Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells.
Identifieur interne : 000602 ( Main/Exploration ); précédent : 000601; suivant : 000603Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells.
Auteurs : Neal G. Ravindra [États-Unis] ; Mia Madel Alfajaro [États-Unis] ; Victor Gasque [États-Unis, France] ; Jin Wei [États-Unis] ; Renata B. Filler [États-Unis] ; Nicholas C. Huston [États-Unis] ; Han Wan [États-Unis] ; Klara Szigeti-Buck [États-Unis] ; Bao Wang [États-Unis] ; Ruth R. Montgomery [États-Unis] ; Stephanie C. Eisenbarth [États-Unis] ; Adam Williams [États-Unis] ; Anna Marie Pyle [États-Unis] ; Akiko Iwasaki [États-Unis] ; Tamas L. Horvath [États-Unis] ; Ellen F. Foxman [États-Unis] ; David Van Dijk [États-Unis] ; Craig B. Wilen [États-Unis]Source :
- bioRxiv : the preprint server for biology ; 2020.
Abstract
SARS-CoV-2, the causative agent of COVID-19, has resulted in more than 3,000,000 infections and 200,000 deaths. There are currently no approved drugs or vaccines for the treatment or prevention of COVID-19. Enhanced understanding of SARS-CoV-2 infection and pathogenesis is critical for the development of therapeutics. To reveal insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2 we performed single-cell RNA sequencing of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface cultures over a time-course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as the major target of infection, which we confirmed by electron microscopy. Over the course of infection, cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell intrinsic expression of type I and type III IFNs and IL6 but not IL1. This results in expression of interferon stimulated genes in both infected and bystander cells. Here, we have conducted an in-depth analysis of SARS-CoV-2 infection in HBECs and provide a detailed characterization of genes, cell types, and cell state changes associated with the infection.
DOI: 10.1101/2020.05.06.081695
PubMed: 32511382
PubMed Central: PMC7263511
Affiliations:
- France, États-Unis
- Auvergne-Rhône-Alpes, Connecticut, Maryland, Rhône-Alpes, Île-de-France
- Lyon, Paris
- Université Claude Bernard Lyon 1
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Wilen</name><affiliation wicri:level="2"><nlm:affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Immunobiology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32511382</idno><idno type="pmid">32511382</idno><idno type="doi">10.1101/2020.05.06.081695</idno><idno type="pmc">PMC7263511</idno><idno type="wicri:Area/Main/Corpus">000F14</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000F14</idno><idno type="wicri:Area/Main/Curation">000F14</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000F14</idno><idno type="wicri:Area/Main/Exploration">000F14</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells.</title><author><name sortKey="Ravindra, Neal G" sort="Ravindra, Neal G" uniqKey="Ravindra N" first="Neal G" last="Ravindra">Neal G. Ravindra</name><affiliation wicri:level="2"><nlm:affiliation>Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Computer Science, Yale University, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Alfajaro, Mia Madel" sort="Alfajaro, Mia Madel" uniqKey="Alfajaro M" first="Mia Madel" last="Alfajaro">Mia Madel Alfajaro</name><affiliation wicri:level="2"><nlm:affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Immunobiology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Gasque, Victor" sort="Gasque, Victor" uniqKey="Gasque V" first="Victor" last="Gasque">Victor Gasque</name><affiliation wicri:level="2"><nlm:affiliation>Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Computer Science, Yale University, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Université Claude Bernard Lyon 1, Faculté de Médecine Lyon Est, Lyon, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université Claude Bernard Lyon 1, Faculté de Médecine Lyon Est, Lyon</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Rhône-Alpes</region><settlement type="city">Lyon</settlement></placeName><orgName type="university">Université Claude Bernard Lyon 1</orgName></affiliation><affiliation wicri:level="3"><nlm:affiliation>Département de Bioinformatique, Univ Evry, Université Paris-Saclay, Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Département de Bioinformatique, Univ Evry, Université Paris-Saclay, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Wei, Jin" sort="Wei, Jin" uniqKey="Wei J" first="Jin" last="Wei">Jin Wei</name><affiliation wicri:level="2"><nlm:affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Immunobiology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Filler, Renata B" sort="Filler, Renata B" uniqKey="Filler R" first="Renata B" last="Filler">Renata B. Filler</name><affiliation wicri:level="2"><nlm:affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Immunobiology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Huston, Nicholas C" sort="Huston, Nicholas C" uniqKey="Huston N" first="Nicholas C" last="Huston">Nicholas C. Huston</name><affiliation wicri:level="2"><nlm:affiliation>Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Wan, Han" sort="Wan, Han" uniqKey="Wan H" first="Han" last="Wan">Han Wan</name><affiliation wicri:level="2"><nlm:affiliation>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Szigeti Buck, Klara" sort="Szigeti Buck, Klara" uniqKey="Szigeti Buck K" first="Klara" last="Szigeti-Buck">Klara Szigeti-Buck</name><affiliation wicri:level="2"><nlm:affiliation>Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Comparative Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Neuroscience, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Wang, Bao" sort="Wang, Bao" uniqKey="Wang B" first="Bao" last="Wang">Bao Wang</name><affiliation wicri:level="2"><nlm:affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Immunobiology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Montgomery, Ruth R" sort="Montgomery, Ruth R" uniqKey="Montgomery R" first="Ruth R" last="Montgomery">Ruth R. Montgomery</name><affiliation wicri:level="2"><nlm:affiliation>Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Internal Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Eisenbarth, Stephanie C" sort="Eisenbarth, Stephanie C" uniqKey="Eisenbarth S" first="Stephanie C" last="Eisenbarth">Stephanie C. Eisenbarth</name><affiliation wicri:level="2"><nlm:affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Immunobiology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Williams, Adam" sort="Williams, Adam" uniqKey="Williams A" first="Adam" last="Williams">Adam Williams</name><affiliation wicri:level="2"><nlm:affiliation>The Jackson Laboratory, Farmington, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Jackson Laboratory, Farmington, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Pyle, Anna Marie" sort="Pyle, Anna Marie" uniqKey="Pyle A" first="Anna Marie" last="Pyle">Anna Marie Pyle</name><affiliation wicri:level="2"><nlm:affiliation>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Chevy Chase, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Iwasaki, Akiko" sort="Iwasaki, Akiko" uniqKey="Iwasaki A" first="Akiko" last="Iwasaki">Akiko Iwasaki</name><affiliation wicri:level="2"><nlm:affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Immunobiology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Chevy Chase, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Horvath, Tamas L" sort="Horvath, Tamas L" uniqKey="Horvath T" first="Tamas L" last="Horvath">Tamas L. Horvath</name><affiliation wicri:level="2"><nlm:affiliation>Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Comparative Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Foxman, Ellen F" sort="Foxman, Ellen F" uniqKey="Foxman E" first="Ellen F" last="Foxman">Ellen F. Foxman</name><affiliation wicri:level="2"><nlm:affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Immunobiology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Van Dijk, David" sort="Van Dijk, David" uniqKey="Van Dijk D" first="David" last="Van Dijk">David Van Dijk</name><affiliation wicri:level="2"><nlm:affiliation>Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Computer Science, Yale University, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Wilen, Craig B" sort="Wilen, Craig B" uniqKey="Wilen C" first="Craig B" last="Wilen">Craig B. Wilen</name><affiliation wicri:level="2"><nlm:affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Immunobiology, Yale School of Medicine, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author></analytic><series><title level="j">bioRxiv : the preprint server for biology</title><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">SARS-CoV-2, the causative agent of COVID-19, has resulted in more than 3,000,000 infections and 200,000 deaths. There are currently no approved drugs or vaccines for the treatment or prevention of COVID-19. Enhanced understanding of SARS-CoV-2 infection and pathogenesis is critical for the development of therapeutics. To reveal insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2 we performed single-cell RNA sequencing of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface cultures over a time-course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as the major target of infection, which we confirmed by electron microscopy. Over the course of infection, cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell intrinsic expression of type I and type III IFNs and IL6 but not IL1. This results in expression of interferon stimulated genes in both infected and bystander cells. Here, we have conducted an in-depth analysis of SARS-CoV-2 infection in HBECs and provide a detailed characterization of genes, cell types, and cell state changes associated with the infection.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32511382</PMID><DateRevised><Year>2020</Year><Month>07</Month><Day>24</Day></DateRevised><Article PubModel="Electronic"><Journal><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>May</Month><Day>07</Day></PubDate></JournalIssue><Title>bioRxiv : the preprint server for biology</Title><ISOAbbreviation>bioRxiv</ISOAbbreviation></Journal><ArticleTitle>Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">2020.05.06.081695</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1101/2020.05.06.081695</ELocationID><Abstract><AbstractText>SARS-CoV-2, the causative agent of COVID-19, has resulted in more than 3,000,000 infections and 200,000 deaths. There are currently no approved drugs or vaccines for the treatment or prevention of COVID-19. Enhanced understanding of SARS-CoV-2 infection and pathogenesis is critical for the development of therapeutics. To reveal insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2 we performed single-cell RNA sequencing of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface cultures over a time-course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as the major target of infection, which we confirmed by electron microscopy. Over the course of infection, cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell intrinsic expression of type I and type III IFNs and IL6 but not IL1. This results in expression of interferon stimulated genes in both infected and bystander cells. Here, we have conducted an in-depth analysis of SARS-CoV-2 infection in HBECs and provide a detailed characterization of genes, cell types, and cell state changes associated with the infection.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ravindra</LastName><ForeName>Neal G</ForeName><Initials>NG</Initials><AffiliationInfo><Affiliation>Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science, Yale University, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Alfajaro</LastName><ForeName>Mia Madel</ForeName><Initials>MM</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gasque</LastName><ForeName>Victor</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science, Yale University, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Université Claude Bernard Lyon 1, Faculté de Médecine Lyon Est, Lyon, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Département de Bioinformatique, Univ Evry, Université Paris-Saclay, Paris, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Jin</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Filler</LastName><ForeName>Renata B</ForeName><Initials>RB</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Huston</LastName><ForeName>Nicholas C</ForeName><Initials>NC</Initials><AffiliationInfo><Affiliation>Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wan</LastName><ForeName>Han</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Szigeti-Buck</LastName><ForeName>Klara</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Bao</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Montgomery</LastName><ForeName>Ruth R</ForeName><Initials>RR</Initials><AffiliationInfo><Affiliation>Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eisenbarth</LastName><ForeName>Stephanie C</ForeName><Initials>SC</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Williams</LastName><ForeName>Adam</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>The Jackson Laboratory, Farmington, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pyle</LastName><ForeName>Anna Marie</ForeName><Initials>AM</Initials><AffiliationInfo><Affiliation>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Iwasaki</LastName><ForeName>Akiko</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Horvath</LastName><ForeName>Tamas L</ForeName><Initials>TL</Initials><AffiliationInfo><Affiliation>Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Foxman</LastName><ForeName>Ellen F</ForeName><Initials>EF</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van Dijk</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science, Yale University, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wilen</LastName><ForeName>Craig B</ForeName><Initials>CB</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>K08 AI119139</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>K08 AI128043</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 AI141609</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R21 AI133440</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D000076942">Preprint</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>05</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>bioRxiv</MedlineTA><NlmUniqueID>101680187</NlmUniqueID></MedlineJournalInfo><CoiStatement>Declaration of interests: The authors declare no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>6</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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