Molecular Characterization of the FCoV-like Canine Coronavirus HLJ-071 in China

Abstract Background According to differences in antigens and genetic composition, canine coronavirus (CCoV) consists of two genotypes, CCoV-Ⅰ and CCoV-Ⅱ. Recently, CCoVs with mutant variations have been found to be pantropic and pathogenic in dogs. Results In this study, we isolated a CCoV, designated HLJ-071, from a dead 5-week-old female Welsh Corgi with severe diarrhea and vomiting. Sequence analysis suggested that HLJ-071 bears a complete ORF3abc when compared with classic CCoV isolates (1–71, K378 and S378). In addition, a variable region was located between the S gene and the open reading frames (ORF) 3a gene, in which HLJ-071 has a deletion of 104 nucleotides (nts) when compared with classic CCoV strains 1–71, S378 and K378. Phylogenetic analysis based on the S gene and complete sequences showed that HLJ-071 is closely related to Feline Coronavirus (FCoV) II. Recombination analysis suggested that HLJ-071 originated from the recombination of FCoV 79-1683, FCoV DF2 and CCoV A76. Finally, cell tropism experiments suggested that HLJ-071 is able to replicate in canine macrophages/monocytes. Conclusion The present study involved the isolation and genetic characterization of a variant CCoV strain. The spike protein and ORF3abc of CCoV might play a key role in viral tropism, which could affect replication in monocyte/macrophage cells. This will provide essential information for further understanding the evolution of CCoV in China.

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Molecular characterization of the FCoV-like canine coronavirus HLJ-071 in China

BMC Veterinary Research ◽

10.1186/s12917-021-03073-8 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Zhige Tian ◽

Qing Pan ◽

Miaomiao Zheng ◽

Ying Deng ◽

Peng Guo ◽

...

Keyword(s):

Genetic Characterization ◽

Point Mutations ◽

Variable Region ◽

Cell Tropism ◽

Essential Information ◽

Severe Diarrhea ◽

S Gene ◽

Canine Coronavirus ◽

Complete Sequences

Abstract Background According to the differences of antigen and genetic composition, canine coronavirus (CCoV) consists of two genotypes, CCoV-I and CCoV-II. Since 2004, CCoVs with point mutations or deletions of NSPs are contributing to the changes in tropism and virulence in dogs. Results In this study, we isolated a CCoV, designated HLJ-071, from a dead 5-week-old female Welsh Corgi with severe diarrhea and vomit. Sequence analysis suggested that HLJ-071 bearing a complete ORF3abc compared with classic CCoV isolates (1-71, K378 and S378). In addition, a variable region was located between S gene and ORF 3a gene, in which a deletion with 104 nts for HLJ-071 when compared with classic CCoV strains 1-71, S378 and K378. Phylogenetic analysis based on the S gene and complete sequences showed that HLJ-071 was closely related to FCoV II. Recombination analysis suggested that HLJ-071 originated from the recombination of FCoV 79-1683, FCoV DF2 and CCoV A76. Finally, according to cell tropism experiments, it suggested that HLJ-071 could replicate in canine macrophages/monocytes cells. Conclusion The present study involved the isolation and genetic characterization of a variant CCoV strain and spike protein and ORF3abc of CCoV might play a key role in viral tropism, which could affect the replication in monocyte/macrophage cells. It will provide essential information for further understanding the evolution in China.

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Identification of Canine Coronavirus Strains from Feces by S Gene Nested PCR and Molecular Characterization of a New Australian Isolate

Journal of Clinical Microbiology ◽

10.1128/jcm.39.3.1036-1041.2001 ◽

2001 ◽

Vol 39 (3) ◽

pp. 1036-1041 ◽

Cited By ~ 21

Author(s):

M. J. Naylor ◽

G. A. Harrison ◽

R. P. Monckton ◽

S. McOrist ◽

P. R. Lehrbach ◽

...

Keyword(s):

Molecular Characterization ◽

Nested Pcr ◽

Australian Isolate ◽

S Gene ◽

Canine Coronavirus

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Characterization of Marek's disease virus insertion and deletion mutants that lack US1 (ICP22 homolog), US10, and/or US2 and neighboring short-component open reading frames.

Journal of Virology ◽

10.1128/jvi.68.12.8239-8253.1994 ◽

1994 ◽

Vol 68 (12) ◽

pp. 8239-8253 ◽

Cited By ~ 37

Author(s):

M S Parcells ◽

A S Anderson ◽

J L Cantello ◽

R W Morgan

Keyword(s):

Disease Virus ◽

Marek's Disease Virus ◽

Open Reading Frames ◽

Marek's Disease ◽

Deletion Mutants ◽

Marek’S Disease Virus ◽

Insertion And Deletion ◽

Short Component ◽

Reading Frames

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Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽

10.3390/v13010027 ◽

2020 ◽

Vol 13 (1) ◽

pp. 27

Author(s):

Jun Kwon ◽

Sang Guen Kim ◽

Hyoun Joong Kim ◽

Sib Sankar Giri ◽

Sang Wha Kim ◽

...

Keyword(s):

Morphological Traits ◽

Open Reading Frames ◽

Genome Comparison ◽

The Novel ◽

Promising Alternative ◽

Isolation And Characterization ◽

Global Issue ◽

Reading Frames ◽

Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

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Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions

npj Genomic Medicine ◽

10.1038/s41525-020-00167-4 ◽

2021 ◽

Vol 6 (1) ◽

Cited By ~ 2

Author(s):

Chaitanya Erady ◽

Adam Boxall ◽

Shraddha Puntambekar ◽

N. Suhas Jagannathan ◽

Ruchi Chauhan ◽

...

Keyword(s):

Transcript Level ◽

Open Reading Frames ◽

The Cancer Genome Atlas ◽

Small Subset ◽

Cancer Tissue ◽

Post Translational Modifications ◽

Cancer Genome Atlas ◽

Systematic Identification ◽

Reading Frames

AbstractUncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that remain unexplored for novel therapeutic opportunities. To our knowledge, no systematic identification and characterization of transcripts encoding nORFs or their translation products in cancer, or in any other physiological process has been performed. We use our curated nORFs database (nORFs.org), together with RNA-Seq data from The Cancer Genome Atlas (TCGA) and Genotype-Expression (GTEx) consortiums, to identify transcripts containing nORFs that are expressed frequently in cancer or matched normal tissue across 22 cancer types. We show nORFs are subject to extensive dysregulation at the transcript level in cancer tissue and that a small subset of nORFs are associated with overall patient survival, suggesting that nORFs may have prognostic value. We also show that nORF products can form protein-like structures with post-translational modifications. Finally, we perform in silico screening for inhibitors against nORF-encoded proteins that are disrupted in stomach and esophageal cancer, showing that they can potentially be targeted by inhibitors. We hope this work will guide and motivate future studies that perform in-depth characterization of nORF functions in cancer and other diseases.

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Lights and Shadows in the Genetics of Syndromic and Non-Syndromic Hearing Loss in the Italian Population

Genes ◽

10.3390/genes11111237 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1237

Author(s):

Anna Morgan ◽

Stefania Lenarduzzi ◽

Beatrice Spedicati ◽

Elisabetta Cattaruzzi ◽

Flora Maria Murru ◽

...

Keyword(s):

Hearing Loss ◽

Disease Genes ◽

Italian Population ◽

Essential Information ◽

Whole Exome ◽

Relevant Role ◽

Multiplex Ligation Probe Amplification ◽

Syndromic Hearing Loss

Hearing loss (HL), both syndromic (SHL) and non-syndromic (NSHL), is the most common sensory disorder, affecting ~460 million people worldwide. More than 50% of the congenital/childhood cases are attributable to genetic causes, highlighting the importance of genetic testing in this class of disorders. Here we applied a multi-step strategy for the molecular diagnosis of HL in 125 patients, which included: (1) an accurate clinical evaluation, (2) the analysis of GJB2, GJB6, and MT-RNR1 genes, (3) the evaluation STRC-CATSPER2 and OTOA deletions via Multiplex Ligation Probe Amplification (MLPA), (4) Whole Exome Sequencing (WES) in patients negative to steps 2 and 3. Our approach led to the characterization of 50% of the NSHL cases, confirming both the relevant role of the GJB2 (20% of cases) and STRC deletions (6% of cases), and the high genetic heterogeneity of NSHL. Moreover, due to the genetic findings, 4% of apparent NSHL patients have been re-diagnosed as SHL. Finally, WES characterized 86% of SHL patients, supporting the role of already know disease-genes. Overall, our approach proved to be efficient in identifying the molecular cause of HL, providing essential information for the patients’ future management.

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Size-based characterization of adalimumab and TNF-α interactions using flow induced dispersion analysis: assessment of avidity-stabilized multiple bound species

Scientific Reports ◽

10.1038/s41598-021-84113-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Morten E. Pedersen ◽

Ragna M. S. Haegebaert ◽

Jesper Østergaard ◽

Henrik Jensen

Keyword(s):

Protein Interactions ◽

Free Ligand ◽

Local Environment ◽

Dispersion Analysis ◽

Surface Immobilization ◽

Covalent Bonds ◽

Essential Information ◽

Tnf Α

AbstractThe understanding and characterization of protein interactions is crucial for elucidation of complicated biomolecular processes as well as for the development of new biopharmaceutical therapies. Often, protein interactions involve multiple binding, avidity, oligomerization, and are dependent on the local environment. Current analytical methodologies are unable to provide a detailed mechanistic characterization considering all these parameters, since they often rely on surface immobilization, cannot measure under biorelevant conditions, or do not feature a structurally-related readout for indicating formation of multiple bound species. In this work, we report the use of flow induced dispersion analysis (FIDA) for in-solution characterization of complex protein interactions under in vivo like conditions. FIDA is an immobilization-free ligand binding methodology employing Taylor dispersion analysis for measuring the hydrodynamic radius (size) of biomolecular complexes. Here, the FIDA technology is utilized for a size-based characterization of the interaction between TNF-α and adalimumab. We report concentration-dependent complex sizes, binding affinities (Kd), kinetics, and higher order stoichiometries, thus providing essential information on the TNF-α–adalimumab binding mechanism. Furthermore, it is shown that the avidity stabilized complexes involving formation of multiple non-covalent bonds are formed on a longer timescale than the primary complexes formed in a simple 1 to 1 binding event.

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