Genetic characterization of human adenoviruses in patients using metagenomic next-generation sequencing in Hubei, China, from 2018 to 2019

Bin Fang; Juan Lai; Yongfeng Liu; Tian-Tian Yu; Xiao Yu; Xiang Li; Lijun Dong; Xin Zhang; Wei Yang; Qin Yan; Lei Sun; Lin-Lin Liu

doi:10.3389/fmicb.2023.1153728

Genetic characterization of human adenoviruses in patients using metagenomic next-generation sequencing in Hubei, China, from 2018 to 2019

Front Microbiol. 2023 Mar 16:14:1153728. doi: 10.3389/fmicb.2023.1153728. eCollection 2023.

Authors

Bin Fang¹, Juan Lai², Yongfeng Liu², Tian-Tian Yu³, Xiao Yu¹, Xiang Li¹, Lijun Dong², Xin Zhang², Wei Yang², Qin Yan², Lei Sun², Lin-Lin Liu¹

Affiliations

¹ Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China.
² GeneMind Biosciences Company Limited, Shenzhen, China.
³ School of Public Health, Department of Nutritional Hygiene and Toxicology, Wuhan University of Science and Technology, Wuhan, China.

Abstract

Objectives: This study aimed to characterize the genomic epidemiology of human adenoviruses (HAdVs) in Hubei, China, using metagenomic next-generation sequencing (mNGS).

Methods: In total, 25 HAdV-positive samples collected from 21 pediatric patients were sequenced and subjected to mNGS using the NextSeq 550 and GenoLab M sequencing platforms. The metagenomic data were assembled de novo for molecular typing, phylogenetic and recombination analyzes.

Results: We assembled 50 HAdV genomes, 88% (22/25) genomes from GenoLab M, and 84% (21/25) genomes from NextSeq 550 have perfect alignments to reference genomes with greater than 90%. The most fully assembled 25 genomes were categorized into 7 HAdV genotypes, the most abundant of which were HAdV-B3 (9/25) and HAdV-C2 (6/25). Phylogenetic analyzes revealed that the newly isolated HAdV-B3 strains diverged into separate clusters according to their genotypes. Vigilance is needed that HAdV-B3 isolates have begun to form new distinct clusters. High nucleotide identity was observed in the whole genome level within the same HAdV genotypes, while marked differences of three capsid genes across HAdV genotypes were noted. The high nucleotide diversity regions were concordant with the reported hypervariable regions. Further, three recombinant strains were identified: S64 and S71 originated from the parental strains HAdV-B14 and HAdV-B11, and S28 originated from HAdV-C1, HAdV-C5, and HAdV-CBJ113. GenoLab M and NextSeq 550 showed comparable performance with respect to data yield, duplication rate, human ratio, and assembly completeness.

Conclusion: The sequencing quality and assembly accuracy showed that mNGS assembled genomes can be used for subsequently HAdV genotyping and genomic characterization. The high nucleotide diversity of capsid genes and high frequency of recombination events has highlighted the necessity for HAdV epidemiological surveillance in China.

Keywords: genetic characterization; human adenovirus; metagenomic next-generation sequencing; phylogenetic analysis; recombination analysis.