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Clin Microbiol Infect. 2016 May;22(5):458.e1-9. doi: 10.1016/j.cmi.2016.01.006. Epub 2016 Jan 21.

Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China.

Author information

1
Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China.
2
State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China.
3
Key Laboratory of Major Diseases in Children and National Key Discipline of Paediatrics Capital Medical University, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.
4
Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China. Electronic address: tanwj28@163.com.

Abstract

Severe acute respiratory infection (SARI) in children is thought to be mainly caused by infection with various viruses, some of which have been well characterized; however, analyses of respiratory tract viromes among children with SARI versus those without are limited. In this study, nasopharyngeal swabs from children with and without SARI (135 versus 15) were collected in China between 2008 and 2010 and subjected to multiplex metagenomic analyses using a next-generation sequencing platform. The results show that members of the Paramyxoviridae, Coronaviridae, Parvoviridae, Orthomyxoviridae, Picornaviridae, Anelloviridae and Adenoviridae families represented the most abundant species identified (>50% genome coverage) in the respiratory tracts of children with SARI. The viral population found in the respiratory tracts of children without SARI was less diverse and mainly dominated by the Anelloviridae family with only a small proportion of common epidemic respiratory viruses. Several almost complete viral genomes were assembled, and the genetic diversity was determined among several samples based on next-generation sequencing. This research provides comprehensive mapping of the viromes of children with SARI and indicates high heterogeneity of known viruses present in the childhood respiratory tract, which may benefit the detection and prevention of respiratory disease.

KEYWORDS:

Children; metagenomics; next-generation sequencing; severe acute respiratory tract infection; virome

PMID:
26802214
DOI:
10.1016/j.cmi.2016.01.006
[Indexed for MEDLINE]
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