Next-generation Sequencing Study of Pathogens in Serum from Patients with Febrile Jaundice in Sierra Leone.

Yi Zhang; Fei YE; Lian Xu Xia; Ling Wei Zhu; Idrissa Laybohr Kamara; Ke Qiang Huang; Yong Zhang; Jun Liu; Brima Kargbo; Ji Wang; Mi Fang Liang; Jing Dong Song; Xue Jun MA; Gui Zhen WU

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Next-generation Sequencing Study of Pathogens in Serum from Patients with Febrile Jaundice in Sierra Leone.

Author: Yi ZHANG ^{1
,

2} ; Fei YE ^{1
,

2} ; Lian Xu XIA ^{3
,

4} ; Ling Wei ZHU ^{3
,

5} ; Idrissa Laybohr KAMARA ⁶ ; Ke Qiang HUANG ⁷ ; Yong ZHANG ⁷ ; Jun LIU ⁷ ; Brima KARGBO ⁸ ; Ji WANG ⁷ ; Mi Fang LIANG ⁷ ; Jing Dong SONG ^{1
,

2} ; Xue Jun MA ⁹ ; Gui Zhen WU ⁷
Author Information

1. National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
2. Sierra Leone-China Friendship Biological Safety Laboratory, Freetown, Sierra-Leone.
3. Sierra Leone-China Friendship Biological Safety Laboratory, Freetown, Sierra-Leone
4. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
5. Chinese Center for Disease Control and Prevention, Beijing 102206, China.
6. Sierra Leone-China Friendship Biological Safety Laboratory, Freetown, Sierra-Leone.
7. National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
8. Sierra Leone Ministry of Health and Sanitation Freetown, Sierra-Leone.
9. Key Laboratory of Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
Publication Type:Journal Article
Keywords: Febrile jaundice; Next-generation sequencing; Sierra Leone; Virus
MeSH: Adolescent; Adult; Case-Control Studies; Female; Fever; epidemiology; virology; Humans; Jaundice; epidemiology; virology; Male; Sequence Analysis; Sierra Leone; epidemiology; Young Adult
From: Biomedical and Environmental Sciences 2019;32(5):363-370
CountryChina
Language:English
Abstract: OBJECTIVE:People in Western Africa suffer greatly from febrile jaundice, which is caused by a variety of pathogens. However, yellow fever virus (YFV) is the only pathogen under surveillance in Sierra Leone owing to the undeveloped medical and public health system there. Most of the results of YFV identification are negative. Elucidation of the pathogen spectrum is required to reduce the prevalence of febrile jaundice.
METHODS:In the present study, we used Ion Torrent semiconductor sequencing to profile the pathogen spectrum in archived YFV-negative sera from 96 patients in Sierra Leone who presented with unexplained febrile jaundice.
RESULTS:The most frequently identified sequencing reads belonged to the following pathogens: cytomegalovirus (89.58%), Epstein-Barr virus (55.21%), hepatitis C virus (34.38%), rhinovirus (28.13%), hepatitis A virus (20.83%), coxsackievirus (10.42%), Ebola virus (8.33%), hepatitis E virus (8.33%), lyssavirus (4.17%), leptospirosis (4.17%), chikungunya virus (2.08%), Crimean-Congo hemorrhagic fever virus (1.04%), and hepatitis B virus (1.04%).
CONCLUSION:The distribution of sequencing reads suggests a broader spectrum of pathogens for consideration in clinical diagnostics and epidemiological surveillance in Sierra Leone.