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

Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases
Yu WangWenjie Tan

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 hete...Continue Reading

References

Jan 22, 2005·Current Opinion in Pediatrics·Jean E Klig, Nikhil B Shah
Apr 10, 2008·PLoS Pathogens·Stacy R FinkbeinerDavid Wang
Feb 13, 2009·Journal of Virology·Joseph G VictoriaEric Delwart
Sep 30, 2009·PloS One·Appolinaire DjikengDavid J Spiro
Dec 26, 2009·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Daniele FocosiMario Petrini
Feb 23, 2010·Virology·Beatrix CoetzeeJohan T Burger
Sep 9, 2011·Journal of Virology·Tongling ShanEric Delwart
Sep 13, 2011·PLoS Pathogens·Tung G PhanEric L Delwart
Jun 22, 2012·PloS One·Kristine M WylieGregory A Storch
Apr 15, 2014·Journal of Infection in Developing Countries·Zhen LinAlberto J León
May 6, 2014·Veterinary Microbiology·Terry Fei Fan NgEric Delwart
Nov 19, 2014·American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons·J C YoungR G Collman
Feb 13, 2015·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Terry NolanSylvia Taylor
Apr 14, 2015·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Jan ZollWillem J G Melchers
Aug 8, 2015·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Carrie L ByingtonAndrew T Pavia

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Citations

Mar 25, 2017·Critical Reviews in Microbiology·Lisa BillardSophie Vallet
Mar 21, 2017·Nature Reviews. Microbiology·Wing Ho ManDebby Bogaert
Feb 2, 2018·Frontiers in Immunology·Sudhanshu ShekharFernanda Cristina Petersen
May 13, 2018·BMC Infectious Diseases·Lili XuZhengde Xie
Oct 7, 2017·Current Medicinal Chemistry·Giulia FreerMauro Pistello
Jul 5, 2019·Clinical Microbiology Reviews·Marianne F L van den BroekSarah Lebeer
Sep 24, 2020·BMC Infectious Diseases·Mohammad T Al BatainehQutayba Hamid
Sep 23, 2016·American Journal of Respiratory and Critical Care Medicine·Alicia B MitchellAllan R Glanville
Feb 15, 2020·BMC Pulmonary Medicine·Raquel NazarethPaulo Paixão
Jul 28, 2020·Frontiers in Bioengineering and Biotechnology·Yang LiXuejun Ma
Nov 30, 2017·Emerging Topics in Life Sciences·Geraint B Rogers
May 31, 2021·Trends in Microbiology·Andrea IorioLorenza Putignani
Jun 25, 2021·Journal of Medical Microbiology·Matthew Flynn, James Dooley
Dec 7, 2021·Frontiers in Medicine·Kotakonda ArunasriSisinthy Shivaji

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Datasets Mentioned

BETA
SRR2040553
SRR2040557

Methods Mentioned

BETA
Illumina sequencing
PCR

Software Mentioned

SOAP Aligner
SAS
- Toolkit
SOAP no
MEGA
FASTX
MAFFT
CLC Genomic Workbench

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