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1. Multiplex qPCR Discriminates Variants of Concern to Enhance Global Surveillance of SARS-CoV-2

Author

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

Published
2023
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2. Neutralizing antibodies against the SARS-CoV-2 Delta and Omicron variants following heterologous CoronaVac plus BNT162b2 booster vaccination

Author

Pérez-Then, Eddy, Lucas, Carolina, Monteiro, Valter Silva, Miric, Marija, Brache, Vivian, Cochon, Leila, Vogels, Chantal B. F., Malik, Amyn A., De la Cruz, Elena, Jorge, Aidelis, De los Santos, Margarita, Leon, Patricia, Breban, Mallery I., Billig, Kendall, Yildirim, Inci, Pearson, Claire, Downing, Randy, Gagnon, Emily, Muyombwe, Anthony, Razeq, Jafar, Campbell, Melissa, Ko, Albert I., Omer, Saad B., Grubaugh, Nathan D., Vermund, Sten H., and Iwasaki, Akiko

Published
2022
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3. Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota

Author

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., and Grubaugh, Nathan D.

Published
2022
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4. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA

Author

Altajar, Ahmad, DeJesus, Alexandra, Brito, Anderson, Watkins, Anne E., Muyombwe, Anthony, Blumenstiel, Brendan S., Neal, Caleb, Kalinich, Chaney C., Liu, Chen, Loreth, Christine, Castaldi, Christopher, Pearson, Claire, Bernard, Clare, Nolet, Corey M., Ferguson, David, Buzby, Erika, Laszlo, Eva, Reagan, Faye L., Vicente, Gina, Rooke, Heather M., Munger, Heidi, Johnson, Hillary, Tikhonova, Irina R., Ott, Isabel M., Razeq, Jafar, Meldrim, James C., Brown, Jessica, Wang, Jianhui, Vostok, Johanna, Beauchamp, John P., Grimsby, Jonna L., Hall, Joshua, Messer, Katelyn S., Larkin, Katie L., Vernest, Kyle, Madoff, Lawrence C., Green, Lisa M., Webber, Lori, Gagne, Luc, Ulcena, Maesha A., Ray, Marianne C., Fisher, Marissa E., Barter, Mary, Lee, Matthew D., DeFelice, Matthew T., Cipicchio, Michelle C., Smith, Natasha L., Lennon, Niall J., Fitzgerald, Nicholas A., Kerantzas, Nicholas, Hui, Pei, Harrington, Rachel, Downing, Randy, Haye, Rashida, Lynch, Ryan, Anderson, Scott E., Hennigan, Scott, English, Sean, Cofsky, Seana, Clancy, Selina, Mane, Shrikant, Ash, Stephanie, Baez, Stephanie, Fleming, Steve, Murphy, Steven, Chaluvadi, Sushma, Alpert, Tara, Rivard, Trevor, Schulz, Wade, Mandese, Zoe M., Earnest, Rebecca, Uddin, Rockib, Matluk, Nicholas, Renzette, Nicholas, Turbett, Sarah E., Siddle, Katherine J., 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., and Grubaugh, Nathan D.

Published
2022
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5. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA

Author

Earnest, Rebecca, primary, Uddin, Rockib, additional, Matluk, Nicholas, additional, Renzette, Nicholas, additional, Turbett, Sarah E., additional, Siddle, Katherine J., additional, Loreth, Christine, additional, Adams, Gordon, additional, Tomkins-Tinch, Christopher H., additional, Petrone, Mary E., additional, Rothman, Jessica E., additional, Breban, Mallery I., additional, Koch, Robert Tobias, additional, Billig, Kendall, additional, Fauver, Joseph R., additional, Vogels, Chantal B.F., additional, Bilguvar, Kaya, additional, De Kumar, Bony, additional, Landry, Marie L., additional, Peaper, David R., additional, Kelly, Kevin, additional, Omerza, Greg, additional, Grieser, Heather, additional, Meak, Sim, additional, Martha, John, additional, Dewey, Hannah B., additional, Kales, Susan, additional, Berenzy, Daniel, additional, Carpenter-Azevedo, Kristin, additional, King, Ewa, additional, Huard, Richard C., additional, Novitsky, Vlad, additional, Howison, Mark, additional, Darpolor, Josephine, additional, Manne, Akarsh, additional, Kantor, Rami, additional, Smole, Sandra C., additional, Brown, Catherine M., additional, Fink, Timelia, additional, Lang, Andrew S., additional, Gallagher, Glen R., additional, Pitzer, Virginia E., additional, Sabeti, Pardis C., additional, Gabriel, Stacey, additional, MacInnis, Bronwyn L., additional, Tewhey, Ryan, additional, Adams, Mark D., additional, Park, Daniel J., additional, Lemieux, Jacob E., additional, Grubaugh, Nathan D., additional, Altajar, Ahmad, additional, DeJesus, Alexandra, additional, Brito, Anderson, additional, Watkins, Anne E., additional, Muyombwe, Anthony, additional, Blumenstiel, Brendan S., additional, Neal, Caleb, additional, Kalinich, Chaney C., additional, Liu, Chen, additional, Castaldi, Christopher, additional, Pearson, Claire, additional, Bernard, Clare, additional, Nolet, Corey M., additional, Ferguson, David, additional, Buzby, Erika, additional, Laszlo, Eva, additional, Reagan, Faye L., additional, Vicente, Gina, additional, Rooke, Heather M., additional, Munger, Heidi, additional, Johnson, Hillary, additional, Tikhonova, Irina R., additional, Ott, Isabel M., additional, Razeq, Jafar, additional, Meldrim, James C., additional, Brown, Jessica, additional, Wang, Jianhui, additional, Vostok, Johanna, additional, Beauchamp, John P., additional, Grimsby, Jonna L., additional, Hall, Joshua, additional, Messer, Katelyn S., additional, Larkin, Katie L., additional, Vernest, Kyle, additional, Madoff, Lawrence C., additional, Green, Lisa M., additional, Webber, Lori, additional, Gagne, Luc, additional, Ulcena, Maesha A., additional, Ray, Marianne C., additional, Fisher, Marissa E., additional, Barter, Mary, additional, Lee, Matthew D., additional, DeFelice, Matthew T., additional, Cipicchio, Michelle C., additional, Smith, Natasha L., additional, Lennon, Niall J., additional, Fitzgerald, Nicholas A., additional, Kerantzas, Nicholas, additional, Hui, Pei, additional, Harrington, Rachel, additional, Downing, Randy, additional, Haye, Rashida, additional, Lynch, Ryan, additional, Anderson, Scott E., additional, Hennigan, Scott, additional, English, Sean, additional, Cofsky, Seana, additional, Clancy, Selina, additional, Mane, Shrikant, additional, Ash, Stephanie, additional, Baez, Stephanie, additional, Fleming, Steve, additional, Murphy, Steven, additional, Chaluvadi, Sushma, additional, Alpert, Tara, additional, Rivard, Trevor, additional, Schulz, Wade, additional, and Mandese, Zoe M., additional

Published
2022
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6. SARS-CoV-2 Delta outbreak among fully vaccinated nursing home residents likely initiated by a fully vaccinated staff member – Connecticut, July–August 2021

Author

Bart, Stephen M, Harizaj, Adora, Pearson, Claire L, Conteh, Tiara, Grogan, Erin, Downing, Randy, Kirking, Hannah L, Tate, Jacqueline E, Jernigan, John A, and Leung, Vivian

Subjects
SARS-CoV-2 transmission, Connecticut, AcademicSubjects/MED00290, SARS-CoV-2, Brief Report, COVID-19, COVID-19 vaccines, Humans, long-term care facilities, Disease Outbreaks, Nursing Homes
Abstract

During July-August 2021, a coronavirus disease 2019 (COVID-19) outbreak involving 21 residents (all fully vaccinated) and 10 staff (9 fully vaccinated) occurred in a Connecticut nursing home. The outbreak was likely initiated by a fully vaccinated staff member and propagated by fully vaccinated persons. Prior COVID-19 was protective among vaccinated residents.

Published
2021

7. Immunogenicity of heterologous BNT162b2 booster in fully vaccinated individuals with CoronaVac against SARS-CoV-2 variants Delta and Omicron: the Dominican Republic Experience

Author

Pérez-Then, Eddy, primary, Lucas, Carolina, additional, Monteiro, Valter Silva, additional, Miric, Marija, additional, Brache, Vivian, additional, Cochon, Leila, additional, Vogels, Chantal B. F., additional, De la Cruz, Elena, additional, Jorge, Aidelis, additional, De los Santos, Margarita, additional, Leon, Patricia, additional, Breban, Mallery I., additional, Billig, Kendall, additional, Yildirim, Inci, additional, Pearson, Claire, additional, Downing, Randy, additional, Gagnon, Emily, additional, Muyombwe, Anthony, additional, Razeq, Jafar, additional, Campbell, Melissa, additional, Ko, Albert, additional, Omer, Saad B., additional, Grubaugh, Nathan D., additional, Vermund, Sten H., additional, and Iwasaki, Akiko, additional

Published
2021
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8. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta Outbreak Among Fully Vaccinated Nursing Home Residents Likely Initiated by a Fully Vaccinated Staff Member – Connecticut, July–August 2021

Author

Bart, Stephen M, primary, Harizaj, Adora, additional, Pearson, Claire L, additional, Conteh, Tiara, additional, Grogan, Erin, additional, Downing, Randy, additional, Kirking, Hannah L, additional, Tate, Jacqueline E, additional, Jernigan, John A, additional, and Leung, Vivian, additional

Published
2021
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9. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

Author

Vogels, Chantal BF, 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 AE, Brazil-UK CADDE Genomic Network, Singh, Lavanya, Tegally, Houriiyah, Anyaneji, Ugochukwu J, Network for Genomic Surveillance in South Africa, 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, and Grubaugh, Nathan D

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.

Published
2021

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

Author

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

Published
2021
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11. Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States

Author

Alpert, Tara, primary, Brito, Anderson F., additional, Lasek-Nesselquist, Erica, additional, Rothman, Jessica, additional, Valesano, Andrew L., additional, MacKay, Matthew J., additional, Petrone, Mary E., additional, Breban, Mallery I., additional, Watkins, Anne E., additional, Vogels, Chantal B.F., additional, Kalinich, Chaney C., additional, Dellicour, Simon, additional, Russell, Alexis, additional, Kelly, John P., additional, Shudt, Matthew, additional, Plitnick, Jonathan, additional, Schneider, Erasmus, additional, Fitzsimmons, William J., additional, Khullar, Gaurav, additional, Metti, Jessica, additional, Dudley, Joel T., additional, Nash, Megan, additional, Beaubier, Nike, additional, Wang, Jianhui, additional, Liu, Chen, additional, Hui, Pei, additional, Muyombwe, Anthony, additional, Downing, Randy, additional, Razeq, Jafar, additional, Bart, Stephen M., additional, Grills, Ardath, additional, Morrison, Stephanie M., additional, Murphy, Steven, additional, Neal, Caleb, additional, Laszlo, Eva, additional, Rennert, Hanna, additional, Cushing, Melissa, additional, Westblade, Lars, additional, Velu, Priya, additional, Craney, Arryn, additional, Cong, Lin, additional, Peaper, David R., additional, Landry, Marie L., additional, Cook, Peter W., additional, Fauver, Joseph R., additional, Mason, Christopher E., additional, Lauring, Adam S., additional, St. George, Kirsten, additional, MacCannell, Duncan R., additional, and Grubaugh, Nathan D., additional

Published
2021
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12. Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States

Author

Alpert, Tara, primary, Brito, Anderson F., additional, Lasek-Nesselquist, Erica, additional, Rothman, Jessica, additional, Valesano, Andrew L., additional, MacKay, Matthew J., additional, Petrone, Mary E., additional, Breban, Mallery I., additional, Watkins, Anne E., additional, Vogels, Chantal B.F., additional, Kalinich, Chaney C., additional, Dellicour, Simon, additional, Russell, Alexis, additional, Kelly, John P., additional, Shudt, Matthew, additional, Plitnick, Jonathan, additional, Schneider, Erasmus, additional, Fitzsimmons, William J., additional, Khullar, Gaurav, additional, Metti, Jessica, additional, Dudley, Joel T., additional, Nash, Megan, additional, Beaubier, Nike, additional, Wang, Jianhui, additional, Liu, Chen, additional, Hui, Pei, additional, Muyombwe, Anthony, additional, Downing, Randy, additional, Razeq, Jafar, additional, Bart, Stephen M., additional, Grills, Ardath, additional, Morrison, Stephanie M., additional, Murphy, Steven, additional, Neal, Caleb, additional, Laszlo, Eva, additional, Rennert, Hanna, additional, Cushing, Melissa, additional, Westblade, Lars, additional, Velu, Priya, additional, Craney, Arryn, additional, Fauntleroy, Kathy A., additional, Peaper, David R., additional, Landry, Marie L., additional, Cook, Peter W., additional, Fauver, Joseph R., additional, Mason, Christopher E., additional, Lauring, Adam S., additional, George, Kirsten St., additional, MacCannell, Duncan R., additional, and Grubaugh, Nathan D., additional

Published
2021
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13. Changing US Epidemiology of NDM-Producing Carbapenem-Resistant Enterobacteriaceae, 2017–2019

Author

Shugart, Alicia, primary, Mahon, Garrett, additional, Epstein, Lauren, additional, Huang, Jennifer Y., additional, McAllister, Gillian, additional, Lawsin, Adrian, additional, Sula, Erisa, additional, Halpin, Alison Laufer, additional, Smith, Amanda, additional, Carman, Rebekah, additional, Cassidy, P. Maureen, additional, Morey, Karim, additional, Paranandi, Anu, additional, Downing, Randy, additional, Noel, Diane, additional, Kallen, Alexander J., additional, and Walters, Maroya Spalding, additional

Published
2020
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14. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

Author

Fauver, Joseph R., primary, Petrone, Mary E., additional, Hodcroft, Emma B., additional, Shioda, Kayoko, additional, Ehrlich, Hanna Y., additional, Watts, Alexander G., additional, Vogels, Chantal B.F., additional, Brito, Anderson F., additional, Alpert, Tara, additional, Muyombwe, Anthony, additional, Razeq, Jafar, additional, Downing, Randy, additional, Cheemarla, Nagarjuna R., additional, Wyllie, Anne L., additional, Kalinich, Chaney C., additional, Ott, Isabel M., additional, Quick, Joshua, additional, Loman, Nicholas J., additional, Neugebauer, Karla M., additional, Greninger, Alexander L., additional, Jerome, Keith R., additional, Roychoudhury, Pavitra, additional, Xie, Hong, additional, Shrestha, Lasata, additional, Huang, Meei-Li, additional, Pitzer, Virginia E., additional, Iwasaki, Akiko, additional, Omer, Saad B., additional, Khan, Kamran, additional, Bogoch, Isaac I., additional, Martinello, Richard A., additional, Foxman, Ellen F., additional, Landry, Marie L., additional, Neher, Richard A., additional, Ko, Albert I., additional, and Grubaugh, Nathan D., additional

Published
2020
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15. Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology

Author

Fauver, Joseph R., primary, Petrone, Mary E., additional, Hodcroft, Emma B., additional, Shioda, Kayoko, additional, Ehrlich, Hanna Y., additional, Watts, Alexander G., additional, Vogels, Chantal B.F., additional, Brito, Anderson F., additional, Alpert, Tara, additional, Muyombwe, Anthony, additional, Razeq, Jafar, additional, Downing, Randy, additional, Cheemarla, Nagarjuna R., additional, Wyllie, Anne L., additional, Kalinich, Chaney C., additional, Ott, Isabel, additional, Quick, Joshua, additional, Loman, Nicholas J., additional, Neugebauer, Karla M., additional, Greninger, Alexander L., additional, Jerome, Keith R., additional, Roychoudhury, Pavitra, additional, Xie, Hong, additional, Shrestha, Lasata, additional, Huang, Meei-Li, additional, Pitzer, Virginia E., additional, Iwasaki, Akiko, additional, Omer, Saad B., additional, Khan, Kamran, additional, Bogoch, Isaac I., additional, Martinello, Richard A., additional, Foxman, Ellen F., additional, Landry, Marie L., additional, Neher, Richard A., additional, Ko, Albert I., additional, and Grubaugh, Nathan D., additional

Published
2020
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16. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta Outbreak Among Fully Vaccinated Nursing Home Residents Likely Initiated by a Fully Vaccinated Staff Member – Connecticut, July–August 2021.

Author

Bart, Stephen M, Harizaj, Adora, Pearson, Claire L, Conteh, Tiara, Grogan, Erin, Downing, Randy, Kirking, Hannah L, Tate, Jacqueline E, Jernigan, John A, and Leung, Vivian

Subjects
IMMUNIZATION, MEDICAL personnel, NURSING care facilities, COVID-19, COVID-19 pandemic, SICK people
Abstract

During July–August 2021, a coronavirus disease 2019 (COVID-19) outbreak involving 21 residents (all fully vaccinated) and 10 staff (9 fully vaccinated) occurred in a Connecticut nursing home. The outbreak was likely initiated by a fully vaccinated staff member and propagated by fully vaccinated persons. Prior COVID-19 was protective among vaccinated residents. [ABSTRACT FROM AUTHOR]

Published
2022
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17. Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages.

Author

Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CBF, Gardner LM, Pitzer VE, St George K, Adams MD, and Grubaugh ND

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 t ) 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 R t 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.

Published
2021
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18. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.

Author

Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, Goes de Jesus J, Morales Claro I, Magalhães Ferreira G, Crispim MAE, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, and Grubaugh ND

Subjects
COVID-19 diagnosis, COVID-19 genetics, DNA Primers, Humans, Multiplex Polymerase Chain Reaction methods, Mutation, Polyproteins genetics, Viral Proteins genetics, COVID-19 virology, SARS-CoV-2 genetics
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., Competing Interests: The authors have declared that no competing interests exist.

Published
2021
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19. PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern.

Author

Vogels CBF, Breban MI, Alpert T, Petrone ME, Watkins AE, Ott IM, de Jesus JG, Claro IM, Ferreira GM, Crispim MAE, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, and Grubaugh ND

Abstract

With the emergence of SARS-CoV-2 variants that may increase transmissibility and/or cause escape from immune responses 1-3 , 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 UK 4,5 could be serendipitously detected by the ThermoFisher 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 that lack spike Δ69-70, such as B.1.351 (also 501Y.V2) detected in South Africa 6 and P.1 (also 501Y.V3) recently detected in Brazil 7 . We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all three 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 variants of concern 8 . Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence spread of B.1.1.7, B.1.351, and P.1.

Published
2021
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20. Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States.

Author

Alpert T, Brito AF, Lasek-Nesselquist E, Rothman J, Valesano AL, MacKay MJ, Petrone ME, Breban MI, Watkins AE, Vogels CBF, Kalinich CC, Dellicour S, Russell A, Kelly JP, Shudt M, Plitnick J, Schneider E, Fitzsimmons WJ, Khullar G, Metti J, Dudley JT, Nash M, Beaubier N, Wang J, Liu C, Hui P, Muyombwe A, Downing R, Razeq J, Bart SM, Grills A, Morrison SM, Murphy S, Neal C, Laszlo E, Rennert H, Cushing M, Westblade L, Velu P, Craney A, Fauntleroy KA, Peaper DR, Landry ML, Cook PW, Fauver JR, Mason CE, Lauring AS, George KS, MacCannell DR, and Grubaugh ND

Abstract

The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response., Competing Interests: Declarations of Interests M.J.M, G.K., J.M., J.T.D., M.N., N.B., and C.E.M. work for Tempus Labs. K.S.G. receives research support from Thermo Fisher for the development of assays for the detection and characterization of viruses. All other authors declare no competing interests.

Published
2021
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21. Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology.

Author

Fauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J, Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott I, Quick J, Loman NJ, Neugebauer KM, Greninger AL, Jerome KR, Roychoudhury P, Xie H, Shrestha L, Huang ML, Pitzer VE, Iwasaki A, Omer SB, Khan K, Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, and Grubaugh ND

Abstract

Since its emergence and detection in Wuhan, China in late 2019, the novel coronavirus SARS-CoV-2 has spread to nearly every country around the world, resulting in hundreds of thousands of infections to date. The virus was first detected in the Pacific Northwest region of the United States in January, 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March. To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the U.S., we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. Our phylogenetic analysis places the majority of these genomes with viruses sequenced from Washington state. By coupling our genomic data with domestic and international travel patterns, we show that early SARS-CoV-2 transmission in Connecticut was likely driven by domestic introductions. Moreover, the risk of domestic importation to Connecticut exceeded that of international importation by mid-March regardless of our estimated impacts of federal travel restrictions. This study provides evidence for widespread, sustained transmission of SARS-CoV-2 within the U.S. and highlights the critical need for local surveillance.

Published
2020
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