Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique

doi:10.1007/s11427-016-0244-8

. 2017 Mar;60(3):279-286.

doi: 10.1007/s11427-016-0244-8. Epub 2016 Dec 2.

Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique

Xiaohui Zou¹, Guangpeng Tang², Xiang Zhao¹, Yan Huang², Tao Chen¹, Mingyu Lei², Wenbing Chen¹, Lei Yang¹, Wenfei Zhu¹, Li Zhuang², Jing Yang¹, Zhaomin Feng¹, Dayan Wang¹, Dingming Wang³, Yuelong Shu⁴

Affiliations

¹ National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
² Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China.
³ Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China. cfswdm@gzscdc.org.
⁴ National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China. yshu@cnic.org.cn.

PMID: 27921234
PMCID: PMC7088591
DOI: 10.1007/s11427-016-0244-8

Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique

Xiaohui Zou et al. Sci China Life Sci. 2017 Mar.

. 2017 Mar;60(3):279-286.

doi: 10.1007/s11427-016-0244-8. Epub 2016 Dec 2.

Authors

Affiliations

¹ National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
² Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China.
³ Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China. cfswdm@gzscdc.org.
⁴ National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China. yshu@cnic.org.cn.

PMID: 27921234
PMCID: PMC7088591
DOI: 10.1007/s11427-016-0244-8

Abstract

Many viruses can cause respiratory diseases in humans. Although great advances have been achieved in methods of diagnosis, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province, China. A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS. An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples. Human rhinovirus C was the virus most frequently detected and was identified in seven samples. Human measles virus, adenovirus B 55 and coxsackievirus A10 were also identified. Metagenomic sequencing also provided virus genomic sequences, which enabled genotype characterization and phylogenetic analysis. For cases of multiple infection, metagenomic sequencing afforded information regarding the quantity of each virus in the sample, which could be used to evaluate each viruses' role in the disease. Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.

Keywords: metagenomics; next-generation sequencing; unexplained pneumonia.

PubMed Disclaimer

Cited by

A Case of Adult Epstein-Barr Virus-Associated Pneumonia with Multiple Cavitary Pulmonary Lesions Confirmed by Lung Biopsy mNGS: A Case Report.
Zhuang S, Yu X, Zhang Y, Chen X. Zhuang S, et al. Infect Drug Resist. 2023 Dec 7;16:7507-7513. doi: 10.2147/IDR.S434929. eCollection 2023. Infect Drug Resist. 2023. PMID: 38089957 Free PMC article.
Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.
Sandybayev N, Beloussov V, Strochkov V, Solomadin M, Granica J, Yegorov S. Sandybayev N, et al. Microorganisms. 2022 Nov 24;10(12):2327. doi: 10.3390/microorganisms10122327. Microorganisms. 2022. PMID: 36557580 Free PMC article. Review.
Advantages and challenges of metagenomic sequencing for the diagnosis of pulmonary infectious diseases.
Chen Y, Fan LC, Chai YH, Xu JF. Chen Y, et al. Clin Respir J. 2022 Oct;16(10):646-656. doi: 10.1111/crj.13538. Epub 2022 Sep 6. Clin Respir J. 2022. PMID: 36068680 Free PMC article. Review.
A Retrospective Paired Comparison Between Untargeted Next Generation Sequencing and Conventional Microbiology Tests With Wisely Chosen Metagenomic Sequencing Positive Criteria.
Qin H, Peng J, Liu L, Wu J, Pan L, Huang X, Huang M, Qiu H, Du B; China Critical Care Clinical Trials Group (CCCCTG). Qin H, et al. Front Med (Lausanne). 2021 Oct 6;8:686247. doi: 10.3389/fmed.2021.686247. eCollection 2021. Front Med (Lausanne). 2021. PMID: 34692715 Free PMC article.
Inactivation and risk control of pathogenic microorganisms in municipal sludge treatment: A review.
Li M, Song G, Liu R, Huang X, Liu H. Li M, et al. Front Environ Sci Eng. 2022;16(6):70. doi: 10.1007/s11783-021-1504-5. Epub 2021 Sep 25. Front Environ Sci Eng. 2022. PMID: 34608423 Free PMC article. Review.

See all "Cited by" articles

References

1. Assiri A., McGeer A., Perl T.M., Price C.S., Al Rabeeah A.A., Cummings D.A.T., Alabdullatif Z.N., Assad M., Almulhim A., Makhdoom H., Madani H., Alhakeem R., Al-Tawfiq J.A., Cotten M., Watson S.J., Kellam P., Zumla A.I., Memish Z.A., Memish Z.A. Hospital outbreak of middle east respiratory syndrome coronavirus. N Engl J Med. 2013;369:407–416. doi: 10.1056/NEJMoa1306742. - DOI - PMC - PubMed
1. Briese T., Renwick N., Venter M., Jarman R.G., Ghosh D., Köndgen S., Shrestha S.K., Hoegh A.M., Casas I., Adjogoua E.V., Akoua-Koffi C., Myint K.S., Williams D.T., Chidlow G. v. d., Berg R., Calvo C., Koch O., Palacios G., Kapoor V., Villari J., Dominguez S.R., Holmes K.V., Harnett G., Smith D., Mackenzie J.S., Ellerbrok H., Schweiger B., Schønning K., Chadha M.S., Leendertz F.H., Mishra A.C., Gibbons R.V., Holmes E.C., Lipkin W.I. Global distribution of novel rhinovirus genotype. Emerg Infect Dis. 2008;14:944–947. doi: 10.3201/eid1406.080271. - DOI - PMC - PubMed
1. Dabisch-Ruthe M., Vollmer T., Adams O., Knabbe C., Dreier J. Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay. BMC Infect Dis. 2012;12:163. doi: 10.1186/1471-2334-12-163. - DOI - PMC - PubMed
1. Ding Y., Wang H., Shen H., Li Z., Geng J., Han H., Cai J., Li X., Kang W., Weng D., Lu Y., Wu D., He L., Yao K. The clinical pathology of severe acute respiratory syndrome (SARS): a report from China. J Pathol. 2003;200:282–289. doi: 10.1002/path.1440. - DOI - PMC - PubMed
1. Du J., Yang L., Ren X., Zhang J., Dong J., Sun L., Zhu Y., Yang F., Zhang S., Wu Z., Jin Q. Genetic diversity of coronaviruses in Miniopterus fuliginosus bats. Sci China Life Sci. 2016;59:604–614. doi: 10.1007/s11427-016-5039-0. - DOI - PMC - PubMed

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

LinkOut - more resources

Full Text Sources
Other Literature Sources
- scite Smart Citations

[1] Assiri A., McGeer A., Perl T.M., Price C.S., Al Rabeeah A.A., Cummings D.A.T., Alabdullatif Z.N., Assad M., Almulhim A., Makhdoom H., Madani H., Alhakeem R., Al-Tawfiq J.A., Cotten M., Watson S.J., Kellam P., Zumla A.I., Memish Z.A., Memish Z.A. Hospital outbreak of middle east respiratory syndrome coronavirus. N Engl J Med. 2013;369:407–416. doi: 10.1056/NEJMoa1306742. - DOI - PMC - PubMed

[2] Assiri A., McGeer A., Perl T.M., Price C.S., Al Rabeeah A.A., Cummings D.A.T., Alabdullatif Z.N., Assad M., Almulhim A., Makhdoom H., Madani H., Alhakeem R., Al-Tawfiq J.A., Cotten M., Watson S.J., Kellam P., Zumla A.I., Memish Z.A., Memish Z.A. Hospital outbreak of middle east respiratory syndrome coronavirus. N Engl J Med. 2013;369:407–416. doi: 10.1056/NEJMoa1306742. - DOI - PMC - PubMed

[3] Briese T., Renwick N., Venter M., Jarman R.G., Ghosh D., Köndgen S., Shrestha S.K., Hoegh A.M., Casas I., Adjogoua E.V., Akoua-Koffi C., Myint K.S., Williams D.T., Chidlow G. v. d., Berg R., Calvo C., Koch O., Palacios G., Kapoor V., Villari J., Dominguez S.R., Holmes K.V., Harnett G., Smith D., Mackenzie J.S., Ellerbrok H., Schweiger B., Schønning K., Chadha M.S., Leendertz F.H., Mishra A.C., Gibbons R.V., Holmes E.C., Lipkin W.I. Global distribution of novel rhinovirus genotype. Emerg Infect Dis. 2008;14:944–947. doi: 10.3201/eid1406.080271. - DOI - PMC - PubMed

[4] Briese T., Renwick N., Venter M., Jarman R.G., Ghosh D., Köndgen S., Shrestha S.K., Hoegh A.M., Casas I., Adjogoua E.V., Akoua-Koffi C., Myint K.S., Williams D.T., Chidlow G. v. d., Berg R., Calvo C., Koch O., Palacios G., Kapoor V., Villari J., Dominguez S.R., Holmes K.V., Harnett G., Smith D., Mackenzie J.S., Ellerbrok H., Schweiger B., Schønning K., Chadha M.S., Leendertz F.H., Mishra A.C., Gibbons R.V., Holmes E.C., Lipkin W.I. Global distribution of novel rhinovirus genotype. Emerg Infect Dis. 2008;14:944–947. doi: 10.3201/eid1406.080271. - DOI - PMC - PubMed

[5] Dabisch-Ruthe M., Vollmer T., Adams O., Knabbe C., Dreier J. Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay. BMC Infect Dis. 2012;12:163. doi: 10.1186/1471-2334-12-163. - DOI - PMC - PubMed

[6] Dabisch-Ruthe M., Vollmer T., Adams O., Knabbe C., Dreier J. Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay. BMC Infect Dis. 2012;12:163. doi: 10.1186/1471-2334-12-163. - DOI - PMC - PubMed

[7] Ding Y., Wang H., Shen H., Li Z., Geng J., Han H., Cai J., Li X., Kang W., Weng D., Lu Y., Wu D., He L., Yao K. The clinical pathology of severe acute respiratory syndrome (SARS): a report from China. J Pathol. 2003;200:282–289. doi: 10.1002/path.1440. - DOI - PMC - PubMed

[8] Ding Y., Wang H., Shen H., Li Z., Geng J., Han H., Cai J., Li X., Kang W., Weng D., Lu Y., Wu D., He L., Yao K. The clinical pathology of severe acute respiratory syndrome (SARS): a report from China. J Pathol. 2003;200:282–289. doi: 10.1002/path.1440. - DOI - PMC - PubMed

[9] Du J., Yang L., Ren X., Zhang J., Dong J., Sun L., Zhu Y., Yang F., Zhang S., Wu Z., Jin Q. Genetic diversity of coronaviruses in Miniopterus fuliginosus bats. Sci China Life Sci. 2016;59:604–614. doi: 10.1007/s11427-016-5039-0. - DOI - PMC - PubMed

[10] Du J., Yang L., Ren X., Zhang J., Dong J., Sun L., Zhu Y., Yang F., Zhang S., Wu Z., Jin Q. Genetic diversity of coronaviruses in Miniopterus fuliginosus bats. Sci China Life Sci. 2016;59:604–614. doi: 10.1007/s11427-016-5039-0. - DOI - PMC - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique

Affiliations

Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique

Authors

Affiliations

Abstract

Similar articles

Cited by

References

MeSH terms

LinkOut - more resources

Full Text Sources

Other Literature Sources