Molecular characterization, phylogenetic and variation analyses of SARS-CoV-2 strains in Turkey

Aims: We present the sequence and single-nucleotide polymorphism (SNP) analysis for 47 complete genomes for SARS-CoV-2 isolates on Turkish patients. Methods: The Illumina MiSeq platform was used for sequencing the libraries. The SNPs were detected by using Genome Analysis Toolkit – HaplotypeCaller v.3.8.0 and were inspected on GenomeBrowse v2.1.2. Results: All viral genome sequences of our isolates were located in lineage B under the different clusters, such as B.1 (n = 3), B.1.1 (n = 28) and B.1.9 (n = 16). According to the Global Initiative on Sharing All Influenza Data nomenclature, all of our complete genomes were placed in G, GR and GH clades. In our study, 549 total and 53 unique SNPs were detected. Conclusion: The results indicate that the SARS-CoV-2 sequences of our isolates have great similarity with all Turkish and European sequences.

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Molecular Characterization, Phylogenetic and Variation Analyzes of SARS-CoV-2 strains in Turkey

10.1101/2020.09.11.293183 ◽

2020 ◽

Author(s):

Karamese Murat ◽

Ozgur Didem ◽

Tutuncu Emin Ediz

Keyword(s):

Illumina Miseq ◽

Composite Likelihood ◽

Likelihood Method ◽

Neighbor Joining ◽

Genome Sequences ◽

Illumina Miseq Platform ◽

Complete Genomes ◽

Genome Analysis Toolkit ◽

Miseq Platform ◽

Turkish Patients

ABSTRACTIntroductionWe present the sequence analysis for 47 complete genomes for SARS-CoV-2 isolates on Turkish patients. To identify their genetic similarity, phylogenetic analysis was performed by comparing the worldwide SARS-CoV-2 sequences, selected from GISAID, to the complete genomes from Turkish isolates. In addition, we focused on the variation analysis to show the mutations on SARS-CoV-2 genomes.MethodsIllumina MiSeq platform was used for sequencing the libraries. The raw reads were aligned to the known SARS-CoV-2 genome (GenBank: MN908947.3) using the Burrows-Wheeler aligner (v.0.7.1). The phylogenetic tree was constructer using Phylip v.3.6 with Neighbor-Joining and composite likelihood method. The variants were detected by using Genome Analysis Toolkit-HaplotypeCaller v.3.8.0 and were inspected on GenomeBrowse v2.1.2.ResultsAll viral genome sequences of our isolates was located in lineage B under the different clusters such as B.1 (n=3), B.1.1 (n=28), and B.1.9 (n=16). According to the GISAID nomenclature, all our complete genomes were placed in G, GR and GH clades. Five hundred forty-nine total and 53 unique variants were detected. All 47 genomes exhibited different kinds of variants. The distinct variants consist of 274 missense, 225 synonymous, and 50 non-coding alleles.ConclusionThe results indicated that the SARS-CoV-2 sequences of our isolates have great similarity with all Turkish and European sequences. Further studies should be performed for better comparison of strains, after more complete genome sequences will be released. We also believe that collecting and sharing any data about SARS-CoV-2 virus and COVID-19 will be effective and may help the related studies.

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Synergistic effect of genetic polymorphisms in TLR6 and TLR10 genes on the risk of pulmonary tuberculosis in a Moldavian population

Innate Immunity ◽

10.1177/17534259211029996 ◽

2021 ◽

pp. 175342592110299

Author(s):

Alexander Varzari ◽

Igor V. Deyneko ◽

Elena Tudor ◽

Harald Grallert ◽

Thomas Illig

Keyword(s):

Pulmonary Tuberculosis ◽

Interaction Analysis ◽

P Value ◽

Fisher Exact Test ◽

Snp Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Exact Test ◽

Pulmonary Tb ◽

The Republic

Polymorphisms in genes that control immune function and regulation may influence susceptibility to pulmonary tuberculosis (TB). In this study, 14 polymorphisms in 12 key genes involved in the immune response ( VDR, MR1, TLR1, TLR2, TLR10, SLC11A1, IL1B, IL10, IFNG, TNF, IRAK1, and FOXP3) were tested for their association with pulmonary TB in 271 patients with TB and 251 community-matched controls from the Republic of Moldova. In addition, gene–gene interactions involved in TB susceptibility were analyzed for a total of 43 genetic loci. Single nucleotide polymorphism (SNP) analysis revealed a nominal association between TNF rs1800629 and pulmonary TB (Fisher exact test P = 0.01843). In the pairwise interaction analysis, the combination of the genotypes TLR6 rs5743810 GA and TLR10 rs11096957 GT was significantly associated with an increased genetic risk of pulmonary TB (OR = 2.48, 95% CI = 1.62–3.85; Fisher exact test P value = 1.5 × 10−5, significant after Bonferroni correction). In conclusion, the TLR6 rs5743810 and TLR10 rs11096957 two-locus interaction confers a significantly higher risk for pulmonary TB; due to its high frequency in the population, this SNP combination may serve as a novel biomarker for predicting TB susceptibility.

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Whole-Genome Single-Nucleotide-Polymorphism Analysis for Discrimination of Clostridium botulinum Group I Strains

Applied and Environmental Microbiology ◽

10.1128/aem.03934-13 ◽

2014 ◽

Vol 80 (7) ◽

pp. 2125-2132 ◽

Cited By ~ 23

Author(s):

Narjol Gonzalez-Escalona ◽

Ruth Timme ◽

Brian H. Raphael ◽

Donald Zink ◽

Shashi K. Sharma

Keyword(s):

Single Nucleotide Polymorphism ◽

Clostridium Botulinum ◽

Toxin Gene ◽

Polymorphism Analysis ◽

Snp Analysis ◽

Whole Genome ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Content Type ◽

Group I

ABSTRACTClostridium botulinumis a genetically diverse Gram-positive bacterium producing extremely potent neurotoxins (botulinum neurotoxins A through G [BoNT/A-G]). The complete genome sequences of three strains harboring only the BoNT/A1 nucleotide sequence are publicly available. Although these strains contain a toxin cluster (HA+OrfX−) associated with hemagglutinin genes, little is known about the genomes of subtype A1 strains (termed HA−OrfX+) that lack hemagglutinin genes in the toxin gene cluster. We sequenced the genomes of three BoNT/A1-producingC. botulinumstrains: two strains with the HA+OrfX−cluster (69A and 32A) and one strain with the HA−OrfX+cluster (CDC297). Whole-genome phylogenic single-nucleotide-polymorphism (SNP) analysis of these strains along with other publicly availableC. botulinumgroup I strains revealed five distinct lineages. Strains 69A and 32A clustered with theC. botulinumtype A1 Hall group, and strain CDC297 clustered with theC. botulinumtype Ba4 strain 657. This study reports the use of whole-genome SNP sequence analysis for discrimination ofC. botulinumgroup I strains and demonstrates the utility of this analysis in quickly differentiatingC. botulinumstrains harboring identical toxin gene subtypes. This analysis further supports previous work showing that strains CDC297 and 657 likely evolved from a common ancestor and independently acquired separate BoNT/A1 toxin gene clusters at distinct genomic locations.

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Leptin gene polymorphism of Ongole Grade cattle based on single nucleotide polymorphism

Journal of the Indonesian Tropical Animal Agriculture ◽

10.14710/jitaa.43.4.309-314 ◽

2018 ◽

Vol 43 (4) ◽

pp. 309

Author(s):

N. Hilmia ◽

D. Rahmat ◽

D. Dudi

Keyword(s):

Amino Acids ◽

Single Nucleotide Polymorphism ◽

Gene Polymorphism ◽

Direct Sequencing ◽

Snp Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Exon 2 ◽

Specific Allele ◽

Polymerase Chain

Point mutation on exon 2 of leptin gene, which changes amino acid encoding from Arginine to Cysteine, may alters the physiological function of the leptin hormone. This study aimed to identify leptin gene polymorphism of Ongole Grade (OG) cattle based on Single Nucleotide Polymorphism (SNP). The DNA sample was taken from 48 head of OG cattle at Balai Pengembangan Perbibitan Ternak Sapi Potong(BPPT SP) Cijeungjing West Java, which was isolated from white blood cell using the high salt method. Amplification of DNA was done by Polymerase Chain Reaction (PCR), followed by direct sequencing to obtain nucleotide sequence. The SNP analysis was carried out from alignment of sequencing result using Bioedit and MEGA 5.2 program. The results indicated in exon 2 leptin gene of OG cattle there was one synonymous SNPs that did not changeamino acids Serine encoding on g.1025T >C/S17S, while two non synonymous SNPaltered amino acids encoding, those were g.1047C> T /R25C and g.1048G>A/R25H. Those mutations changed amino acids encoding from Arginine to Cysteine and Arginine to Histidine respectively.In OG cattle, the frequency of A allele (44.8%) was higher than C allele (33.3%) and T allele (21.9%). Six genotypes were also identified, i.e. AA (41.7%), CC (20.8%), CT (20.8%), CA(4.2%), TT (10.4%) and TA (2.1 %). Heterozigosity of OG cattle based on leptin gene was 0.65 that was a high category. The A allele was a specific allele on Indonesian local cattle.

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Single Nucleotide Polymorphism (SNP) Analysis of Metallothionein 2A Gene in White and Black Females

Epidemiology ◽

10.1097/01.ede.0000362580.51072.d9 ◽

2009 ◽

Vol 20 ◽

pp. S171

Author(s):

Jane McElroy ◽

Elizabeth Bryda ◽

Robert Schnabel ◽

Stephanie McKay ◽

Jeremy Taylor

Keyword(s):

Single Nucleotide Polymorphism ◽

Snp Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Black Females

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P.7.b.005 Arginine vasopressin receptor gene-based single nucleotide polymorphism (SNP) analysis in ADHD

European Neuropsychopharmacology ◽

10.1016/s0924-977x(09)71109-5 ◽

2009 ◽

Vol 19 ◽

pp. S686

Author(s):

D. van West ◽

J. Del-Favero ◽

D. Deboutte ◽

C. Van Broeckhoven ◽

S. Claes

Keyword(s):

Single Nucleotide Polymorphism ◽

Arginine Vasopressin ◽

Receptor Gene ◽

Vasopressin Receptor ◽

Snp Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide

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Novel Genotyping and Quantitative Analysis of Neuraminidase Inhibitor Resistance-Associated Mutations in Influenza A Viruses by Single-Nucleotide Polymorphism Analysis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00316-11 ◽

2011 ◽

Vol 55 (10) ◽

pp. 4718-4727 ◽

Cited By ~ 15

Author(s):

Susu Duan ◽

David A. Boltz ◽

Jiang Li ◽

Christine M. Oshansky ◽

Henju Marjuki ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Influenza Viruses ◽

Polymorphism Analysis ◽

Snp Analysis ◽

Pandemic H1n1 ◽

Wild Type ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Inhibitor Resistance ◽

Public Health Epidemiology

ABSTRACTNeuraminidase (NA) inhibitors are among the first line of defense against influenza virus infection. With the increased worldwide use of the drugs, antiviral susceptibility surveillance is increasingly important for effective clinical management and for public health epidemiology. Effective monitoring requires effective resistance detection methods. We have developed and validated a novel genotyping method for rapid detection of established NA inhibitor resistance markers in influenza viruses by single nucleotide polymorphism (SNP) analysis. The multi- or monoplex SNP analysis based on single nucleotide extension assays was developed to detect NA mutations H275Y and I223R/V in pandemic H1N1 viruses, H275Y in seasonal H1N1 viruses, E119V and R292K in seasonal H3N2 viruses, and H275Y and N295S in H5N1 viruses. The SNP analysis demonstrated high sensitivity for low-content NA amplicons (0.1 to 1 ng/μl) and showed 100% accordant results against a panel of defined clinical isolates. The monoplex assays for the H275Y NA mutation allowed precise and accurate quantification of the proportions of wild-type and mutant genotypes in virus mixtures (5% to 10% discrimination), with results comparable to those of pyrosequencing. The SNP analysis revealed the lower growth fitness of an H275Y mutant compared to the wild-type pandemic H1N1 virus by quantitatively genotyping progeny viruses grown in normal human bronchial epithelial cells. This novel method offers high-throughput screening capacity, relatively low costs, and the wide availability of the necessary equipment, and thus it could provide a much-needed approach for genotypic screening of NA inhibitor resistance in influenza viruses.

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Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections

Journal of Clinical Microbiology ◽

10.1128/jcm.00517-18 ◽

2018 ◽

Vol 56 (9) ◽

Cited By ~ 15

Author(s):

Anna Janowicz ◽

Fabrizio De Massis ◽

Massimo Ancora ◽

Cesare Cammà ◽

Claudio Patavino ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Multilocus Sequence Typing ◽

Core Genome ◽

Brucella Melitensis ◽

Reference Sequence ◽

Snp Analysis ◽

Phylogenetic Distance ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Content Type

ABSTRACT The use of whole-genome sequencing (WGS) using next-generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through single-nucleotide polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome multilocus sequence typing (cgMLST) has not been explored so far. The current study developed an allele-based cgMLST method and compared its performance to that of the genome-wide SNP approach and the traditional multilocus variable-number tandem repeat analysis (MLVA) on a defined sample collection. The data set was comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 isolates with unknown epidemiological status, composed of human and animal samples collected in Italy. The cgMLST scheme generated in this study contained 2,704 targets of the B. melitensis 16M reference genome. We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be ≤6 loci in the cgMLST and ≤7 in WGS SNP analysis. Higher phylogenetic distance resolution was achieved with cgMLST and SNP analysis than with MLVA, particularly for strains belonging to the same lineage, thereby allowing diverse and unrelated genotypes to be identified with greater confidence. The application of a cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen, and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.

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Heterozygous Single-Nucleotide Polymorphism Genotypes at Heat Shock Protein 70 Gene Potentially Influence Thermo-Tolerance Among Four Zebu Breeds of Nigeria

Frontiers in Genetics ◽

10.3389/fgene.2021.642213 ◽

2021 ◽

Vol 12 ◽

Author(s):

Gbolabo Olaitan Onasanya ◽

George Mutani Msalya ◽

Aranganoor Kannan Thiruvenkadan ◽

Chirukandoth Sreekumar ◽

Gopalan Krishnaswamy Tirumurugaan ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Heat Shock ◽

Heat Shock Protein ◽

Genetic Variants ◽

Heat Shock Protein 70 ◽

Genotypic Frequency ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Unique Snps

Genetic variants at heat shock protein 70 gene and their influence on heat stress (HS) tolerance were studied among selected Nigeria zebu, namely, 25 White Fulani (WF), 21 Sokoto Gudali (SG), 21 Red Bororo (RB), and 23 Ambala (AM). Detection of single nucleotide polymorphism (SNP) followed by determination of genotype and genotypic frequency was made among the selected breeds. The heat tolerance coefficient (HTC) was determined from thermo-related parameters including body temperature, rectal temperature, and respiratory rate. Thermo-Tolerance was evaluated through the SNP–thermo-parameter relationship. Statistical analyses were done using the GLM procedure in SAS. A quantitative real-time/high-resolution melting-based assay detected twelve genetic variants. Five of these were common and shared across all breeds of cattle. Of the remaining seven variants, three were specifically identified in AM, two in SG, and two in RB. Also, SNPs were evaluated and four unique SNPs (C151T, C146T, G90A, and C219A) were identified. Heterozygous animals had lower HTC suggesting their potential to withstand HS than homozygous counterparts. The WF and RB animals had significantly lower values for all parameters (BT, RT, RR, and HTC) compared to AM and SG breeds. Thermo-related parameters were significantly different (P < 0.001), and it is recommended that screening of SNPs in zebu is needed to enable selection for improved thermo-tolerance.

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Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis

Applied and Environmental Microbiology ◽

10.1128/aem.03103-15 ◽

2015 ◽

Vol 82 (3) ◽

pp. 822-831 ◽

Cited By ~ 21

Author(s):

Marina Morganti ◽

Erika Scaltriti ◽

Paolo Cozzolino ◽

Luca Bolzoni ◽

Gabriele Casadei ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Food Chain ◽

Snp Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Production Chain ◽

Content Type ◽

Routine Monitoring ◽

Parma Ham ◽

Qualitative Pattern

ABSTRACTThe quantitative and qualitative patterns of environmental contamination byListeria monocytogeneswere investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive forL. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality ofL. monocytogeneswithin plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread ofL. monocytogeneswithin and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments.

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