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Molecular characterization of the complete genome sequence of human Parechovirus 1 in Pakistan
1Department of Biosciences, COMSATS University (CUI), Park Road, Tarlai Kalan, Chak Shahzad, Islamabad, 45550, Pakistan.
Insights
This study sequenced two complete human parechovirus 1 (HPeV1) genomes from Pakistani children with gastroenteritis. Phylogenetic analysis revealed their global similarity, aiding future HPeV1 prevention and treatment strategies.
Area of Science:
- Virology
- Genomics
- Public Health
Background:
- Human parechoviruses (HPeVs) are common in young children.
- HPeV1 is the most prevalent genotype, causing respiratory and gastrointestinal illness.
- Previous Pakistani studies lacked complete HPeV genome data.
Purpose of the Study:
- To obtain and analyze the complete genomes of two HPeV1 strains from Pakistan.
- To understand the genetic relatedness and potential recombination of these HPeV1 strains.
Main Methods:
- Whole genome sequencing of HPeV1 strains (PAK419, PAK663) using Illumina HiSeq.
- Phylogenetic analysis of obtained genome sequences.
- SimPlot analysis to detect intergenotypic recombination.
Main Results:
- Complete genome sequences of two HPeV1 strains (PAK419, PAK663) were obtained.
- These strains showed 97% amino acid similarity to Dutch HPeV1 strains and clustered globally.
- An RGD motif crucial for host cell entry was identified in the VP1 protein.
- Evidence of intergenotypic recombination was found in the non-structural region.
Conclusions:
- The full genomes of these Pakistani HPeV1 strains provide valuable data.
- This information can contribute to developing preventive and treatment measures for HPeV infections.
Abstract:
Human parechoviruses (HPeVs) are highly common pathogens in children under 2 years of age. Of the 19 distinct HPeV genotypes identified worldwide, HPeV1 is still the most prevalent type associated with respiratory and gastrointestinal symptoms in infants and young children. Pakistan's previous studies have focused only on the detection and partial sequencing of HPeV genotypes. In the present study, we have obtained the complete genomes of 2 HPeV1 strains (PAK419 and PAK663) from children using NGS method on Illumina Hiseq Platform. These samples were collected from children suffering from acute gastroenteritis in Rawalpindi, Pakistan during 2016. The near complete genome sequences obtained for two HPeV1 strains (PAK419 and PAK663) consist of total 6877 nucleotides with a single, large open reading frame (ORF) encoding a polyprotein gene. Phylogenetic analysis showed that both HPeV1 strains exhibited maximum amino acid similarity (97 %) to HPeV1 strains from The Nederlands (2007-863, GQ183034) and clustered closely with this and with other HPeV1 strains isolated from other countries in the world (Ethiopia, Taiwan, Russia and Brazil). A motif of arginine-glycine-aspartic acid (RGD) in the VP1 (Outer capsid protein) C-terminus region that is suggested to help virus entry into the host cell also identified in PAK419 and PAK663. SimPlot analysis revealed that intergenotypic recombination events may have take place in the non-structural region between both HPeV1 strains (PAK419, PAK663), two major strains of HPeV1 (GQ183034 and MG873157) and four minor strains of HPeV4 (AM235750), HPeV7 (EU556224), HPeV15 (MN265386) and HPeV18 (KT879915). The full genome of HPeV1 strains characterized in the current study will provide complete information on these newly isolated strains for further preventive or treatment measures.
