Molecular characterization of echovirus 13 uncovering high genetic diversity and identification of new genotypes in Pakistan

Abstract

Echovirus 13 (E-13) is reported worldwide and is mostly related to aseptic meningitis but it is also isolated from cases of acute flaccid paralysis (AFP). Unfortunately, all studies conducted on non polio enterovirus in Pakistan only confirm E-13 isolation based on microneutralization assay but there is lack of molecular epidemiological data on this serotype. In this study, 113 stool samples were collected from AFP patients during 2008–2010. An enterovirus primer mediated real-time reverse transcriptase polymerase chain reaction, a standard microneutralization assay and sequencing of viral protein 1 gene (VP1) identified the predominant serotype E-13. For molecular characterization, genetic relationship between 12 clinical isolates of echovirus 13 was investigated by partial sequencing of viral protein 1 gene. These strains, combined with related sequences from GenBank were divided phylogenetically into two different genogroups A and B (>30% divergence) and were found genetically distinct from the circulating strains in the world. Additionally, phylogenic grouping pattern revealed that the study strains clustered into three distinct subgroups (A3, A7 and B3) having >23% nucleotide divergence representing three new genotypes. The genotype A7 seems to be restricted geographically. In conclusion, the current study provides an overview of the molecular epidemiology and evolution of E-13 in the country. This study strongly suggests that enterovirus surveillance system should be established in the country to determine the temporal and geographical trends and disease pattern of different enterovirus serotypes in the community.