scholarly journals The Gut Viral Metagenome Analysis of Domestic Dogs Captures Snapshot of Viral Diversity and Potential Risk of Coronavirus

2021 ◽  
Vol 8 ◽  
Author(s):  
Ying Shi ◽  
Jie Tao ◽  
Benqiang Li ◽  
Xiaohui Shen ◽  
Jinghua Cheng ◽  
...  
Keyword(s):  
Potential Risk ◽  
Association Studies ◽  
Companion Animals ◽  
Plant Viruses ◽  
Viral Diversity ◽  
Canis Lupus Familiaris ◽  
Human Beings ◽  
Canine Coronavirus ◽  
Detection Frequency ◽  
Prediction And Prevention

The close relations between dogs (Canis lupus familiaris) and humans lay a foundation for cross species transmissions of viruses. The co-existence of multiplex viruses in the host accelerate viral variations. For effective prediction and prevention of potential epidemic or even pandemic, the metagenomics method was used to investigate the gut virome status of 45 domestic healthy dogs which have extensive contact with human beings. A total of 248.6 GB data (505, 203, 006 valid reads, 150 bp in length) were generated and 325, 339 contigs, which were best matched with viral genes, were assembled from 46, 832, 838 reads. In the aggregate, 9,834 contigs (3.02%) were confirmed for viruses. The top 30 contigs with the most reads abundance were mapped to DNA virus families Circoviridae, Parvoviridae and Herpesviridae; and RNA virus families Astroviridae, Coronaviridae and Picornaviridae, respectively. Numerous sequences were assigned to animal virus families of Astroviridae, Coronaviridae, Circoviridae, etc.; and phage families of Microviridae, Siphoviridae, Ackermannviridae, Podoviridae, Myoviridae and the unclassified phages. Further, several sequences were homologous with the insect and plant viruses, which reflects the diet and habitation of dogs. Significantly, canine coronavirus was uniquely identified in all the samples with high abundance, and the phylogenetic analysis therefore showed close relationship with the human coronavirus strain 229E and NL63, indicating the potential risk of canine coronavirus to infect humans by obtaining the ability of cross-species transmission. This study emphasizes the high detection frequency of virus harbored in the enteric tract of healthy contacted animal, and expands the knowledge of the viral diversity and the spectrum for further disease-association studies, which is meaningful for elucidating the epidemiological and biological role of companion animals in public health.

Genetic Data Analysis

2021 ◽  
pp. 358-372
Author(s):  
M. Shamila ◽  
Amit Kumar Tyagi
Keyword(s):  
Data Analysis ◽  
Association Studies ◽  
Single Gene ◽  
Genetic Data ◽  
Building Blocks ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Human Beings ◽  
Genome Wide ◽  
Genetic Data Analysis

Genome-wide association studies (GWAS) or genetic data analysis is used to discover common genetic factors which influence the health of human beings and become a part of a disease. The concept of using genomics has increased in recent years, especially in e-healthcare. Today there is huge improvement required in this field or genomics. Note that the terms genomics and genetics are not similar terms here. Basically, the human genome is made up of DNA, which consists of four different chemical building blocks (called bases and abbreviated A, T, C, and G). Based on this, we differentiate each and every human being living on earth. The term ‘genetics' originated from the Greek word ‘genetikos'. It means ‘origin'. In simple terms, genetics can be defined as a branch of biology, which deals with the study of the functionalities and composition of a single gene in an organism. There are mainly three branches of genetics, which include classical genetics, molecular genetics, and population genetics.

scholarly journals A novel canis lupus familiaris reference genome improves variant resolution for use in breed-specific GWAS

2021 ◽  
Vol 4 (4) ◽  
pp. e202000902 ◽  
Author(s):  
Robert A Player ◽  
Ellen R Forsyth ◽  
Kathleen J Verratti ◽  
David W Mohr ◽  
Alan F Scott ◽  
...  
Keyword(s):  
Canis Lupus ◽  
Reference Genome ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Canis Lupus Familiaris ◽  
High Molecular Weight Dna ◽  
Short Read ◽  
Genome Wide ◽  
The Cost

Reference genome fidelity is critically important for genome wide association studies, yet most vary widely from the study population. A typical whole genome sequencing approach implies short-read technologies resulting in fragmented assemblies with regions of ambiguity. Further information is lost by economic necessity when genotyping populations, as lower resolution technologies such as genotyping arrays are commonly used. Here, we present a phased reference genome for Canis lupus familiaris using high molecular weight DNA-sequencing technologies. We tested wet laboratory and bioinformatic approaches to demonstrate a minimum workflow to generate the 2.4 gigabase genome for a Labrador Retriever. The de novo assembly required eight Oxford Nanopore R9.4 flowcells (∼23X depth) and running a 10X Genomics library on the equivalent of one lane of an Illumina NovaSeq S1 flowcell (∼88X depth), bringing the cost of generating a nearly complete reference genome to less than $10K (USD). Mapping of short-read data from 10 Labrador Retrievers against this reference resulted in 1% more aligned reads versus the current reference (CanFam3.1, P < 0.001), and a 15% reduction of variant calls, increasing the chance of identifying true, low-effect size variants in a genome-wide association studies. We believe that by incorporating the cost to produce a full genome assembly into any large-scale genotyping project, an investigator can improve study power, decrease costs, and optimize the overall scientific value of their study.

scholarly journals Polygenic approaches to detect gene–environment interactions when external information is unavailable

2018 ◽  
Vol 20 (6) ◽  
pp. 2236-2252 ◽  
Author(s):  
Wan-Yu Lin ◽  
Ching-Chieh Huang ◽  
Yu-Li Liu ◽  
Shih-Jen Tsai ◽  
Po-Hsiu Kuo
Keyword(s):  
Association Studies ◽  
Genetic Risk Score ◽  
External Information ◽  
Analysis Tool ◽  
Genome Wide Association Studies ◽  
Adaptive Combination ◽  
Gene Environment ◽  
Prediction And Prevention ◽  
Main Effects ◽  
Polygenic Approach

Abstract The exploration of ‘gene–environment interactions’ (G × E) is important for disease prediction and prevention. The scientific community usually uses external information to construct a genetic risk score (GRS), and then tests the interaction between this GRS and an environmental factor (E). However, external genome-wide association studies (GWAS) are not always available, especially for non-Caucasian ethnicity. Although GRS is an analysis tool to detect G × E in GWAS, its performance remains unclear when there is no external information. Our ‘adaptive combination of Bayes factors method’ (ADABF) can aggregate G × E signals and test the significance of G × E by a polygenic test. We here explore a powerful polygenic approach for G × E when external information is unavailable, by comparing our ADABF with the GRS based on marginal effects of SNPs (GRS-M) and GRS based on SNP × E interactions (GRS-I). ADABF is the most powerful method in the absence of SNP main effects, whereas GRS-M is generally the best test when single-nucleotide polymorphisms main effects exist. GRS-I is the least powerful test due to its data-splitting strategy. Furthermore, we apply these methods to Taiwan Biobank data. ADABF and GRS-M identified gene × alcohol and gene × smoking interactions on blood pressure (BP). BP-increasing alleles elevate more BP in drinkers (smokers) than in nondrinkers (nonsmokers). This work provides guidance to choose a polygenic approach to detect G × E when external information is unavailable.

scholarly journals Occurrence of antimicrobial resistance and virulence genes, and distribution of enterococcal clonal complex 17 from animals and human beings in Korea

2012 ◽  
Vol 24 (5) ◽  
pp. 924-931 ◽  
Author(s):  
Ka Hee Kwon ◽  
Sun Young Hwang ◽  
Bo Youn Moon ◽  
Young Kyung Park ◽  
Sook Shin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Clonal Complex ◽  
Opportunistic Infections ◽  
Companion Animals ◽  
Companion Animal ◽  
Human Beings ◽  
Erythromycin Resistance ◽  
Food Animal ◽  
Resistance Rates

Enterococci are major zoonotic bacteria that cause opportunistic infections in human beings and animals. Moreover, pathogenic strains can be disseminated between human beings and animals, particularly companion animals that come into frequent contact with people. Recently, Enterococcus faecium clonal complex 17 (CC17) has emerged as a pandemic clone. Most CC17 strains are ampicillin resistant and possess virulence genes such as esp and hyl. Despite the possible dissemination of CC17 between human beings and animals, prevalence data about CC17 in animals is limited. In the present study, the phenotypes and genotypes of antimicrobial resistance were compared, as well as virulence gene profiles from 184 enterococci strains isolated from chickens, pigs, companion animals, and human patients in Korea. Ampicillin-resistant E. faecium (AREF) strains were selected, and multilocus sequence typing was performed to investigate the dispersion of CC17 among animals and human beings. The companion animal and human isolates showed high resistance rates to ampicillin and ciprofloxacin, whereas food animal isolates showed high tetracycline and erythromycin resistance rates. Ampicillin-resistant E. faecium was only detected in human (21/21 E. faecium, 100%) and companion animal (3/5 E. faecium, 60%) isolates, and all human AREF strains and 1 canine AREF strain were confirmed as CC17. In conclusion, the occurrence of antimicrobial resistance and virulence genes, and the distribution of enterococcal CC17 in companion animal enterococcal strains were similar to those of human strains rather than to those of food animal strains.

Phyto-metabolites; An Impregnable Shield against Plant Viruses

2018 ◽  
Vol 13 (1) ◽  
pp. 1934578X1801300 ◽  
Author(s):  
Waqar Islam ◽  
Muhammad Adnan ◽  
Muhammad Tayyab ◽  
Mubasher Hussain ◽  
Saif Ul Islam
Keyword(s):  
Integrated Management ◽  
Plant Viruses ◽  
Insect Vector ◽  
Human Beings ◽  
Virus Diseases ◽  
Primary And Secondary Metabolites ◽  
Vector Population ◽  
Alternative Means ◽  
Management Approaches ◽  
Resistant Genotypes

Worldwide, economically important crops are under continuous threat from plant viruses as they reproduce within the host and spread via various biological and non biological means. The problem can be minimized via application of integrated management approaches involving utilization of resistant genotypes and reducing the insect vector population. But such strategies are rarely applied in developing countries and farmers prefer to use chemicals against all type of diseases. But increasing use of pesticides is a leading cause of disaster to our ecosystem so alternative means such as phyto-metabolites should be explored for eco friendly management of plant viruses. So here we have reviewed about different phyto-metabolites that can be effectively and potentially used against various plant virus diseases. We further explained about the various primary and secondary metabolites such as alkaloids, essential oils, flavonoids, polysaccharides and proteins. The review highlights the recent advances in the field of phyto-metabolites utilization against plant viruses and sums up via hoping through prospects that future drugs will be safer for human beings and our ecosystem.

scholarly journals Detection and Molecular Characterization of Canine Alphacoronavirus in Free-Roaming Dogs, Bangladesh

Viruses ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 67
Author(s):  
Mohammad Enayet Hossain ◽  
Ariful Islam ◽  
Shariful Islam ◽  
Md Kaisar Rahman ◽  
Mojnu Miah ◽  
...  
Keyword(s):  
Genetic Recombination ◽  
Companion Animals ◽  
Cross Sectional Study ◽  
Interspecies Transmission ◽  
Full Genome Sequencing ◽  
Cross Sectional ◽  
Canine Coronavirus ◽  
Three Samples ◽  
The Uk

Canine coronavirus (CCoV) is widespread among the dog population and causes gastrointestinal disorders, and even fatal cases. As the zoonotic transmission of viruses from animals to humans has become a worldwide concern nowadays, it is necessary to screen free-roaming dogs for their common pathogens due to their frequent interaction with humans. We conducted a cross-sectional study to detect and characterize the known and novel Corona, Filo, Flavi, and Paramyxoviruses in free-roaming dogs in Bangladesh. Between 2009–10 and 2016–17, we collected swab samples from 69 dogs from four districts of Bangladesh, tested using RT-PCR and sequenced. None of the samples were positive for Filo, Flavi, and Paramyxoviruses. Only three samples (4.3%; 95%CI: 0.9–12.2) tested positive for Canine Coronavirus (CCoV). The CCoV strains identified were branched with strains of genotype CCoV-II with distinct distances. They are closely related to CCoVs from the UK, China, and other CoVs isolated from different species, which suggests genetic recombination and interspecies transmission of CCoVs. These findings indicate that CCoV is circulating in dogs of Bangladesh. Hence, we recommend future studies on epidemiology and genetic characterization with full-genome sequencing of emerging coronaviruses in companion animals in Bangladesh.

scholarly journals Feline and Canine Coronaviruses: Common Genetic and Pathobiological Features

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Sophie Le Poder
Keyword(s):  
Infectious Disease ◽  
Severe Acute Respiratory Syndrome ◽  
Host Cell ◽  
Companion Animals ◽  
Cell Tropism ◽  
Human Coronavirus ◽  
Feline Infectious Peritonitis ◽  
Canine Coronavirus ◽  
Coronavirus Infection ◽  
Systemic Infections

A new human coronavirus responsible for severe acute respiratory syndrome (SARS) was identified in 2003, which raised concern about coronaviruses as agents of serious infectious disease. Nevertheless, coronaviruses have been known for about 50 years to be major agents of respiratory, enteric, or systemic infections of domestic and companion animals. Feline and canine coronaviruses are widespread among dog and cat populations, sometimes leading to the fatal diseases known as feline infectious peritonitis (FIP) and pantropic canine coronavirus infection in cats and dogs, respectively. In this paper, different aspects of the genetics, host cell tropism, and pathogenesis of the feline and canine coronaviruses (FCoV and CCoV) will be discussed, with a view to illustrating how study of FCoVs and CCoVs can improve our general understanding of the pathobiology of coronaviruses.

scholarly journals Diabetes as a potential risk for periodontitis: association studies

2020 ◽  
Vol 83 (1) ◽  
pp. 40-45 ◽  
Author(s):  
Robert J. Genco ◽  
Wenche S. Borgnakke
Keyword(s):  
Potential Risk ◽  
Association Studies

Genetic effects, gene-lifestyle interactions, and type 2 diabetes

Open Medicine ◽  
2008 ◽  
Vol 3 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Lu Qi
Keyword(s):  
Type 2 Diabetes ◽  
Genetic Variants ◽  
Positional Cloning ◽  
Association Studies ◽  
Dietary Habit ◽  
Genetic Components ◽  
Genome Wide ◽  
Prediction And Prevention ◽  
Intervention Trials

AbstractType 2 diabetes has become a major public health challenge worldwide. It is now widely accepted that genetic components affect the development of type 2 diabetes, in concert with environmental factors such as lifestyle and diet. Traditional linkage mapping, positional cloning, and candidate gene-based association studies have identified a few genetic variants in genes such as TCF7L2, PPARG, and KCNJ11 that are reproducibly related to the risk of type 2 diabetes. To date, about ten genome-wide association (GWA) studies have been published. These studies discovered new susceptibility genes for type 2 diabetes and provide novel insight into the diabetes etiology. In addition, data especially from lifestyle intervention trials display promising evidence that the genetic variants may interact with changes of dietary habit and physical activity in predisposing to type 2 diabetes. The gene-lifestyle interactions merit extensive exploration in large, prospective studies. The findings from these areas will substantially improve the prediction and prevention of type 2 diabetes.

scholarly journals Contamination of the urban environment with excrements of companion animals as an underestimated source of Staphylococcus species posing a threat to public health

2020 ◽  
Vol 68 (1) ◽  
pp. 12-19
Author(s):  
Aleksandra Trościańczyk ◽  
Aneta Nowakiewicz ◽  
Sebastian Gnat ◽  
Magdalena Wójcik ◽  
Sylwia Wdowiak-Wróbel ◽  
...  
Keyword(s):  
Public Health ◽  
Gastrointestinal Tract ◽  
Urban Space ◽  
Potential Risk ◽  
Companion Animals ◽  
Individual Resistance ◽  
Phenotypic Resistance ◽  
Restriction Sites ◽  
High Level ◽  
Genotypic Characteristics

AbstractThe aim of the study was to assess the incidence, resistance, virulence, and genotypic characteristics of Staphylococcus spp. residing in the gastrointestinal tract of dogs and cats, as a group of animals causing potential contamination of the urban space. A high percentage of strains resistant to penicillin (58%), oxacillin (9%) and tetracycline (60%) were found. All isolates resistant to penicillin, kanamycin, or chloramphenicol carried genes responsible for individual resistance (blaZ, aph(3′)-IIIa, and cat (pC194)/cat (pC223), respectively. The mecA gene was detected in 45% of the oxacillin-resistant Staphylococcus pseudintermedius strains. The amplification of DNA fragments surrounding rare restriction sites analysis demonstrated high heterogeneity of genotypic profiles correlating with phenotypic resistance profiles. Multilocus sequence typing analysis classified the methicillin-resistant S. pseudintermedius strains as ST71, ST890, and the totally new ST1047. The presence of a high level of resistance among Staphylococcus strains may suggest a potential risk of transfer of these bacteria between companion animals and humans.

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