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  1. Article ; Online: Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.

    Washington, Nicole L / Gangavarapu, Karthik / Zeller, Mark / Bolze, Alexandre / Cirulli, Elizabeth T / Schiabor Barrett, Kelly M / Larsen, Brendan B / Anderson, Catelyn / White, Simon / Cassens, Tyler / Jacobs, Sharoni / Levan, Geraint / Nguyen, Jason / Ramirez, Jimmy M / Rivera-Garcia, Charlotte / Sandoval, Efren / Wang, Xueqing / Wong, David / Spencer, Emily /
    Robles-Sikisaka, Refugio / Kurzban, Ezra / Hughes, Laura D / Deng, Xianding / Wang, Candace / Servellita, Venice / Valentine, Holly / De Hoff, Peter / Seaver, Phoebe / Sathe, Shashank / Gietzen, Kimberly / Sickler, Brad / Antico, Jay / Hoon, Kelly / Liu, Jingtao / Harding, Aaron / Bakhtar, Omid / Basler, Tracy / Austin, Brett / MacCannell, Duncan / Isaksson, Magnus / Febbo, Phillip G / Becker, David / Laurent, Marc / McDonald, Eric / Yeo, Gene W / Knight, Rob / Laurent, Louise C / de Feo, Eileen / Worobey, Michael / Chiu, Charles Y / Suchard, Marc A / Lu, James T / Lee, William / Andersen, Kristian G

    Cell

    2021  Volume 184, Issue 10, Page(s) 2587–2594.e7

    Abstract: The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has ... gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing ... to its early emergence. We found that, while the fraction of B.1.1.7 varied by state, the variant increased ...

    Abstract The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of this variant in the United States (US), tracking it back to its early emergence. We found that, while the fraction of B.1.1.7 varied by state, the variant increased at a logistic rate with a roughly weekly doubling rate and an increased transmission of 40%-50%. We revealed several independent introductions of B.1.1.7 into the US as early as late November 2020, with community transmission spreading it to most states within months. We show that the US is on a similar trajectory as other countries where B.1.1.7 became dominant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.
    MeSH term(s) COVID-19/genetics ; COVID-19/mortality ; COVID-19/transmission ; Female ; Humans ; Male ; Models, Biological ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; SARS-CoV-2/pathogenicity ; United States/epidemiology
    Language English
    Publishing date 2021-03-30
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2021.03.052
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.

    Washington, Nicole L / Gangavarapu, Karthik / Zeller, Mark / Bolze, Alexandre / Cirulli, Elizabeth T / Barrett, Kelly M Schiabor / Larsen, Brendan B / Anderson, Catelyn / White, Simon / Cassens, Tyler / Jacobs, Sharoni / Levan, Geraint / Nguyen, Jason / Ramirez, Jimmy M / Rivera-Garcia, Charlotte / Sandoval, Efren / Wang, Xueqing / Wong, David / Spencer, Emily /
    Robles-Sikisaka, Refugio / Kurzban, Ezra / Hughes, Laura D / Deng, Xianding / Wang, Candace / Servellita, Venice / Valentine, Holly / De Hoff, Peter / Seaver, Phoebe / Sathe, Shashank / Gietzen, Kimberly / Sickler, Brad / Antico, Jay / Hoon, Kelly / Liu, Jingtao / Harding, Aaron / Bakhtar, Omid / Basler, Tracy / Austin, Brett / Isaksson, Magnus / Febbo, Phillip G / Becker, David / Laurent, Marc / McDonald, Eric / Yeo, Gene W / Knight, Rob / Laurent, Louise C / de Feo, Eileen / Worobey, Michael / Chiu, Charles / Suchard, Marc A / Lu, James T / Lee, William / Andersen, Kristian G

    medRxiv : the preprint server for health sciences

    2021  

    Abstract: ... on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant ... As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first ... proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing ...

    Abstract As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.
    Language English
    Publishing date 2021-02-07
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.02.06.21251159
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

    Washington, Nicole L. / Gangavarapu, Karthik / Zeller, Mark / Bolze, Alexandre / Cirulli, Elizabeth T. / Schiabor Barrett, Kelly M. / Larsen, Brendan B. / Anderson, Catelyn / White, Simon / Cassens, Tyler / Jacobs, Sharoni / Levan, Geraint / Nguyen, Jason / Ramirez, Jimmy M. / Rivera-Garcia, Charlotte / Sandoval, Efren / Wang, Xueqing / Wong, David / Spencer, Emily /
    Robles-Sikisaka, Refugio / Kurzban, Ezra / Hughes, Laura D / Deng, Xianding / Wang, Candace / Servellita, Venice / Valentine, Holly / De Hoff, Peter / Seaver, Phoebe / Sathe, Shashank / Gietzen, Kimberly / Sickler, Brad / Antico, Jay / Hoon, Kelly / Liu, Jingtao / Harding, Aaron / Bakhtar, Omid / Basler, Tracy / Austin, Brett / Isaksson, Magnus / Febbo, Phil / Becker, David / Laurent, Marc / McDonald, Eric / Yeo, Gene W. / Knight, Rob / Laurent, Louise C. / de Feo, Eileen / Worobey, Michael / Chiu, Charles / Suchard, Marc A. / Lu, James T. / Lee, William / Andersen, Kristian G.

    medRxiv

    Abstract: ... on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant ... As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first ... proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing ...

    Abstract As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.
    Keywords covid19
    Language English
    Publishing date 2021-02-07
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.02.06.21251159
    Database COVID19

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  4. Article ; Online: Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations.

    Shen, Lishuang / Bard, Jennifer Dien / Triche, Timothy J / Judkins, Alexander R / Biegel, Jaclyn A / Gai, Xiaowu

    Emerging microbes & infections

    2021  Volume 10, Issue 1, Page(s) 1293–1299

    Abstract: The SARS-CoV-2 B.1.1.7 lineage is highly infectious and as of April 2021 accounted for 92% of COVID ... it constituted 36.8% of all B.1.1.7 isolates in Washington. Phylogenetic analysis and transmission inference ... mutations of B.1.1.7, HV69-70del and Y144del. It is surface exposed and may alter NTD tertiary configuration ...

    Abstract The SARS-CoV-2 B.1.1.7 lineage is highly infectious and as of April 2021 accounted for 92% of COVID-19 cases in Europe and 59% of COVID-19 cases in the U.S. It is defined by the N501Y mutation in the receptor-binding domain (RBD) of the Spike (S) protein, and a few other mutations. These include two mutations in the N terminal domain (NTD) of the S protein, HV69-70del and Y144del (also known as Y145del due to the presence of tyrosine at both positions). We recently identified several emerging SARS-CoV-2 variants of concerns, characterized by Membrane (M) protein mutations, including I82T and V70L. We now identify a sub-lineage of B.1.1.7 that emerged through sequential acquisitions of M:V70L in November 2020 followed by a novel S:D178H mutation first observed in early February 2021. The percentage of B.1.1.7 isolates in the US that belong to this sub-lineage increased from 0.15% in February 2021 to 1.8% in April 2021. To date, this sub-lineage appears to be U.S.-specific with reported cases in 31 states, including Hawaii. As of April 2021, it constituted 36.8% of all B.1.1.7 isolates in Washington. Phylogenetic analysis and transmission inference with Nextstrain suggest this sub-lineage likely originated in either California or Washington. Structural analysis revealed that the S:D178H mutation is in the NTD of the S protein and close to two other signature mutations of B.1.1.7, HV69-70del and Y144del. It is surface exposed and may alter NTD tertiary configuration or accessibility, and thus has the potential to affect neutralization by NTD directed antibodies.
    MeSH term(s) Binding Sites ; Humans ; Models, Molecular ; Mutation ; Phylogeny ; Protein Domains ; Protein Structure, Tertiary ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; Sequence Analysis, RNA ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; United States ; Viral Matrix Proteins/genetics ; Whole Genome Sequencing/methods
    Chemical Substances Spike Glycoprotein, Coronavirus ; Viral Matrix Proteins ; membrane protein, SARS-CoV-2 ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2021-06-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2681359-2
    ISSN 2222-1751 ; 2222-1751
    ISSN (online) 2222-1751
    ISSN 2222-1751
    DOI 10.1080/22221751.2021.1943540
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations

    Shen, Lishuang / Dien Bard, Jennifer / Triche, Timothy J / Judkins, Alexander R / Biegel, Jaclyn A / Gai, Xiaowu

    medRxiv

    Abstract: The SARS-CoV-2 B.1.1.7 lineage is highly infectious and as of April 2021 accounted for 92% of COVID ... As of April 2021 it constituted 36.8% of all B.1.1.7 isolates in Washington. Phylogenetic analysis and ... to two other signature mutations of B.1.1.7, HV69-70del and Y144del. It is surface exposed and may alter ...

    Abstract The SARS-CoV-2 B.1.1.7 lineage is highly infectious and as of April 2021 accounted for 92% of COVID-19 cases in Europe and 59% of COVID-19 cases in the U.S. It is defined by the N501Y mutation in the receptor binding domain (RBD) of the Spike (S) protein, and a few other mutations. These include two mutations in the N terminal domain (NTD) of the S protein, HV69-70del and Y144del (also known as Y145del due to the presence of tyrosine at both positions). We recently identified several emerging SARS-CoV-2 variants of concerns, characterized by Membrane (M) protein mutations, including I82T and V70L. We now identify a sub-lineage of B.1.1.7 that emerged through sequential acquisitions of M:V70L in November 2020 followed by a novel S:D178H mutation first observed in early February 2021. The percentage of B.1.1.7 isolates in the U.S. that belong to this sub-lineage increased from 0.15% in February 2021 to 1.8% in April 2021. To date this sub-lineage appears to be U.S.-specific with reported cases in 31 states, including Hawaii. As of April 2021 it constituted 36.8% of all B.1.1.7 isolates in Washington. Phylogenetic analysis and transmission inference with Nextstrain suggests this sub-lineage likely originated in either California or Washington. Structural analysis revealed that the S:D178H mutation is in the NTD of the S protein and close to two other signature mutations of B.1.1.7, HV69-70del and Y144del. It is surface exposed and may alter NTD tertiary configuration or accessibility, and thus has the potential to affect neutralization by NTD directed antibodies.
    Keywords covid19
    Language English
    Publishing date 2021-05-18
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.05.14.21257247
    Database COVID19

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