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  1. Article ; Online: Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study.

    Shaw, Alexander G / Mampuela, Tresor Kabeya / Lofiko, Emmanuel Lokilo / Pratt, Catherine / Troman, Catherine / Bujaki, Erika / O'Toole, Áine / Akello, Joyce Odeke / Aziza, Adrienne Amuri / Lusamaki, Eddy Kinganda / Makangara, Jean Claude / Akonga, Marceline / Lay, Yvonne / Nsunda, Bibiche / White, Bailey / Jorgensen, David / Pukuta, Elizabeth / Riziki, Yogolelo / Rankin, Kathleen E /
    Rambaut, Andrew / Ahuka-Mundeke, Steve / Muyembe, Jean-Jacques / Martin, Javier / Grassly, Nicholas C / Mbala-Kingebeni, Placide

    Nature microbiology

    2023  Volume 8, Issue 9, Page(s) 1634–1640

    Abstract: Timely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a ... ...

    Abstract Timely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a promising fast method. Here we report prospective testing of stool samples from suspected polio cases, and their contacts, in the Democratic Republic of the Congo between 10 August 2021 and 4 February 2022. DDNS detected polioviruses in 62/2,339 (2.7%) of samples, while gold standard combination of cell culture, quantitative PCR and Sanger sequencing detected polioviruses in 51/2,339 (2.2%) of the same samples. DDNS provided case confirmation in 7 days (median) in routine surveillance conditions. DDNS enabled confirmation of three serotype 2 circulating vaccine-derived poliovirus outbreaks 23 days (mean) earlier (range 6-30 days) than the gold standard method. The mean sequence similarity between sequences obtained by the two methods was 99.98%. Our data confirm the feasibility of implementing DDNS in a national poliovirus laboratory.
    MeSH term(s) Poliovirus/genetics ; Nanopore Sequencing ; Polymerase Chain Reaction ; Dansyl Compounds
    Chemical Substances dimethylaminonaphthalene-5-sulfonaminoethylmethylamine (74686-82-1) ; Dansyl Compounds
    Language English
    Publishing date 2023-08-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-023-01453-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo.

    Kinganda-Lusamaki, Eddy / Black, Allison / Mukadi, Daniel B / Hadfield, James / Mbala-Kingebeni, Placide / Pratt, Catherine B / Aziza, Amuri / Diagne, Moussa M / White, Bailey / Bisento, Nella / Nsunda, Bibiche / Akonga, Marceline / Faye, Martin / Faye, Ousmane / Edidi-Atani, Francois / Matondo-Kuamfumu, Meris / Mambu-Mbika, Fabrice / Bulabula, Junior / Di Paola, Nicholas /
    Pauthner, Matthias G / Andersen, Kristian G / Palacios, Gustavo / Delaporte, Eric / Sall, Amadou Alpha / Peeters, Martine / Wiley, Michael R / Ahuka-Mundeke, Steve / Bedford, Trevor / Tamfum, Jean-Jacques Muyembe

    Nature medicine

    2021  Volume 27, Issue 4, Page(s) 710–716

    Abstract: On 1 August 2018, the Democratic Republic of the Congo (DRC) declared its tenth Ebola virus disease (EVD) outbreak. To aid the epidemiologic response, the Institut National de Recherche Biomédicale (INRB) implemented an end-to-end genomic surveillance ... ...

    Abstract On 1 August 2018, the Democratic Republic of the Congo (DRC) declared its tenth Ebola virus disease (EVD) outbreak. To aid the epidemiologic response, the Institut National de Recherche Biomédicale (INRB) implemented an end-to-end genomic surveillance system, including sequencing, bioinformatic analysis and dissemination of genomic epidemiologic results to frontline public health workers. We report 744 new genomes sampled between 27 July 2018 and 27 April 2020 generated by this surveillance effort. Together with previously available sequence data (n = 48 genomes), these data represent almost 24% of all laboratory-confirmed Ebola virus (EBOV) infections in DRC in the period analyzed. We inferred spatiotemporal transmission dynamics from the genomic data as new sequences were generated, and disseminated the results to support epidemiologic response efforts. Here we provide an overview of how this genomic surveillance system functioned, present a full phylodynamic analysis of 792 Ebola genomes from the Nord Kivu outbreak and discuss how the genomic surveillance data informed response efforts and public health decision making.
    MeSH term(s) Congo/epidemiology ; Disease Outbreaks ; Ebola Vaccines/immunology ; Ebolavirus/genetics ; Genome, Viral ; Genomics ; Hemorrhagic Fever, Ebola/epidemiology ; Hemorrhagic Fever, Ebola/genetics ; Hemorrhagic Fever, Ebola/transmission ; Hemorrhagic Fever, Ebola/virology ; Phylogeny ; Recurrence ; Reinfection/virology ; Sequence Analysis, DNA ; Spatio-Temporal Analysis
    Chemical Substances Ebola Vaccines
    Language English
    Publishing date 2021-04-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-021-01302-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 4212: Show issues Location:
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    Zs.MG 39: Show issues

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  3. Article ; Online: Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease.

    Mbala-Kingebeni, Placide / Pratt, Catherine / Mutafali-Ruffin, Mbusa / Pauthner, Matthias G / Bile, Faustin / Nkuba-Ndaye, Antoine / Black, Allison / Kinganda-Lusamaki, Eddy / Faye, Martin / Aziza, Amuri / Diagne, Moussa M / Mukadi, Daniel / White, Bailey / Hadfield, James / Gangavarapu, Karthik / Bisento, Nella / Kazadi, Donatien / Nsunda, Bibiche / Akonga, Marceline /
    Tshiani, Olivier / Misasi, John / Ploquin, Aurelie / Epaso, Victor / Sana-Paka, Emilia / N'kasar, Yannick Tutu Tshia / Mambu, Fabrice / Edidi, Francois / Matondo, Meris / Bula Bula, Junior / Diallo, Boubacar / Keita, Mory / Belizaire, Marie R D / Fall, Ibrahima S / Yam, Abdoulaye / Mulangu, Sabue / Rimoin, Anne W / Salfati, Elias / Torkamani, Ali / Suchard, Marc A / Crozier, Ian / Hensley, Lisa / Rambaut, Andrew / Faye, Ousmane / Sall, Amadou / Sullivan, Nancy J / Bedford, Trevor / Andersen, Kristian G / Wiley, Michael R / Ahuka-Mundeke, Steve / Muyembe Tamfum, Jean-Jacques

    The New England journal of medicine

    2021  Volume 384, Issue 13, Page(s) 1240–1247

    Abstract: During the 2018-2020 Ebola virus disease (EVD) outbreak in North Kivu province in the Democratic Republic of Congo, EVD was diagnosed in a patient who had received the recombinant vesicular stomatitis virus-based vaccine expressing a ZEBOV glycoprotein ( ... ...

    Abstract During the 2018-2020 Ebola virus disease (EVD) outbreak in North Kivu province in the Democratic Republic of Congo, EVD was diagnosed in a patient who had received the recombinant vesicular stomatitis virus-based vaccine expressing a ZEBOV glycoprotein (rVSV-ZEBOV) (Merck). His treatment included an Ebola virus (EBOV)-specific monoclonal antibody (mAb114), and he recovered within 14 days. However, 6 months later, he presented again with severe EVD-like illness and EBOV viremia, and he died. We initiated epidemiologic and genomic investigations that showed that the patient had had a relapse of acute EVD that led to a transmission chain resulting in 91 cases across six health zones over 4 months. (Funded by the Bill and Melinda Gates Foundation and others.).
    MeSH term(s) Adult ; Bayes Theorem ; Democratic Republic of the Congo/epidemiology ; Ebola Vaccines/immunology ; Ebolavirus/genetics ; Ebolavirus/isolation & purification ; Fatal Outcome ; Genome, Viral ; Hemorrhagic Fever, Ebola/diagnosis ; Hemorrhagic Fever, Ebola/epidemiology ; Hemorrhagic Fever, Ebola/therapy ; Hemorrhagic Fever, Ebola/transmission ; Humans ; Male ; Mutation ; Phylogeny ; RNA, Viral/blood ; Recurrence
    Chemical Substances Ebola Vaccines ; RNA, Viral
    Language English
    Publishing date 2021-03-31
    Publishing country United States
    Document type Case Reports ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMoa2024670
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Ua VI Zs.34: Show issues Location:
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