Metagenomic identification of diverse animal hepaciviruses and pegiviruses

2020 ◽  
Author(s):  
Ashleigh F. Porter ◽  
John H.-O. Pettersson ◽  
Wei-Shan Chang ◽  
Erin Harvey ◽  
Karrie Rose ◽  
...  
Keyword(s):  
Large Scale ◽  
Animal Species ◽  
Rna Virus ◽  
Mammalian Species ◽  
Evolutionary Time ◽  
Virus Family ◽  
Ixodes Holocyclus ◽  
Short Read Archive ◽  
Novel Variant ◽  
Additional Support

AbstractThe RNA virus family Flaviviridae harbours several important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently divided into four genera - Hepacivirus, Pegivirus, Pestivirus and Flavivirus – each of which have a diverse host range. Members of the genus Hepacivirus are associated with a diverse array of animal species, including humans and non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa including humans. Using a combination of meta-transcriptomic and whole genome sequencing we identified four novel hepaciviruses and one novel variant of a known virus, in five species of native Australian wildlife, expanding our knowledge of the diversity in this important group of RNA viruses. The infected hosts comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). The addition of these novel viruses led to the identification of a distinct marsupial clade within the hepacivirus phylogeny that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Gecko and avian associated hepacivirus lineages were also identified. In addition, by mining the short-read archive (SRA) database we identified another five novel members of Flaviviridae, comprising three new hepaciviruses from avian and primate hosts, as well as two primate-associated pegiviruses. The large-scale phylogenetic analysis of these novel hepacivirus and pegivirus genomes provides additional support for virus-host co-divergence over evolutionary time-scales.

scholarly journals Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Ashleigh F Porter ◽  
John H -O Pettersson ◽  
Wei-Shan Chang ◽  
Erin Harvey ◽  
Karrie Rose ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Animal Species ◽  
Rna Viruses ◽  
Mammalian Species ◽  
Virus Transmission ◽  
Whole Genome ◽  
Ixodes Holocyclus ◽  
Positive Sense ◽  
Novel Variant ◽  
History Of

Abstract The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus, and hepatitis C virus. The Flaviviridae are currently divided into four genera—Hepacivirus, Pegivirus, Pestivirus, and Flavivirus—each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole-genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the SRA database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci- and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co-divergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the diversity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.

scholarly journals SARS-CoV-2 vaccines strategies: a comprehensive review of phase 3 candidates

npj Vaccines ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Nikolaos C. Kyriakidis ◽  
Andrés López-Cortés ◽  
Eduardo Vásconez González ◽  
Alejandra Barreto Grimaldos ◽  
Esteban Ortiz Prado
Keyword(s):  
Neutralizing Antibodies ◽  
Large Scale ◽  
Vaccine Development ◽  
Rna Virus ◽  
Protein S ◽  
Effective Vaccine ◽  
Phase 3 ◽  
Vaccine Candidates ◽  
Advantages And Disadvantages ◽  
The World

AbstractThe new SARS-CoV-2 virus is an RNA virus that belongs to the Coronaviridae family and causes COVID-19 disease. The newly sequenced virus appears to originate in China and rapidly spread throughout the world, becoming a pandemic that, until January 5th, 2021, has caused more than 1,866,000 deaths. Hence, laboratories worldwide are developing an effective vaccine against this disease, which will be essential to reduce morbidity and mortality. Currently, there more than 64 vaccine candidates, most of them aiming to induce neutralizing antibodies against the spike protein (S). These antibodies will prevent uptake through the human ACE-2 receptor, thereby limiting viral entrance. Different vaccine platforms are being used for vaccine development, each one presenting several advantages and disadvantages. Thus far, thirteen vaccine candidates are being tested in Phase 3 clinical trials; therefore, it is closer to receiving approval or authorization for large-scale immunizations.

COVID-19 personal protective behaviors during mass events: Lessons from observational measures in Wales, UK.

2021 ◽  
Author(s):  
Ashley Gould ◽  
Lesley Lewis ◽  
Lowri Evans ◽  
Leanne Greening ◽  
Holly Howe-Davies ◽  
...  
Keyword(s):  
Large Scale ◽  
Protective Behaviors ◽  
Mass Gatherings ◽  
Observational Measures ◽  
Behavioral Observations ◽  
The Government ◽  
Additional Support ◽  
The Uk ◽  
Trained Observers ◽  
Personal Protective Behaviors

Within the context of reopening society in the summer of 2021, as the UK moved away from ’lockdown,’ the Government of Wales piloted the return on organised ‘mass gatherings’ of people at a number of test events. Behavioral observations were made at two of the test events to support this process. The research was particularly interested in four key factors: How (1) context within a venue, (2) environmental design, (3) staffing and social norms, and (4) time across an event, affected personal protective behaviors of social distancing, face covering use, and hand hygiene. Data collection was undertaken by trained observers across the above factors. Findings suggest that adherence of attendees was generally high, but with clear indications that levels were shaped in a systematic way by the environment, situational cues, and the passage of time during the events. Some instances of large-scale non-adherence to personal protective behaviors were documented. Overall, there were three main situations where behavioral adherence broke down, under conditions where: (1) staff were not present; (2) there was a lack of environmental signalling (including physical interventions or communications); and (3) later into the events when circumstances were less constrained and individuals appeared less cognitively vigilant. Behavioral observations at events can add precision and identify critical risk situations where/when extra effort is required. The findings suggest a liberal paternal approach whereby state authorities, health authorities and other key organisations can help nudge individuals towards COVID-safe behaviors. Finally, an individual’s intentions are not always matched by their actions, and so behavioral insights can help identify situations and contexts where people are most likely to require additional support to ensure COVID-19 personal protective behaviors are followed and hence protecting themselves and others.

Dog Models of Aging

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Audrey Ruple ◽  
Evan MacLean ◽  
Noah Snyder-Mackler ◽  
Kate E. Creevy ◽  
Daniel Promislow
Keyword(s):  
Large Scale ◽  
Mammalian Species ◽  
Annual Review ◽  
Publication Date ◽  
Companion Dogs ◽  
Age Related ◽  
Key Concepts ◽  
Similarities And Differences ◽  
Laboratory Models ◽  
Unique Potential

As the most phenotypically diverse mammalian species that shares human environments and access to sophisticated healthcare, domestic dogs have unique potential to inform our understanding of the determinants of aging. Here we outline key concepts in the study of aging and illustrate the value of research with dogs, which can improve dog health and support translational discoveries. We consider similarities and differences in aging and age-related diseases in dogs and humans and summarize key advances in our understanding of genetic and environmental risk factors for morbidity and mortality in dogs. We address health outcomes ranging from cancer to cognitive function and highlight emerging research opportunities from large-scale cohort studies in companion dogs. We conclude that studying aging in dogs could overcome many limitations of laboratory models, most notably, the ability to assess how aging-associated pathways influence aging in real-world environments similar to those experienced by humans. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Differential enrichment of yeast DNA in SARS-CoV-2 and related genomes supports synthetic origin hypothesis

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 912
Author(s):  
Andreas Martin Lisewski
Keyword(s):  
Large Scale ◽  
The Other ◽  
Yeast Cells ◽  
Virus Family ◽  
Spike Gene ◽  
Viral Replicase ◽  
Genomic Editing ◽  
Chromosomal Sequences ◽  
Bat Coronavirus ◽  
Origin Hypothesis

Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should be also considered.    Results: Here we show that the genomes from SARS-CoV-2 and from SARS-CoV-1 are differentially enriched with short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for virus replication, host cell invasion, and host immune response. Specifically, for SARS-CoV-2, we identify two sites: one at the start of the viral replicase domain, and the other at the end of the spike gene past its critical domain junction; for SARS-CoV-1, one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain. As yeast is not a natural host for this virus family, we propose a directed passage model for viral constructs, including virus replicase, in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential sequence homology data across yeast chromosomes congruent with chromosomes harboring specific auxotrophic markers further support this passage model. Model and data together allow us to infer a hypothetical tripartite genome assembly scheme for the synthetic biogenesis of SARS-CoV-2 and SARS-CoV-1.   Conclusions: These results provide evidence that the genome sequences of SARS-CoV-1, SARS-CoV-2, but not that of RaTG13, BANAL-20-52 and all other closest SARS coronavirus family members identified, are carriers of distinct homology signals that might point to large-scale genomic editing during a passage of directed replication and chromosomal integration inside genetically modified yeast cells.

scholarly journals Exploiting the Reverse Vaccinology Approach to Design Novel Subunit Vaccine against Ebola Virus

2020 ◽  
Author(s):  
Md. Asad Ullah ◽  
Bishajit Sarkar ◽  
Syed Sajidul Islam
Keyword(s):  
Molecular Docking ◽  
Mhc Class Ii ◽  
Large Scale ◽  
Matrix Protein ◽  
Ebola Virus ◽  
Rna Virus ◽  
Docking Study ◽  
Dynamics Simulation ◽  
Molecular Docking Study ◽  
Class I Mhc

AbstractEbola virus is a highly pathogenic RNA virus that causes haemorrhagic fever in human. With very high mortality rate, Ebola virus is considered as one of the dangerous viruses in the world. Although, the Ebola outbreaks claimed many lives in the past, no satisfactory treatment or vaccine have been discovered yet to fight against Ebola. For this reason, in this study, various tools of bioinformatics and immunoinformatics were used to design possible vaccines against Zaire Ebola virus strain Mayinga-76. To construct the vaccine, three potential antigenic proteins of the virus, matrix protein VP40, envelope glycoprotein and nucleoprotein were selected against which the vaccines would be designed. The MHC class-I, MHC class-II and B-cell epitopes were determined and after robust analysis through various tools and molecular docking analysis, three vaccine candidates, designated as EV-1, EV-2 and EV-3, were constructed. Since the highly conserved epitopes were used for vaccine construction, these vaccine constructs are also expected to be effective on other strains of Ebola virus like strain Gabon-94 and Kikwit-95. Next, the molecular docking study on these vaccine constructs were analyzed by molecular docking study and EV-1 emerged as the best vaccine construct. Later, molecular dynamics simulation study revealed the good performances as well as good stability of the vaccine protein. Finally, codon adaptation and in silico cloning were conducted to design a possible plasmid (pET-19b plasmid vector was used) for large scale, industrial production of the EV-1 vaccine.

scholarly journals Nutritional and Functional Properties of Colostrum in Puppies and Kittens

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3260
Author(s):  
Luciana Rossi ◽  
Ana Elena Valdez Lumbreras ◽  
Simona Vagni ◽  
Matteo Dell’Anno ◽  
Valentino Bontempo
Keyword(s):  
High Risk ◽  
Infectious Diseases ◽  
Functional Properties ◽  
Animal Species ◽  
Mammalian Species ◽  
Companion Animals ◽  
Glycogen Storage ◽  
Passive Immunity ◽  
Hepatic Glycogen ◽  
Therapeutic Effects

The present review aims toward a better understanding of the nutrition of newborn puppies and kittens. The post-natal period is very sensitive in dogs and cats, as in other animal species. During the first two weeks of life, puppies and kittens are at high risk of dehydration, hypothermia, and hypoglycemia, as well as infectious diseases as they start to acquire the physiological functions of the adult. Neonatal hepatic glycogen storage is low, and newborns depend on colostrum intake to survive. Colostrum provides immunoglobulins and other important substances such as lipids and carbohydrates. Immunoglobulins are central to the immunological link that occurs when the mother transfers passive immunity. The mechanism of transfer varies among mammalian species, but in this review, we focused our attention on dogs and cats. Furthermore, there are components of colostrum which, although their presence is not absolutely necessary, play an important role in nutrition. These components have received considerable interest because of their presumed safety and potential nutritional and therapeutic effects both in humans and animals; however, unfortunately, there are few recent studies in companion animals. Here, we have gathered the published articles that describe studies involving different species of animals, emphasizing companion animals. In particular, the purpose of this narrative of the nutritional and functional proprieties of queens’ and bitches’ colostrum.

scholarly journals On the Order of Gene Distribution on Chromosomes Across the Animal Kingdom

2019 ◽  
Author(s):  
Abdullah A. Toor ◽  
Amir A. Toor
Keyword(s):  
Gene Frequency ◽  
Large Scale ◽  
Animal Species ◽  
Square Root ◽  
Animal Kingdom ◽  
Gene Distribution ◽  
Complement Gene ◽  
Gene Dispersion ◽  
Average Gene ◽  
Animal Genomes

SummaryBackgroundThe large-scale pattern of distribution of genes on the chromosomes in the known animal genomes is not well characterized. We hypothesized that individual genes will be distributed on chromosomes in a mathematically ordered manner across the animal kingdom.ResultsTwenty-one animal genomes reported in the NCBI database were examined. Numerically, there was a trend towards increasing overall gene content with increasing size of the genome as reflected by the chromosomal complement. Gene frequency on individual chromosomes in each animal genome was analyzed and demonstrated uniformity of proportions within each animal with respect to both average gene frequency on individual chromosomes and gene distribution across the unique genomes. Further, average gene distribution across animal species followed a relationship whereby it was, approximately, inversely proportional to the square root of the number of chromosomes in the unique animal genomes, consistent with the notion that there is an ordered increase in gene dispersion as the complexity of the genome increased. To further corroborate these findings a derived measure, termed gene spacing on chromosomes correlated with gene frequency and gene distribution.ConclusionAs animal species have evolved, the distribution of their genes on individual chromosomes and within their genomes, when viewed on a large scale is not random, but follows a mathematically ordered process, such that as the complexity of the organism increases, the genes become less densely distributed on the chromosomes and more dispersed across the genome.

scholarly journals Frequent birth-and-death events throughout perforin-1 evolution

2020 ◽  
Author(s):  
Miguel Araujo-Voces ◽  
Victor Quesada
Keyword(s):  
Preliminary Analysis ◽  
Large Scale ◽  
Mammalian Species ◽  
Genomic Data ◽  
Start Codon ◽  
High Similarity ◽  
Gene Encoding ◽  
Coding Sequences ◽  
Copy Numbers ◽  
Multiple Species

Abstract Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.

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