Using Early Data to Estimate the Actual Infection Fatality Ratio from COVID-19 in France.
Identifieur interne : 000284 ( Main/Exploration ); précédent : 000283; suivant : 000285Using Early Data to Estimate the Actual Infection Fatality Ratio from COVID-19 in France.
Auteurs : Lionel Roques [France] ; Etienne K. Klein [France] ; Julien Papaïx [France] ; Antoine Sar [Suisse] ; Samuel Soubeyrand [France]Source :
- Biology [ 2079-7737 ] ; 2020.
Abstract
The number of screening tests carried out in France and the methodology used to target the patients tested do not allow for a direct computation of the actual number of cases and the infection fatality ratio (IFR). The main objective of this work is to estimate the actual number of people infected with COVID-19 and to deduce the IFR during the observation window in France. We develop a `mechanistic-statistical' approach coupling a SIR epidemiological model describing the unobserved epidemiological dynamics, a probabilistic model describing the data acquisition process and a statistical inference method. The actual number of infected cases in France is probably higher than the observations: we find here a factor ×8 (95%-CI: 5-12) which leads to an IFR in France of 0.5% (95%-CI: 0.3-0.8) based on hospital death counting data. Adjusting for the number of deaths in nursing homes, we obtain an IFR of 0.8% (95%-CI: 0.45-1.25). This IFR is consistent with previous findings in China (0.66%) and in the UK (0.9%) and lower than the value previously computed on the Diamond Princess cruse ship data (1.3%).
DOI: 10.3390/biology9050097
PubMed: 32397286
PubMed Central: PMC7284549
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Using Early Data to Estimate the Actual Infection Fatality Ratio from COVID-19 in France.</title><author><name sortKey="Roques, Lionel" sort="Roques, Lionel" uniqKey="Roques L" first="Lionel" last="Roques">Lionel Roques</name><affiliation wicri:level="3"><nlm:affiliation>INRAE, BioSP, 84914 Avignon, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRAE, BioSP, 84914 Avignon</wicri:regionArea><placeName><region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region><settlement type="city">Avignon</settlement></placeName></affiliation></author><author><name sortKey="Klein, Etienne K" sort="Klein, Etienne K" uniqKey="Klein E" first="Etienne K" last="Klein">Etienne K. Klein</name><affiliation wicri:level="3"><nlm:affiliation>INRAE, BioSP, 84914 Avignon, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRAE, BioSP, 84914 Avignon</wicri:regionArea><placeName><region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region><settlement type="city">Avignon</settlement></placeName></affiliation></author><author><name sortKey="Papaix, Julien" sort="Papaix, Julien" uniqKey="Papaix J" first="Julien" last="Papaïx">Julien Papaïx</name><affiliation wicri:level="3"><nlm:affiliation>INRAE, BioSP, 84914 Avignon, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRAE, BioSP, 84914 Avignon</wicri:regionArea><placeName><region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region><settlement type="city">Avignon</settlement></placeName></affiliation></author><author><name sortKey="Sar, Antoine" sort="Sar, Antoine" uniqKey="Sar A" first="Antoine" last="Sar">Antoine Sar</name><affiliation wicri:level="1"><nlm:affiliation>Medicentre Moutier, 2740 Moutier, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Medicentre Moutier, 2740 Moutier</wicri:regionArea><wicri:noRegion>2740 Moutier</wicri:noRegion></affiliation></author><author><name sortKey="Soubeyrand, Samuel" sort="Soubeyrand, Samuel" uniqKey="Soubeyrand S" first="Samuel" last="Soubeyrand">Samuel Soubeyrand</name><affiliation wicri:level="3"><nlm:affiliation>INRAE, BioSP, 84914 Avignon, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRAE, BioSP, 84914 Avignon</wicri:regionArea><placeName><region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region><settlement type="city">Avignon</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32397286</idno><idno type="pmid">32397286</idno><idno type="doi">10.3390/biology9050097</idno><idno type="pmc">PMC7284549</idno><idno type="wicri:Area/Main/Corpus">001347</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001347</idno><idno type="wicri:Area/Main/Curation">001347</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">001347</idno><idno type="wicri:Area/Main/Exploration">001347</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Using Early Data to Estimate the Actual Infection Fatality Ratio from COVID-19 in France.</title><author><name sortKey="Roques, Lionel" sort="Roques, Lionel" uniqKey="Roques L" first="Lionel" last="Roques">Lionel Roques</name><affiliation wicri:level="3"><nlm:affiliation>INRAE, BioSP, 84914 Avignon, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRAE, BioSP, 84914 Avignon</wicri:regionArea><placeName><region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region><settlement type="city">Avignon</settlement></placeName></affiliation></author><author><name sortKey="Klein, Etienne K" sort="Klein, Etienne K" uniqKey="Klein E" first="Etienne K" last="Klein">Etienne K. Klein</name><affiliation wicri:level="3"><nlm:affiliation>INRAE, BioSP, 84914 Avignon, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRAE, BioSP, 84914 Avignon</wicri:regionArea><placeName><region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region><settlement type="city">Avignon</settlement></placeName></affiliation></author><author><name sortKey="Papaix, Julien" sort="Papaix, Julien" uniqKey="Papaix J" first="Julien" last="Papaïx">Julien Papaïx</name><affiliation wicri:level="3"><nlm:affiliation>INRAE, BioSP, 84914 Avignon, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRAE, BioSP, 84914 Avignon</wicri:regionArea><placeName><region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region><settlement type="city">Avignon</settlement></placeName></affiliation></author><author><name sortKey="Sar, Antoine" sort="Sar, Antoine" uniqKey="Sar A" first="Antoine" last="Sar">Antoine Sar</name><affiliation wicri:level="1"><nlm:affiliation>Medicentre Moutier, 2740 Moutier, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Medicentre Moutier, 2740 Moutier</wicri:regionArea><wicri:noRegion>2740 Moutier</wicri:noRegion></affiliation></author><author><name sortKey="Soubeyrand, Samuel" sort="Soubeyrand, Samuel" uniqKey="Soubeyrand S" first="Samuel" last="Soubeyrand">Samuel Soubeyrand</name><affiliation wicri:level="3"><nlm:affiliation>INRAE, BioSP, 84914 Avignon, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRAE, BioSP, 84914 Avignon</wicri:regionArea><placeName><region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region><settlement type="city">Avignon</settlement></placeName></affiliation></author></analytic><series><title level="j">Biology</title><idno type="ISSN">2079-7737</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The number of screening tests carried out in France and the methodology used to target the patients tested do not allow for a direct computation of the actual number of cases and the infection fatality ratio (IFR). The main objective of this work is to estimate the actual number of people infected with COVID-19 and to deduce the IFR during the observation window in France. We develop a `mechanistic-statistical' approach coupling a SIR epidemiological model describing the unobserved epidemiological dynamics, a probabilistic model describing the data acquisition process and a statistical inference method. The actual number of infected cases in France is probably higher than the observations: we find here a factor ×8 (95%-CI: 5-12) which leads to an IFR in France of 0.5% (95%-CI: 0.3-0.8) based on hospital death counting data. Adjusting for the number of deaths in nursing homes, we obtain an IFR of 0.8% (95%-CI: 0.45-1.25). This IFR is consistent with previous findings in China (0.66%) and in the UK (0.9%) and lower than the value previously computed on the Diamond Princess cruse ship data (1.3%).</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32397286</PMID><DateRevised><Year>2020</Year><Month>06</Month><Day>20</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Print">2079-7737</ISSN><JournalIssue CitedMedium="Print"><Volume>9</Volume><Issue>5</Issue><PubDate><Year>2020</Year><Month>May</Month><Day>08</Day></PubDate></JournalIssue><Title>Biology</Title><ISOAbbreviation>Biology (Basel)</ISOAbbreviation></Journal><ArticleTitle>Using Early Data to Estimate the Actual Infection Fatality Ratio from COVID-19 in France.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E97</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/biology9050097</ELocationID><Abstract><AbstractText>The number of screening tests carried out in France and the methodology used to target the patients tested do not allow for a direct computation of the actual number of cases and the infection fatality ratio (IFR). The main objective of this work is to estimate the actual number of people infected with COVID-19 and to deduce the IFR during the observation window in France. We develop a `mechanistic-statistical' approach coupling a SIR epidemiological model describing the unobserved epidemiological dynamics, a probabilistic model describing the data acquisition process and a statistical inference method. The actual number of infected cases in France is probably higher than the observations: we find here a factor ×8 (95%-CI: 5-12) which leads to an IFR in France of 0.5% (95%-CI: 0.3-0.8) based on hospital death counting data. Adjusting for the number of deaths in nursing homes, we obtain an IFR of 0.8% (95%-CI: 0.45-1.25). This IFR is consistent with previous findings in China (0.66%) and in the UK (0.9%) and lower than the value previously computed on the Diamond Princess cruse ship data (1.3%).</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Roques</LastName><ForeName>Lionel</ForeName><Initials>L</Initials><Identifier Source="ORCID">0000-0001-6647-7221</Identifier><AffiliationInfo><Affiliation>INRAE, BioSP, 84914 Avignon, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Klein</LastName><ForeName>Etienne K</ForeName><Initials>EK</Initials><AffiliationInfo><Affiliation>INRAE, BioSP, 84914 Avignon, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Papaïx</LastName><ForeName>Julien</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>INRAE, BioSP, 84914 Avignon, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sar</LastName><ForeName>Antoine</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Medicentre Moutier, 2740 Moutier, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Soubeyrand</LastName><ForeName>Samuel</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>INRAE, BioSP, 84914 Avignon, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>MEDIA</GrantID><Agency>INRAE</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>05</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Biology (Basel)</MedlineTA><NlmUniqueID>101587988</NlmUniqueID><ISSNLinking>2079-7737</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Bayesian inference</Keyword><Keyword MajorTopicYN="N">COVID-19</Keyword><Keyword MajorTopicYN="N">SIR model</Keyword><Keyword MajorTopicYN="N">case fatality rate</Keyword><Keyword MajorTopicYN="N">infection fatality ratio</Keyword><Keyword MajorTopicYN="N">mechanistic-statistical model</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>04</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>04</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>05</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>5</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>5</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>5</Month><Day>14</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32397286</ArticleId><ArticleId IdType="pii">biology9050097</ArticleId><ArticleId IdType="doi">10.3390/biology9050097</ArticleId><ArticleId IdType="pmc">PMC7284549</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Lancet. 2020 Mar 28;395(10229):1054-1062</Citation><ArticleIdList><ArticleId IdType="pubmed">32171076</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2020 May 13;:</Citation><ArticleIdList><ArticleId IdType="pubmed">32404476</ArticleId></ArticleIdList></Reference><Reference><Citation>J Math Biol. 2019 Jul;79(2):765-789</Citation><ArticleIdList><ArticleId IdType="pubmed">31098663</ArticleId></ArticleIdList></Reference><Reference><Citation>Lancet Infect Dis. 2020 Jun;20(6):669-677</Citation><ArticleIdList><ArticleId IdType="pubmed">32240634</ArticleId></ArticleIdList></Reference><Reference><Citation>Euro Surveill. 2020 Mar;25(12):</Citation><ArticleIdList><ArticleId IdType="pubmed">32234121</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2016 Mar 17;11(3):e0151217</Citation><ArticleIdList><ArticleId IdType="pubmed">26986201</ArticleId></ArticleIdList></Reference><Reference><Citation>J Travel Med. 2020 Mar 13;27(2):</Citation><ArticleIdList><ArticleId IdType="pubmed">32052846</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Med. 2020 May;26(5):672-675</Citation><ArticleIdList><ArticleId IdType="pubmed">32296168</ArticleId></ArticleIdList></Reference><Reference><Citation>JAMA. 2020 Mar 11;:</Citation><ArticleIdList><ArticleId IdType="pubmed">32159775</ArticleId></ArticleIdList></Reference><Reference><Citation>J Theor Biol. 2011 Apr 7;274(1):43-51</Citation><ArticleIdList><ArticleId IdType="pubmed">21237178</ArticleId></ArticleIdList></Reference><Reference><Citation>Biology (Basel). 2020 Mar 08;9(3):</Citation><ArticleIdList><ArticleId IdType="pubmed">32182724</ArticleId></ArticleIdList></Reference><Reference><Citation>Lancet Infect Dis. 2020 May;20(5):533-534</Citation><ArticleIdList><ArticleId IdType="pubmed">32087114</ArticleId></ArticleIdList></Reference><Reference><Citation>Int J Infect Dis. 2020 Mar;92:214-217</Citation><ArticleIdList><ArticleId IdType="pubmed">32007643</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>France</li><li>Suisse</li></country><region><li>Provence-Alpes-Côte d'Azur</li></region><settlement><li>Avignon</li></settlement></list><tree><country name="France"><region name="Provence-Alpes-Côte d'Azur"><name sortKey="Roques, Lionel" sort="Roques, Lionel" uniqKey="Roques L" first="Lionel" last="Roques">Lionel Roques</name></region><name sortKey="Klein, Etienne K" sort="Klein, Etienne K" uniqKey="Klein E" first="Etienne K" last="Klein">Etienne K. Klein</name><name sortKey="Papaix, Julien" sort="Papaix, Julien" uniqKey="Papaix J" first="Julien" last="Papaïx">Julien Papaïx</name><name sortKey="Soubeyrand, Samuel" sort="Soubeyrand, Samuel" uniqKey="Soubeyrand S" first="Samuel" last="Soubeyrand">Samuel Soubeyrand</name></country><country name="Suisse"><noRegion><name sortKey="Sar, Antoine" sort="Sar, Antoine" uniqKey="Sar A" first="Antoine" last="Sar">Antoine Sar</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/CovidFranceV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000284 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000284 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= CovidFranceV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:32397286
|texte= Using Early Data to Estimate the Actual Infection Fatality Ratio from COVID-19 in France.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:32397286" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a CovidFranceV1
| This area was generated with Dilib version V0.6.37. |  |