Serial interval and time-varying reproduction number estimation for COVID-19 in western Iran.
Identifieur interne : 000131 ( Main/Corpus ); précédent : 000130; suivant : 000132Serial interval and time-varying reproduction number estimation for COVID-19 in western Iran.
Auteurs : F. Najafi ; N. Izadi ; S-S Hashemi-Nazari ; F. Khosravi-Shadmani ; R. Nikbakht ; E. ShakibaSource :
- New microbes and new infections [ 2052-2975 ] ; 2020.
Abstract
There is no report on the serial interval (SI) of coronavirus disease 2019 (COVID-19) in Iran, the present report aims to estimate the SI and time-varying R of COVID-19 in western Iran. In this study, there were 1477 confirmed, probable and suspected cases of severe acute respiratory syndrome coronavirus 2 for Kermanshah from 22 February to 9 April. The close contacts of the confirmed cases were identified using telephone follow up of patients and their contacts. The SI distribution was used as an alternative. We fitted different models using the clinical onset dates of patients with their close contact (infector-infectee). Also, we applied a 'serial interval from sample' approach as a Bayesian methodology for estimating reproduction number. From 22 February to 29 March, 247 COVID-19 cases were confirmed by RT-PCR. Close contact between 21 patients (21 infector-infectee pairs), including 12 primary cases and 21 secondary cases, was confirmed. The mean and standard deviation of the SI were estimated as 5.71 and 3.89 days. The R varied from 0.79 to 1.88 for a 7-day time-lapse and ranged from 0.92 to 1.64 for a 14-day time-lapse on raw data. Also, the R varied from 0.83 to 1.84 for 7-day time-lapse and from 0.95 to 1.54 for a 14-day time-lapse using moving average data, respectively. It can be concluded that the low reproduction number for COVID-19 in Kermanshah province is an indication of the effectiveness of preventive and interventive programmes such as quarantine and isolation. Consequently, continuing these preventive measures is highly recommended.
DOI: 10.1016/j.nmni.2020.100715
PubMed: 32566233
PubMed Central: PMC7293842
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Izadi</name><affiliation><nlm:affiliation>Student Research Committee, Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical SciencesTehran, Iran.</nlm:affiliation></affiliation></author><author><name sortKey="Hashemi Nazari, S S" sort="Hashemi Nazari, S S" uniqKey="Hashemi Nazari S" first="S-S" last="Hashemi-Nazari">S-S Hashemi-Nazari</name><affiliation><nlm:affiliation>Prevention of Cardiovascular Disease Research Center, Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran.</nlm:affiliation></affiliation></author><author><name sortKey="Khosravi Shadmani, F" sort="Khosravi Shadmani, F" uniqKey="Khosravi Shadmani F" first="F" last="Khosravi-Shadmani">F. Khosravi-Shadmani</name><affiliation><nlm:affiliation>Research Centre for Environmental Determinants of Health, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.</nlm:affiliation></affiliation></author><author><name sortKey="Nikbakht, R" sort="Nikbakht, R" uniqKey="Nikbakht R" first="R" last="Nikbakht">R. Nikbakht</name><affiliation><nlm:affiliation>Department of Biostatistics, Faculty of Health, Mazandaran University of Medical Sciences, Sari, Iran.</nlm:affiliation></affiliation></author><author><name sortKey="Shakiba, E" sort="Shakiba, E" uniqKey="Shakiba E" first="E" last="Shakiba">E. Shakiba</name><affiliation><nlm:affiliation>Research Centre for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32566233</idno><idno type="pmid">32566233</idno><idno type="doi">10.1016/j.nmni.2020.100715</idno><idno type="pmc">PMC7293842</idno><idno type="wicri:Area/Main/Corpus">000131</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000131</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Serial interval and time-varying reproduction number estimation for COVID-19 in western Iran.</title><author><name sortKey="Najafi, F" sort="Najafi, F" uniqKey="Najafi F" first="F" last="Najafi">F. Najafi</name><affiliation><nlm:affiliation>Department of Epidemiology, Research Centre for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran.</nlm:affiliation></affiliation></author><author><name sortKey="Izadi, N" sort="Izadi, N" uniqKey="Izadi N" first="N" last="Izadi">N. Izadi</name><affiliation><nlm:affiliation>Student Research Committee, Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical SciencesTehran, Iran.</nlm:affiliation></affiliation></author><author><name sortKey="Hashemi Nazari, S S" sort="Hashemi Nazari, S S" uniqKey="Hashemi Nazari S" first="S-S" last="Hashemi-Nazari">S-S Hashemi-Nazari</name><affiliation><nlm:affiliation>Prevention of Cardiovascular Disease Research Center, Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran.</nlm:affiliation></affiliation></author><author><name sortKey="Khosravi Shadmani, F" sort="Khosravi Shadmani, F" uniqKey="Khosravi Shadmani F" first="F" last="Khosravi-Shadmani">F. Khosravi-Shadmani</name><affiliation><nlm:affiliation>Research Centre for Environmental Determinants of Health, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.</nlm:affiliation></affiliation></author><author><name sortKey="Nikbakht, R" sort="Nikbakht, R" uniqKey="Nikbakht R" first="R" last="Nikbakht">R. Nikbakht</name><affiliation><nlm:affiliation>Department of Biostatistics, Faculty of Health, Mazandaran University of Medical Sciences, Sari, Iran.</nlm:affiliation></affiliation></author><author><name sortKey="Shakiba, E" sort="Shakiba, E" uniqKey="Shakiba E" first="E" last="Shakiba">E. Shakiba</name><affiliation><nlm:affiliation>Research Centre for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran.</nlm:affiliation></affiliation></author></analytic><series><title level="j">New microbes and new infections</title><idno type="ISSN">2052-2975</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">There is no report on the serial interval (SI) of coronavirus disease 2019 (COVID-19) in Iran, the present report aims to estimate the SI and time-varying R of COVID-19 in western Iran. In this study, there were 1477 confirmed, probable and suspected cases of severe acute respiratory syndrome coronavirus 2 for Kermanshah from 22 February to 9 April. The close contacts of the confirmed cases were identified using telephone follow up of patients and their contacts. The SI distribution was used as an alternative. We fitted different models using the clinical onset dates of patients with their close contact (infector-infectee). Also, we applied a 'serial interval from sample' approach as a Bayesian methodology for estimating reproduction number. From 22 February to 29 March, 247 COVID-19 cases were confirmed by RT-PCR. Close contact between 21 patients (21 infector-infectee pairs), including 12 primary cases and 21 secondary cases, was confirmed. The mean and standard deviation of the SI were estimated as 5.71 and 3.89 days. The R varied from 0.79 to 1.88 for a 7-day time-lapse and ranged from 0.92 to 1.64 for a 14-day time-lapse on raw data. Also, the R varied from 0.83 to 1.84 for 7-day time-lapse and from 0.95 to 1.54 for a 14-day time-lapse using moving average data, respectively. It can be concluded that the low reproduction number for COVID-19 in Kermanshah province is an indication of the effectiveness of preventive and interventive programmes such as quarantine and isolation. Consequently, continuing these preventive measures is highly recommended.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32566233</PMID><DateRevised><Year>2020</Year><Month>06</Month><Day>23</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">2052-2975</ISSN><JournalIssue CitedMedium="Print"><Volume>36</Volume><PubDate><Year>2020</Year><Month>Jul</Month></PubDate></JournalIssue><Title>New microbes and new infections</Title><ISOAbbreviation>New Microbes New Infect</ISOAbbreviation></Journal><ArticleTitle>Serial interval and time-varying reproduction number estimation for COVID-19 in western Iran.</ArticleTitle><Pagination><MedlinePgn>100715</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.nmni.2020.100715</ELocationID><Abstract><AbstractText>There is no report on the serial interval (SI) of coronavirus disease 2019 (COVID-19) in Iran, the present report aims to estimate the SI and time-varying R of COVID-19 in western Iran. In this study, there were 1477 confirmed, probable and suspected cases of severe acute respiratory syndrome coronavirus 2 for Kermanshah from 22 February to 9 April. The close contacts of the confirmed cases were identified using telephone follow up of patients and their contacts. The SI distribution was used as an alternative. We fitted different models using the clinical onset dates of patients with their close contact (infector-infectee). Also, we applied a 'serial interval from sample' approach as a Bayesian methodology for estimating reproduction number. From 22 February to 29 March, 247 COVID-19 cases were confirmed by RT-PCR. Close contact between 21 patients (21 infector-infectee pairs), including 12 primary cases and 21 secondary cases, was confirmed. The mean and standard deviation of the SI were estimated as 5.71 and 3.89 days. The R varied from 0.79 to 1.88 for a 7-day time-lapse and ranged from 0.92 to 1.64 for a 14-day time-lapse on raw data. Also, the R varied from 0.83 to 1.84 for 7-day time-lapse and from 0.95 to 1.54 for a 14-day time-lapse using moving average data, respectively. It can be concluded that the low reproduction number for COVID-19 in Kermanshah province is an indication of the effectiveness of preventive and interventive programmes such as quarantine and isolation. Consequently, continuing these preventive measures is highly recommended.</AbstractText><CopyrightInformation>© 2020 The Author(s).</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Najafi</LastName><ForeName>F</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Epidemiology, Research Centre for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Izadi</LastName><ForeName>N</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Student Research Committee, Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical SciencesTehran, Iran.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hashemi-Nazari</LastName><ForeName>S-S</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>Prevention of Cardiovascular Disease Research Center, Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Khosravi-Shadmani</LastName><ForeName>F</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Research Centre for Environmental Determinants of Health, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nikbakht</LastName><ForeName>R</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Biostatistics, Faculty of Health, Mazandaran University of Medical Sciences, Sari, Iran.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shakiba</LastName><ForeName>E</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Research Centre for Environmental Determinants of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>06</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>New Microbes New Infect</MedlineTA><NlmUniqueID>101624750</NlmUniqueID><ISSNLinking>2052-2975</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Coronavirus disease 2019</Keyword><Keyword MajorTopicYN="N">Generation time</Keyword><Keyword MajorTopicYN="N">Iran</Keyword><Keyword MajorTopicYN="N">Serial interval</Keyword><Keyword MajorTopicYN="N">Time-varying reproduction number</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>05</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>06</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>06</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>6</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>6</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>6</Month><Day>23</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32566233</ArticleId><ArticleId IdType="doi">10.1016/j.nmni.2020.100715</ArticleId><ArticleId IdType="pii">S2052-2975(20)30067-6</ArticleId><ArticleId IdType="pii">100715</ArticleId><ArticleId IdType="pmc">PMC7293842</ArticleId></ArticleIdList><pmc-dir>pmcsd</pmc-dir>
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