Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host

AbstractDisease surveillance in wildlife populations presents a logistical challenge, yet is critical in gaining a deeper understanding of the presence and impact of wildlife pathogens. Erinaceus coronavirus (EriCoV), a clade C Betacoronavirus, was first described in Western European hedgehogs (Erinaceus europaeus) in Germany. Here, our objective was to determine whether EriCoV is present, and if it is associated with disease, in Great Britain (GB). An EriCoV-specific BRYT-Green® real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Viral RNA was detected in 10.8% (38) samples; however, the virus was not detected in any of the 61 samples tested from Scotland. The full genome sequence of the British EriCoV strain was determined using next generation sequencing; it shared 94% identity with a German EriCoV sequence. Multivariate statistical models using hedgehog case history data, faecal specimen descriptions and post-mortem examination findings found no significant associations indicative of disease associated with EriCoV in hedgehogs. These findings indicate that the Western European hedgehog is a reservoir host of EriCoV in the absence of apparent disease.

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Erinaceus europaeus europaeus (Western European hedgehog)

An Atlas of Mammalian Chromosomes ◽

10.1007/978-1-4615-6424-9_2 ◽

1968 ◽

pp. 5-7

Author(s):

T. C. Hsu ◽

Kurt Benirschke

Keyword(s):

Erinaceus Europaeus ◽

European Hedgehog ◽

Western European

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Neutralizing antibodies induced by first-generation gp41-stabilized HIV-1 envelope trimers and nanoparticles

10.1101/2020.12.02.408328 ◽

2020 ◽

Author(s):

Sonu Kumar ◽

Xiaohe Lin ◽

Timothy Ngo ◽

Benjamin Shapero ◽

Cindy Sou ◽

...

Keyword(s):

Cell Sorting ◽

Neutralizing Antibodies ◽

First Generation ◽

Heptad Repeat ◽

X Ray ◽

X Ray Crystallography ◽

Clade C ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing ◽

Hiv 1

ABSTRACTAntigen-specific B-cell sorting and next-generation sequencing (NGS) were combined to isolate HIV-1 neutralizing antibodies (NAbs) from mice and rabbits immunized with BG505 trimers and nanoparticles. Three mouse NAbs potently neutralize BG505.T332N and recognize a glycan epitope centered at the C3/V4 region, as revealed by electron microscopy (EM), x-ray crystallography, and epitope mapping. Three potent NAbs were sorted from rabbit B cells that target glycan holes on the BG505 envelope glycoprotein (Env) and account for a significant portion of autologous NAb response. We then determined a 3.4Å-resolution crystal structure for the clade C transmitted/founder Du172.17 Env with a redesigned heptad repeat 1 (HR1) bend. This clade C Env, as a soluble trimer and attached to a ferritin nanoparticle, along with a clade A Q482-d12 Env trimer, elicited distinct NAb responses in rabbits. Our study demonstrates that nanoparticles presenting gp41-stabilized trimers can induce potent NAb responses in mice and rabbits with Env-dependent breadth.TEASERMouse and rabbit NAbs elicited by gp41-stabilized trimers and nanoparticles neutralize autologous HIV-1 by targeting different epitopes

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Investigating the Role of the Eurasian Badger (Meles meles) in the Nationwide Distribution of the Western European Hedgehog (Erinaceus europaeus) in England

Animals ◽

10.3390/ani9100759 ◽

2019 ◽

Vol 9 (10) ◽

pp. 759 ◽

Cited By ~ 4

Author(s):

Hof ◽

Allen ◽

Bright

Keyword(s):

Spatial Scales ◽

Agricultural Practices ◽

Meles Meles ◽

Erinaceus Europaeus ◽

Related Factors ◽

Eurasian Badger ◽

European Hedgehog ◽

Intraguild Predator ◽

Western European

Biodiversity is declining globally, which calls for effective conservation measures. It is, therefore, important to investigate the drivers behind species presence at large spatial scales. The Western European hedgehog (Erinaceus europaeus) is one of the species facing declines in parts of its range. Yet, drivers of Western European hedgehog distribution at large spatial scales remain largely unknown. At local scales, the Eurasian badger (Meles meles), an intraguild predator of the Western European hedgehog, can affect both the abundance and the distribution of the latter. However, the Western European hedgehog and the Eurasian badger have shown to be able to co-exist at a landscape scale. We investigated whether the Eurasian badger may play a role in the likelihood of the presence of the Western European hedgehog throughout England by using two nationwide citizen science surveys. Although habitat-related factors explained more variation in the likelihood of Western European hedgehog presence, our results suggest that Eurasian badger presence negatively impacts the likelihood of Western European hedgehog presence. Intraguild predation may, therefore, be influencing the nationwide distribution of hedgehogs in England, and further research is needed about how changes in badger densities and intensifying agricultural practices that remove shelters like hedgerows may influence hedgehog presence.

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Full Genome Sequence of the Western Reserve Strain of Vaccinia Virus Determined by Third-Generation Sequencing

Genome Announcements ◽

10.1128/genomea.01570-17 ◽

2018 ◽

Vol 6 (11) ◽

Cited By ~ 3

Author(s):

István Prazsák ◽

Dóra Tombácz ◽

Attila Szűcs ◽

Béla Dénes ◽

Michael Snyder ◽

...

Keyword(s):

Vaccinia Virus ◽

Genome Sequence ◽

Laboratory Strain ◽

Full Genome Sequence ◽

Content Type ◽

Third Generation Sequencing ◽

Oxford Nanopore ◽

The Pacific ◽

Generation Sequencing ◽

Western Reserve

ABSTRACT The vaccinia virus is a large, complex virus belonging to the Poxviridae family. Here, we report the complete, annotated genome sequence of the neurovirulent Western Reserve laboratory strain of this virus, which was sequenced on the Pacific Biosciences RS II and Oxford Nanopore MinION platforms.

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Multivariate statistical techniques for metagenomic analysis of microbial community recovered from environmental samples

Journal of Bio-Science ◽

10.3329/jbs.v24i0.37486 ◽

2018 ◽

Vol 24 ◽

pp. 45-53 ◽

Cited By ~ 1

Author(s):

Z Akond ◽

M Alam ◽

MS Ahmed ◽

MNH Mollah

Keyword(s):

Microbial Communities ◽

Microbial Mats ◽

Statistical Techniques ◽

Multivariate Statistical ◽

Linear Discriminant ◽

Metabolic Functions ◽

Metabolic Variables ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing ◽

Shed Light

High-throughput big dataset generated through next generation sequencing (NGS) of DNA samples helps identify key differences in the function and taxonomy between microbial communities as well as shed light on the diversity of microbes, cooperation and evolution in any particular ecosystem. During this study, three statistical techniques namely, Random Forest (RF), Multidimensional Scaling (MDS) and Linear Discriminant Analysis (LDA) approaches were employed for functional analysis of 212 publicly available metagenomic datasets within and between 10 environments against 27 metabolic functions. RF generates the 8 most important metabolic variables along with MDS and LDA among which Photosynthesis has the highest score (70.20); Phages, prophages has the second highest score (61.31) and Membrane Transport was found to have the eighth highest score (45.29). The MDS plot was found useful to visualize the separation of the microbes from human or animal hosts from other samples along the first dimension and the separation of the aquatic and mat communities along the second dimension. LDA analyses compared the extent of the microbial samples into three broad groups: the human and animal associated samples, the microbial mats, and the aquatic samples. RF showed that phage activity is a major difference between host-associated microbial communities and free-living. The MDS and LDA techniques suggest that mat communities were unique from both the animal associated metagenomes and the aquatic samples with differences in the vitamin and cofactor metabolism.J. bio-sci. 24: 45-53, 2016

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Insights Into the Etiology of Polerovirus-Induced Pepper Yellows Disease

Phytopathology ◽

10.1094/phyto-07-16-0254-r ◽

2017 ◽

Vol 107 (12) ◽

pp. 1567-1576 ◽

Cited By ~ 7

Author(s):

Leonidas Lotos ◽

Antonio Olmos ◽

Chrysoula Orfanidou ◽

Konstantinos Efthimiou ◽

Apostolos Avgelis ◽

...

Keyword(s):

Sequence Similarity ◽

Full Genome Sequence ◽

Yellow Leaf ◽

Common Ancestry ◽

Full Genome ◽

Small Interfering Rnas ◽

The Common ◽

Leaf Curl Virus ◽

Pepper Vein Yellows Virus ◽

Generation Sequencing

The study of an emerging yellows disease of pepper crops (pepper yellows disease [PYD]) in Greece led to the identification of a polerovirus closely related to Pepper vein yellows virus (PeVYV). Recovery of its full genome sequence by next-generation sequencing of small interfering RNAs allowed its characterization as a new poleroviruses, which was provisionally named Pepper yellows virus (PeYV). Transmission experiments revealed its association with the disease. Sequence similarity and phylogenetic analysis highlighted the common ancestry of the three poleroviruses (PeVYV, PeYV, and Pepper yellow leaf curl virus [PYLCV]) currently reported to be associated with PYD, even though significant genetic differences were identified among them, especially in the C-terminal region of P5 and the 3′ noncoding region. Most of the differences observed can be attributed to a modular type of evolution, which produces mosaic-like variants giving rise to these different poleroviruses Overall, similar to other polerovirus-related diseases, PYD is caused by at least three species (PeVYV, PeYV, and PYLCV) belonging to this group of closely related pepper-infecting viruses.

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Desmoplastic Ganglioglioma of the Spinal Cord in a Western European Hedgehog (Erinaceus Europaeus)

Journal of Veterinary Diagnostic Investigation ◽

10.1177/104063871002200623 ◽

2010 ◽

Vol 22 (6) ◽

pp. 978-983 ◽

Cited By ~ 5

Author(s):

Reiner Ulrich ◽

Alexandra C. Stan ◽

Michael Fehr ◽

Carolin Mallig ◽

Christina Puff

Keyword(s):

Spinal Cord ◽

Erinaceus Europaeus ◽

European Hedgehog ◽

Western European

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Occurrence of the amphibian chytrid fungus Batrachochytrium dendrobatidis in introduced and native species from two regions of France

Amphibia-Reptilia ◽

10.1163/15685381-00002845 ◽

2012 ◽

Vol 33 (3-4) ◽

pp. 415-422 ◽

Cited By ~ 3

Author(s):

Martin Ouellet ◽

Tony Dejean ◽

Patrick Galois

Keyword(s):

Disease Surveillance ◽

Native Species ◽

Batrachochytrium Dendrobatidis ◽

Infectious Agent ◽

Reservoir Host ◽

Chytrid Fungus ◽

Water Frog ◽

American Bullfrog ◽

Precautionary Measures ◽

Amphibian Chytrid Fungus

To investigate the occurrence of the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) in France, we examined 575 amphibians collected between 1875 and 2008 for the presence of the infection in the epidermis. We confirmed Bd in seven of the 15 stations investigated in the Aquitaine and Poitou-Charentes regions. Histological examination revealed the presence of the infectious agent associated with mild epidermal changes in 25 of 493 (5.1%) amphibians sampled in 2007-2008. The overall occurrence was 21.9% (21/96) in the introduced American bullfrog (Lithobates catesbeianus) and 2.3% (4/172) in the native European water frog complex (Pelophylax sp.). These prevalence data should be viewed as conservative giving the limitation of histology. Morbidity and mortality attributable to chytridiomycosis were not observed in these two species during this period. The introduced African clawed frog (Xenopus laevis) and all native museum specimens tested negative for chytrid infection. Unlike L. catesbeianus, Pelophylax sp. is broadly distributed at local and regional scales and whether or not this complex could act as a reservoir host in the dissemination of Bd remains to be determined. The presence of the chytrid fungus in amphibian populations from different locations in southwestern France calls for disease surveillance and for precautionary measures to avoid the spread of this emerging disease.

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Genetic and Antigenetic Characterization of the Novel Kotalahti Bat Lyssavirus (KBLV)

Viruses ◽

10.3390/v13010069 ◽

2021 ◽

Vol 13 (1) ◽

pp. 69

Author(s):

Sten Calvelage ◽

Niina Tammiranta ◽

Tiina Nokireki ◽

Tuija Gadd ◽

Elisa Eggerbauer ◽

...

Keyword(s):

Novel Species ◽

Reservoir Host ◽

The Novel ◽

Ion Torrent ◽

Sequence Analyses ◽

Cross Neutralization ◽

Next Generation Sequencing Ngs ◽

Demarcation Criteria ◽

Generation Sequencing

There is a growing diversity of bat-associated lyssaviruses in the Old World. In August 2017, a dead Brandt’s bat (Myotis brandtii) tested positive for rabies and based on partial sequence analysis, the novel Kotalahti bat lyssavirus (KBLV) was identified. Because the bat was in an autolyzed state, isolation of KBLV was neither successful after three consecutive cell passages on cells nor in mice. Next generation sequencing (NGS) was applied using Ion Torrent ™ S5 technology coupled with target enrichment via hybridization-based capture (myBaits®) was used to sequence 99% of the genome, comprising of 11,878 nucleotides (nt). KBLV is most closely related to EBLV-2 (78.7% identity), followed by KHUV (79.0%) and BBLV (77.6%), supporting the assignment as phylogroup I lyssavirus. Interestingly, all of these lyssaviruses were also isolated from bat species of the genus Myotis, thus supporting that M. brandtii is likely the reservoir host. All information on antigenic and genetic divergence fulfil the species demarcation criteria by ICTV, so that we recommend KBLV as a novel species within the Lyssavirus genus. Next to sequence analyses, assignment to phylogroup I was functionally corroborated by cross-neutralization of G-deleted RABV, pseudotyped with KBLV-G by sera from RABV vaccinated humans. This suggests that conventional RABV vaccines also confer protection against the novel KBLV.

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