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  1. Article ; Online: Incidence of Medically Attended Acute Respiratory Illnesses Due to Respiratory Viruses Across the Life Course During the 2018/19 Influenza Season.

    Jackson, Michael L / Starita, Lea / Kiniry, Erika / Phillips, C Hallie / Wellwood, Stacie / Cho, Shari / Kiavand, Anahita / Truong, Melissa / Han, Peter / Richardson, Matthew / Wolf, Caitlin R / Heimonen, Jessica / Nickerson, Deborah A / Chu, Helen Y

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

    2021  Volume 73, Issue 5, Page(s) 802–807

    Abstract: Background: Although multiple respiratory viruses circulate in humans, few studies have compared the incidence of different viruses across the life course. We estimated the incidence of outpatient illness due to 12 different viruses during November 2018 ...

    Abstract Background: Although multiple respiratory viruses circulate in humans, few studies have compared the incidence of different viruses across the life course. We estimated the incidence of outpatient illness due to 12 different viruses during November 2018 through April 2019 in a fully enumerated population.
    Methods: We conducted active surveillance for ambulatory care visits for acute respiratory illness (ARI) among members of Kaiser Permanente Washington (KPWA). Enrolled patients provided respiratory swab specimens which were tested for 12 respiratory viruses using reverse transcription polymerase chain reaction (RT-PCR). We estimated the cumulative incidence of infection due to each virus overall and by age group.
    Results: The KPWA population under surveillance included 202 562 individuals, of whom 2767 (1.4%) were enrolled in the study. Influenza A(H3N2) was the most commonly detected virus, with an overall incidence of 21 medically attended illnesses per 1000 population; the next most common viruses were influenza A(H1N1) (18 per 1000), coronaviruses (13 per 1000), respiratory syncytial virus (RSV, 13 per 1000), and rhinovirus (9 per 1000). RSV was the most common cause of medically attended ARI among children aged 1-4 years; coronaviruses were the most common among adults aged ≥65 years.
    Conclusions: Consistent with other studies focused on single viruses, we found that influenza and RSV were major causes of acute respiratory illness in persons of all ages. In comparison, coronaviruses and rhinovirus were also important pathogens. Prior to the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), coronaviruses were the second-most common cause of medically attended ARI during the 2018/19 influenza season.
    Language English
    Publishing date 2021-02-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1099781-7
    ISSN 1537-6591 ; 1058-4838
    ISSN (online) 1537-6591
    ISSN 1058-4838
    DOI 10.1093/cid/ciab131
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Ribosomal RNA sequences of Clostridium piliforme isolated from rodent and rabbit: re-examining the phylogeny of the Tyzzer's disease agent and development of a diagnostic polymerase chain reaction assay.

    Feldman, Sanford H / Kiavand, Anahita / Seidelin, Michel / Reiske, Heinz R

    Journal of the American Association for Laboratory Animal Science : JAALAS

    2006  Volume 45, Issue 5, Page(s) 65–73

    Abstract: We used polymerase chain reaction (PCR) technology to amplify the 16S rRNA gene, the intergenic spacer, and most of the 23S rRNA gene from 6 isolates (2 mice, 1 hamster, 1 rat, and 2 rabbit isolates) of the Tyzzer's disease agent (Clostridium piliforme) ... ...

    Abstract We used polymerase chain reaction (PCR) technology to amplify the 16S rRNA gene, the intergenic spacer, and most of the 23S rRNA gene from 6 isolates (2 mice, 1 hamster, 1 rat, and 2 rabbit isolates) of the Tyzzer's disease agent (Clostridium piliforme) and C. colinum. Sequence similarity searches of GenBank identified 45 closely related bacteria, which we used for phylogenetic analysis by parsimony and maximum-likelihood methods using Escherichia coli to root the resulting phylogram. Microorganisms identified as C. piliforme form 3 clusters within a single clade; the nearest related distinguishable species is C. colinum. Other bacterial clades closely related to C. piliforme are clostridia previously identified by molecular methods in the bovine, porcine, and human gastrointestinal tracts. DNA sequence alignment highlighting sequence differences were used to design a rodent and rabbit C. piliforme-specific PCR assay, which targets a 639-basepair region at the 3' end of the 16S rRNA gene and the 5' end of the intergenic spacer. We used this PCR assay to examine 4 rat fecal samples from C. piliformeseropositive rats and reexamine 2 rabbit fecal samples previously identified as containing DNA sequences consistent with C. piliforme infection by 16S PCR assay. Our new assay did not detect the presence of C. piliforme DNA sequences in either the rat or rabbit fecal DNA samples, consistent with the absence of clinical disease in the colonies evaluated.
    MeSH term(s) Animals ; Bacterial Infections ; Clostridium/genetics ; Clostridium/isolation & purification ; Cricetinae ; Feces/microbiology ; Mice ; Molecular Diagnostic Techniques/methods ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Rabbits ; Rats ; Rodent Diseases/microbiology ; Rodent Diseases/pathology ; Sensitivity and Specificity
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2006-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1559-6109
    ISSN 1559-6109
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: A sensitive liquid chromatography/mass spectrometry-based assay for quantitation of amino-containing moieties in lipid A.

    Kalhorn, Thomas F / Kiavand, Anahita / Cohen, Ilana E / Nelson, Amanda K / Ernst, Robert K

    Rapid communications in mass spectrometry : RCM

    2009  Volume 23, Issue 3, Page(s) 433–442

    Abstract: A novel sensitive liquid chromatography/mass spectrometry-based assay was developed for the quantitation of aminosugars, including 2-amino-2-deoxyglucose (glucosamine, GlcN), 2-amino-2-deoxygalactose (galactosamine, GalN), and 4-amino-4-deoxyarabinose ( ... ...

    Abstract A novel sensitive liquid chromatography/mass spectrometry-based assay was developed for the quantitation of aminosugars, including 2-amino-2-deoxyglucose (glucosamine, GlcN), 2-amino-2-deoxygalactose (galactosamine, GalN), and 4-amino-4-deoxyarabinose (aminoarabinose, AraN), and for ethanolamine (EtN), present in lipid A. This assay enables the identification and quantitation of all amino-containing moieties present in lipopolysaccharide or lipid A from a single sample. The method was applied to the analysis of lipid A (endotoxin) isolated from a variety of biosynthetic and regulatory mutants of Salmonella enterica serovar Typhimurium and Francisella tularensis subspecies novicida. Lipid A is treated with trifluoroacetic acid to liberate and deacetylate individual aminosugars and mass tagged with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate, which reacts with primary and secondary amines. The derivatives are separated using reversed-phase chromatography and analyzed using a single quadrupole mass spectrometer to detect quantities as small as 20 fmol. GalN was detected only in Francisella and AraN only in Salmonella, while GlcN was detected in lipid A samples from both species of bacteria. Additionally, we found an approximately 10-fold increase in the level of AraN in lipid A isolated from Salmonella grown in magnesium-limited versus magnesium-replete conditions. Salmonella with defined mutations in lipid A synthesis and regulatory genes were used to further validate the assay. Salmonella with null mutations in the phoP, pmrE, and prmF genes were unable to add AraN to their lipid A, while Salmonella with constitutively active phoP and pmrA exhibited AraN modification of lipid A even in the normally repressive magnesium-replete growth condition. The described assay produces excellent repeatability and reproducibility for the detection of amino-containing moieties in lipid A from a variety of bacterial sources.
    MeSH term(s) Amino Sugars/analysis ; Arabinose/analogs & derivatives ; Arabinose/analysis ; Chromatography, Liquid/methods ; Ethanolamine/analysis ; Francisella tularensis/chemistry ; Francisella tularensis/genetics ; Francisella tularensis/metabolism ; Galactosamine/analysis ; Glucosamine/analysis ; Linear Models ; Lipid A/chemistry ; Mass Spectrometry/methods ; Models, Chemical ; Mutation ; Reproducibility of Results ; Salmonella typhi/chemistry ; Salmonella typhi/genetics ; Salmonella typhi/metabolism ; Sensitivity and Specificity
    Chemical Substances Amino Sugars ; Lipid A ; aminoarabinose ; Ethanolamine (5KV86114PT) ; Galactosamine (7535-00-4) ; Arabinose (B40ROO395Z) ; Glucosamine (N08U5BOQ1K)
    Language English
    Publishing date 2009-01-07
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 58731-x
    ISSN 1097-0231 ; 0951-4198
    ISSN (online) 1097-0231
    ISSN 0951-4198
    DOI 10.1002/rcm.3900
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The Seattle Flu Study: a multiarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology.

    Chu, Helen Y / Boeckh, Michael / Englund, Janet A / Famulare, Michael / Lutz, Barry / Nickerson, Deborah A / Rieder, Mark / Starita, Lea M / Adler, Amanda / Brandstetter, Elisabeth / Frazer, Chris D / Han, Peter D / Gulati, Reena K / Hadfield, James / Jackson, Michael / Kiavand, Anahita / Kimball, Louise E / Lacombe, Kirsten / Newman, Kira /
    Sibley, Thomas R / Logue, Jennifer K / Lyon, Victoria Rachel / Wolf, Caitlin R / Zigman Suchsland, Monica / Shendure, Jay / Bedford, Trevor

    BMJ open

    2020  Volume 10, Issue 10, Page(s) e037295

    Abstract: Introduction: Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterise, and potentially contain new and emerging influenza ... ...

    Abstract Introduction: Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterise, and potentially contain new and emerging influenza strains at both an individual and population level. The objective of this study is to use data gathered simultaneously from community and hospital sites to develop a model of how influenza enters and spreads in a population.
    Methods and analysis: Starting in the 2018-2019 season, we have been enrolling individuals with acute respiratory illness from community sites throughout the Seattle metropolitan area, including clinics, childcare facilities, Seattle-Tacoma International Airport, workplaces, college campuses and homeless shelters. At these sites, we collect clinical data and mid-nasal swabs from individuals with at least two acute respiratory symptoms. Additionally, we collect residual nasal swabs and data from individuals who seek care for respiratory symptoms at four regional hospitals. Samples are tested using a multiplex molecular assay, and influenza whole genome sequencing is performed for samples with influenza detected. Geospatial mapping and computational modelling platforms are in development to characterise the regional spread of influenza and other respiratory pathogens.
    Ethics and dissemination: The study was approved by the University of Washington's Institutional Review Board (STUDY00006181). Results will be disseminated through talks at conferences, peer-reviewed publications and on the study website (www.seattleflu.org).
    MeSH term(s) Genomics ; Humans ; Influenza, Human/epidemiology ; Prevalence ; Prospective Studies ; Seasons
    Keywords covid19
    Language English
    Publishing date 2020-10-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2599832-8
    ISSN 2044-6055 ; 2044-6055
    ISSN (online) 2044-6055
    ISSN 2044-6055
    DOI 10.1136/bmjopen-2020-037295
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology

    Chu, Helen Y. / Boeckh, Michael / Englund, Janet A. / Famulare, Michael / Lutz, Barry R. / Nickerson, Deborah A / Rieder, Mark J. / Starita, Lea M / Adler, Amanda / Brandstetter, Elisabeth / Frazar, Chris D. / Han, Peter D. / Gularti, Reena K. / Hadfield, James / Jackson, Michael L. / Kiavand, Anahita / Kimball, Louise E. / Lacombe, Kirsten / Logue, Jennifer /
    Lyon, Victoria / Newman, Kira L. / Sibley, Thomas R. / Zigman Suschsland, Monica L. / Wolf, Caitlin / Shendure, Jay / Bedford, Trevor

    Abstract: Introduction. Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterize, and potentially contain new and emerging influenza ... ...

    Abstract Introduction. Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterize, and potentially contain new and emerging influenza strains at a population level. The objective of this study is to use data gathered simultaneously from community and hospital sites to develop a model of how influenza enters and spreads in a population. Methods and Analysis. Starting in the 2018-19 season, we have been enrolling individuals with acute respiratory illness from community sites throughout the Seattle metropolitan area, including clinics, childcare facilities, Seattle-Tacoma International Airport, workplaces, college campuses, and homeless shelters. At these sites, we collect clinical data and mid-nasal swabs from individuals with at least two acute respiratory symptoms. Additionally, we collect residual nasal swabs and data from individuals who seek care for respiratory symptoms at four regional hospitals. Samples are tested using a multiplex molecular assay, and influenza whole genome sequencing is performed for samples with influenza detected. Geospatial mapping and computational modeling platforms are in development to characterize the regional spread of influenza and other respiratory pathogens. Ethics and Dissemination. The study was approved by the University of Washington's Institutional Review Board. Results will be disseminated through talks at conferences, peer-reviewed publications, and on the study website (www.seattleflu.org).
    Keywords covid19
    Publisher MedRxiv
    Document type Article ; Online
    DOI 10.1101/2020.03.02.20029595
    Database COVID19

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  6. Article: Cryptic transmission of SARS-CoV-2 in Washington State.

    Bedford, Trevor / Greninger, Alexander L / Roychoudhury, Pavitra / Starita, Lea M / Famulare, Michael / Huang, Meei-Li / Nalla, Arun / Pepper, Gregory / Reinhardt, Adam / Xie, Hong / Shrestha, Lasata / Nguyen, Truong N / Adler, Amanda / Brandstetter, Elisabeth / Cho, Shari / Giroux, Danielle / Han, Peter D / Fay, Kairsten / Frazar, Chris D /
    Ilcisin, Misja / Lacombe, Kirsten / Lee, Jover / Kiavand, Anahita / Richardson, Matthew / Sibley, Thomas R / Truong, Melissa / Wolf, Caitlin R / Nickerson, Deborah A / Rieder, Mark J / Englund, Janet A / Hadfield, James / Hodcroft, Emma B / Huddleston, John / Moncla, Louise H / Müller, Nicola F / Neher, Richard A / Deng, Xianding / Gu, Wei / Federman, Scot / Chiu, Charles / Duchin, Jeff / Gautom, Romesh / Melly, Geoff / Hiatt, Brian / Dykema, Philip / Lindquist, Scott / Queen, Krista / Tao, Ying / Uehara, Anna / Tong, Suxiang / MacCannell, Duncan / Armstrong, Gregory L / Baird, Geoffrey S / Chu, Helen Y / Shendure, Jay / Jerome, Keith R

    medRxiv : the preprint server for health sciences

    2020  

    Abstract: Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. ... ...

    Abstract Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We found that the large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, before active community surveillance was implemented. We estimate a common ancestor of this outbreak clade as occurring between 18 January and 9 February 2020. From genomic data, we estimate an exponential doubling between 2.4 and 5.1 days. These results highlight the need for large-scale community surveillance for SARS-CoV-2 introductions and spread and the power of pathogen genomics to inform epidemiological understanding.
    Keywords covid19
    Language English
    Publishing date 2020-04-06
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.04.02.20051417
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Cryptic transmission of SARS-CoV-2 in Washington state.

    Bedford, Trevor / Greninger, Alexander L / Roychoudhury, Pavitra / Starita, Lea M / Famulare, Michael / Huang, Meei-Li / Nalla, Arun / Pepper, Gregory / Reinhardt, Adam / Xie, Hong / Shrestha, Lasata / Nguyen, Truong N / Adler, Amanda / Brandstetter, Elisabeth / Cho, Shari / Giroux, Danielle / Han, Peter D / Fay, Kairsten / Frazar, Chris D /
    Ilcisin, Misja / Lacombe, Kirsten / Lee, Jover / Kiavand, Anahita / Richardson, Matthew / Sibley, Thomas R / Truong, Melissa / Wolf, Caitlin R / Nickerson, Deborah A / Rieder, Mark J / Englund, Janet A / Hadfield, James / Hodcroft, Emma B / Huddleston, John / Moncla, Louise H / Müller, Nicola F / Neher, Richard A / Deng, Xianding / Gu, Wei / Federman, Scot / Chiu, Charles / Duchin, Jeffrey S / Gautom, Romesh / Melly, Geoff / Hiatt, Brian / Dykema, Philip / Lindquist, Scott / Queen, Krista / Tao, Ying / Uehara, Anna / Tong, Suxiang / MacCannell, Duncan / Armstrong, Gregory L / Baird, Geoffrey S / Chu, Helen Y / Shendure, Jay / Jerome, Keith R

    Science (New York, N.Y.)

    2020  Volume 370, Issue 6516, Page(s) 571–575

    Abstract: After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission ... ...

    Abstract After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.
    MeSH term(s) Bayes Theorem ; Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/transmission ; Genome, Viral ; Humans ; Likelihood Functions ; Pandemics ; Phylogeny ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/transmission ; SARS-CoV-2 ; Washington/epidemiology
    Keywords covid19
    Language English
    Publishing date 2020-09-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abc0523
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Cryptic transmission of SARS-CoV-2 in Washington State

    Bedford, Trevor / Greninger, Alexander L. / Roychoudhury, Pavitra / Starita, Lea M / Famulare, Michael / Huang, Meei-Li / Nalla, Arun / Pepper, Gregory / Reinhardt, Adam / Xie, Hong / Shrestha, Lasata / Nguyen, Truong N / Adler, Amanda / Brandstetter, Elisabeth / Cho, Shari / Giroux, Danielle / Han, Peter D / Fay, Kairsten / Frazar, Chris D /
    Ilcisin, Misja / Lacombe, Kirsten / Lee, Jover / Kiavand, Anahita / Richardson, Matthew / Sibley, Thomas R / Truong, Melissa / Wolf, Caitlin R / Nickerson, Deborah A / Rieder, Mark J / Englund, Janet A / the Seattle Flu Study Investigators / Hadfield, James / Hodcroft, Emma B / Huddleston, John / Moncla, Louise H / Müller, Nicola F / Neher, Richard A / Deng, Xianding / Gu, Wei / Federman, Scot / Chiu, Charles / Duchin, Jeff / Gautom, Romesh / Melly, Geoff / Hiatt, Brian / Dykema, Philip / Lindquist, Scott / Queen, Krista / Tao, Ying / Uehara, Anna / Tong, Suxiang / MacCannell, Duncan / Armstrong, Gregory L / Baird, Geoffrey S / Chu, Helen Y / Shendure, Jay / Jerome, Keith R

    medRxiv

    Abstract: Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. ... ...

    Abstract Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We found that the large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, before active community surveillance was implemented. We estimate a common ancestor of this outbreak clade as occurring between 18 January and 9 February 2020. From genomic data, we estimate an exponential doubling between 2.4 and 5.1 days. These results highlight the need for large-scale community surveillance for SARS-CoV-2 introductions and spread and the power of pathogen genomics to inform epidemiological understanding.
    Keywords covid19
    Language English
    Publishing date 2020-04-16
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.04.02.20051417
    Database COVID19

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  9. Article ; Online: Cryptic transmission of SARS-CoV-2 in Washington State

    Bedford, Trevor / Greninger, Alexander L. / Roychoudhury, Pavitra / Starita, Lea M / Famulare, Michael / Huang, Meei-Li / Nalla, Arun / Pepper, Gregory / Reinhardt, Adam / Xie, Hong / Shrestha, Lasata / Nguyen, Truong N / Adler, Amanda / Brandstetter, Elisabeth / Cho, Shari / Giroux, Danielle / Han, Peter D / Fay, Kairsten / Frazar, Chris D /
    Ilcisin, Misja / Lacombe, Kirsten / Lee, Jover / Kiavand, Anahita / Richardson, Matthew / Sibley, Thomas R / Truong, Melissa / Wolf, Caitlin R / Nickerson, Deborah A / Rieder, Mark J / Englund, Janet A / the Seattle Flu Study Investigators / Hadfield, James / Hodcroft, Emma B / Huddleston, John / Moncla, Louise H / Müller, Nicola F / Neher, Richard A / Deng, Xianding / Gu, Wei / Federman, Scot / Chiu, Charles / Duchin, Jeff / Gautom, Romesh / Melly, Geoff / Hiatt, Brian / Dykema, Philip / Lindquist, Scott / Queen, Krista / Tao, Ying / Uehara, Anna / Tong, Suxiang / MacCannell, Duncan / Armstrong, Gregory L / Baird, Geoffrey S / Chu, Helen Y / Jerome, Keith R

    medRxiv

    Abstract: Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. ... ...

    Abstract Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We found that the large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, before active community surveillance was implemented. We estimate a common ancestor of this outbreak clade as occurring between 18 January and 9 February 2020. From genomic data, we estimate an exponential doubling between 2.4 and 5.1 days. These results highlight the need for large-scale community surveillance for SARS-CoV-2 introductions and spread and the power of pathogen genomics to inform epidemiological understanding.
    Keywords covid19
    Language English
    Publishing date 2020-04-06
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.04.02.20051417
    Database COVID19

    Kategorien

  10. Article: Cryptic transmission of SARS-CoV-2 in Washington state

    Bedford, Trevor / Greninger, Alexander L / Roychoudhury, Pavitra / Starita, Lea M / Famulare, Michael / Huang, Meei-Li / Nalla, Arun / Pepper, Gregory / Reinhardt, Adam / Xie, Hong / Shrestha, Lasata / Nguyen, Truong N / Adler, Amanda / Brandstetter, Elisabeth / Cho, Shari / Giroux, Danielle / Han, Peter D / Fay, Kairsten / Frazar, Chris D /
    Ilcisin, Misja / Lacombe, Kirsten / Lee, Jover / Kiavand, Anahita / Richardson, Matthew / Sibley, Thomas R / Truong, Melissa / Wolf, Caitlin R / Nickerson, Deborah A / Rieder, Mark J / Englund, Janet A / Hadfield, James / Hodcroft, Emma B / Huddleston, John / Moncla, Louise H / Müller, Nicola F / Neher, Richard A / Deng, Xianding / Gu, Wei / Federman, Scot / Chiu, Charles / Duchin, Jeffrey S / Gautom, Romesh / Melly, Geoff / Hiatt, Brian / Dykema, Philip / Lindquist, Scott / Queen, Krista / Tao, Ying / Uehara, Anna / Tong, Suxiang

    Science

    Abstract: After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission ... ...

    Abstract After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #760213
    Database COVID19

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