scholarly journals Virome analysis of ticks in a forest region of Liaoning, China: characterization of a novel hepe-like virus sequence

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Zijun Yang ◽  
Ju Zhang ◽  
Shixing Yang ◽  
Xiaochun Wang ◽  
Quan Shen ◽  
...  
Keyword(s):  
Animal Health ◽  
Viral Metagenomics ◽  
Liaoning Province ◽  
Haemaphysalis Longicornis ◽  
Adeno Associated Virus ◽  
Forest Region ◽  
Close Relationship ◽  
Virus Sequence ◽  
Viral Sequences

Abstract Background Ticks (class Arachnida, subclass Acari) are vectors of transmitting a broad range of pathogenic microorganisms, protozoa, and viruses affecting humans and animals. Liaoning Province is rich in forests where different animals and, abundant Haemaphysalis longicornis ticks exist. Methods Using viral metagenomics, we analyzed the virome in 300 Haemaphysalis longicornis ticks collected from June to August 2015 in the forested region of Liaoning Province, China. Results From the 300 ticks, 1,218,388 high-quality reads were generated, of which 5643 (0.463%) reads showed significant sequence identity to known viruses. Sequence and phylogenetic analysis revealed that viral sequences showing a close relationship with Dabieshan tick virus, Aleutian mink disease virus, adeno-associated virus, Gokushovirus, avian gyrovirus 2 were present in the virome of these ticks. However, the significance of these viruses to human and animal health requires further investigation. Notably, an hepe-like virus, named tick-borne hepe-like virus sequence, was obtained and was highly prevalent in these ticks with a rate of 50%. Nevertheless, one constraint of our study was the limited geographical distribution of the sampled ticks. Conclusion Our study offers an overview of the virome in ticks from a forest region of Liaoning Province and provides further awareness of the viral diversity of ticks.

scholarly journals Lethal Encephalitis of Unknown Origin—Elucidation by Metagenomics

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 59
Author(s):  
Martin Beer
Keyword(s):  
Point Of Care ◽  
Animal Health ◽  
Unknown Origin ◽  
Emerging Viruses ◽  
Viral Pathogens ◽  
Point Of Care Diagnostics ◽  
Close Relationship ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Novel and (re)emerging viruses cause frequent threats to both human and animal health. Diagnostic metagenomics using unbiased next-generation sequencing (NGS) is the key method for the identification of new pathogens. With today’s available state-of-the-art platforms, NGS can be broadly used to also identify novel and unknown pathogens in different sample materials (even in point-of-care diagnostics) or to characterize the complete genomes of all types of pathogens. Nevertheless, the extreme numbers of sequence fragments resulting from NGS analyses requires not only novel diagnostic pipelines including powerful software tools for big data analysis but also a new dimension of knowledge and resources. We therefore developed and validated a universal workflow for metagenome diagnostics for the analysis of disease syndromes in both animals and humans. The metagenomics pipeline will be presented, and several examples with the detection and characterization of novel viruses will be shown. The power of diagnostic metagenomics will be presented with different examples focusing on lethal encephalitis cases in both animals and humans where we were able to identify a series of novel or unexpected viral pathogens. Furthermore, the detection of zoonotic pathogens was only possible by a “one-health” approach and the close relationship between veterinary and human medicine. The major aim of the presentation is to give an idea about the capabilities of modern NGS-based metagenomics and to learn more about the newly detected viral pathogens. Since a large proportion of severe encephalitis cases still remain unexplained, a main conclusion is the recommendation that those cases should be analyzed by using a modern and powerful metagenomics workflow.

scholarly journals Clades of Adeno-Associated Viruses Are Widely Disseminated in Human Tissues

2004 ◽  
Vol 78 (12) ◽  
pp. 6381-6388 ◽  
Author(s):  
Guangping Gao ◽  
Luk H. Vandenberghe ◽  
Mauricio R. Alvira ◽  
You Lu ◽  
Roberto Calcedo ◽  
...  
Keyword(s):  
Gene Therapy ◽  
Molecular Techniques ◽  
Molecular Forms ◽  
Clinical Samples ◽  
Human Tissues ◽  
Adeno Associated Virus ◽  
Sequence Characterization ◽  
Gene Therapy Vectors ◽  
Viral Sequences

ABSTRACT The potential for using Adeno-associated virus (AAV) as a vector for human gene therapy has stimulated interest in the Dependovirus genus. Serologic data suggest that AAV infections are prevalent in humans, although analyses of viruses and viral sequences from clinical samples are extremely limited. Molecular techniques were used in this study to successfully detect endogenous AAV sequences in 18% of all human tissues screened, with the liver and bone marrow being the most predominant sites. Sequence characterization of rescued AAV DNAs indicated a diverse array of molecular forms which segregate into clades whose members share functional and serologic similarities. One of the most predominant human clades is a hybrid of two previously described AAV serotypes, while another clade was found in humans and several species of nonhuman primates, suggesting a cross-species transmission of this virus. These data provide important information regarding the biology of parvoviruses in humans and their use as gene therapy vectors.

scholarly journals Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 405
Author(s):  
Anna Matysiak ◽  
Michal Kabza ◽  
Justyna A. Karolak ◽  
Marcelina M. Jaworska ◽  
Malgorzata Rydzanicz ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Ocular Surface ◽  
Molecular Techniques ◽  
Corneal Tissue ◽  
Rna Seq ◽  
Microbiome Composition ◽  
Viral Sequences ◽  
Pcr Techniques ◽  
Unmapped Reads

The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into Proteobacteria, Firmicutes, and Actinobacteria phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity.

Identification and genetic characterization of avian-origin H3N2 canine influenza viruses isolated from the Liaoning province of China in 2012

Virus Genes ◽  
2014 ◽  
Vol 49 (2) ◽  
pp. 342-347 ◽  
Author(s):  
Xinyan Yang ◽  
Chunguo Liu ◽  
Fei Liu ◽  
Dafei Liu ◽  
Yan Chen ◽  
...  
Keyword(s):  
Genetic Characterization ◽  
Influenza Viruses ◽  
Liaoning Province ◽  
Avian Origin ◽  
Canine Influenza

scholarly journals Characterization of Two Novel Polyomaviruses of Birds by Using Multiply Primed Rolling-Circle Amplification of Their Genomes

2006 ◽  
Vol 80 (7) ◽  
pp. 3523-3531 ◽  
Author(s):  
Reimar Johne ◽  
Walter Wittig ◽  
Daniel Fernández-de-Luco ◽  
Ursula Höfle ◽  
Hermann Müller
Keyword(s):  
Rolling Circle Amplification ◽  
Large Tumor ◽  
Rolling Circle ◽  
Reading Frame ◽  
Field Samples ◽  
Close Relationship ◽  
Avian Polyomavirus ◽  
Avian Group ◽  
Pyrrhula Pyrrhula

ABSTRACT Polyomaviruses are small nonenveloped particles with a circular double-stranded genome, approximately 5 kbp in size. The mammalian polyomaviruses mainly cause persistent subclinical infections in their natural nonimmunocompromised hosts. In contrast, the polyomaviruses of birds—avian polyomavirus (APV) and goose hemorrhagic polyomavirus (GHPV)—are the primary agents of acute and chronic disease with high mortality rates in young birds. Screening of field samples of diseased birds by consensus PCR revealed the presence of two novel polyomaviruses in the liver of an Eurasian bullfinch (Pyrrhula pyrrhula griseiventris) and in the spleen of a Eurasian jackdaw (Corvus monedula), tentatively designated as finch polyomavirus (FPyV) and crow polyomavirus (CPyV), respectively. The genomes of the viruses were amplified by using multiply primed rolling-circle amplification and cloned. Analysis of the FPyV and CPyV genome sequences revealed a close relationship to APV and GHPV, indicating the existence of a distinct avian group among the polyomaviruses. The main characteristics of this group are (i) involvement in fatal disease, (ii) the existence of an additional open reading frame in the 5′ region of the late mRNAs, and (iii) a different manner of DNA binding of the large tumor antigen compared to that of the mammalian polyomaviruses.

scholarly journals The legacy of building in the mountain. A report from the Grisons

ARCHALP ◽  
2021 ◽  
Author(s):  
Gordian Blumenthal ◽  
Ramun Capaul
Keyword(s):  
Cultural Landscape ◽  
Cultural Influences ◽  
Design Work ◽  
Space Planning ◽  
Human Needs ◽  
Cultural Aspects ◽  
Close Relationship ◽  
The Alps ◽  
The Many

“In the Alps, the cultural landscape changes with the way people live and act. Social structures and economic conditions shape human needs and define the appearance of the territory and landscape, contributing to the development of specific settlement and housing models, in close relationship with the place. The local typology and construction technologies, developed throughout the history, thus embody the responses to the particular local housing needs, characterizing the places according to different cultural influences. These conditions, together with the influences of the environmental and natural context, as well as the cultural aspects linked to the traditions of the local communities, today are still distinctive elements of the characterization of the villages and mountain valleys. The essay, starting from design experiences conducted personally by the architects in their region of origin – the Grisons – explores the many suggestions that the “legacy” of the different ways of building in the mountains offered for their design work. From space planning to materials, from construction solutions to typology, the architectural projects of Capaul & Blumenthal, both in the case of the recovery of the existing heritage and in the case of new buildings, seem to move from a clever re-interpretation of the complex heritage that combines savoir faire, knowledge, inspirations and materials, to seek careful answers to the current problems of the Alpine world.”

scholarly journals Identification and Evolutionary Characterization of Papillomavirus Sequences in New World Monkeys (Genera Sapajus and Alouatta) from Argentina

2021 ◽  
Author(s):  
Candelaria Sanchez Fernandez ◽  
Elisa M Bolatti ◽  
Andres C.A. Culasso ◽  
Diego Chouhy ◽  
Martin M Kowalewski ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Pcr Primers ◽  
Host Tree ◽  
New World Monkeys ◽  
Alouatta Caraya ◽  
Captive Populations ◽  
L1 Protein ◽  
Viral Sequences ◽  
Northeastern Argentina

Abstract Objective: In this study, we investigated the occurrence of papillomavirus (PV) infection in non-human primates (NHP, Platyrrhine) of northeastern Argentina by using broad-spectrum PCR primers at the L1 gene. In addition, we conducted a phylogenetic and coalescence analysis of viral sequences to explore their evolutionary history and evaluate the co-speciation hypothesis in the context of primate evolution. Methods: We obtained samples of 57 individuals from wild and captive populations of Alouatta caraya, Sapajus nigritus and Sapajus cay. We assessed PV infection by PCR amplification with the CUT primer system and sequencing of 337 bp (112 amino acids) of the L1 protein. The viral sequences were analyzed by phylogenetic and Bayesian coalescence methods to estimate the age of the most common recent ancestor (tMCRA) with BEAST, v1.4.8 software. We evaluated viral/host tree congruence with TreeMap v3.0. Results: We identified two novel putative PV sequences of the genus Gamma- PV in Sapajus sp and Alouatta caraya (SPV1 and AcPV1, respectively). The tMRCA of SPV1 was estimated at 11,941,682 years before present (ybp) and that of AcPV1 at 46,638,071 ybp, both predating the coalescence times of their hosts: 6.4 million years (MYA) and 6.8 MYA, respectively. Based on the comparison of primate and viral phylogenies, we could not reject the null hypothesis that the PV tree is no more congruent with the host tree than a random tree would be (P>0.05). Thus, a model of virus-host coevolution was rejected. Conclusion: This study presents the first report of PV infection in Platyrrhine species from Argentina, expands the range of described hosts for these viruses, and proposes new scenarios for their origin and dispersal.

scholarly journals Characterization of an MLP Homologue from Haemaphysalis longicornis (Acari: Ixodidae) Ticks

Pathogens ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 284
Author(s):  
Jin Luo ◽  
Hui Shen ◽  
Qiaoyun Ren ◽  
Guiquan Guan ◽  
Bo Zhao ◽  
...  
Keyword(s):  
Muscle Development ◽  
Developmental Stages ◽  
Rabbit Antiserum ◽  
Haemaphysalis Longicornis ◽  
Mrna Levels ◽  
Muscle Lim Protein ◽  
Rapid Amplification ◽  
Differentiation And Proliferation ◽  
Phosphate Buffered Saline

Members of the cysteine-rich protein (CRP) family are known to participate in muscle development in vertebrates. Muscle LIM protein (MLP) belongs to the CRP family and has an important function in the differentiation and proliferation of muscle cells. In this study, the full-length cDNA encoding MLP from Haemaphysalis longicornis (H. longicornis; HLMLP) ticks was obtained by 5′ rapid amplification of cDNA ends (RACE). To verify the transcriptional status of MLP in ticks, HLMLP gene expression was assessed during various developmental stages by real-time PCR (RT-PCR). Interestingly, HLMLP expression in the integument was significantly (P < 0.01) higher than that observed in other tested tissues of engorged adult ticks. In addition, HLMLP mRNA levels were significantly downregulated in response to thermal stress at 4 °C for 48 h. Furthermore, recombinant HLMLP was expressed in Escherichia coli, and Western blot analysis showed that rabbit antiserum against H. longicornis adults recognized HLMLP and MLPs from different ticks. Ten 3-month-old rabbits that had never been exposed to ticks were used for the immunization and challenge experiments. The rabbits were divided into two groups of five rabbits each, where rabbits in the first group were immunized with HLMLP, while those in the second group were immunized with phosphate-buffered saline (PBS) diluent as controls. The vaccination of rabbits with the recombinant HLMLP conferred partial protective immunity against ticks, resulting in 20.00% mortality and a 17.44% reduction in the engorgement weight of adult ticks. These results suggest that HLMLP is not ideal as a candidate for use in anti-tick vaccines. However, the results of this study generated novel information on the MLP gene in H. longicornis and provide a basis for further investigation of the function of this gene that could potentially lead to a better understanding of the mechanism of myofiber determination and transformation

scholarly journals Characterization of the Intestinal Microbiota of Broiler Breeders With Different Egg Laying Rate

2020 ◽  
Vol 7 ◽  
Author(s):  
Zengqiao Yang ◽  
Chunhua Zhang ◽  
Jianping Wang ◽  
Pietro Celi ◽  
Xuemei Ding ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Feed Efficiency ◽  
Animal Health ◽  
Negative Relationship ◽  
Egg Laying ◽  
Ovary Cell ◽  
Feed Conversion ◽  
Broiler Breeders ◽  
Gastrointestinal Microbiota

The gastrointestinal microbiota plays a pivotal role in maintaining animal health, immunity and reproductive performances. However, literature about the relationship between microbiota and reproductive performance is limited. The aim of the present study was to determine differences in the intestinal microbiota of broiler breeders with different egg laying rate. A total of 200 AA+ parent broiler breeders (41-week-old) were separated into two groups according to their different egg laying rate [average egg laying rate group (AR: 78.57 ± 0.20%) and high egg laying rate group (HR: 90.79 ± 0.43%). Feed conversion ratio (FCR), ovary cell apoptosis rate (ApoCR) and relative abdominal fat weight were lower (p = 0.01), while the hatchability rate of qualified egg was higher (p = 0.04) in HR group than that in AR group. Phascolarctobacterium abundance were lower (p = 0.012) in ileum of HR birds. Romboutsia (genus) in ileum was negatively related to the feed efficiency (r = −0.58, p &lt; 0.05), Firmicutes (phylum) and Lactobacillus (genus) abundances in cecum were positively related to the egg laying rate (ELR) (r = 0.35 and 0.48, p &lt; 0.05), feed efficiency (r = 0.42 and 0.43, p &lt; 0.05), while Spirochaetes (phylum) and Sphaerochaeta (genus) abundances in cecum were negatively related to the ELR (r = −0.43 and −0.70, p &lt; 0.05), feed efficiency (r = 0.54 and 0.48, p &lt; 0.05), and positively related to ApoCR (r = 0.46 and 0.47, p &lt; 0.05). Our results suggested that microbiota, such as Firmicutes (phylum) and Lactobacillus (genus) have positive relationship, while Spirochaetes (phylum) and Romboutsia (genus) abundances exert negative relationship with broiler breeders' reproductive performances.

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