The emergence of novel Iranian variants in sheeppox and goatpox viral envelope proteins with remarkably altered putative binding affinities with the host receptor

Alwan, Haider; Torabi, Maryam; Nourani, Hossein; Al-Shuhaib, Mohammed Baqur S.

doi:10.1007/s11262-023-01987-z

Cited by 4 publications

(2 citation statements)

References 47 publications

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“…For each gene fragment, neighbour-joining trees were constructed using NCBI-BLASTn for sequence comparison and iTOL for visualization. Sequences were colorcoded for enhanced differentiation as per Alwan et al (2023).…”

Section: Phylogenetic Tree Constructionmentioning

confidence: 99%

Genetic diversity and phylogenetic positioning of Entamoeba histolytica isolates from stool samples of patients from few Hospitals at Diyala governorate

Mohamed,

Ahmed,

Mohsin

2024

JANS

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Entamoeba histolytica is a protozoan parasite that causes amoebiasis, an infection primarily affecting the intestines. The study aimed to determine the phylogenetic placement of six isolates of E. histolytica that were amplified from three genetic loci, rRNA, cysteine proteinase, and amoebapore C to evaluate the genetic variation pattern of each sequence. DNA extracted from cultured and frozen stool samples using PrestoTM Stool DNA Extraction Kit and Geneaid kits was analyzed for E. histolytica diversity in amoebiasis patients at Baquba General Hospital from March-June 2023. Polymerase chaing kreaction (PCR) and sequencing of virulence genes (rRNA, cysteine proteinase, amoebapore C) followed by phylogenetic analysis revealed genetic variation and potential implications for pathogenicity. The conducted sequencing reactions confirmed the precise identification of the examined samples, which were determined to be attributed to variable isolates of E. histolytica. Aligning the rRNA sequences of samples A1 and A2 with the most closely related rRNA sequences of E. histolytica (GenBank acc. no. OP925909.1) revealed the presence of two nucleic acid variants (212C>T in A1, and 427G>C in A1 and A2) not present in the reference sequences. Aligning the cysteine proteinase sequences of samples B1 and B2 with the most closely related genomic DNA sequences of E. histolytica (GenBank acc. no. X91642.1) revealed the presence of four nucleic acid variants (95A>T and 96A>T in B1 and B2, and 246A>T and 247A>T in B2) not present in the reference sequences. Translation of nucleic acid sequences to amino acid residues showed that both 95A>T and 96A>T variants caused a missense effect of p.46E>V, while both 246A>T and 247A>T variants showed another missense effect of p.97T>S. Aligning the amoebapore C sequences of samples C1 and C2 with the most closely related genomic sequences of E. histolytica (GenBank acc. no. X76903.1) revealed their entire similarity. It was inferred from the tree that the investigated protozoan samples occupied distinct phylogenetic positions and were suitable for the vicinity of various clinical isolates that were isolated from several locations worldwide. However, the rRNA-based tree provided ample genetic diversity with more effective discrimination compared with the other used loci.

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Section: Phylogenetic Tree Constructionmentioning

confidence: 99%

Genetic diversity and phylogenetic positioning of Entamoeba histolytica isolates from stool samples of patients from few Hospitals at Diyala governorate

Mohamed,

Ahmed,

Mohsin

2024

JANS

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“…Given its pivotal role in subsequent molecular biology experiments, the extensively utilized DNA sequencing methodologies demand vigilant attention to any nucleic acid variations. Owing to its feasibility and cost-effectiveness, Sanger DNA sequencing has found extensive application in pivotal domains other than clinical analysis, spanning biodiversity [14], animal production [15], microbial pathogenesis [16], medical genetics [17], and other recent applications, such as in silico computations [18]. Despite having developed multiple approaches to next-generation sequencing, Sanger biochemistry continues to serve as the foundation for sequencing production in numerous post-PCR genotyping protocols [19].…”

Section: Introductionmentioning

confidence: 99%

Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis

Al-Shuhaib,

Hashim

2023

Journal of Genetic Engineering and Biotechnology

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Background Sanger dideoxy sequencing is vital in clinical analysis due to its accuracy, ability to analyze genetic markers like SNPs and STRs, capability to generate reliable DNA profiles, and its role in resolving complex clinical cases. The precision and robustness of Sanger sequencing contribute significantly to the scientific basis of clinical investigations. Main body of the abstract Though the reading of chromatograms seems to be a routine step, many errors conducted in PCR may lead to consequent limitations in the readings of AGCT peaks. These errors are possibly associated with improper DNA amplification and its subsequent interpretation of DNA sequencing files, such as noisy peaks, artifacts, and confusion between double-peak technical errors, heterozygosity, and double infection potentials. Thus, it is not feasible to read nucleic acid sequences without giving serious attention to these technical problems. To ensure the accuracy of DNA sequencing outcomes, it is also imperative to detect and rectify technical challenges that may lead to misinterpretation of the DNA sequence, resulting in errors and incongruities in subsequent analyses. Short conclusion This overview sheds light on prominent technical concerns that can emerge prior to and during the interpretation of DNA chromatograms in Sanger sequencing, along with offering strategies to address them effectively. The significance of identifying and tackling these technical limitations during the chromatogram analysis is underscored in this review. Recognizing these concerns can aid in enhancing the quality of downstream analyses for Sanger sequencing results, which holds notable improvement in accuracy, reliability, and ability to provide crucial genetic information in clinical analysis.

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The emergence of a novel SARS-CoV-2 variant with higher efficiency of binding with the human host cell receptors in Iraqi subjects

Al-Mousawi,

Musafer,

Alattabi

et al. 2023

Biologia

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The emergence of novel Iranian variants in sheeppox and goatpox viral envelope proteins with remarkably altered putative binding affinities with the host receptor

Cited by 4 publications

References 47 publications

Genetic diversity and phylogenetic positioning of Entamoeba histolytica isolates from stool samples of patients from few Hospitals at Diyala governorate

Genetic diversity and phylogenetic positioning of Entamoeba histolytica isolates from stool samples of patients from few Hospitals at Diyala governorate

Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis

The emergence of a novel SARS-CoV-2 variant with higher efficiency of binding with the human host cell receptors in Iraqi subjects

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