scholarly journals Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae)

2009 ◽  
Vol 83 (21) ◽  
pp. 11233-11243 ◽  
Author(s):  
Stephanie D. Friedman ◽  
Fred J. Genthner ◽  
Jennifer Gentry ◽  
Mark D. Sobsey ◽  
Jan Vinjé
Keyword(s):  
Complete Genome ◽  
Catalytic Domain ◽  
Phylogenetic Analyses ◽  
Detailed Knowledge ◽  
Genome Sequences ◽  
Virus Family ◽  
Sequence Identity ◽  
The Family ◽  
The Individual ◽  
Male Specific

ABSTRACT Male-specific single-stranded RNA (FRNA) coliphages belong to the family Leviviridae. They are classified into two genera (Levivirus and Allolevivirus), which can be subdivided into four genogroups (genogroups I and II in Levivirus and genogroups III and IV in Allolevivirus). Relatively few strains have been completely characterized, and hence, a detailed knowledge of this virus family is lacking. In this study, we sequenced and characterized the complete genomes of 19 FRNA strains (10 Levivirus strains and 9 Allolevivirus strains) and compared them to the 11 complete genome sequences available in GenBank. Nucleotide similarities among strains of Levivirus genogroups I and II were 75% to 99% and 83 to 94%, respectively, whereas similarities among strains of Allolevivirus genogroups III and IV ranged from 70 to 96% and 75 to 95%, respectively. Although genogroup I strain fr and genogroup III strains MX1 and M11 share only 70 to 78% sequence identity with strains in their respective genogroups, phylogenetic analyses of the complete genome and the individual genes suggest that strain fr should be grouped in Levivirus genogroup I and that the MX1 and M11 strains belong in Allolevivirus genogroup III. Strains within each genus share >50% sequence identity, whereas between the two genera, strains have <40% nucleotide sequence identity. Overall, amino acid composition, nucleotide similarities, and replicase catalytic domain location contributed to phylogenetic assignments. A conserved eight-nucleotide signature at the 3′ end of the genome distinguishes leviviruses (5′ ACCACCCA 3′) from alloleviviruses (5′ TCCTCCCA 3′).

scholarly journals Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1017
Author(s):  
Hirohisa Mekata ◽  
Tomohiro Okagawa ◽  
Satoru Konnai ◽  
Takayuki Miyazawa
Keyword(s):  
Phylogenetic Analyses ◽  
Foamy Virus ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Virus Family ◽  
Bovine Foamy Virus ◽  
Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

The complete genome sequences of two isolates of cnidium vein yellowing virus, a tentative new member of the family Secoviridae

2015 ◽  
Vol 160 (11) ◽  
pp. 2911-2914 ◽  
Author(s):  
Ran Hee Yoo ◽  
Fumei Zhao ◽  
Seungmo Lim ◽  
Davaajargal Igori ◽  
Sang-Mok Kim ◽  
...  
Keyword(s):  
Complete Genome ◽  
Genome Sequences ◽  
The Family ◽  
Yellowing Virus

scholarly journals Complete Genome Sequences of Chikungunya Viruses Isolated from Plasma Specimens Collected from Haitians in 2014

2017 ◽  
Vol 5 (15) ◽  
Author(s):  
Sarah K. White ◽  
J. Glenn Morris ◽  
Maha A. Elbadry ◽  
Valery Madsen Beau De Rochars ◽  
Bernard A. Okech ◽  
...  
Keyword(s):  
Human Plasma ◽  
Complete Genome ◽  
Chikungunya Virus ◽  
Phylogenetic Analyses ◽  
Genomic Sequences ◽  
Genome Sequences ◽  
Chikungunya Fever ◽  
Asian Lineage ◽  
Virus Isolates

ABSTRACT Ten chikungunya virus isolates from human plasma collected in Haiti from May to August 2014, in the midst of a chikungunya fever outbreak, were fully sequenced. The resulting genomic sequences are nearly identical, and phylogenetic analyses indicate they belong to the Asian lineage of the virus.

scholarly journals Complete Genome Sequence of Human Coronavirus OC43 Isolated from Mexico

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
B. T. Taboada ◽  
P. Isa ◽  
M. A. Espinoza ◽  
F. E. Aponte ◽  
M. A. Arias-Ortiz ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genome Sequences ◽  
Human Coronavirus ◽  
Sequence Identity ◽  
New Generation Sequencing ◽  
New Generation ◽  
Metagenomic Approach ◽  
Generation Sequencing

We report the complete genome sequence of the first Mexican human coronavirus (HCoV) OC43, obtained by new-generation sequencing and a metagenomic approach, isolated from a child hospitalized with pneumonia. The genome is closely related to the other OC43 genome sequences available, ranging from 99.8% to 98.2% nucleotide sequence identity.

scholarly journals Are Human P[14] Rotavirus Strains the Result of Interspecies Transmissions from Sheep or Other Ungulates That Belong to the Mammalian Order Artiodactyla?

2009 ◽  
Vol 83 (7) ◽  
pp. 2917-2929 ◽  
Author(s):  
Jelle Matthijnssens ◽  
Christiaan A. Potgieter ◽  
Max Ciarlet ◽  
Viviana Parreño ◽  
Vito Martella ◽  
...  
Keyword(s):  
Complete Genome ◽  
Human Population ◽  
Animal Species ◽  
Genetic Relatedness ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Genome Sequences ◽  
Lama Guanicoe ◽  
Bovine Rotavirus ◽  
Genomic Relatedness

ABSTRACT A limited number of human G6P[14] rotavirus strains that cause gastroenteritis in humans have been isolated in Europe and Australia. The complete genome sequences were determined for five of these human strains—B10925-97 (isolated in Belgium in 1997), 111/05-27 (Italy, 2005), PA169 (Italy, 1987), MG6 (Australia, 1993), and Hun5 (Hungary, 1997)—and their genetic relatedness to animal rotavirus strains was evaluated by sequencing the complete genome of the sheep rotavirus OVR762 (G8P[14]; Spain, 2002), the guanaco (Lama guanicoe) rotavirus strains Arg/Chubut/99 and Arg/Río Negro/98 (G8P[14] and G8P[1], respectively; Argentina, 1999 and 1998), the sable antelope strain RC-18/08 (G6P[14]; South Africa, 2008), and the bovine rotavirus strain Arg/B383/98 (G15P[11]; Argentina, 1998). These analyses revealed an overall consensus genomic constellation (G6/G8)-P[14]-I2-(R2/R5)-C2-M2-(A3/A11)-N2-T6-(E2/E12)-H3, together with a few gene reassortments, and the phylogenetic analyses confirmed that the P[14] human strains evaluated in this study were closely related to rotavirus strains isolated from sheep, cattle, goats, guanacos, and antelopes and to rabbits (albeit to a lesser extent), suggesting that one (or more) of these animal species might be the source of the human G6P[14] strains. The main feature of the genotype and phylogenetic analyses was the close overall genomic relatedness between the five human G6P[14] rotavirus strains and the ovine and antelope rotavirus strains. Taken together, these data strongly suggest a common origin for the human P[14] strains and those of the even-toed ungulates belonging to the mammalian order Artiodactyla, with sheep probably playing a key role in the interspecies transmission responsible for the introduction of P[14] rotavirus strains into the human population.

scholarly journals Complete Genome Sequences of Grapevine Yellow Speckle Viroid 1 and Hop Stunt Viroid Assembled from the Transcriptome of Ixeridium dentatum Plants

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Joong-Hwan Lee ◽  
Seungmo Lim ◽  
Seung-Won Lee ◽  
Ran Hee Yoo ◽  
Davaajargal Igori ◽  
...  
Keyword(s):  
Complete Genome ◽  
Transcriptome Data ◽  
Genome Sequences ◽  
First Report ◽  
Stunt Viroid ◽  
Hop Stunt Viroid ◽  
The Family

Here, we report complete genome sequences of grapevine yellow speckle viroid 1 (GYSVd1) and hop stunt viroid (HSVd), members of the family Pospiviroidae , assembled from the transcriptome data generated from Ixeridium dentatum plants. To our knowledge, this is the first report of GYSVd1 and HSVd in I. dentatum .

Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae

Holzforschung ◽  
2018 ◽  
Vol 72 (4) ◽  
pp. 337-345 ◽  
Author(s):  
Yu Song ◽  
Xin Yao ◽  
Bing Liu ◽  
Yunhong Tan ◽  
Richard T. Corlett
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Inverted Repeats ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Tropical Asia ◽  
Length Difference ◽  
The Family ◽  
Genomic Analyses

AbstractAlseodaphneis a genus of timber trees (ca. 40 spp.) belonging to thePerseagroup of the Lauraceae. It is widely distributed in tropical Asia, but is often confused withDehaasiaandNothaphoebe, and the systematics of the genus is unclear. Here, the complete chloroplast genome sequences ofA. semecarpifoliawill be reported, the type species ofAlseodaphne, and two China-endemic species,A. gracilisandA. huanglianshanensis. The three plastomes were 153 051 bp, 153 099 bp and 153 070 bp, respectively. Comparative genomic analyses indicate that the threeAlseodaphneplastomes have similar genome size and those are very different with previously published plastomes of Lauraceae in length. The length difference is directly caused by inverted repeats expansion/contraction. Four highly variable loci includingpsbD-trnM,ndhF-rpl32,rpl32-trnLandycf1among the threeAlseodaphnespecies were identified as useful plastid candidate barcodes forAlseodaphneand Lauraceae species. Phylogenetic analyses based on 12 complete plastomes of Lauraceae species confirm a monophyleticPerseagroup comprising species ofAlseodaphne,Phoebe,PerseaandMachilus.

scholarly journals Complete Genome Sequences of BK Polyomavirus Strains from Two Patients with Urinary Tract Infection, Sequenced Using the Ion Torrent Platform

2017 ◽  
Vol 5 (46) ◽  
Author(s):  
Graham Rose ◽  
Kyriaki Ranellou ◽  
Raju Misra ◽  
Colin Crump ◽  
David Wooldridge ◽  
...  
Keyword(s):  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Tract Infection ◽  
Complete Genome ◽  
Phylogenetic Analyses ◽  
Ion Torrent ◽  
Genome Sequences ◽  
Transplant Patients ◽  
Bk Polyomavirus ◽  
Kidney Transplant Patients

ABSTRACT BK polyomavirus is an important pathogen in kidney transplant patients. We report here two complete genome sequences, those of isolates CAMB-1035 and CAMB-1055, identified in two urine samples tested for urinary tract infection at a hospital in eastern England, United Kingdom. Variation and phylogenetic analyses indicate that both isolates belong to subtype Ib-1.

scholarly journals Multiple Introductions of Rabbit Hemorrhagic Disease Virus Lagovirus europaeus/GI.2 in Africa

Biology ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 883
Author(s):  
Faten Ben Chehida ◽  
Ana M. Lopes ◽  
João V. Côrte-Real ◽  
Soufien Sghaier ◽  
Rim Aouini ◽  
...  
Keyword(s):  
Disease Virus ◽  
Complete Genome ◽  
Phylogenetic Analyses ◽  
Rabbit Hemorrhagic Disease Virus ◽  
Economic Losses ◽  
Hemorrhagic Disease ◽  
Genome Sequences ◽  
Rabbit Hemorrhagic Disease ◽  
Multiple Introductions ◽  
New Genotype

Rabbit hemorrhagic disease (RHD) causes high mortality and morbidity in European rabbits (Oryctolagus cuniculus). In Africa, the presence of the causative agent, the rabbit hemorrhagic disease virus (RHDV), was first confirmed in 1992 (genotype Lagovirus europaeus/GI.1). In 2015, the new genotype Lagovirus europaeus/GI.2 (RHDV2/b) was detected in Tunisia. Currently, GI.2 strains are present in several North and Sub-Saharan African countries. Considerable economic losses have been observed in industrial and traditional African rabbitries due to RHDV. Like other RNA viruses, this virus presents high recombination rates, with the emergence of GI.2 being associated with a recombinant strain. Recombination events have been detected with both pathogenic (GI.1b and GII.1) and benign (GI.3 and GI.4) strains. We obtained complete genome sequences of Tunisian GI.2 strains collected between 2018 and 2020 and carried out phylogenetic analyses. The results revealed that Tunisian strains are GI.3P-GI.2 strains that were most likely introduced from Europe. In addition, the results support the occurrence of multiple introductions of GI.2 into Africa, stressing the need for characterizing complete genome sequences of the circulating lagoviruses to uncover their origin. Continued monitoring and control of rabbit trade will grant a better containment of the disease and reduce the disease-associated economic losses.

scholarly journals Coding-Complete Genome Sequences of an Iteradensovirus and an Alphapermutotetra-Like Virus Identified from the Pine Processionary Moth (Thaumetopoea pityocampa) in Portugal

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Franck Dorkeld ◽  
Réjane Streiff ◽  
Carole Kerdelhué ◽  
Mylène Ogliastro
Keyword(s):  
Complete Genome ◽  
Open Reading Frames ◽  
Thaumetopoea Pityocampa ◽  
Data Sets ◽  
Genome Sequences ◽  
Virus Family ◽  
Content Type ◽  
Pine Processionary Moth ◽  
Transcriptomic Data ◽  
Reading Frames

ABSTRACT The coding-complete genome sequences of an iteradensovirus (family Parvoviridae) and an alphapermutotetra-like virus (family Permutotetraviridae) were discovered from transcriptomic data sets obtained from Thaumetopoea pityocampa larvae collected in Portugal. Each of the coding-complete genome sequences of these viruses contains three main open reading frames (ORFs).

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