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Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Related Experiment Video

Updated: May 25, 2025

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SARS-CoV-2 XEC: A Genome-Based Survey.

Fabio Scarpa1, Francesco Branda2, Giancarlo Ceccarelli3

  • 1Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy.

Microorganisms
|February 26, 2025
PubMed
Summary

A novel SARS-CoV-2 recombinant, XEC, emerged from lineages KP.3.3 and KS.1.1. Despite mutations for immune evasion, XEC shows limited spread and appears to be an evolutionary dead-end.

Keywords:
SARS-CoV-2XEC recombinantevolutionary trajectorygenetic diversitygenomic surveillancepandemic monitoringphylogenomic analysisspike protein mutationsviral recombination

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Area of Science:

  • Virology
  • Genomics
  • Molecular Biology

Background:

  • Recombination is a key driver in the evolution of SARS-CoV-2 variants.
  • The emergence of novel recombinant lineages necessitates detailed genomic and structural characterization.

Purpose of the Study:

  • To perform a comprehensive genomic and structural analysis of the SARS-CoV-2 XEC recombinant.
  • To understand the evolutionary trajectory and public health implications of XEC.

Main Methods:

  • Phylogenomic analyses to determine evolutionary relationships.
  • Identification of genomic breakpoints and mutational analysis.
  • Bayesian Skyline Plot analysis for population dynamics.

Main Results:

  • XEC is a recombinant of KP.3.3 and KS.1.1, with a breakpoint in the spike protein gene.
  • Mutations in XEC are associated with immune evasion and receptor binding, but lack novel changes in conserved epitopes.
  • XEC exhibits limited geographical spread, low genetic variability, and a stable but declining population size, suggesting an evolutionary dead-end.

Conclusions:

  • XEC, while possessing some immune-evasive mutations, is unlikely to become a significant public health threat.
  • Ongoing genomic surveillance is crucial for monitoring the emergence and characteristics of viral recombinants.
  • Distinguishing between variants of concern and those with limited epidemiological impact is vital.