Genetic characterizations and molecular epidemiology of human echovirus 30 isolated from Ningxia, China

Abstract

In October 2017, a small outbreak of echovirus 30 (E30) associated with aseptic meningitis in nine cases occurred at a primary school in the Ningxia Hui Autonomous Region. That year, we observed a significant increase in E30 levels in an acute flaccid paralysis (AFP) case surveillance system. To investigate their phylogenetic relationships, we determined the whole genomic sequences of 12 strains isolated from aseptic meningitis cases, AFP cases, and healthy children. We found that the E30 strains circulating in Ningxia belong to two lineages (H and J). The strains isolated in 2010, 2012, and 2016 belonged to the H lineage. In 2017, a new lineage, J, emerged as the dominant lineage. Phylogenetic trees were constructed based on the whole genome and P1, P2, and P3 regions; clustering with other types of enterovirus species B was found, suggesting that recombination events had occurred. The recombination sites were mainly in regions 2B, 2C, and 3D. This study confirmed that the E30 strains in Ningxia in 2010, 2012, and 2016 had different recombination patterns and were recombined with different enteroviruses. The 2017 epidemic E30 originated from another new lineage with a complex recombination pattern and formed an independent transmission chain in Ningxia.

Keywords

• Echovirus 30 (E30)
• Complete genome sequence
• Molecular epidemiology