Improved inference of time-varying reproduction numbers during infectious disease outbreaks
Identifieur interne : 000016 ( France/Analysis ); précédent : 000015; suivant : 000017Improved inference of time-varying reproduction numbers during infectious disease outbreaks
Auteurs : R. N. Thompson [Royaume-Uni] ; J. E. Stockwin [Royaume-Uni] ; R. D. Van Gaalen [Pays-Bas] ; J. A. Polonsky [Suisse] ; Z. N. Kamvar [Royaume-Uni] ; P. A. Demarsh [Canada] ; E. Dahlqwist [Suède] ; S. Li [Suède] ; E. Miguel [France] ; T. Jombart [Royaume-Uni] ; J. Lessler [États-Unis] ; S. Cauchemez [France] ; A. Cori [Royaume-Uni]Source :
- Epidemics [ 1755-4365 ] ; 2019.
Abstract
Real-time estimation of reproduction numbers during outbreaks can guide control. Using up-to-date serial interval data and accounting for imported cases is vital. We develop a framework for estimating pathogen transmissibility appropriately. We demonstrate it using data from outbreaks of influenza, Ebola and MERS. Our approach is implemented in R package
Url:
DOI: 10.1016/j.epidem.2019.100356
PubMed: 31624039
PubMed Central: 7105007
Affiliations:
- Canada, France, Pays-Bas, Royaume-Uni, Suisse, Suède, États-Unis
- Angleterre, Canton de Genève, Languedoc-Roussillon, Occitanie (région administrative), Oxfordshire, Québec, Île-de-France
- Genève, Montpellier, Montréal, Oxford
- Université McGill, Université d'Oxford, Université de Genève
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PMC:7105007Le document en format XML
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Thompson</name><affiliation wicri:level="4"><nlm:aff id="aff0005">Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS</wicri:regionArea><orgName type="university">Université d'Oxford</orgName><placeName><settlement type="city">Oxford</settlement><region type="nation">Angleterre</region><region type="région" nuts="1">Oxfordshire</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff0010">Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG</wicri:regionArea><orgName type="university">Université d'Oxford</orgName><placeName><settlement type="city">Oxford</settlement><region type="nation">Angleterre</region><region type="région" nuts="1">Oxfordshire</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff0015">Christ Church, University of Oxford, St Aldates, Oxford OX1 1DP, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Christ Church, University of Oxford, St Aldates, Oxford OX1 1DP</wicri:regionArea><orgName type="university">Université d'Oxford</orgName><placeName><settlement type="city">Oxford</settlement><region type="nation">Angleterre</region><region type="région" nuts="1">Oxfordshire</region></placeName></affiliation></author><author><name sortKey="Stockwin, J E" sort="Stockwin, J E" uniqKey="Stockwin J" first="J. 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Miguel</name><affiliation wicri:level="3"><nlm:aff id="aff0055">MIVEGEC, IRD, University of Montpellier, CNRS, Montpellier, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>MIVEGEC, IRD, University of Montpellier, CNRS, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Jombart, T" sort="Jombart, T" uniqKey="Jombart T" first="T." last="Jombart">T. 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N." last="Thompson">R. N. Thompson</name><affiliation wicri:level="4"><nlm:aff id="aff0005">Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS</wicri:regionArea><orgName type="university">Université d'Oxford</orgName><placeName><settlement type="city">Oxford</settlement><region type="nation">Angleterre</region><region type="région" nuts="1">Oxfordshire</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff0010">Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG</wicri:regionArea><orgName type="university">Université d'Oxford</orgName><placeName><settlement type="city">Oxford</settlement><region type="nation">Angleterre</region><region type="région" nuts="1">Oxfordshire</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff0015">Christ Church, University of Oxford, St Aldates, Oxford OX1 1DP, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Christ Church, University of Oxford, St Aldates, Oxford OX1 1DP</wicri:regionArea><orgName type="university">Université d'Oxford</orgName><placeName><settlement type="city">Oxford</settlement><region type="nation">Angleterre</region><region type="région" nuts="1">Oxfordshire</region></placeName></affiliation></author><author><name sortKey="Stockwin, J E" sort="Stockwin, J E" uniqKey="Stockwin J" first="J. E." last="Stockwin">J. E. Stockwin</name><affiliation wicri:level="4"><nlm:aff id="aff0020">Lady Margaret Hall, University of Oxford, Norham Gardens, Oxford OX2 6QA, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Lady Margaret Hall, University of Oxford, Norham Gardens, Oxford OX2 6QA</wicri:regionArea><orgName type="university">Université d'Oxford</orgName><placeName><settlement type="city">Oxford</settlement><region type="nation">Angleterre</region><region type="région" nuts="1">Oxfordshire</region></placeName></affiliation></author><author><name sortKey="Van Gaalen, R D" sort="Van Gaalen, R D" uniqKey="Van Gaalen R" first="R. D." last="Van Gaalen">R. D. Van Gaalen</name><affiliation wicri:level="1"><nlm:aff id="aff0025">Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven</wicri:regionArea><wicri:noRegion>3720 BA Bilthoven</wicri:noRegion></affiliation></author><author><name sortKey="Polonsky, J A" sort="Polonsky, J A" uniqKey="Polonsky J" first="J. A." last="Polonsky">J. A. Polonsky</name><affiliation wicri:level="1"><nlm:aff id="aff0030">World Health Organization, Avenue Appia, Geneva 1202, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>World Health Organization, Avenue Appia, Geneva 1202</wicri:regionArea><wicri:noRegion>Geneva 1202</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:aff id="aff0075">Faculty of Medicine, University of Geneva, 1 Rue Michel-Servet, Geneva 1211, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Faculty of Medicine, University of Geneva, 1 Rue Michel-Servet, Geneva 1211</wicri:regionArea><orgName type="university">Université de Genève</orgName><placeName><settlement type="city">Genève</settlement><region nuts="3" type="region">Canton de Genève</region></placeName></affiliation></author><author><name sortKey="Kamvar, Z N" sort="Kamvar, Z N" uniqKey="Kamvar Z" first="Z. N." last="Kamvar">Z. N. Kamvar</name><affiliation wicri:level="1"><nlm:aff id="aff0035">MRC Centre for Global Infectious Disease Analysis, Imperial College London, Faculty of Medicine, London W2 1PG, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC Centre for Global Infectious Disease Analysis, Imperial College London, Faculty of Medicine, London W2 1PG</wicri:regionArea><wicri:noRegion>London W2 1PG</wicri:noRegion></affiliation></author><author><name sortKey="Demarsh, P A" sort="Demarsh, P A" uniqKey="Demarsh P" first="P. A." last="Demarsh">P. A. Demarsh</name><affiliation wicri:level="4"><nlm:aff id="aff0040">The Surveillance Lab, McGill University, 1140 Pine Avenue West, Montreal H3A 1A3, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>The Surveillance Lab, McGill University, 1140 Pine Avenue West, Montreal H3A 1A3</wicri:regionArea><orgName type="university">Université McGill</orgName><placeName><settlement type="city">Montréal</settlement><region type="state">Québec</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="aff0045">Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, 130 Colonnade Road, Ottawa, Ontario, K1A 0K9, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, 130 Colonnade Road, Ottawa, Ontario, K1A 0K9</wicri:regionArea><wicri:noRegion>K1A 0K9</wicri:noRegion></affiliation></author><author><name sortKey="Dahlqwist, E" sort="Dahlqwist, E" uniqKey="Dahlqwist E" first="E." last="Dahlqwist">E. Dahlqwist</name><affiliation wicri:level="1"><nlm:aff id="aff0050">Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm</wicri:regionArea><wicri:noRegion>171 77 Stockholm</wicri:noRegion></affiliation></author><author><name sortKey="Li, S" sort="Li, S" uniqKey="Li S" first="S." last="Li">S. Li</name><affiliation wicri:level="1"><nlm:aff id="aff0050">Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm</wicri:regionArea><wicri:noRegion>171 77 Stockholm</wicri:noRegion></affiliation></author><author><name sortKey="Miguel, E" sort="Miguel, E" uniqKey="Miguel E" first="E." last="Miguel">E. Miguel</name><affiliation wicri:level="3"><nlm:aff id="aff0055">MIVEGEC, IRD, University of Montpellier, CNRS, Montpellier, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>MIVEGEC, IRD, University of Montpellier, CNRS, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Jombart, T" sort="Jombart, T" uniqKey="Jombart T" first="T." last="Jombart">T. Jombart</name><affiliation wicri:level="1"><nlm:aff id="aff0035">MRC Centre for Global Infectious Disease Analysis, Imperial College London, Faculty of Medicine, London W2 1PG, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC Centre for Global Infectious Disease Analysis, Imperial College London, Faculty of Medicine, London W2 1PG</wicri:regionArea><wicri:noRegion>London W2 1PG</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff0060">Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT</wicri:regionArea><wicri:noRegion>London WC1E 7HT</wicri:noRegion></affiliation></author><author><name sortKey="Lessler, J" sort="Lessler, J" uniqKey="Lessler J" first="J." last="Lessler">J. Lessler</name><affiliation wicri:level="1"><nlm:aff id="aff0065">Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205</wicri:regionArea><wicri:noRegion>21205</wicri:noRegion></affiliation></author><author><name sortKey="Cauchemez, S" sort="Cauchemez, S" uniqKey="Cauchemez S" first="S." last="Cauchemez">S. Cauchemez</name><affiliation wicri:level="3"><nlm:aff id="aff0070">Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris 75015, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris 75015</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Cori, A" sort="Cori, A" uniqKey="Cori A" first="A." last="Cori">A. Cori</name><affiliation wicri:level="1"><nlm:aff id="aff0035">MRC Centre for Global Infectious Disease Analysis, Imperial College London, Faculty of Medicine, London W2 1PG, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>MRC Centre for Global Infectious Disease Analysis, Imperial College London, Faculty of Medicine, London W2 1PG</wicri:regionArea><wicri:noRegion>London W2 1PG</wicri:noRegion></affiliation></author></analytic><series><title level="j">Epidemics</title><idno type="ISSN">1755-4365</idno><idno type="eISSN">1878-0067</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Highlights</title><p><list list-type="simple" id="lis0005"><list-item id="lsti0005"><label>•</label><p id="par0005">Real-time estimation of reproduction numbers during outbreaks can guide control.</p></list-item><list-item id="lsti0010"><label>•</label><p id="par0010">Using up-to-date serial interval data and accounting for imported cases is vital.</p></list-item><list-item id="lsti0015"><label>•</label><p id="par0015">We develop a framework for estimating pathogen transmissibility appropriately.</p></list-item><list-item id="lsti0020"><label>•</label><p id="par0020">We demonstrate it using data from outbreaks of influenza, Ebola and MERS.</p></list-item><list-item id="lsti0025"><label>•</label><p id="par0025">Our approach is implemented in R package <italic>EpiEstim</italic> and online application <italic>EpiEstim App</italic>.</p></list-item></list></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Al Tawfiq, J A" uniqKey="Al Tawfiq J">J.A. 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Jalava</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van De Kassteele, J" uniqKey="Van De Kassteele J">J. van de Kassteele</name></author><author><name sortKey="Eilers, P H C" uniqKey="Eilers P">P.H.C. Eilers</name></author><author><name sortKey="Wallinga, J" uniqKey="Wallinga J">J. Wallinga</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Gaalen, R D" uniqKey="Van Gaalen R">R.D. van Gaalen</name></author><author><name sortKey="Van De Kassteele, J" uniqKey="Van De Kassteele J">J. van de Kassteele</name></author><author><name sortKey="Hahne, S J M" uniqKey="Hahne S">S.J.M. Hahné</name></author><author><name sortKey="Bruijning Verhagen, P" uniqKey="Bruijning Verhagen P">P. Bruijning-Verhagen</name></author><author><name sortKey="Wallinga, J" uniqKey="Wallinga J">J. Wallinga</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vink, M A" uniqKey="Vink M">M.A. Vink</name></author><author><name sortKey="Bootsma, M C J" uniqKey="Bootsma M">M.C.J. Bootsma</name></author><author><name sortKey="Wallinga, J" uniqKey="Wallinga J">J. Wallinga</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wallinga, J" uniqKey="Wallinga J">J. Wallinga</name></author><author><name sortKey="Teunis, P" uniqKey="Teunis P">P. Teunis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wallinga, J" uniqKey="Wallinga J">J. Wallinga</name></author><author><name sortKey="Lipsitch, M" uniqKey="Lipsitch M">M. Lipsitch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wallinga, J" uniqKey="Wallinga J">J. Wallinga</name></author><author><name sortKey="Van Boven, M" uniqKey="Van Boven M">M. van Boven</name></author><author><name sortKey="Lipsitch, M" uniqKey="Lipsitch M">M. Lipsitch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="White, S M" uniqKey="White S">S.M. White</name></author><author><name sortKey="Bullock, J M" uniqKey="Bullock J">J.M. Bullock</name></author><author><name sortKey="Hooftman, D A P" uniqKey="Hooftman D">D.A.P. Hooftman</name></author><author><name sortKey="Chapman, D S" uniqKey="Chapman D">D.S. Chapman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Who Ebola Response Team" uniqKey="Who Ebola Response Team">WHO Ebola Response Team</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wilder Smith, A" uniqKey="Wilder Smith A">A. Wilder-Smith</name></author><author><name sortKey="Monath, T P" uniqKey="Monath T">T.P. Monath</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wiratsudakul, A" uniqKey="Wiratsudakul A">A. Wiratsudakul</name></author><author><name sortKey="Triampo, W" uniqKey="Triampo W">W. Triampo</name></author><author><name sortKey="Laosiritaworn, Y" uniqKey="Laosiritaworn Y">Y. Laosiritaworn</name></author><author><name sortKey="Modchang, C" uniqKey="Modchang C">C. Modchang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ypma, R J" uniqKey="Ypma R">R.J. Ypma</name></author><author><name sortKey="Donker, T" uniqKey="Donker T">T. Donker</name></author><author><name sortKey="Van Ballegooijen, W M" uniqKey="Van Ballegooijen W">W.M. van Ballegooijen</name></author><author><name sortKey="Wallinga, J" uniqKey="Wallinga J">J. Wallinga</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Canada</li><li>France</li><li>Pays-Bas</li><li>Royaume-Uni</li><li>Suisse</li><li>Suède</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Canton de Genève</li><li>Languedoc-Roussillon</li><li>Occitanie (région administrative)</li><li>Oxfordshire</li><li>Québec</li><li>Île-de-France</li></region><settlement><li>Genève</li><li>Montpellier</li><li>Montréal</li><li>Oxford</li></settlement><orgName><li>Université McGill</li><li>Université d'Oxford</li><li>Université de Genève</li></orgName></list><tree><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Thompson, R N" sort="Thompson, R N" uniqKey="Thompson R" first="R. N." last="Thompson">R. N. Thompson</name></region><name sortKey="Cori, A" sort="Cori, A" uniqKey="Cori A" first="A." last="Cori">A. Cori</name><name sortKey="Jombart, T" sort="Jombart, T" uniqKey="Jombart T" first="T." last="Jombart">T. Jombart</name><name sortKey="Jombart, T" sort="Jombart, T" uniqKey="Jombart T" first="T." last="Jombart">T. Jombart</name><name sortKey="Kamvar, Z N" sort="Kamvar, Z N" uniqKey="Kamvar Z" first="Z. N." last="Kamvar">Z. N. Kamvar</name><name sortKey="Stockwin, J E" sort="Stockwin, J E" uniqKey="Stockwin J" first="J. E." last="Stockwin">J. E. Stockwin</name><name sortKey="Thompson, R N" sort="Thompson, R N" uniqKey="Thompson R" first="R. N." last="Thompson">R. N. Thompson</name><name sortKey="Thompson, R N" sort="Thompson, R N" uniqKey="Thompson R" first="R. N." last="Thompson">R. N. Thompson</name></country><country name="Pays-Bas"><noRegion><name sortKey="Van Gaalen, R D" sort="Van Gaalen, R D" uniqKey="Van Gaalen R" first="R. D." last="Van Gaalen">R. D. Van Gaalen</name></noRegion></country><country name="Suisse"><noRegion><name sortKey="Polonsky, J A" sort="Polonsky, J A" uniqKey="Polonsky J" first="J. A." last="Polonsky">J. A. Polonsky</name></noRegion><name sortKey="Polonsky, J A" sort="Polonsky, J A" uniqKey="Polonsky J" first="J. A." last="Polonsky">J. A. Polonsky</name></country><country name="Canada"><region name="Québec"><name sortKey="Demarsh, P A" sort="Demarsh, P A" uniqKey="Demarsh P" first="P. A." last="Demarsh">P. A. Demarsh</name></region><name sortKey="Demarsh, P A" sort="Demarsh, P A" uniqKey="Demarsh P" first="P. A." last="Demarsh">P. A. Demarsh</name></country><country name="Suède"><noRegion><name sortKey="Dahlqwist, E" sort="Dahlqwist, E" uniqKey="Dahlqwist E" first="E." last="Dahlqwist">E. Dahlqwist</name></noRegion><name sortKey="Li, S" sort="Li, S" uniqKey="Li S" first="S." last="Li">S. Li</name></country><country name="France"><region name="Occitanie (région administrative)"><name sortKey="Miguel, E" sort="Miguel, E" uniqKey="Miguel E" first="E." last="Miguel">E. Miguel</name></region><name sortKey="Cauchemez, S" sort="Cauchemez, S" uniqKey="Cauchemez S" first="S." last="Cauchemez">S. Cauchemez</name></country><country name="États-Unis"><noRegion><name sortKey="Lessler, J" sort="Lessler, J" uniqKey="Lessler J" first="J." last="Lessler">J. Lessler</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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