scholarly journals Consensus proposals for classification of the family Hepeviridae

2014 ◽  
Vol 95 (10) ◽  
pp. 2223-2232 ◽  
Author(s):  
Donald B. Smith ◽  
Peter Simmonds ◽  
Shahid Jameel ◽  
Suzanne U. Emerson ◽  
Tim J. Harrison ◽  
...  
Keyword(s):  
Mammalian Species ◽  
Cutthroat Trout ◽  
Hepatitis E ◽  
Amino Acid Sequences ◽  
Sequence Information ◽  
Virus Species ◽  
Wide Range ◽  
The Family ◽  
Novel Variants

The family Hepeviridae consists of positive-stranded RNA viruses that infect a wide range of mammalian species, as well as chickens and trout. A subset of these viruses infects humans and can cause a self-limiting acute hepatitis that may become chronic in immunosuppressed individuals. Current published descriptions of the taxonomical divisions within the family Hepeviridae are contradictory in relation to the assignment of species and genotypes. Through analysis of existing sequence information, we propose a taxonomic scheme in which the family is divided into the genera Orthohepevirus (all mammalian and avian hepatitis E virus (HEV) isolates) and Piscihepevirus (cutthroat trout virus). Species within the genus Orthohepevirus are designated Orthohepevirus A (isolates from human, pig, wild boar, deer, mongoose, rabbit and camel), Orthohepevirus B (isolates from chicken), Orthohepevirus C (isolates from rat, greater bandicoot, Asian musk shrew, ferret and mink) and Orthohepevirus D (isolates from bat). Proposals are also made for the designation of genotypes within the human and rat HEVs. This hierarchical system is congruent with hepevirus phylogeny, and the three classification levels (genus, species and genotype) are consistent with, and reflect discontinuities in the ranges of pairwise distances between amino acid sequences. Adoption of this system would include the avoidance of host names in taxonomic identifiers and provide a logical framework for the assignment of novel variants.

scholarly journals A Novel Hepe-Like Virus from Farmed Giant Freshwater Prawn Macrobrachium rosenbergii

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 323 ◽  
Author(s):  
Xuan Dong ◽  
Tao Hu ◽  
Qingyuan Liu ◽  
Chen Li ◽  
Yani Sun ◽  
...  
Keyword(s):  
Hepatitis E Virus ◽  
Phylogenetic Analyses ◽  
Mammalian Species ◽  
Macrobrachium Rosenbergii ◽  
Hepatitis E ◽  
Freshwater Prawn ◽  
Giant Freshwater Prawn ◽  
Wide Range ◽  
The Family ◽  
Virus Genomes

The family Hepeviridae includes several positive-stranded RNA viruses, which infect a wide range of mammalian species, chicken, and trout. However, few hepatitis E viruses (HEVs) have been characterized from invertebrates. In this study, a hepevirus, tentatively named Crustacea hepe-like virus 1 (CHEV1), from the economically important crustacean, the giant freshwater prawn Macrobrachium rosenbergii, was characterized. The complete genome consisted of 7750 nucleotides and had a similar structure to known hepatitis E virus genomes. Phylogenetic analyses suggested it might be a novel hepe-like virus within the family Hepeviridae. To our knowledge, this is the first hepe-like virus characterized from crustaceans.

scholarly journals Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

2021 ◽  
Vol 20 (7) ◽  
pp. 911-927
Author(s):  
Lucia Muggia ◽  
Yu Quan ◽  
Cécile Gueidan ◽  
Abdullah M. S. Al-Hatmi ◽  
Martin Grube ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Species ◽  
Sister Group ◽  
Asexual Propagation ◽  
Dna Sequence Data ◽  
Wide Range ◽  
The Family ◽  
Rock Inhabiting Fungi ◽  
Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

Old versus new characters for systematics: Cautionary tales from virology

1990 ◽  
Vol 3 (1) ◽  
pp. 159
Author(s):  
A Gibbs ◽  
A Ding ◽  
J Howe ◽  
P Keese ◽  
A MacKenzie ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Recombination ◽  
Large Subunit ◽  
Molecular Taxonomy ◽  
Amino Acid Sequences ◽  
Sequence Information ◽  
Molecular Sequence ◽  
Taxonomic Methods ◽  
Cautionary Tales

Molecular sequence information about viruses has mostly confirmed the groupings devised by traditional taxonomic methods, but shown in addition that the genes of related species may differ in number, arrangement, orientation and in sequence homology. It has also revealed that true genetic recombination between viruses has been common, even among those with RNA genomes, indeed most virus groups seem to have arisen y recombination. Thus, there is an unexpected wealth of genetic chaos hidden behind the fatade of the phenotype, and it is possible that the difficulties that plant taxonomists have had in identifying the relationships of the major groupings of plants could have similar causes. Nonetheless, molecular taxonomy does give sensible results and this is illustrated by a classification of the large subunit Rubisco proteins of 21 plant species based on their amino acid sequences.

scholarly journals Characterization and complete genome sequences of two novel variants of the family Closteroviridae from Chinese kiwifruit

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242362
Author(s):  
Xin Feng ◽  
Rui-lian Lai ◽  
Min-xia Gao ◽  
Wen-guang Chen ◽  
Ru-jian Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Organization ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Viral Genomes ◽  
Relationship Analysis ◽  
The Family ◽  
Novel Variants ◽  
Rapid Amplification

Two distinct closterovirus-like genome sequences (termed AdV-1 v1 and v2) were identified in Actinidia chinensis var. deliciosa ‘Miliang-1’ that had no disease symptoms using high-throughput sequencing. Using overlapping reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends, the genomic sequences of AdV-1 v1 and v2 were confirmed as 17,646 and 18,578 nucleotides in length, respectively. The two complete genomes contained 9 and 15 open reading frames, respectively, coding for proteins having domains typical of Closteroviridae, such as RNA-dependent RNA polymerase (RdRp), heat shock protein 70 homolog (HSP70h) and coat protein (CP). Sequence analysis showed that the amino acid sequences of RdRp, HSP70h, and CP of the two variants exhibited high similarity (> 80%), while their genomic organization was somewhat different. This suggested that the two viral genomes identified here are variants of the family Closteroviridae in a single kiwifruit host. Furthermore, phylogenetic relationship analysis revealed that the two variants had a closer relationship with the unclassified virus Persimmon virus B (PeVB) and Actinidia virus 1 (AcV-1) than with other members of the family Closteroviridae, as did their genomic organization. It is speculated that the two variants, together with PeVB and AcV-1 belong to a new subfamily of Closteroviridae.

2. The different types of trust

2018 ◽  
Author(s):  
Richard Clements ◽  
Ademola Abass
Keyword(s):  
Modern World ◽  
Family Wealth ◽  
Wide Range ◽  
The Family ◽  
Different Types ◽  
Complete Series ◽  
Explanatory Text ◽  
The Many ◽  
Primary Materials

Titles in the Complete series combine extracts from a wide range of primary materials with clear explanatory text to provide readers with a complete introductory resource. This chapter examines the different types of trust, how they are used, and the nature of a trust. The many uses of trusts in the modern world, from pensions to the ownership of the family home and the preservation of family wealth are explained. The discussions cover the meanings of trust and property; what trusts are used for; what an equitable interest is; classification of trusts; resulting trusts; constructive trusts; implied trusts; Quistclose-type trusts; and wills and intestacies.

scholarly journals Serologic Analysis of Hepatitis E Virus Infection in Patients with Kidney-Related Illnesses

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 64
Author(s):  
Martynas Simanavičius ◽  
Arūnė Verbickaitė ◽  
Paulius Lukas Tamošiūnas ◽  
Ernesta Mačionienė ◽  
Indrė Kučinskaitė-Kodzė
Keyword(s):  
Hepatitis E Virus ◽  
Rna Virus ◽  
Mammalian Species ◽  
Hepatitis E ◽  
Transplant Recipients ◽  
Kidney Transplant Recipients ◽  
The Family ◽  
Life Threatening ◽  
Globally Distributed ◽  
Undercooked Pork

Hepatitis E is a globally distributed human disease caused by the hepatitis E virus (HEV). HEV is a positive-sense, single-stranded RNA virus that belongs to the family Hepeviridae. Within the genus Orthohepevirus, seven HEV genotypes infect various mammalian hosts. HEV genotypes HEV-1 to HEV-4 and HEV-7 can infect humans. HEV-3 is zoonotic with the domestic pig, wild boar, deer and other mammalian species as reservoirs. HEV-3 is an underestimated emerging threat which is spread across Europe. It is transmitted through undercooked pork meat or other products, and with blood components through transfusions. HEV-3 infection in immunocompetent patients is self-limiting and clinically asymptomatic. However, immunocompromised individuals are at a high risk of developing chronic hepatitis E. Chronic infection may lead to life-threatening liver cirrhosis. Patients with kidney transplants or kidney-related illnesses are in this risk group. In this study, a serologic analysis of blood samples obtained from kidney transplant recipients, patients with chronic kidney disease, patients under dialysis and healthy controls was performed. A prevalence of anti-HEV antibodies was assessed by commercial and in-house ELISAs.

scholarly journals Novel Mammalian Herpesviruses and Lineages within the Gammaherpesvirinae: Cospeciation and Interspecies Transfer

2008 ◽  
Vol 82 (7) ◽  
pp. 3509-3516 ◽  
Author(s):  
Bernhard Ehlers ◽  
Güzin Dural ◽  
Nezlisah Yasmum ◽  
Tiziana Lembo ◽  
Benoit de Thoisy ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Phylogenetic Analyses ◽  
Mammalian Species ◽  
Amino Acid Sequences ◽  
Mammalian Host ◽  
Virus Species ◽  
Branching Pattern ◽  
Long Distance ◽  
Bayesian Monte Carlo ◽  
Long Distance Pcr

ABSTRACT Novel members of the subfamily Gammaherpesvirinae, hosted by eight mammalian species from six orders (Primates, Artiodactyla, Perissodactyla, Carnivora, Scandentia, and Eulipotyphla), were discovered using PCR with pan-herpesvirus DNA polymerase (DPOL) gene primers and genus-specific glycoprotein B (gB) gene primers. The gB and DPOL sequences of each virus species were connected by long-distance PCR, and contiguous sequences of approximately 3.4 kbp were compiled. Six additional gammaherpesviruses from four mammalian host orders (Artiodactyla, Perissodactyla, Primates, and Proboscidea), for which only short DPOL sequences were known, were analyzed in the same manner. Together with available corresponding sequences for 31 other gammaherpesviruses, alignments of encoded amino acid sequences were made and used for phylogenetic analyses by maximum-likelihood and Bayesian Monte Carlo Markov chain methods to derive a tree which contained two major loci of unresolved branching details. The tree was rooted by parallel analyses that included alpha- and betaherpesvirus sequences. This gammaherpesvirus tree contains 11 major lineages and presents the widest view to date of phylogenetic relationships in any subfamily of the Herpesviridae, as well as the most complex in the number of deep lineages. The tree's branching pattern can be interpreted only in part in terms of the cospeciation of virus and host lineages, and a substantial incidence of the interspecies transfer of viruses must also be invoked.

scholarly journals Identification of HLA-A*24:02-restricted CTL candidate epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2 and analysis of their conservation using the mutation database of SARS-CoV-2 variants

2021 ◽  
Author(s):  
Akira Takagi ◽  
Masanori Matsui
Keyword(s):  
Neutralizing Antibodies ◽  
Viral Evolution ◽  
Critical Role ◽  
Amino Acid Sequences ◽  
Viral Control ◽  
Mutation Database ◽  
Wide Range ◽  
Novel Variants ◽  
Near Future ◽  
Original Virus

COVID-19 vaccines are currently being administrated worldwide and playing a critical role in controlling the pandemic. They have been designed to elicit neutralizing antibodies against Spike protein of the original SARS-CoV-2, and hence they are less effective against SARS-CoV-2 variants with mutated Spike than the original virus. It is possible that novel variants with abilities of enhanced transmissibility and/or immunoevasion will appear in the near future and perfectly escape from vaccine-elicited immunity. Therefore, the current vaccines may need to be improved to compensate for the viral evolution. For this purpose, it may be beneficial to take advantage of CD8+ cytotoxic T lymphocytes (CTLs). Several lines of evidence suggest the contribution of CTLs on the viral control in COVID-19, and CTLs target a wide range of proteins involving comparatively conserved non-structural proteins. Here, we identified twenty-two HLA-A*24:02-restricted CTL candidate epitopes derived from the non-structural polyprotein 1a (pp1a) of SARS-CoV-2 using computational algorithms, HLA-A*24:02 transgenic mice and the peptide-encapsulated liposomes. We focused on pp1a and HLA-A*24:02 because pp1a is relatively conserved and HLA-A*24:02 is predominant in East Asians such as Japanese. The conservation analysis revealed that the amino acid sequences of 7 out of the 22 epitopes were hardly affected by a number of mutations in the Sequence Read Archive database of SARS-CoV-2 variants. The information of such conserved epitopes might be useful for designing the next-generation COVID-19 vaccine that is universally effective against any SARS-CoV-2 variants by the induction of both anti-Spike neutralizing antibodies and CTLs specific for conserved epitopes.

scholarly journals POPULATION GENETICS ANALYSIS OF Garlic virus A, Garlic virus B, Garlic virus C AND Garlic virus X

2019 ◽  
Vol 18 (3) ◽  
Author(s):  
Maria Bereda ◽  
Elżbieta Paduch-Cichal
Keyword(s):  
Population Size ◽  
Negative Selection ◽  
Balancing Selection ◽  
Amino Acid Sequences ◽  
Virus Species ◽  
Nucleic Acid Binding ◽  
The Family ◽  
Virus C ◽  
Garlic Virus ◽  
Pressure Analysis

Garlic virus A (GarV-A), Garlic virus B (GarV-B), Garlic virus C (GarV-C) and Garlic virus X (GarV-X) are members of the genus Allexivirus in the family Alphaflexiviridae. In this study, we collected 10, 30, 10 and 14 isolates of GarV-A, GarV-B, GarV-C and GarV-X, respectively, from different parts of Poland. All sequences of coat protein (CP) and nucleic-acid binding protein (NABP) regions of Allexivirus isolates available in GenBank were also included in this study. The nucleotide and amino acid sequences identities within each population differed substantially depending on the region of the genome and virus species. The results of selection pressure analysis showed that populations of each Allexivirus underwent negative selection, but the extent of the negative selection varied. It was also concluded that the GarV-A and GarV-C populations underwent a decrease in population size or balancing selection, while the GarV-B and GarV-X populations underwent an increase in population size. It was concluded that both populations of GarV-X evolved independently in each respective area, in contrast to populations of GarV-A, GarV-B and GarV-C.

scholarly journals Flaviviridae — addition to the family

2019 ◽  
pp. 4-10
Author(s):  
I. V. Kruglov
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Homo Sapiens ◽  
Virus Species ◽  
Phylogenetic Relation ◽  
New Members ◽  
Wide Range ◽  
The Family ◽  
History Of ◽  
Flying Fox

This review article analyzes and summarizes the history of the replenishment of the family Flaviviridae with new members over the last several decades on the example of the youngest genera of this family - Hepacivirus and Pegivirus .It all started in 1966 when surgeon George Barker, who had hepatitis, had blood serum taken in containing an unknown virus. This virus was named GBV , by patient initials. Samples of the serum were frozen. A nucleic acid recognized as corresponding to the genomes of 2 separate virus species was isolated from the tested material in 1995. These viruses were named GBV-A and GBV-B . By this time, the hepatitis C virus had already been discovered, which was assigned to the Flaviviridae family, where a separate, third genus of Hepacivirus was allocated for it.In 2010, a more distantly related virus (named GBV-D ) was found in bats (Indian flying fox - lat. Pteropus giganteus ). GBV-B , which causes acute hepatitis in experimentally infected tamarines, became the second species in the genus Hepacivirus to company with hepatitis C virus. The remaining GB viruses based on phylogenetic relation-ships, genome organization, and pathogenetic properties were proposed in 2011 to be classified as members of the fourth genus in the Flaviviridae family. This genus was named Pegivirus (pe - persistence, g - GB).11 species of viruses have now been identified in the genus Pegivirus . They are indicated by letters in the order of the Latin alphabet - from Pegivirus A to Pegivirus K. And 14 species of viruses have now been identified in the genus Hepacivirus . So the story of the investigation, which began in 1966 with the discovery of the previously unknown GBV virus, has so far concluded with the discovery of two new genera of the family Flaviviridae. Numerous members of these two genera infect and also persist among a wide range of species belonging to different orders of the mammalian class, including Homo Sapiens .

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