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  1. Article ; Online: Analysis of the time course of COVID-19 cases and deaths from countries with extensive testing allows accurate early estimates of the age specific symptomatic CFR values.

    Rothman, Jessica E / Eidelberg, David / Rothman, Samantha L / Holford, Theodore R / Rothman, Douglas L

    PloS one

    2021  Volume 16, Issue 8, Page(s) e0253843

    Abstract: Background: Knowing the true infected and symptomatic case fatality ratios (IFR and CFR) for COVID-19 is of high importance for epidemiological model projections. Early in the pandemic many locations had limited testing and reporting, so that standard ... ...

    Abstract Background: Knowing the true infected and symptomatic case fatality ratios (IFR and CFR) for COVID-19 is of high importance for epidemiological model projections. Early in the pandemic many locations had limited testing and reporting, so that standard methods for determining IFR and CFR required large adjustments for missed cases. We present an alternate approach, based on results from the countries at the time that had a high test to positive case ratio to estimate symptomatic CFR.
    Methods: We calculated age specific (0-69, 70-79, 80+ years old) time corrected crude symptomatic CFR values from 7 countries using two independent time to fatality correction methods. Data was obtained through May 7, 2020. We applied linear regression to determine whether the mean of these coefficients had converged to the true symptomatic CFR values. We then tested these coefficients against values derived in later studies as well as a large random serological study in NYC at that time.
    Results: The age dependent symptomatic CFR values accurately predicted the percentage of the population infected as reported by two random testing studies in NYC. They also were in good agreement with later studies that estimated age specific IFR and CFR values from serological studies and more extensive data sets available later in the pandemic.
    Conclusions: We found that for regions with extensive testing it is possible to get early accurate symptomatic CFR coefficients. These values, in combination with an estimate of the age dependence of infection, allows symptomatic CFR values and percentage of the population that is infected to be determined in similar regions with limited testing.
    MeSH term(s) Adolescent ; Adult ; Age Distribution ; Aged ; Aged, 80 and over ; COVID-19/epidemiology ; COVID-19/mortality ; Cause of Death ; Child ; Child, Preschool ; Disease Outbreaks/statistics & numerical data ; Europe/epidemiology ; Female ; Humans ; Infant ; Infant, Newborn ; Israel/epidemiology ; Linear Models ; Male ; Middle Aged ; Models, Statistical ; Mortality ; New Zealand/epidemiology ; Republic of Korea/epidemiology ; Young Adult
    Language English
    Publishing date 2021-08-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0253843
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics.

    Allicock, Orchid M / Petrone, Mary E / Yolda-Carr, Devyn / Breban, Mallery / Walsh, Hannah / Watkins, Anne E / Rothman, Jessica E / Farhadian, Shelli F / Grubaugh, Nathan D / Wyllie, Anne L

    BMC infectious diseases

    2022  Volume 22, Issue 1, Page(s) 284

    Abstract: Background: There is an urgent need to expand testing for SARS-CoV-2 and other respiratory pathogens as the global community struggles to control the COVID-19 pandemic. Current diagnostic methods can be affected by supply chain bottlenecks and require ... ...

    Abstract Background: There is an urgent need to expand testing for SARS-CoV-2 and other respiratory pathogens as the global community struggles to control the COVID-19 pandemic. Current diagnostic methods can be affected by supply chain bottlenecks and require the assistance of medical professionals, impeding the implementation of large-scale testing. Self-collection of saliva may solve these problems, as it can be completed without specialized training and uses generic materials.
    Methods: We observed 30 individuals who self-collected saliva using four different collection devices and analyzed their feedback. Two of these devices, a funnel and bulb pipette, were used to evaluate at-home saliva collection by 60 individuals. SARS-CoV-2-spiked saliva samples were subjected to temperature cycles designed to simulate the conditions the samples might be exposed to during the summer and winter seasons and sensitivity of detection was evaluated.
    Results: All devices enabled the safe, unsupervised self-collection of saliva. The quantity and quality of the samples received were acceptable for SARS-CoV-2 diagnostic testing, as determined by human RNase P detection. There was no significant difference in SARS-CoV-2 nucleocapsid gene (N1) detection between the freshly spiked samples and those incubated with the summer and winter profiles.
    Conclusion: We demonstrate inexpensive, generic, buffer free collection devices suitable for unsupervised and home saliva self-collection.
    MeSH term(s) COVID-19/diagnosis ; Humans ; Nucleocapsid Proteins ; Pandemics ; SARS-CoV-2 ; Saliva
    Chemical Substances Nucleocapsid Proteins
    Language English
    Publishing date 2022-03-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041550-3
    ISSN 1471-2334 ; 1471-2334
    ISSN (online) 1471-2334
    ISSN 1471-2334
    DOI 10.1186/s12879-022-07285-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics.

    Allicock, Orchid M / Petrone, Mary E / Yolda-Carr, Devyn / Breban, Mallery / Walsh, Hannah / Watkins, Anne E / Rothman, Jessica E / Farhadian, Shelli F / Grubaugh, Nathan D / Wyllie, Anne L

    medRxiv : the preprint server for health sciences

    2021  

    Abstract: There is an urgent need to expand testing for SARS-CoV-2 and other respiratory pathogens as the global community struggles to control the COVID-19 pandemic. Current diagnostic methods can be affected by supply chain bottlenecks and require the assistance ...

    Abstract There is an urgent need to expand testing for SARS-CoV-2 and other respiratory pathogens as the global community struggles to control the COVID-19 pandemic. Current diagnostic methods can be affected by supply chain bottlenecks and require the assistance of medical professionals, impeding the implementation of large-scale testing. Self-collection of saliva may solve these problems, as it can be completed without specialized training and uses generic materials. In this study, we observed thirty individuals who self-collected saliva using four different collection devices and analyzed their feedback. Two of these devices, a funnel and bulb pipette, were used to evaluate at-home saliva collection by 60 individuals. All devices enabled the safe, unsupervised self-collection of saliva. The quantity and quality of the samples received were acceptable for SARS-CoV-2 diagnostic testing, as determined by RNase P detection. Here, we demonstrate inexpensive, generic, buffer free collection devices suitable for unsupervised and home saliva self-collection.
    Language English
    Publishing date 2021-07-03
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.02.01.21250946
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity.

    Lucas, Carolina / Vogels, Chantal B F / Yildirim, Inci / Rothman, Jessica E / Lu, Peiwen / Monteiro, Valter / Gehlhausen, Jeff R / Campbell, Melissa / Silva, Julio / Tabachnikova, Alexandra / Peña-Hernandez, Mario A / Muenker, M Catherine / Breban, Mallery I / Fauver, Joseph R / Mohanty, Subhasis / Huang, Jiefang / Shaw, Albert C / Ko, Albert I / Omer, Saad B /
    Grubaugh, Nathan D / Iwasaki, Akiko

    Nature

    2021  Volume 600, Issue 7889, Page(s) 523–529

    Abstract: The emergence of SARS-CoV-2 variants with mutations in major neutralizing antibody-binding sites can affect humoral immunity induced by infection or ... ...

    Abstract The emergence of SARS-CoV-2 variants with mutations in major neutralizing antibody-binding sites can affect humoral immunity induced by infection or vaccination
    MeSH term(s) 2019-nCoV Vaccine mRNA-1273/immunology ; Adult ; Aged ; Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; BNT162 Vaccine/immunology ; COVID-19/epidemiology ; COVID-19/virology ; Female ; Health Personnel/statistics & numerical data ; Humans ; Immunity, Humoral ; Male ; Middle Aged ; Mutation ; Retrospective Studies ; SARS-CoV-2/classification ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology ; T-Lymphocytes/immunology ; Vaccines, Synthetic/immunology ; mRNA Vaccines/immunology
    Chemical Substances Antibodies, Neutralizing ; Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; Vaccines, Synthetic ; mRNA Vaccines ; spike protein, SARS-CoV-2 ; 2019-nCoV Vaccine mRNA-1273 (EPK39PL4R4) ; BNT162 Vaccine (N38TVC63NU)
    Language English
    Publishing date 2021-10-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-021-04085-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota.

    Petrone, Mary E / Rothman, Jessica E / Breban, Mallery I / Ott, Isabel M / Russell, Alexis / Lasek-Nesselquist, Erica / Badr, Hamada / Kelly, Kevin / Omerza, Greg / Renzette, Nicholas / Watkins, Anne E / Kalinich, Chaney C / Alpert, Tara / Brito, Anderson F / Earnest, Rebecca / Tikhonova, Irina R / Castaldi, Christopher / Kelly, John P / Shudt, Matthew /
    Plitnick, Jonathan / Schneider, Erasmus / Murphy, Steven / Neal, Caleb / Laszlo, Eva / Altajar, Ahmad / Pearson, Claire / Muyombwe, Anthony / Downing, Randy / Razeq, Jafar / Niccolai, Linda / Wilson, Madeline S / Anderson, Margaret L / Wang, Jianhui / Liu, Chen / Hui, Pei / Mane, Shrikant / Taylor, Bradford P / Hanage, William P / Landry, Marie L / Peaper, David R / Bilguvar, Kaya / Fauver, Joseph R / Vogels, Chantal B F / Gardner, Lauren M / Pitzer, Virginia E / St George, Kirsten / Adams, Mark D / Grubaugh, Nathan D

    Communications biology

    2022  Volume 5, Issue 1, Page(s) 439

    Abstract: SARS-CoV-2 variants shaped the second year of the COVID-19 pandemic and the discourse around effective control measures. Evaluating the threat posed by a new variant is essential for adapting response efforts when community transmission is detected. In ... ...

    Abstract SARS-CoV-2 variants shaped the second year of the COVID-19 pandemic and the discourse around effective control measures. Evaluating the threat posed by a new variant is essential for adapting response efforts when community transmission is detected. In this study, we compare the dynamics of two variants, Alpha and Iota, by integrating genomic surveillance data to estimate the effective reproduction number (R
    MeSH term(s) COVID-19/epidemiology ; Genomics ; Humans ; Pandemics ; SARS-CoV-2/genetics ; United States/epidemiology
    Language English
    Publishing date 2022-05-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-022-03347-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA.

    Earnest, Rebecca / Uddin, Rockib / Matluk, Nicholas / Renzette, Nicholas / Turbett, Sarah E / Siddle, Katherine J / Loreth, Christine / Adams, Gordon / Tomkins-Tinch, Christopher H / Petrone, Mary E / Rothman, Jessica E / Breban, Mallery I / Koch, Robert Tobias / Billig, Kendall / Fauver, Joseph R / Vogels, Chantal B F / Bilguvar, Kaya / De Kumar, Bony / Landry, Marie L /
    Peaper, David R / Kelly, Kevin / Omerza, Greg / Grieser, Heather / Meak, Sim / Martha, John / Dewey, Hannah B / Kales, Susan / Berenzy, Daniel / Carpenter-Azevedo, Kristin / King, Ewa / Huard, Richard C / Novitsky, Vlad / Howison, Mark / Darpolor, Josephine / Manne, Akarsh / Kantor, Rami / Smole, Sandra C / Brown, Catherine M / Fink, Timelia / Lang, Andrew S / Gallagher, Glen R / Pitzer, Virginia E / Sabeti, Pardis C / Gabriel, Stacey / MacInnis, Bronwyn L / Tewhey, Ryan / Adams, Mark D / Park, Daniel J / Lemieux, Jacob E / Grubaugh, Nathan D

    Cell reports. Medicine

    2022  Volume 3, Issue 4, Page(s) 100583

    Abstract: The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%-80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with ... ...

    Abstract The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%-80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant's respective emergence period, finding that Delta emerged 1.37-2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63%-167% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95% CI 3.1-10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta's enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability.
    MeSH term(s) COVID-19/epidemiology ; Humans ; New England/epidemiology ; Public Health ; SARS-CoV-2/genetics
    Language English
    Publishing date 2022-03-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
    ISSN 2666-3791
    ISSN (online) 2666-3791
    DOI 10.1016/j.xcrm.2022.100583
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages.

    Petrone, Mary E / Rothman, Jessica E / Breban, Mallery I / Ott, Isabel M / Russell, Alexis / Lasek-Nesselquist, Erica / Kelly, Kevin / Omerza, Greg / Renzette, Nicholas / Watkins, Anne E / Kalinich, Chaney C / Alpert, Tara / Brito, Anderson F / Earnest, Rebecca / Tikhonova, Irina R / Castaldi, Christopher / Kelly, John P / Shudt, Matthew / Plitnick, Jonathan /
    Schneider, Erasmus / Murphy, Steven / Neal, Caleb / Laszlo, Eva / Altajar, Ahmad / Pearson, Claire / Muyombwe, Anthony / Downing, Randy / Razeq, Jafar / Niccolai, Linda / Wilson, Madeline S / Anderson, Margaret L / Wang, Jianhui / Liu, Chen / Hui, Pei / Mane, Shrikant / Taylor, Bradford P / Hanage, William P / Landry, Marie L / Peaper, David R / Bilguvar, Kaya / Fauver, Joseph R / Vogels, Chantal B F / Gardner, Lauren M / Pitzer, Virginia E / St George, Kirsten / Adams, Mark D / Grubaugh, Nathan D

    medRxiv : the preprint server for health sciences

    2021  

    Abstract: Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control measures. Evaluating the public health threat posed by a new variant is essential for appropriately adapting ... ...

    Abstract Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control measures. Evaluating the public health threat posed by a new variant is essential for appropriately adapting response efforts when community transmission is detected. However, this assessment requires that a true comparison can be made between the new variant and its predecessors because factors other than the virus genotype may influence spread and transmission. In this study, we develop a framework that integrates genomic surveillance data to estimate the relative effective reproduction number (R
    Language English
    Publishing date 2021-07-02
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.07.01.21259859
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA.

    Earnest, Rebecca / Uddin, Rockib / Matluk, Nicholas / Renzette, Nicholas / Siddle, Katherine J / Loreth, Christine / Adams, Gordon / Tomkins-Tinch, Christopher H / Petrone, Mary E / Rothman, Jessica E / Breban, Mallery I / Koch, Robert Tobias / Billig, Kendall / Fauver, Joseph R / Vogels, Chantal B F / Turbett, Sarah / Bilguvar, Kaya / De Kumar, Bony / Landry, Marie L /
    Peaper, David R / Kelly, Kevin / Omerza, Greg / Grieser, Heather / Meak, Sim / Martha, John / Dewey, Hannah H / Kales, Susan / Berenzy, Daniel / Carpenter-Azevedo, Kristin / King, Ewa / Huard, Richard C / Smole, Sandra C / Brown, Catherine M / Fink, Timelia / Lang, Andrew S / Gallagher, Glen R / Sabeti, Pardis C / Gabriel, Stacey / MacInnis, Bronwyn L / Tewhey, Ryan / Adams, Mark D / Park, Daniel J / Lemieux, Jacob E / Grubaugh, Nathan D

    medRxiv : the preprint server for health sciences

    2021  

    Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more ... ...

    Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more transmissible than Alpha, allowing Delta to become the globally dominant variant. However, it was unclear if the ostensible difference in relative transmissibility was due mostly to innate properties of Delta's infectiousness or differences in the study populations. To investigate, we formed a partnership with SARS-CoV-2 genomic surveillance programs from all six New England US states. By comparing logistic growth rates, we found that Delta emerged 37-163% faster than Alpha in early 2021 (37% Massachusetts, 75% New Hampshire, 95% Maine, 98% Rhode Island, 151% Connecticut, and 163% Vermont). We next computed variant-specific effective reproductive numbers and estimated that Delta was 58-120% more transmissible than Alpha across New England (58% New Hampshire, 68% Massachusetts, 76% Connecticut, 85% Rhode Island, 98% Maine, and 120% Vermont). Finally, using RT-PCR data, we estimated that Delta infections generate on average ∼6 times more viral RNA copies per mL than Alpha infections. Overall, our evidence indicates that Delta's enhanced transmissibility could be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on the underlying immunity and behavior of distinct populations.
    Language English
    Publishing date 2021-10-07
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.10.06.21264641
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.

    Vogels, Chantal B F / Breban, Mallery I / Ott, Isabel M / Alpert, Tara / Petrone, Mary E / Watkins, Anne E / Kalinich, Chaney C / Earnest, Rebecca / Rothman, Jessica E / Goes de Jesus, Jaqueline / Morales Claro, Ingra / Magalhães Ferreira, Giulia / Crispim, Myuki A E / Singh, Lavanya / Tegally, Houriiyah / Anyaneji, Ugochukwu J / Hodcroft, Emma B / Mason, Christopher E / Khullar, Gaurav /
    Metti, Jessica / Dudley, Joel T / MacKay, Matthew J / Nash, Megan / Wang, Jianhui / Liu, Chen / Hui, Pei / Murphy, Steven / Neal, Caleb / Laszlo, Eva / Landry, Marie L / Muyombwe, Anthony / Downing, Randy / Razeq, Jafar / de Oliveira, Tulio / Faria, Nuno R / Sabino, Ester C / Neher, Richard A / Fauver, Joseph R / Grubaugh, Nathan D

    PLoS biology

    2021  Volume 19, Issue 5, Page(s) e3001236

    Abstract: With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It ... ...

    Abstract With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69-70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.
    MeSH term(s) COVID-19/diagnosis ; COVID-19/genetics ; COVID-19/virology ; DNA Primers ; Humans ; Multiplex Polymerase Chain Reaction/methods ; Mutation ; Polyproteins/genetics ; SARS-CoV-2/genetics ; Viral Proteins/genetics
    Chemical Substances DNA Primers ; ORF1ab polyprotein, SARS-CoV-2 ; Polyproteins ; Viral Proteins
    Language English
    Publishing date 2021-05-07
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126776-5
    ISSN 1545-7885 ; 1544-9173
    ISSN (online) 1545-7885
    ISSN 1544-9173
    DOI 10.1371/journal.pbio.3001236
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages

    Petrone, Mary E. / Rothman, Jessica E. / Breban, Mallery I. / Ott, Isabel M. / Russell, Alexis / Lasek-Nesselquist, Erica / Kelly, Kevin / Omerza, Greg / Renzette, Nicholas / Watkins, Anne E. / Kalinich, Chaney C. / Alpert, Tara / Brito, Anderson F. / Earnest, Rebecca / Tikhonova, Irina R. / Castaldi, Christopher / Kelly, John P. / Shudt, Matthew / Plitnick, Jonathan /
    Schneider, Erasmus / Murphy, Steven / Neal, Caleb / Laszlo, Eva / Altajar, Ahmad / Pearson, Claire / Muyombwe, Anthony / Downing, Randy / Razeq, Jafar / Niccolai, Linda / Wilson, Madeline S. / Anderson, Margaret L. / Wang, Jianhui / Liu, Chen / Hui, Pei / Mane, Shrikant / Taylor, Bradford P. / Hanage, William P. / Landry, Marie L. / Peaper, David R. / Bilguvar, Kaya / Fauver, Joseph R. / Vogels, Chantal B.F. / Gardner, Lauren M. / Pitzer, Virginia E. / George, Kirsten St. / Adams, Mark D. / Grubaugh, Nathan D.

    medRxiv

    Abstract: Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control measures. Evaluating the public health threat posed by a new variant is essential for appropriately adapting ... ...

    Abstract Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control measures. Evaluating the public health threat posed by a new variant is essential for appropriately adapting response efforts when community transmission is detected. However, this assessment requires that a true comparison can be made between the new variant and its predecessors because factors other than the virus genotype may influence spread and transmission. In this study, we develop a framework that integrates genomic surveillance data to estimate the relative effective reproduction number (Rt) of co-circulating lineages. We use Connecticut, a state in the northeastern United States in which the SARS-CoV-2 variants B.1.1.7 and B.1.526 co-circulated in early 2021, as a case study for implementing this framework. We find that the Rt of B.1.1.7 was 6-10% larger than that of B.1.526 in Connecticut in the midst of a COVID-19 vaccination campaign. To assess the generalizability of this framework, we apply it to genomic surveillance data from New York City and observe the same trend. Finally, we use discrete phylogeography to demonstrate that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of B.1.1.7 were larger than those resulting from B.1.526 introductions. Our framework, which uses open-source methods requiring minimal computational resources, may be used to monitor near real-time variant dynamics in a myriad of settings.
    Keywords covid19
    Language English
    Publishing date 2021-07-02
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.07.01.21259859
    Database COVID19

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