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

Biomedical and Environmental Sciences 2019年第5期32卷 363-370页

作者： ZHANG Yi YE Fei XIA Lian Xu ZHU Ling Wei IDRISSA Laybohr Kamara HUANG Ke Qiang ZHANG Yong LIU Jun brima kargbo WANG Ji LIANG Mi Fang SONG Jing Dong MA Xue Jun WU Gui Zhen National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and PreventionBeijing 102206China Sierra Leone-China Friendship Biological Safety Laboratory FreetownSierra-Leone National Institute for Communicable Disease Control and Prevention Chinese Center for Disease Control and PreventionBeijing 102206China Chinese Center for Disease Control and Prevention Beijing 102206China Sierra Leone Ministry of Health and Sanitation Freetown Sierra-Leone Key Laboratory of Medical Virology National Health and Family Planning CommissionNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China

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.

关键词： Sierra Leone Febrile jaundice Next‐generation sequencing Virus

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Serological Investigation of Laboratory-Confirmed and Suspected Ebola Virus Disease Patients During the Late Phase of the Ebola Outbreak in Sierra Leone

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Virologica Sinica 2018年第4期33卷 323-334页

作者： Yang Liu YuLan Sun Wei Wu AQian Li XianDa Yang Shuo Zhang Chuan Li QiuDong Su ShaoJian Cai DaPeng Sun HaiYang Hu Zhe Zhang XiuXu Yang Idrissa Kamara Sheku Koroma Gerald Bangura Alie Tia Abdul Kamara Matt Lebby brima kargbo Jiandong Li Shiwen Wang XiaoPing Dong YueLong Shu WenBo Xu George F. Gao GuiZhen Wu DeXin Li William J. Liu MiFang Liang Key Laboratory of Medical Virology and Viral Diseases Ministry of Health National Institute for Viral Disease Control and Prevention (IVDC) Chinese Center for Disease Control and Prevention (China CDC) Beijing 102206 China Beijing Center for Disease Control and Prevention (Beijing CDC China) Beijing 100013 China Jilin Provincial Center for Disease Control and Prevention (Jilin CDC China) Jilin 130021 China Fujian Provincial Center for Disease Control and Prevention (Fujian CDC China) Fuzhou 350001 China Shandong Provincial Center for Disease Control and Prevention (Shandong CDC China) Jinan 250014 China Jiangsu Provincial Center for Disease Control and Prevention (Jiangsu CDC China) Nanjing 210009 China Beijing Institute of Biotechnology Beijing 100071 China Sierra Leone-China Friendship Biological Safety Laboratory (SLE-CHN Bio-safety Lab) Freetown 999127 Sierra Leone The Ministry of Health and Sanitation (MoHS SL) Freetown 999127 Sierra Leone CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China

This study aimed to investigate the serological characteristics of Ebola virus(EBOV) infection during the late phase of the Ebola outbreak in Sierra Leone. In total, 877 blood samples from 694 suspected Ebola virus disease(EVD) cases assessed from March to December 2015, were analyzed via real-time reverse transcription polymerase chain reaction(RT-PCR) for viral RNA and enzyme-linked immunosorbent assay(ELISA) and Luminex to detect antibodies against EBOV. Viral load and EBOV-specific IgM/IgG titers displayed a declining trend during March to December 2015. Viral RNA load decreased rapidly at earlier stages after disease onset, while EBOV-specific IgM and IgG still persisted in 58.1%(18/31) and 93.5%(29/31) of the confirmed EVD patients and in 3.8%(25/663) and 17.8%(118/663) of the RNA-negative suspected patients in the later phase, respectively. Dynamic analysis of longitudinally collected samples from eight EVD patients revealed typically reversed trends of declining viral load and increasing IgM and/or IgG titers in response to the EBOV *** present results indicate that certain populations of Sierra Leone developed immunity to an EBOV infection in the late phase of the outbreak, providing novel insights into the risk assessment of EBOV infections among human populations.

关键词： Ebola virus (EBOV) Late phase Serologic investigation IgM IgG

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HIV prevalence in suspected Ebola cases during the 2014-2016 Ebola epidemic in Sierra Leone

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Infectious Diseases of Poverty 2019年第2期8卷 87-90页

作者： William J.Liu Hai-Yang Hu Qiu-Dong Su Zhe Zhang Yang Liu Yu-Lan Sun Xian-Da Yang Da-Peng Sun Shao-Jian Cai Xiu-Xu Yang Idrissa Kamara Abdul Kamara Matt Lebby brima kargbo Patricia Ongpin Xiao-Ping Dong Yue-Long Shu Wen-Bo Xu Gui-Zhen Wu Michael Gboun George F.Gao NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and Prevention(China CDC)Beijing 102206China Jiangsu Provincial Center for Disease control and Prevention Nanjing 210009China Beijing Institute of Biotechnology Beijing 100071China. Beijing Center for Disease Prevention and Control Beijing 100013China Jilin Provincial Center for Disease control and Prevention Changchun 130021China Shandong Provincial Center for Disease control and Prevention Jinan 250014China Fujian Provincial Center for Disease control and Prevention Fuzhou 350001China The Ministry of Health and Sanitation FreetownSierra Leone UNAIDS FreetownSierra Leone Chinese Center for Disease Control and Prevention Beijing 102206China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of Sciences(CAS)Beijing 100101China Sierra Leone-China Friendship Biological Safety Laboratory FreetownSierra Leone

Background:The 2014-2016 Ebola virus epidemic in West Africa was the largest outbreak of Ebola virus disease(EVD)in *** the influence of other prevalent diseases such as human immunodeficiency virus infection and acquired immune deficiency syndrome(HIV/AIDS)will help improve treatment and supportive care of patients with *** presentation:We examined HIV and hepatitis C virus(HCV)antibody prevalence among suspected EVD cases from the Sierra Leone-China Friendship Biological Safety Laboratory during the epidemic in Sierra *** and HCV antibodies were tested in 678 EVD-negative samples by enzyme-linked immunosorbent assay.A high HIV prevalence(17.6%)and low HCV prevalence(0.22%)were observed among the suspected ***,we found decreased HIV positive rates among the suspected cases over the course of the *** suggests a potentially beneficial effect of an improved public health system after assistance from the World Health Organization and other international aid ***:This EVD epidemic had a considerable impact on the public health system and influenced the prevalence of HIV found among suspected cases in Sierra Leone,but also provided an opportunity to establish a better surveillance network for infectious diseases.

关键词： HIV HCV Ebola Prevalence Sierra Leone

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Intra-host Ebola viral adaption during human infection

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Biosafety and Health 2019年第1期1卷 14-24页

作者： William JLiu Weifeng Shi Wuyang Zhu Cong Jin Shumei Zou Ji Wang Yuehua Ke Xiaofeng Li Mi Liu Tao Hu Hang Fan Yigang Tong Xiang Zhao Wenbin Chen Yuhui Zhao Di Liu Gary Wong Chengchao Chen Chunyu Geng Weiwei Xie Hui Jiang Idrissa Laybor Kamara Abdul Kamara Matt Lebby brima kargbo Xiangguo Qiu Yu Wang Xiaofeng Liang Mifang Liang Xiaoping Dong Guizhen Wu George F.Gao Yuelong Shu NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China Shandong Universities Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases Taishan Medical UniversityTaian 271000China Institute of Disease Control and Prevention Academy of Military Medical SciencesBeijing 100071China State Key Laboratory of Pathogen and Biosecurity Institute of Microbiology and EpidemiologyAcademy of Military Medical SciencesBeijing 100071China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China BGI-Shenzhen Shenzhen 518083China Sierra Leone Ministry of Health and Sanitation FreetownSierra Leone Special Pathogens Program National Microbiology LaboratoryPublic Health Agency of CanadaWinnipegCanada Chinese Center for Disease Control and Prevention Beijing 102206China Public Health School(Shenzhen) Sun Yat-sen UniversityShenzhen 510006China

The onsite next generation sequencing(NGS)of Ebola virus(EBOV)genomes during the 2013–2016 Ebola epidemic in Western Africa provides an opportunity to trace the origin,transmission,and evolution of this ***,we have diagnosed a cohort of EBOV patients in Sierra Leone in 2015,during the late phase of the *** surviving EBOV patients had a recovery process characterized by decreasing viremia,fever,and biochemical *** genomes sequenced through the longitudinal blood samples of these patients showed dynamic intra-host substitutions of the virus during acute infection,including the previously described short stretches of 13 serial TNC ***,within individual patients,samples collected during the early phase of infection possessed Ts at these nucleotide sites,whereas they were replaced by Cs in samples collected in the later phase,suggesting that these short stretches of TNC mutations could emerge *** addition,up to a total of 35 nucleotide sites spanning the EBOV genome were mutated *** study showed the dynamic intra-host adaptation of EBOV during patient recovery and gave more insight into the complex EBOV-host interactions.

关键词： Ebola virus Intra-host Nucleotide Variation Adaptation Genome sequencing Clinical manifestations Blood biochemistry

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