between ZYMV genomic sequences from PNG and its neighboring countries, Australia and East Timor; the closest match between a PNG and any other genomic sequence was a 92.8% nucleotide identity with a sequence in major phylogroup A’s minor phylogroup VI from Japan. When the RDP5.2 recombination analysis program was used to compare 66 ZYMV sequences, evidence was obtained of 30 firm recombination events involving 41 sequences, and all isolates from PNG were recombinants. There were 21 sequences without recombination events in major phylogroup A, whereas there were only 4 such sequences within major phylogroup B. ZYMV’s P1, Cl, N1a-Pro, P3, CP, and NIb regions contained the highest evidence of recombination breakpoints. Following removal of recombinant sequences, seven minor phylogroups were absent (I, III, IV, V, VI, VII, and VIII), leaving only minor phylogroups II and IX. By contrast, when a phylogenetic tree was constructed using recombinant sequences with their recombinationally derived tracts removed before analysis, five previous minor phylogroups remained unchanged within major phylogroup A (II, III, IV, V, and VII) while four formed two new merged phylogroups (I/VI and VIII/IX). Absence of genetic connectivity between PNG, Australian, and East Timorese ZYMV sequences, and the 92.8% nucleotide identity between a PNG sequence and the closest sequence from elsewhere, suggest that a single introduction may have occurred followed by subsequent evolution to adapt to the PNG environment. The need for enhanced biosecurity measures to protect against potentially damaging virus movements crossing the seas separating neighboring countries in this region of the world is discussed.

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The genomic sequence ofExiguobacterium chiriqhuchastr. N139 reveals a species that thrives in cold waters and extreme environmental conditions

PeerJ ◽

10.7717/peerj.3162 ◽

2017 ◽

Vol 5 ◽

pp. e3162 ◽

Cited By ~ 5

Author(s):

Ana Gutiérrez-Preciado ◽

Carlos Vargas-Chávez ◽

Mariana Reyes-Prieto ◽

Omar F. Ordoñez ◽

Diego Santos-García ◽

...

Keyword(s):

Acid Metabolism ◽

High Salinity ◽

Genomic Sequence ◽

Ultraviolet B ◽

Comparative Genomic ◽

Ultraviolet B Radiation ◽

Genomic Analyses ◽

High Concentrations ◽

And Coping ◽

Cold Lake

We report the genome sequence ofExiguobacterium chiriqhuchastr. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of theExiguobacteriumgenomes available suggest that our strain belongs to the same species as the previously reportedE. pavilionensisstr. RW-2 andExiguobacteriumstr. GIC 31. We describe this species and propose thechiriqhuchaname to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bpE. chiriqhuchastr. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that conferE. chiriqhuchastr. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.

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Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus

Clinical Infectious Diseases ◽

10.1093/cid/ciz234 ◽

2019 ◽

Vol 70 (3) ◽

pp. 464-473 ◽

Cited By ~ 3

Author(s):

Won-Keun Kim ◽

Jin Sun No ◽

Daesang Lee ◽

Jaehun Jung ◽

Hayne Park ◽

...

Keyword(s):

Genomic Sequence ◽

Disease Risk ◽

Hemorrhagic Fever ◽

Epidemiological Surveillance ◽

Likelihood Method ◽

Comparative Genomic ◽

Novel Approach ◽

Epidemiological Surveys ◽

Outbreak Areas ◽

Complete Sequences

Abstract Background Endemic outbreaks of hantaviruses pose a critical public health threat worldwide. Hantaan orthohantavirus (HTNV) causes hemorrhagic fever with renal syndrome (HFRS) in humans. Using comparative genomic analyses of partial and nearly complete sequences of HTNV from humans and rodents, we were able to localize, with limitations, the putative infection locations for HFRS patients. Partial sequences might not reflect precise phylogenetic positions over the whole-genome sequences; finer granularity of rodent sampling reflects more precisely the circulation of strains. Methods Five HFRS specimens were collected. Epidemiological surveys were conducted with the patients during hospitalization. We conducted active surveillance at suspected HFRS outbreak areas. We performed multiplex polymerase chain reaction–based next-generation sequencing to obtain the genomic sequence of HTNV from patients and rodents. The phylogeny of human- and rodent-derived HTNV was generated using the maximum likelihood method. For phylogeographic analyses, the tracing of HTNV genomes from HFRS patients was defined on the bases of epidemiological interviews, phylogenetic patterns of the viruses, and geographic locations of HTNV-positive rodents. Results The phylogeographic analyses demonstrated genetic clusters of HTNV strains from clinical specimens, with HTNV circulating in rodents at suspected sites of patient infections. Conclusions This study demonstrates a major shift in molecular epidemiological surveillance of HTNV. Active targeted surveillance was performed at sites of suspected infections, allowing the high-resolution phylogeographic analysis to reveal the site of emergence of HTNV. We posit that this novel approach will make it possible to identify infectious sources, perform disease risk assessment, and implement preparedness against vector-borne viruses.

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Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila

BMC Genomics ◽

10.1186/1471-2164-11-271 ◽

2010 ◽

Vol 11 (1) ◽

pp. 271 ◽

Cited By ~ 13

Author(s):

Suzy C.P. Renn ◽

Heather E. Machado ◽

Albyn Jones ◽

Kosha Soneji ◽

Rob J. Kulathinal ◽

...

Keyword(s):

Comparative Genomic Hybridization ◽

Genomic Sequence ◽

Sequence Divergence ◽

Comparative Genomic ◽

Proof Of Concept ◽

Genomic Hybridization

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Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov

10.1101/703363 ◽

2019 ◽

Author(s):

Cristina Merla ◽

Carla Rodrigues ◽

Virginie Passet ◽

Marta Corbella ◽

Harry A. Thorpe ◽

...

Keyword(s):

Mass Spectrometry ◽

Type Strain ◽

Genomic Sequence ◽

Phylogenetic Analyses ◽

Klebsiella Oxytoca ◽

Mass Spectrometry Analysis ◽

Nucleotide Identity ◽

Average Nucleotide Identity ◽

Single Strain ◽

Spectrometry Analysis

AbstractKlebsiella oxytoca causes opportunistic human infections and post-antibiotic haemorrhagic diarrhoea. This Enterobacteriaceae species is genetically heterogeneous and is currently subdivided into seven phylogroups (Ko1 to Ko4, Ko6 to Ko8). Here we investigated the taxonomic status of phylogroups Ko3 and Ko4. Genomic sequence-based phylogenetic analyses demonstrate that Ko3 and Ko4 formed well-defined sequence clusters related to, but distinct from, Klebsiella michiganensis (Ko1), Klebsiella oxytoca (Ko2), K. huaxiensis (Ko8) and K. grimontii (Ko6). The average nucleotide identity of Ko3 and Ko4 were 90.7% with K. huaxiensis and 95.5% with K. grimontii, respectively. In addition, three strains of K. huaxiensis, a species so far described based on a single strain from a urinary tract infection patient in China, were isolated from cattle and human faeces. Biochemical and MALDI-ToF mass spectrometry analysis allowed differentiating Ko3, Ko4 and Ko8 from the other K. oxytoca species. Based on these results, we propose the names Klebsiella spallanzanii for the Ko3 phylogroup, with SPARK_775_C1T (CIP 111695T, DSM 109531T) as type strain, and Klebsiella pasteurii for Ko4, with SPARK_836_C1T (CIP 111696T, DSM 109530T) as type strain. Strains of K. spallanzanii were isolated from human urine, cow faeces and farm surfaces, while strains of K. pasteurii were found in faecal carriage from humans, cows and turtles.Accession numbersThe nucleotide sequences generated in this study were deposited in ENA and are available through the INSDC databases under accession numbers MN091365 (SB6411T = SPARK775C1T), MN091366 (SB6412 T = SPARK836C1T) and MN104661 to MN104677 (16S rRNA), MN076606 to MN076643 (gyrA and rpoB), and MN030558 to MN030567 (blaOXY). Complete genomic sequences were submitted to European Nucleotide Archive under the BioProject number PRJEB15325.AbbreviationsANI, average nucleotide identity; HCCA, a-cyano-4-hydroxycinnamic acid; isDDH, in silico DNA-DNA hybridization; SCAI, Simmons citrate agar with inositol; MALDI57 ToF MS: Matrix-assisted laser desorption/ionization time of flight mass spectrometry

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