@article{fdi:010075730,
  title = {2018 {E}bola virus disease outbreak in {E}quateur {P}rovince, {D}emocratic {R}epublic of the {C}ongo : a retrospective genomic characterisation},
  author = {{M}bala-{K}ingebeni, {P}. and {P}ratt, {C}. {B}. and {W}iley, {M}. {R}. and {D}iagne, {M}. {M}. and {M}akiala-{M}andanda, {S}. and {A}ziza, {A}. and {D}i {P}aola, {N}. and {C}hitty, {J}. {A}. and {D}iop, {M}. and {A}youba, {A}hidjo and {V}idal, {N}icole and {F}aye, {O}. and {F}aye, {O}. and {K}arhemere, {S}. and {A}runa, {A}. and {N}sio, {J}. and {M}ulangu, {F}. and {M}ukadi, {D}. and {M}ukadi, {P}. and {K}ombe, {J}. and {M}ulumba, {A}. and {D}uraffour, {S}. and {L}ikofata, {J}. and {P}ukuta, {E}. and {C}aviness, {K}. and {B}artlett, {M}. {L}. and {G}onzalez, {J}. and {M}inogue, {T}. and {S}ozhamannan, {S}. and {G}ross, {S}. {M}. and {S}chroth, {G}. {P}. and {K}uhn, {J}. {H}. and {D}onaldson, {E}. {F}. and {D}elaporte, {E}. and {S}anchez-{L}ockhart, {M}. and {P}eeters, {M}artine and {M}uyembe-{T}amfum, {J}. {J}. and {S}all, {A}. {A}. and {P}alacios, {G}. and {A}huka-{M}undeke, {S}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground {T}he 2018 {E}bola virus disease ({EVD}) outbreak in {E}quateur {P}rovince, {D}emocratic {R}epublic of the {C}ongo, began on {M}ay 8, and was declared over on {J}uly 24; it resulted in 54 documented cases and 33 deaths. {W}e did a retrospective genomic characterisation of the outbreak and assessed potential therapeutic agents and vaccine (medical countermeasures). {M}ethods {W}e used target-enrichment sequencing to produce {E}bola virus genomes from samples obtained in the 2018 {E}quateur {P}rovince outbreak. {C}ombining these genomes with genomes associated with known outbreaks from {G}en{B}ank, we constructed a maximum-likelihood phylogenetic tree. {I}n-silico analyses were used to assess potential mismatches between the outbreak strain and the probes and primers of diagnostic assays and the antigenic sites of the experimental r{VSVAG}-{ZEBOV}-{GP} vaccine and therapeutics. {A}n in-vitro flow cytometry assay was used to assess the binding capability of the individual components of the monodonal antibody cocktail {ZM}app. {F}indings {A} targeted sequencing approach produced 16 near-complete genomes. {P}hylogenetic analysis of these genomes and 1011 genomes from {G}en{B}ank revealed a distinct cluster, confirming a new {E}bola virus variant, for which we propose the name "{T}umba". {T}his new variant appears to have evolved at a slower rate than other {E}bola virus variants (0.69 x 10(-3) substitutions per site per year with "{T}umba" vs 1.06 x 10(-3) substitutions per site per year without "{T}umba"). {W}e found few sequence mismatches in the assessed assay target regions and antigenic sites. {W}e identified nine amino acid changes in the {E}bola virus surface glycoprotein, of which one resulted in reduced binding of the 13{C}6 antibody within the {ZM}app cocktail. {I}nterpretation {R}etrospectively, we show the feasibility of using genomics to rapidly characterise a new {E}bola virus variant within the timeframe of an outbreak. {P}hylogenetic analysis provides further indications that these variants are evolving at differing rates. {R}apid in-silico analyses can direct in-vitro experiments to quickly assess medical countermeasures.},
  keywords = {{REPUBLIQUE} {DEMOCRATIQUE} {DU} {CONGO}},
  booktitle = {},
  journal = {{L}ancet {I}nfectious {D}iseases},
  volume = {19},
  numero = {6},
  pages = {641--647},
  ISSN = {1473-3099},
  year = {2019},
  DOI = {10.1016/s1473-3099(19)30124-0},
  URL = {https://www.documentation.ird.fr/hor/fdi:010075730},
}