A Large-Scale Outbreak of Echovirus 30 in Gansu Province of China in 2015 and Its Phylodynamic Characterization

Abstract

Background: Echovirus 30 (E-30) has been investigated and reported worldwide and is closely associated with several infectious diseases, including encephalitis; myocarditis; and hand, foot, and mouth disease. Although many E-30 outbreaks associated with encephalitis have been reported around the world, it was not reported in northwest China until 2015.

Methods: The clinical samples, including the feces, serum, throat swabs, and cerebrospinal fluid, were collected for this study and were analyzed for diagnosis. E-30 was isolated and processed according to the standard procedures. The epidemiological and phylogenetic analysis were performed to indicate the characteristics of E-30 outbreaks and phylodynamics of E-30 in China.

Results: The E-30 outbreaks affected nine towns of Gansu Province in 2015, starting at a school of Nancha town and spreading to other towns within 1 month. The epidemiological features showed that children aged 6-15 years were more susceptible to E-30 infection. The genotypes B and C cocirculated in the world, whereas the latter dominated the circulation of E-30 in China. The genome sequences of this outbreak present 99.3-100% similarity among these strains, indicating a genetic-linked aggregate outbreak of E-30 in this study. Two larger genetic diversity expansions and three small fluctuations of E-30 were observed from 1987 to 2016 in China, which revealed the oscillating patterns of E-30 in China. In addition, the coastal provinces of China, such as Zhejiang, Fujian, and Shandong, were initially infected, followed by other parts of the country. The E-30 strains isolated from mainland of China may have originated from Taiwan of China in the last century.

Conclusion: The highly similar E-30 genomes in this outbreak showed an aggregate outbreak of E-30, with nine towns affected. Our results suggested that, although the genetic diversity of E-30 oscillates, the dominant lineages of E-30 in China has complex genetic transmission. The coastal provinces played an important role in E-30 spread, which implied further development of effective countermeasures. This study provides a further insight into the E-30 outbreak and transmission and illustrates the importance of valuable surveillance in the future.

Keywords: echovirus 30 (E-30); encephalitis; molecular epidemiology; phylodynamics; phylogenetic analysis.

FIGURE 1

The overview of flow presented in this study.

FIGURE 2

The number of probable and laboratory-confirmed cases, as well as the isolated E-30 strains reported. The line chart shows the sentinel surveillance data of probable cases reported from June to August, 2015, corresponding to the left vertical coordinates. The bar chart represent the laboratory-confirmed cases and isolated E-30 strains corresponding to the right vertical coordinates.

FIGURE 3

The phylogenetic tree based on the entire VP1 genome of 36 representative strains isolated from 1958 (Bastianni strain of E-30 prototype) to 2016, with the E-21 strain used as an outgroup. The black triangle indicates the strains isolated from this study, and one strain was included for genotyping. The node numbers at each node show the bootstrap support constructed by neighbor-joining method with 1,000 bootstrap replicates. The letters on the right represent the genotypes of E-30, from genotypes A–C.

FIGURE 4

(A) The magnification based on the red box of (B) and the branches colored in red represent the E-30 isolates from the collective outbreak of this study in 2015. (B) The midpoint-rooted maximum likelihood phylogenetic tree of 446 E-30 strains isolated from China. The scale bars represent the substitutions per site per year. The lineages 1 and 2 show the transmission lineages of E-30 in China, including the timespan of E-30 strains.

FIGURE 5

(A) The relative genetic diversity of E-30 sequences in China. The black arrows show the important timescale that the relative genetic diversity of E-30 decrease signally. (B) The maximum clade credibility (MCC) phylogenetic tree based on the entire VP1 coding region in China and colored according to the locations of strains. The detailed information of isolates used in this study, including GenBank accession numbers, locations, and other essential information, are presented in Supplementary Table S1. The lineages 1 and 2 show the transmission lineages of E-30 in China, corresponding to Figure 4.