Related Experiment Video

Updated: Nov 8, 2025

Author Spotlight: Characterizing DNA Replication of Pathogenic Repeats to Uncover Mechanisms of Replication Fork Stalling and Expansion
05:22

Author Spotlight: Characterizing DNA Replication of Pathogenic Repeats to Uncover Mechanisms of Replication Fork Stalling and Expansion

Published on: September 13, 2024

999

Phylogenetic molecular evolution and recombination analysis of complete genome of human parechovirus in Thailand

Thaweesak Chieochansin1,2, Jiratchaya Puenpa3, Yong Poovorawan3

  • 1Siriraj Center of Research Excellence for Cancer Immunotherapy, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Prannok Road, Wanglang, Bangkok Noi, Bangkok, 11170, Thailand. thaweesak.chi@mahidol.ac.th.

Scientific Reports
|April 22, 2021
PubMed

Insights

Human parechovirus (HPeV) shows high genetic diversity due to recombination. This study analyzed HPeV complete genomes from Thailand, revealing a novel recombinant strain, B1091/HPeV14/2011, with implications for future treatments.

Area of Science:

  • Virology
  • Molecular Evolution
  • Genomics

Background:

  • Human parechovirus (HPeV) is a picornavirus causing diverse symptoms, including respiratory, gastrointestinal, and neurological complications.
  • High genetic diversity in HPeV is attributed to its RNA-dependent RNA polymerase (RdRp) lacking proofreading and frequent recombination.
  • Limited data exists on the molecular evolutionary aspects of the complete HPeV genome.

Purpose of the Study:

  • To investigate the phylogenetic, molecular evolution, and recombination patterns of the complete HPeV genome.
  • To analyze HPeV strains isolated in Thailand between 2009 and 2012.
  • To understand the evolutionary dynamics driving HPeV diversity.

Main Methods:

  • Complete genome amplification of 58 HPeV-positive samples using in-house designed primers.
  • Generation of ten overlapping PCR fragments for comprehensive genomic analysis.
  • Direct Sanger sequencing and phylogenetic analysis (whole-genome and VP1), alongside Bootscan analysis for recombination detection.

Main Results:

  • Phylogenetic analysis of complete genomes and VP1 regions generally aligned, confirming established genotypes.
  • A specific strain, B1091/HPeV14/2011, showed discordant phylogenetic placement between whole-genome and VP1 analyses.
  • Bootscan analysis identified B1091/HPeV14/2011 as a recombinant virus, with VP1 from HPeV14 and the remaining genome from HPeV1B.

Conclusions:

  • The study provides crucial insights into the molecular evolution and recombination of HPeV genomes.
  • Identification of a novel recombinant strain highlights the ongoing evolution of HPeV.
  • Findings can accelerate the development of targeted treatment and prophylactic strategies against HPeV infections.

More Related Videos

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins09:40

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

12.4K
Using a Pan-Viral Microarray Assay Virochip to Screen Clinical Samples for Viral Pathogens13:45

Using a Pan-Viral Microarray Assay Virochip to Screen Clinical Samples for Viral Pathogens

Published on: April 27, 2011

19.2K

Related Concept Videos

Viral Mutations00:36

Viral Mutations

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...
36.8K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
6.5K
Viral Recombination00:57

Viral Recombination

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.
24.3K
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
6.3K