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Related Concept Videos

Stages of Infection01:26

Stages of Infection

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Stages of infection describe what happens to a susceptible host once a pathogen invades the human body. The stages of infection are incubation, prodromal, illness, stage of decline, and convalescence. The incubation stage is the period from exposure to a pathogen until symptoms start. The infected person is unaware of impending illness as the pathogens grow and multiply within the body. The duration may vary depending on the type of infection. The incubation period of measles averages ten to...
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Viral Mutations00:36

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A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
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Viral Recombination00:57

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Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
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Pneumonia II: Pathophysiology01:29

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Gene Evolution - Fast or Slow?02:05

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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Exon Recombination02:32

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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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A Mouse Model for the Transition of Streptococcus pneumoniae from Colonizer to Pathogen upon Viral Co-Infection Recapitulates Age-Exacerbated Illness
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Intra-host evolution during SARS-CoV-2 prolonged infection.

Carolina M Voloch1, Ronaldo da Silva Francisco2, Luiz G P de Almeida2

  • 1Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-902, Brazil.

Virus Evolution
|October 13, 2021
PubMed
Summary
This summary is machine-generated.

Prolonged SARS-CoV-2 infection involves increasing intra-host viral diversity, driven by host immunity. This evolution may explain the emergence of immune-resistant variants during the COVID-19 pandemic.

Keywords:
COVID-19RNA-editing enzymesSpike genehelicase geneprolonged infection

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Area of Science:

  • Virology
  • Genomics
  • Immunology

Background:

  • Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections pose challenges to controlling the COVID-19 pandemic.
  • The mechanisms behind prolonged SARS-CoV-2 infection and viral persistence remain unclear.
  • Intra-host single nucleotide variants (iSNVs) may contribute to viral persistence and the emergence of concerning mutations.

Purpose of the Study:

  • To investigate the intra-host evolution of SARS-CoV-2 during prolonged infections.
  • To understand the role of iSNVs in viral persistence and host-pathogen interactions.

Main Methods:

  • Whole-genome sequencing of SARS-CoV-2 from 33 patients with prolonged RT-PCR positivity (average 18 days).
  • Samples were collected at two different time points during the infection.
  • Phylogenetic, populational, and computational analyses were performed on viral sequences.

Main Results:

  • Elevated within-host genomic diversity was observed in later samples, correlating with lower viral loads (higher Ct values).
  • Differential accumulation of missense variants in key proteins (Spike, helicase) and longitudinal acquisition of iSNVs in Spike protein were detected.
  • A distinct mutational profile, characterized by increased A→U and decreased G→A signatures, suggested host innate immune responses.

Conclusions:

  • Host innate immunity plays a significant role in shaping intra-host SARS-CoV-2 diversity during prolonged infections.
  • The observed viral evolution dynamics may contribute to the emergence of variants resistant to host immune responses.
  • Findings offer insights into host-pathogen interactions and potential mechanisms for variant spread in the COVID-19 pandemic.