Epidemiology and Genetic Variabilities of Human Adenovirus Type 55 Reveal Relative Genome Stability Across Time and Geographic Space in China

Abstract

After the first outbreak in China in 2006, human adenovirus type 55 (HAdV-B55) has become a common pathogen causing life threatening pneumonia in northern China. However, HAdV-B55 infection has been rarely reported in southern China. Here, we collected throat swabs from 3,192 hospitalized children with acute respiratory disease (ARD) from May 2017 to April 2019 in Guangzhou, southern China, tested them for HAdV-B55 infection. Only one of 1,399 patients from May 2017 to April 2018 was HAdV-B55 positive; HAdV-B55 infections significantly increased with 10 of 1,792 patients testing positive since May 2018. HAdV-B55-267, isolated from a case of death, was sequenced for whole genomic analysis. Three other strains, HAdV-B55-Y16, -TY12, and -TY26, isolated earlier in patients from Shanxi, northern China, were also sequenced and analyzed. The four HAdV-B55 strains formed similar plaques, grew to similar titers, and resulted in similar typical cell pathogenic effects. HAdV-B55-267 formed a subclade with the prototype strain QS-DLL; strains HAdV-B55-Y16, -TY12, and -TY26 were closely related to strain QZ01. HAdV-B55 could be divided into two subtypes (HAdV-B55-a and -b) according to the presence or absence of the insertion of "CCATATCCGTGTT"; all strains isolated from China except for strain BJ01 belong to subtype b. HAdV-B55-267 had only one non-synonymous substitution comparing with strain QS-DLL, and all HAdV-B55 strains had highly conserved capsid proteins and few non-synonymous substitutions. This study suggests that HAdV-B55 is an important pathogen associated with ARD in Guangzhou since 2018, exhibiting the relative genome stability across time and geographic space in China.

Keywords: China; acute respiratory disease (ARD); comparative genomics; human adenovirus type 55; mutation; virulence.

FIGURE 1

Plaque-forming units in A549 cells infected with HAdV-B55. (A) The plaques of HAdV-B55-Shanxi-Y16, HAdV-B55-TY12, HAdV-B55-TY26, and HAdV-B55-267 isolates formed on day 12–14 post-infection of A549 cells. (B) The CPE phenotype of A549 cells 48 h after infection with HAdV-B55-Shanxi-Y16, HAdV-B55-TY12, HAdV-B55-TY26, and HAdV-B55-267 isolates at an MOI of 2 PFU/cell.

FIGURE 2

Transcriptional map and genomic organization of strain HAdV-B55-267. Early, intermediate, and late transcription units are designated by purple arrows, whereas orange color designates coding regions. Arrows show the transcriptional orientation of the coding transcripts.

FIGURE 3

Phylogenetic analysis of HAdV-B55. The phylogenetic trees based on the whole genomic sequence of adenovirus species B (A) as well as further genomic analysis aligned with the corresponding sequences (B), and hexon (C) or fiber (D) amino acid sequence. HAdV-B includes two subspecies, B1 and B2 (A). HAdV-B55 was divided into two subtypes (HAdV-B55a and HAdV-B55b) according to the presence or absence of the insertions of “CCATATCCGTGTT,” located in the non-coding region of the upstream of E1A poly(A) region (B). Bootstrapped, neighbor-joining trees with 1,000 replicates were constructed using the MEGA 5.05 software with default parameters, and a neighbor-joining method. Bootstrap numbers shown at the nodes indicate the percentages of the 1,000 replications producing the clade. The scale bar indicates the units of nucleotide substitutions per site. The strains sequenced or concerned in this study are labeled with red solid triangles and circles, respectively. The sequences used for phylogenic analysis were retrieved from GenBank and are summarized in Table 2.

FIGURE 4

The distribution of HAdV-B55 in China. The HAdV-B55 strains are labeled with solid red stars. The sequences were retrieved from GenBank and are summarized in Table 2.