scholarly journals Bagaza virus and Israel turkey meningoencephalomyelitis virus are a single virus species

2014 ◽  
Vol 95 (4) ◽  
pp. 883-887 ◽  
Author(s):  
Jovita Fernández-Pinero ◽  
Irit Davidson ◽  
Maia Elizalde ◽  
Shimon Perk ◽  
Yevgeny Khinich ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
International Committee ◽  
Nucleotide Sequences ◽  
Virus Species ◽  
Sequence Comparisons ◽  
Phylogenetic Comparison ◽  
The Family ◽  
Complete Sequences ◽  
Close Genetic Relationship

Bagaza virus (BAGV) and Israel turkey meningoencephalomyelitis virus (ITV) are classified in the genus Flavivirus of the family Flaviviridae. Serologically, they are closely related, belonging to the Ntaya serocomplex. Nucleotide sequences available to date consist of several complete sequences of BAGV isolates, but only partial sequences of ITV isolates. Sequence comparisons of partial envelope (E) and NS5 regions reveal a close genetic relationship between these viruses. Despite this, BAGV and ITV are considered as separate virus species in the database of the International Committee on Taxonomy of Viruses. In this work, complete nucleotide sequences for five ITV isolates are provided, thereby permitting a phylogenetic comparison with other complete sequences of flaviviruses in the Ntaya serogroup. We conclude that BAGV and ITV are the same virus species and propose that both viruses be designated by a new unified name: Avian meningoencephalomyelitis virus.

scholarly journals Viruses Associated with Rusty Mottle and Twisted Leaf Diseases of Sweet Cherry Are Distinct Species

2013 ◽  
Vol 103 (12) ◽  
pp. 1287-1295 ◽  
Author(s):  
D. E. V. Villamor ◽  
K. C. Eastwell
Keyword(s):  
Distinct Species ◽  
Mottle Virus ◽  
Distribution Data ◽  
Virus Species ◽  
Rna Sequences ◽  
Sequence Comparisons ◽  
Protein Coding ◽  
Green Ring ◽  
Virus Rna ◽  
The Family

Virus RNA sequences related to those of the family Betaflexiviridae were amplified from trees affected with the following diseases: cherry twisted leaf, apricot ring pox, cherry necrotic rusty mottle, cherry rusty mottle, and cherry green ring mottle. Phylogenetic analysis of virus sequences obtained from these diseased trees from western North America, along with published sequences of Cherry green ring mottle virus (CGRMV) and Cherry necrotic rusty mottle virus (CNRMV), revealed four major clades. Segregation into these four populations correlated with distinct symptom expression on woody indicators, suggesting that each clade represents a distinct virus species within the family Betaflexiviridae. The viruses occupying each clade were designated clade I: Cherry twisted leaf associated virus, clade II: CNRMV, clade III: Cherry rusty mottle associated virus, and clade IV: CGRMV. Potential recombination events were predicted to occur within and between these viruses, the latter being strongly supported by incongruent phylogenies. Examination of frequency distribution data derived from pairwise sequence comparisons of coat protein coding sequences resulted in a proposal for alternative guidelines for species demarcation for this family of viruses.

scholarly journals Evidence for Frequent Recombination within Species Human Enterovirus B Based on Complete Genomic Sequences of All Thirty-Seven Serotypes

2004 ◽  
Vol 78 (2) ◽  
pp. 855-867 ◽  
Author(s):  
M. Steven Oberste ◽  
Kaija Maher ◽  
Mark A. Pallansch
Keyword(s):  
Complete Genome ◽  
Phylogenetic Analyses ◽  
Human Enterovirus ◽  
Bootstrap Support ◽  
Common Mechanism ◽  
Rna Recombination ◽  
Sequence Comparisons ◽  
Nontranslated Region ◽  
The Family ◽  
Complete Sequences

ABSTRACT The species Human enterovirus B (HEV-B) in the family Picornaviridae consists of coxsackievirus A9; coxsackieviruses B1 to B6; echoviruses 1 to 7, 9, 11 to 21, 24 to 27, and 29 to 33; and enteroviruses 69 and 73. We have determined complete genome sequences for the remaining 22 HEV-B serotypes whose sequences were not represented in public databases and analyzed these in conjunction with previously available complete sequences in GenBank. Members of HEV-B were monophyletic relative to all other human enterovirus species in all regions of the genome except in the 5′-nontranslated region (NTR), where they are known to cluster with members of HEV-A. Within HEV-B, phylogenies constructed from the structural (P1) and nonstructural regions of the genome (P2 and P3) are incongruent, suggesting that recombination had occurred. Similarity plots and bootscanning analysis across the complete genome identified multiple sites at which the phylogeny of a given strain's sequence shifted, indicating potential recombination points. These points are distributed in the 5′-NTR and throughout P2 and P3, but no sites with >80% bootstrap support were identified within the capsid. Individual sequence comparisons and phylogenetic analyses suggest that members of HEV-B have recombined with one another on multiple occasions, resulting in a complex mosaic of sequences derived from multiple parental viruses in the nonstructural regions of the genome. We conclude that RNA recombination is a common mechanism for enterovirus evolution and that recombination within the nonstructural regions of the genome (P2 and P3) has been observed only among members of the same species.

scholarly journals Advanced genebank management of genetic resources of European wild apple, Malus sylvestris, using genome-wide SNP array data

2021 ◽  
Vol 17 (4) ◽  
Author(s):  
Joukje Buiteveld ◽  
Herma JJ Koehorst-van Putten ◽  
Linda Kodde ◽  
Ivo Laros ◽  
Giorgio Tumino ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Genetic Relationship ◽  
Snp Array ◽  
Seed Orchard ◽  
Effective Population ◽  
Malus Sylvestris ◽  
Genebank Management ◽  
Genetic Resources Management ◽  
Genebank Collection ◽  
Close Genetic Relationship

AbstractThe Netherlands’ field genebank collection of European wild apple (Malus sylvestris), consisting of 115 accessions, was studied in order to determine whether duplicates and mistakes had been introduced, and to develop a strategy to optimize the planting design of the collection as a seed orchard. We used the apple 20K Infinium single nucleotide polymorphism (SNP) array, developed in M. domestica, for the first time for genotyping in M. sylvestris. We could readily detect the clonal copies and unexpected duplicates. Thirty-two M. sylvestris accessions (29%) showed a close genetic relationship (parent-child, full-sib, or half-sib) to another accession, which reflects the small effective population size of the in situ populations. Traces of introgression from M. domestica were only found in 7 individuals. This indicates that pollination preferentially took place among the M. sylvestris trees. We conclude that the collection can be considered as mainly pure M. sylvestris accessions. The results imply that it should be managed as one unit when used for seed production. A bias in allele frequencies in the seeds may be prevented by not harvesting all accessions with a close genetic relationship to the others in the seed orchard. We discuss the value of using the SNP array to elaborate the M. sylvestris genetic resources more in depth, including for phasing the markers in a subset of the accessions, as a first step towards genetic resources management at the level of haplotypes.

Flaviviruses excluding dengue

2020 ◽  
pp. 830-845
Author(s):  
Shannan Lee Rossi ◽  
Nikos Vasilakis
Keyword(s):  
Japanese Encephalitis Virus ◽  
Host Range ◽  
Yellow Fever ◽  
Japanese Encephalitis ◽  
Human Infection ◽  
Virus Species ◽  
Human Pathogens ◽  
West Nile ◽  
The Family ◽  
Large Host

The family Flaviviridae currently consists of four recognized genera: Flavivirus, Pestivirus, Hepacivirus, and Pegivirus. Although members of the family have a large host range that includes both vertebrates and invertebrates, only members of the genus Flavivirus are known as arboviruses, vectored either by mosquitoes or ticks. The remaining genera in the family are exclusively found in mammals, and their diversity has greatly expanded with recent virus discoveries. The genus Flavivirus comprises 92 virus species, of which over 40 can cause human infection. Many of these include important human pathogens such as Zika, dengue, yellow fever, West Nile, and Japanese encephalitis virus.

Close genetic relationship between central Thai and Mon people in Thailand revealed by autosomal microsatellites

2020 ◽  
Author(s):  
Suparat Srithawong ◽  
Kanha Muisuk ◽  
Metawee Srikummool ◽  
Jatupol Kampuansai ◽  
Pittayawat Pittayaporn ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Close Genetic Relationship ◽  
Autosomal Microsatellites

scholarly journals Tracing the genetic history of the ‘Cañaris’ from Ecuador and Peru using uniparental DNA markers

BMC Genomics ◽  
2020 ◽  
Vol 21 (S7) ◽  
Author(s):  
José R. Sandoval ◽  
Daniela R. Lacerda ◽  
Marilza M. S. Jota ◽  
Paulo Robles-Ruiz ◽  
Pierina Danos ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Y Chromosome ◽  
Genetic Relationship ◽  
Tandem Repeats ◽  
Geographic Proximity ◽  
Lake Titicaca ◽  
Control Region Sequences ◽  
History Of ◽  
Historical Question ◽  
Close Genetic Relationship

Abstract Background According to history, in the pre-Hispanic period, during the conquest and Inka expansion in Ecuador, many Andean families of the Cañar region would have been displaced to several places of Tawantinsuyu, including Kañaris, a Quechua-speaking community located at the highlands of the Province of Ferreñafe, Lambayeque (Peru). Other families were probably taken from the Central Andes to a place close to Kañaris, named Inkawasi. Evidence of this migration comes from the presence near the Kañaris–Inkawasi communities of a village, a former Inka camp, which persists until the present day. This scenario could explain these toponyms, but it is still controversial. To clarify this historical question, the study presented here focused on the inference of the genetic relationship between ‘Cañaris’ populations, particularly of Cañar and Ferreñafe, compared to other highland populations. We analysed native patrilineal Y chromosome haplotypes composed of 15 short tandem repeats, a set of SNPs, and maternal mitochondrial DNA haplotypes of control region sequences. Results After the genetic comparisons of local populations—three from Ecuador and seven from Peru—, Y chromosome analyses (n = 376) indicated that individuals from the Cañar region do not share Y haplotypes with the Kañaris, or even with those of the Inkawasi. However, some Y haplotypes of Ecuadorian ‘Cañaris’ were associated with haplotypes of the Peruvian populations of Cajamarca, Chivay (Arequipa), Cusco and Lake Titicaca, an observation that is congruent with colonial records. Within the Kañaris and Inkawasi communities there are at least five clans in which several individuals share haplotypes, indicating that they have recent common ancestors. Despite their relative isolation, most individuals of both communities are related to those of the Cajamarca and Chachapoyas in Peru, consistent with the spoken Quechua and their geographic proximity. With respect to mitochondrial DNA haplotypes (n = 379), with the exception of a shared haplotype of the D1 lineage between the Cañar and Kañaris, there are no genetic affinities. Conclusion Although there is no close genetic relationship between the Peruvian Kañaris (including Inkawasi) and Ecuadorian Cañar populations, our results showed some congruence with historical records.

scholarly journals A Newly Identified Virus in the Family Potyviridae Encodes Two Leader Cysteine Proteases in Tandem That Evolved Contrasting RNA Silencing Suppression Functions

2020 ◽  
Vol 95 (1) ◽  
Author(s):  
Li Qin ◽  
Wentao Shen ◽  
Zhongfa Tang ◽  
Weiyao Hu ◽  
Lingna Shangguan ◽  
...  
Keyword(s):  
Rna Silencing ◽  
Rna Viruses ◽  
Evolutionary Relationship ◽  
Cysteine Proteases ◽  
Terminal Region ◽  
Crop Damage ◽  
Virus Species ◽  
Protease Domain ◽  
The Family ◽  
Silencing Suppression

ABSTRACT Potyviridae is the largest family of plant-infecting RNA viruses and includes many agriculturally and economically important viral pathogens. The viruses in the family, known as potyvirids, possess single-stranded, positive-sense RNA genomes with polyprotein processing as a gene expression strategy. The N-terminal regions of potyvirid polyproteins vary greatly in sequence. Previously, we identified a novel virus species within the family, Areca palm necrotic spindle-spot virus (ANSSV), which was predicted to encode two cysteine proteases, HCPro1 and HCPro2, in tandem at the N-terminal region. Here, we present evidence showing self-cleavage activity of these two proteins and define their cis-cleavage sites. We demonstrate that HCPro2 is a viral suppressor of RNA silencing (VSR), and both the variable N-terminal and conserved C-terminal (protease domain) moieties have antisilencing activity. Intriguingly, the N-terminal region of HCPro1 also has RNA silencing suppression activity, which is, however, suppressed by its C-terminal protease domain, leading to the functional divergence of HCPro1 and HCPro2 in RNA silencing suppression. Moreover, the deletion of HCPro1 or HCPro2 in a newly created infectious clone abolishes viral infection, and the deletion mutants cannot be rescued by addition of corresponding counterparts of a potyvirus. Altogether, these data suggest that the two closely related leader proteases of ANSSV have evolved differential and essential functions to concertedly maintain viral viability. IMPORTANCE The Potyviridae represent the largest group of known plant RNA viruses and account for more than half of the viral crop damage worldwide. The leader proteases of viruses within the family vary greatly in size and arrangement and play key roles during the infection. Here, we experimentally demonstrate the presence of a distinct pattern of leader proteases, HCPro1 and HCPro2 in tandem, in a newly identified member within the family. Moreover, HCPro1 and HCPro2, which are closely related and typically characterized with a short size, have evolved contrasting RNA silencing suppression activity and seem to function in a coordinated manner to maintain viral infectivity. Altogether, the new knowledge fills a missing piece in the evolutionary relationship history of potyvirids and improves our understanding of the diversification of potyvirid genomes.

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