Complete genome sequence of a multi-recombinant echovirus 6 strain isolated from CSF in Ahvaz, Southwestern Iran

Samaneh Abbasi; Manoochehr Makvandi; Ali Teimoori; Alireza Samarbaf-Zadeh

doi:10.1016/j.jcma.2017.06.026

Complete genome sequence of a multi-recombinant echovirus 6 strain isolated from CSF in Ahvaz, Southwestern Iran

J Chin Med Assoc. 2018 Apr;81(4):340-347. doi: 10.1016/j.jcma.2017.06.026. Epub 2018 Feb 21.

Authors

Samaneh Abbasi¹, Manoochehr Makvandi², Ali Teimoori¹, Alireza Samarbaf-Zadeh¹

Affiliations

¹ Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Department of Virology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
² Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Department of Virology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. Electronic address: manoochehrmakvandi29@yahoo.com.

PMID: 29475814
DOI: 10.1016/j.jcma.2017.06.026

Abstract

Background: Echovirus 6 (E6), is one of the main enteroviral serotypes, was initially isolated from patients with aseptic meningitis (AM) and is a major cause of hospitalization among children and adults worldwide.

Methods: A cerebrospinal fluid (CSF) sample was collected from patient with clinically suspected aseptic meningitis (AM) in August 2011. Following detection of a virus and subsequent virus serotyping, the whole genome sequence was determined. The sequence of the VP1 region of the isolated strain E6 RA/E6/Ahvaz/Iran/2011 showed 79% (>75%) nucleotide and 94% (>85%) amino acid homology with prototype strain D'Amori. The isolated strain was identified as an E6 serotype. A specimen was cultured in a human rhabdomyosarcoma (RD) cell line. Following propagation, the virus was further analyzed using the plaque assay technique, reverse transcription PCR (RT-PCR), rapid amplification of CDNA ends (RACE), TA cloning, sequencing, phylogenetic analysis, Simplot and boot scanning analyses (ver. 3.5) were applied to find evidence of recombination in the isolated strain.

Results: The isolated Echo6 strain RA/E6/Ahvaz/Iran/2011 has been recorded in GenBank with a partial and complete genome accession numbers (KX619440) (KX198605), respectively. The complete genomic sequence was 7435 nt, with a 742 bp 5' UTR, 117 bp 3' UTR, and an open reading frame (ORF) encoding a polypeptide of 2191 amino acids. The nucleotide analysis of the VP1 and structural genomic regions of the isolated strain showed high similarity with strain E6-10887-99 isolated from patient with facial nerve paresis in Russia in 1999. The recombinations evidence were observed in the isolated strain E6 RA/E6/Ahvaz/Iran/2011 and found to have a high levels of inter-serotypic exchanges in 2C and 3A-3C genomic regions with Echovirus13 and Echovirus14, respectively.

Conclusion: Full genome sequence analysis of enteroviral is required to understand the epidemiological pattern and to evaluate the new enterovirus circulating in community.

Keywords: Enterovirus B; Iran; Molecular sequence data; RD cells; Recombination.

MeSH terms

Capsid Proteins / genetics
Cell Line, Tumor
Echovirus 6, Human / classification
Echovirus 6, Human / genetics*
Echovirus 6, Human / isolation & purification
Female
Humans
Meningitis, Aseptic / cerebrospinal fluid
Meningitis, Aseptic / virology*
Whole Genome Sequencing*

Substances

Capsid Proteins