scholarly journals The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 258 ◽  
Author(s):  
Dominique L. Chaput ◽  
David Bass ◽  
Md. Mehedi Alam ◽  
Neaz Al Hasan ◽  
Grant D. Stentiford ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Geographical Origin ◽  
Rna Virus ◽  
Geographic Origin ◽  
South American ◽  
Reassortment Event ◽  
Coding Regions ◽  
Whole Genomes ◽  
History Of ◽  
Negative Sense

Tilapia lake virus (TiLV), a negative sense RNA virus with a 10 segment genome, is an emerging threat to tilapia aquaculture worldwide, with outbreaks causing over 90% mortality reported on several continents since 2014. Following a severe tilapia mortality event in July 2017, we confirmed the presence of TiLV in Bangladesh and obtained the near-complete genome of this isolate, BD-2017. Phylogenetic analysis of the concatenated 10 segment coding regions placed BD-2017 in a clade with the two isolates from Thailand, separate from the Israeli and South American isolates. However, phylogenetic analysis of individual segments gave conflicting results, sometimes clustering BD-2017 with one of the Israeli isolates, and splitting pairs of isolates from the same region. By comparing patterns of topological difference among segments of quartets of isolates, we showed that TiLV likely has a history of reassortment. Segments 5 and 6, in particular, appear to have undergone a relatively recent reassortment event involving Ecuador isolate EC-2012 and Israel isolate Til-4-2011. The phylogeny of TiLV isolates therefore depends on the segment sequenced. Our findings illustrate the need to exercise caution when using phylogenetic analysis to infer geographic origin and track the movement of TiLV, and we recommend using whole genomes wherever possible.

scholarly journals Molecular Characterization of Leishmania RNA virus 2 in Leishmania major from Uzbekistan

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 830 ◽  
Author(s):  
Yuliya Kleschenko ◽  
Danyil Grybchuk ◽  
Nadezhda S. Matveeva ◽  
Diego H. Macedo ◽  
Evgeny N. Ponirovsky ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cutaneous Leishmaniasis ◽  
Molecular Characterization ◽  
Leishmania Major ◽  
Geographical Origin ◽  
Rna Virus ◽  
Viral Sequences

Here we report sequence and phylogenetic analysis of two new isolates of Leishmania RNA virus 2 (LRV2) found in Leishmania major isolated from human patients with cutaneous leishmaniasis in south Uzbekistan. These new virus-infected flagellates were isolated in the same region of Uzbekistan and the viral sequences differed by only nineteen SNPs, all except one being silent mutations. Therefore, we concluded that they belong to a single LRV2 species. New viruses are closely related to the LRV2-Lmj-ASKH documented in Turkmenistan in 1995, which is congruent with their shared host (L. major) and common geographical origin.

Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7)

2020 ◽  
Vol 142 ◽  
pp. 203-211
Author(s):  
AJ Tighe ◽  
MD Gallagher ◽  
J Carlsson ◽  
I Matejusova ◽  
F Swords ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rna Virus ◽  
Whole Genome ◽  
Pancreas Disease ◽  
Codon Positions ◽  
History Of ◽  
Unique Strain ◽  
Salmon Pancreas Disease Virus

Salmon pancreas disease virus, more commonly known as salmonid alphavirus (SAV), is a single-stranded positive sense RNA virus and the causative agent of pancreas disease and sleeping disease in salmonids. In this study, a unique strain of SAV previously isolated from ballan wrasse was subjected to whole genome sequencing using nanopore sequencing. In order to accurately examine the evolutionary history of this strain in comparison to other SAV strains, a partitioned phylogenetic analysis was performed to account for variation in the rate of evolution for both individual genes and codon positions. Partitioning the genome alignments almost doubled the observed branch lengths in the phylogenetic tree when compared to the more common approach of applying one model of substitution across the genome and significantly increased the statistical fit of the best-fitting models of nucleotide substitution. Based on the genomic data, a valid case can be made for the viral strain examined in this study to be considered a new SAV genotype. In addition, this study adds to a growing number of studies in which SAV has been found to infect non-salmonid fish, and as such we have suggested that the viral species name be amended to the more inclusive ‘piscine alphavirus’.

scholarly journals Influence of HIV Infection on the Natural History of Hepatocellular Carcinoma: Results From a Global Multicohort Study

2019 ◽  
Vol 37 (4) ◽  
pp. 296-304 ◽  
Author(s):  
David J. Pinato ◽  
Elias Allara ◽  
Ting-Yi Chen ◽  
Franco Trevisani ◽  
Beatriz Minguez ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Geographical Origin ◽  
Geographic Origin ◽  
Hiv Positive ◽  
Hiv Seropositivity ◽  
Hiv Rna ◽  
Cell Counts ◽  
Class B ◽  
History Of ◽  
Anticancer Treatment

PURPOSE Conflicting evidence indicates that HIV seropositivity may influence the outcome of patients with hepatocellular carcinoma (HCC), a leading cause of mortality in people with HIV. We aimed to verify whether HIV affected the overall survival (OS) of patients with HCC, independent of treatment and geographic origin. PATIENTS AND METHODS We designed an international multicohort study of patients with HCC accrued from four continents who did not receive any anticancer treatment. We estimated the effect of HIV seropositivity on patients’ OS while accounting for common prognostic factors and demographic characteristics in uni- and multivariable models. RESULTS A total of 1,588 patients were recruited, 132 of whom were HIV positive. Most patients clustered within Barcelona Clinic Liver Cancer (BCLC) C or D criteria (n = 1,168 [74%]) and Child-Turcotte-Pugh (CTP) class B (median score, 7; interquartile range [IQR], 3). At HCC diagnosis, the majority of patients who were HIV-positive (n = 65 [64%]) had been on antiretrovirals for a median duration of 8.3 years (IQR, 8.59 years) and had median CD4+ cell counts of 256 (IQR, 284) with undetectable HIV RNA (n = 68 [52%]). OS decreased significantly throughout BCLC stages 0 to D (16, 12, 7.5, 3.1, and 3 months, respectively; P < .001). Median OS of patients who were HIV-positive was one half that of their HIV-uninfected counterparts (2.2 months [bootstrap 95% CI, 1.2 to 3.1 months] v 4.1 months [95% CI, 3.6 to 4.4 months]). In adjusted analyses, HIV seropositivity increased the hazard of death by 24% ( P = .0333) independent of BCLC ( P < .0001), CTP ( P < .0001), α-fetoprotein ( P < .0001), geographical origin ( P < .0001), and male sex ( P = .0016). Predictors of worse OS in patients who were HIV-positive included CTP ( P = .0071) and α-fetoprotein ( P < .0001). CONCLUSION Despite adequate antiretroviral treatment, HIV seropositivity is associated with decreased survival in HCC, independent of stage, anticancer treatment, and geographical origin. Mechanistic studies investigating the immunobiology of HIV-associated HCC are urgently required.

scholarly journals Analysis of the long control region of bovine papillomavirus type 1 associated with sarcoids in equine hosts indicates multiple cross-species transmission events and phylogeographical structure

2014 ◽  
Vol 95 (12) ◽  
pp. 2748-2756 ◽  
Author(s):  
Hannah Trewby ◽  
Gizachew Ayele ◽  
Giuseppe Borzacchiello ◽  
Sabine Brandt ◽  
M. Saveria Campo ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Control Region ◽  
Long Control Region ◽  
Sequence Variant ◽  
South American ◽  
Bovine Papillomavirus ◽  
Dna Viruses ◽  
Species Association ◽  
Fitness Advantage ◽  
History Of

Papillomaviruses are a family of slowly evolving DNA viruses and their evolution is commonly linked to that of their host species. However, whilst bovine papillomavirus-1 (BPV-1) primarily causes warts in its natural host, the cow, it can also cause locally aggressive and invasive skin tumours in equids, known as sarcoids, and thus provides a rare contemporary example of cross-species transmission of a papillomavirus. Here, we describe the first phylogenetic analysis of BPV-1 in equine sarcoids to our knowledge, allowing us to explore the evolutionary history of BPV-1 and investigate its cross-species association with equids. A phylogenetic analysis of the BPV-1 transcriptional promoter region (the long control region or LCR) was conducted on 15 bovine and 116 equine samples from four continents. Incorporating previous estimates for evolutionary rates in papillomavirus implied that the genetic diversity in the LCR variants was ancient and predated domestication of both equids and cattle. The phylogeny demonstrated geographical segregation into an ancestral group (African, South American and Australian samples), and a more recently derived, largely European clade. Whilst our data are consistent with BPV-1 originating in cattle, we found evidence of multiple, probably relatively recent, cross-species transmission events into horses. We also demonstrated the high prevalence of one particular sequence variant (variant 20), and suggest this may indicate that this variant shows a fitness advantage in equids. Although strong host specificity remains the norm in papillomaviruses, our results demonstrate that exceptions to this rule exist and can become epidemiologically relevant.

scholarly journals Diversity, Virulence, and 2,4-Diacetylphloroglucinol Sensitivity of Gaeumannomyces graminis var. tritici Isolates from Washington State

2009 ◽  
Vol 99 (5) ◽  
pp. 472-479 ◽  
Author(s):  
Youn-Sig Kwak ◽  
Peter A. H. M. Bakker ◽  
Debora C. M. Glandorf ◽  
Jennifer T. Rice ◽  
Timothy C. Paulitz ◽  
...  
Keyword(s):  
Geographical Origin ◽  
Geographic Origin ◽  
Washington State ◽  
Gaeumannomyces Graminis ◽  
Growing Seasons ◽  
History Of ◽  
Pathogenicity Tests ◽  
Polymerase Chain ◽  
Gaeumannomyces Graminis Var Tritici ◽  
Take All

We determined whether isolates of the take-all pathogen Gaeumannomyces graminis var. tritici become less sensitive to 2,4-diacetylphloroglucinol (2,4-DAPG) during wheat monoculture as a result of exposure to the antibiotic over multiple growing seasons. Isolates of G. graminis var. tritici were baited from roots of native grasses collected from noncropped fields and from roots of wheat from fields with different cropping histories near Lind, Ritzville, Pullman, and Almota, WA. Isolates were characterized by using morphological traits, G. graminis variety-specific polymerase chain reaction and pathogenicity tests. The sensitivity of G. graminis var. tritici isolates to 2,4-DAPG was determined by measuring radial growth of each isolate. The 90% effective dose value was 3.1 to 4.4 μg ml–1 for 2,4-DAPG-sensitive isolates, 4.5 to 6.1 μg ml–1 for moderately sensitive isolates, and 6.2 to 11.1 μg ml–1 for less sensitive isolates. Sensitivity of G. graminis var. tritici isolates to 2,4-DAPG was normally distributed in all fields and was not correlated with geographic origin or cropping history of the field. There was no correlation between virulence on wheat and geographical origin, or virulence and sensitivity to 2,4-DAPG. These results indicate that G. graminis var. tritici does not become less sensitive to 2,4-DAPG during extended wheat monoculture.

scholarly journals Genomic analysis on Brazilian strains of Anaplasma marginale

2021 ◽  
Vol 30 (2) ◽  
Author(s):  
Bruno Dall’Agnol ◽  
Anelise Webster ◽  
Ugo Araújo Souza ◽  
Antonela Barbieri ◽  
Fabiana Quoos Mayer ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Anaplasma Marginale ◽  
Surface Proteins ◽  
Reference Sequence ◽  
South American ◽  
Nucleotide Polymorphisms ◽  
Whole Genomes ◽  
History Of ◽  
Vector Borne ◽  
Genome Information

Abstract Anaplasma marginale is a vector-borne pathogen that causes a disease known as anaplasmosis. No sequenced genomes of Brazilian strains are yet available. The aim of this work was to compare whole genomes of Brazilian strains of A. marginale (Palmeira and Jaboticabal) with genomes of strains from other regions (USA and Australia strains). Genome sequencing of Brazilian strains was performed by means of next-generation sequencing. Reads were mapped using the genome of the Florida strain of A. marginale as a reference sequence. Single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) were identified. The data showed that two Brazilian strains grouped together in one particular clade, which grouped in a larger American group together with North American strains. Moreover, some important differences in surface proteins between the two Brazilian isolates can be discerned. These results shed light on the evolutionary history of A. marginale and provide the first genome information on South American isolates. Assessing the genome sequences of strains from different regions is essential for increasing knowledge of the pan-genome of this bacteria.

The oldest sigmodontine rodent revisited and the age of the first South American cricetids

2018 ◽  
Vol 93 (2) ◽  
pp. 368-384 ◽  
Author(s):  
Franck Barbière ◽  
Pablo E. Ortiz ◽  
Ulyses F.J. Pardiñas
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Cranial Morphology ◽  
South American ◽  
Early Pliocene ◽  
Molecular Approaches ◽  
Fossil Material ◽  
History Of ◽  
New Interpretation ◽  
First Time

AbstractNew fossil material ofAuliscomys formosusReig 1978 allows restudy of the oldest known South American representative of the subfamily Sigmodontinae. Description ofAuliscomys formosuswas based on a fragmentary dentary exhumed from the Monte Hermoso Formation of central Argentina. Previous studies allocatedA. formosusto the early Pliocene. A reevaluation of dental and cranial morphology, including for the first time the upper dentition, and the inclusion ofA. formosusin a phylogenetic analysis of the tribe Phyllotini indicate thatA. formosusrepresents a new genus,Kraglievichimys.Kraglievichimysshares a mosaic of characters with the livingAuliscomysOsgood, 1915 andLoxodontomysOsgood, 1947. The taxonomic reassignment ofA. formosusand the possibility that the Monte Hermoso Formation may be younger than early Pliocene in age provide a new understanding of cricetid diversification in South America. Estimates of sigmodontine ancestry by molecular approaches are biased toward older ages, whereas this new interpretation of the history ofK. formosussuggests that the South American history of sigmodontines spans less than 4 million years.UUID:http://zoobank.org/49dd8f60-56b1-4e8a-a044-6cea3a1bd52b

scholarly journals Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop

2016 ◽  
Author(s):  
Markus G. Stetter ◽  
Karl J Schmid
Keyword(s):  
Phylogenetic Trees ◽  
De Novo ◽  
Geographic Origin ◽  
Genotyping By Sequencing ◽  
South American ◽  
Amaranthus Hypochondriacus ◽  
Multispecies Coalescent ◽  
Genome Size Evolution ◽  
History Of ◽  
Weedy Species

AbstractThe genus Amaranthus consists of 50 to 70 species and harbors several cultivated and weedy species of great economic importance. A small number of suitable traits, phenotypic plasticity, gene flow and hybridization made it difficult to establish the taxonomy and phylogeny of the whole genus despite various studies using molecular markers. We inferred the phylogeny of the Amaranthus genus using genotyping by sequencing (GBS) of 94 genebank accessions representing 35 Amaranthus species and measured their genome sizes. SNPs were called by de novo and reference-based methods, for which we used the distant sugarbeet Beta vulgaris and the closely related Amaranthus hypochondriacus as references. SNP counts and proportions of missing data differed between methods, but the resulting phylogenetic trees were highly similar. A distance-based neighbor joing tree of individual accessions and a species tree calculated with the multispecies coalescent supported a previous taxonomic classification into three subgenera although the subgenus A. Acnida consists of two highly differentiated clades. The analysis of the Hybridus complex within the A. Amaranthus subgenus revealed insights on the history of cultivated grain amaranths. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. Wild and cultivated amaranth accessions did not differentiate according to the species assignment but clustered by their geographic origin from South and Central America. Different geographically separated populations of Amaranthus hybridus appear to be the common ancestors of the three cultivated grain species and A. quitensis might be additionally be involved in the evolution of South American grain amaranth (A. caudatus). We also measured genome sizes of the species and observed little variation with the exception of two lineages that showed evidence for a recent polyploidization. With the exception of two lineages, genome sizes are quite similar and indicate that polyploidization did not play a major role in the history of the genus.

scholarly journals Prevalence of Newcastle Disease Diagnosed at the Avian Clinic, Ahmadu Bello University, Zaria, Nigeria: A retrospective survey

2020 ◽  
pp. 60-64
Keyword(s):  
Newcastle Disease ◽  
Management Practices ◽  
Rna Virus ◽  
Viral Disease ◽  
Vaccination History ◽  
History Of ◽  
Single Vaccination ◽  
Almost All ◽  
Negative Sense ◽  
Poor Management

Introduction: Newcastle disease (ND) is a viral disease of birds caused by a negative sense single-stranded RNA virus known as the Newcastle disease virus. It is a disease of almost all species of domestic and wild birds with devastating impacts on poultry health and production. The aim of this study was to determine the prevalence of ND within species, breeds, age and vaccination history from the period of 2014-2018. Methods: A five- year retrospective study (2014-2018) of cases of poultry diseases diagnosed at the Avian Clinic of Veterinary Teaching Hospital (VTH), Ahmadu Bello University (A.B.U), Zaria, Nigeria was conducted, the prevalence of ND within species, breeds, age and vaccination history was determined. Case records file were collected, studied, and clinically diagnosed cases of ND were extracted. Results: It was observed that of the 1,768 poultry cases presented, 754 (42.6%) were confirmed as ND. Most cases were recorded in chickens 710 (40.2%). The prevalence was highest in the improved breed 670 (37.9%) while the local and unknown breeds had prevalence of 4 (0.2%) and 80 (4.5%) respectively. Birds within 8-13 weeks of age had the highest prevalence of 276 (15.4%) while the lowest prevalence of 19 (1.1%) was recorded in birds of unknown ages. Birds with history of incomplete vaccination (single vaccination) had the highest prevalence of 232 (13.1%), while those with complete vaccination history (three rounds of vaccination) had the lowest prevalence of 50 (2.8%). Significance: Poor management practices and improper knowledge of vaccination by the poultry handlers may be responsible for the prevalence pattern of ND recorded. Adequate biosecurity measures and routine vaccination are recommended to minimize the outbreak of ND.

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