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1. SARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity

Author

Peña-Hernández, Mario A., Alfajaro, Mia Madel, Filler, Renata B., Moriyama, Miyu, Keeler, Emma L., Ranglin, Zara E., Kong, Yong, Mao, Tianyang, Menasche, Bridget L., Mankowski, Madeleine C., Zhao, Zhe, Vogels, Chantal B. F., Hahn, Anne M., Kalinich, Chaney C., Zhang, Shuo, Huston, Nicholas, Wan, Han, Araujo-Tavares, Rafael, Lindenbach, Brett D., Homer, Robert, Pyle, Anna Marie, Martinez, David R., Grubaugh, Nathan D., Israelow, Benjamin, Iwasaki, Akiko, and Wilen, Craig B.

Published
2024
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2. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus

Author

Vogels, Chantal B. F., Hill, Verity, Breban, Mallery I., Chaguza, Chrispin, Paul, Lauren M., Sodeinde, Afeez, Taylor-Salmon, Emma, Ott, Isabel M., Petrone, Mary E., Dijk, Dennis, Jonges, Marcel, Welkers, Matthijs R. A., Locksmith, Timothy, Dong, Yibo, Tarigopula, Namratha, Tekin, Omer, Schmedes, Sarah, Bunch, Sylvia, Cano, Natalia, Jaber, Rayah, Panzera, Charles, Stryker, Ian, Vergara, Julieta, Zimler, Rebecca, Kopp, Edgar, Heberlein, Lea, Herzog, Kaylee S., Fauver, Joseph R., Morrison, Andrea M., Michael, Scott F., and Grubaugh, Nathan D.

Published
2024
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3. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean

Author

Taylor-Salmon, Emma, Hill, Verity, Paul, Lauren M., Koch, Robert T., Breban, Mallery I., Chaguza, Chrispin, Sodeinde, Afeez, Warren, Joshua L., Bunch, Sylvia, Cano, Natalia, Cone, Marshall, Eysoldt, Sarah, Garcia, Alezaundra, Gilles, Nicadia, Hagy, Andrew, Heberlein, Lea, Jaber, Rayah, Kassens, Elizabeth, Colarusso, Pamela, Davis, Amanda, Baudin, Samantha, Rico, Edhelene, Mejía-Echeverri, Álvaro, Scott, Blake, Stanek, Danielle, Zimler, Rebecca, Muñoz-Jordán, Jorge L., Santiago, Gilberto A., Adams, Laura E., Paz-Bailey, Gabriela, Spillane, Melanie, Katebi, Volha, Paulino-Ramírez, Robert, Mueses, Sayira, Peguero, Armando, Sánchez, Nelissa, Norman, Francesca F., Galán, Juan-Carlos, Huits, Ralph, Hamer, Davidson H., Vogels, Chantal B. F., Morrison, Andrea, Michael, Scott F., and Grubaugh, Nathan D.

Published
2024
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5. 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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6. Survey of white-footed mice (Peromyscus leucopus) in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses

Author

Earnest, Rebecca, Hahn, Anne M., Feriancek, Nicole M., Brandt, Matthew, Filler, Renata B., Zhao, Zhe, Breban, Mallery I., Vogels, Chantal B. F., Chen, Nicholas F. G., Koch, Robert T., Porzucek, Abbey J., Sodeinde, Afeez, Garbiel, Alexa, Keanna, Claire, Litwak, Hannah, Stuber, Heidi R., Cantoni, Jamie L., Pitzer, Virginia E., Olarte Castillo, Ximena A., Goodman, Laura B., Wilen, Craig B., Linske, Megan A., Williams, Scott C., and Grubaugh, Nathan D.

Published
2023
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9. Analysis of Powassan Virus Genome Sequences from Human Cases Reveals Substantial Genetic Diversity with Implications for Molecular Assay Development.

Author

Klontz, Erik H., Chowdhury, Navid, Holbrook, Nolan, Solomon, Isaac H., Telford 3rd, Sam R., Aliota, Matthew T., Vogels, Chantal B. F., Grubaugh, Nathan D., Helgager, Jeffrey, Hughes, Holly R., Velez, Jason, Piantadosi, Anne, Chiu, Charles Y., Lemieux, Jacob, and Branda, John A.

Subjects
IXODES scapularis, POWASSAN (Disease), GENETIC variation, CEREBROSPINAL fluid, IMMUNOCOMPROMISED patients
Abstract

Powassan virus (POWV) is an emerging tick-borne virus that causes severe meningoencephalitis in the United States, Canada, and Russia. Serology is generally the preferred diagnostic modality, but PCR on cerebrospinal fluid, blood, or urine has an important role, particularly in immunocompromised patients who are unable to mount a serologic response. Although the perceived poor sensitivity of PCR in the general population may be due to the biology of infection and health-seeking behavior (with short viremic periods that end before hospital presentation), limitations in assay design may also contribute. Genome sequences from clinical POWV cases are extremely scarce; PCR assay design has been informed by those available, but the numbers are limited. Larger numbers of genome sequences from tick-derived POWV are available, but it is not known if POWV genomes from human infections broadly mirror genomes from tick hosts, or if human infections are caused by a subset of more virulent strains. We obtained viral genomic data from 10 previously unpublished POWV human infections and showed that they broadly mirror the diversity of genome sequences seen in ticks, including all three major clades (lineage I, lineage II Northeast, and lineage II Midwest). These newly published clinical POWV genome sequences include the first confirmed lineage I infection in the United States, highlighting the relevance of all clades in human disease. An in silico analysis of published POWV PCR assays shows that many assays were optimized against a single clade and have mismatches that may affect their sensitivity when applied across clades. This analysis serves as a launching point for improved PCR design for clinical diagnostics and environmental surveillance. [ABSTRACT FROM AUTHOR]

Published
2024
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10. 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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11. 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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12. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19

Author

Unterman, Avraham, Sumida, Tomokazu S., Nouri, Nima, Yan, Xiting, Zhao, Amy Y., Gasque, Victor, Schupp, Jonas C., Asashima, Hiromitsu, Liu, Yunqing, Cosme, Jr., Carlos, Deng, Wenxuan, Chen, Ming, Raredon, Micha Sam Brickman, Hoehn, Kenneth B., Wang, Guilin, Wang, Zuoheng, DeIuliis, Giuseppe, Ravindra, Neal G., Li, Ningshan, Castaldi, Christopher, Wong, Patrick, Fournier, John, Bermejo, Santos, Sharma, Lokesh, Casanovas-Massana, Arnau, Vogels, Chantal B. F., Wyllie, Anne L., Grubaugh, Nathan D., Melillo, Anthony, Meng, Hailong, Stein, Yan, Minasyan, Maksym, Mohanty, Subhasis, Ruff, William E., Cohen, Inessa, Raddassi, Khadir, Niklason, Laura E., Ko, Albert I., Montgomery, Ruth R., Farhadian, Shelli F., Iwasaki, Akiko, Shaw, Albert C., van Dijk, David, Zhao, Hongyu, Kleinstein, Steven H., Hafler, David A., Kaminski, Naftali, and Dela Cruz, Charles S.

Published
2022
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13. Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques

Author

Baaijens, Jasmijn A., Zulli, Alessandro, Ott, Isabel M., Nika, Ioanna, van der Lugt, Mart J., Petrone, Mary E., Alpert, Tara, Fauver, Joseph R., Kalinich, Chaney C., Vogels, Chantal B. F., Breban, Mallery I., Duvallet, Claire, McElroy, Kyle A., Ghaeli, Newsha, Imakaev, Maxim, Mckenzie-Bennett, Malaika F., Robison, Keith, Plocik, Alex, Schilling, Rebecca, Pierson, Martha, Littlefield, Rebecca, Spencer, Michelle L., Simen, Birgitte B., Hanage, William P., Grubaugh, Nathan D., Peccia, Jordan, and Baym, Michael

Published
2022
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15. Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity

Author

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., and Iwasaki, Akiko

Published
2021
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16. The impact of antigenic distance on Orthopoxvirus Vaccination and Mpox Infection for cross-protective immunity

Author

Crandell, Jameson, primary, Monteiro, Valter Silva, additional, Pischel, Lauren, additional, Fang, Zhenhao, additional, Zhong, Yi, additional, Lawres, Lauren, additional, Conde, Luciana, additional, Meira de Asis, Gustavo, additional, Maciel, Gabriela, additional, Zaleski, Agnieszka, additional, Lira, Guilherme S., additional, Higa, Luiza M., additional, Breban, Mallery I., additional, Vogels, Chantal B. F., additional, Grubaugh, Nathan D., additional, Aoun-Barakat, Lydia, additional, Grifoni, Alba, additional, Sette, Alessandro, additional, Castineiras, Terezinha M., additional, Chen, Sidi, additional, Yildirim, Inci, additional, Vale, Andre M., additional, Omer, Saad B., additional, and Lucas, Carolina, additional

Published
2024
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18. A satellite repeat-derived piRNA controls embryonic development of Aedes

Author

Halbach, Rebecca, Miesen, Pascal, Joosten, Joep, Tasköprü, Ezgi, Rondeel, Inge, Pennings, Bas, and Vogels, Chantal B. F.

Subjects
Embryonic development -- Control -- Genetic aspects -- Analysis, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Tandem repeat elements such as the diverse class of satellite repeats occupy large parts of eukaryotic chromosomes, mostly at centromeric, pericentromeric, telomeric and subtelomeric regions.sup.1. However, some elements are located in euchromatic regions throughout the genome and have been hypothesized to regulate gene expression in cis by modulating local chromatin structure, or in trans via transcripts derived from the repeats.sup.2-4. Here we show that a satellite repeat in the mosquito Aedes aegypti promotes sequence-specific gene silencing via the expression of two PIWI-interacting RNAs (piRNAs). Whereas satellite repeats and piRNA sequences generally evolve extremely quickly.sup.5-7, this locus was conserved for approximately 200 million years, suggesting that it has a central function in mosquito biology. piRNA production commenced shortly after egg laying, and inactivation of the more abundant piRNA resulted in failure to degrade maternally deposited transcripts in the zygote and developmental arrest. Our results reveal a mechanism by which satellite repeats regulate global gene expression in trans via piRNA-mediated gene silencing that is essential for embryonic development. A conserved satellite repeat in the mosquito Aedes aegypti encodes PIWI-interacting RNAs that promote sequence-specific gene silencing in trans and have an essential role in embryonic development., Author(s): Rebecca Halbach [sup.1] , Pascal Miesen [sup.1] , Joep Joosten [sup.1] , Ezgi Tasköprü [sup.1] , Inge Rondeel [sup.1] , Bas Pennings [sup.1] , Chantal B. F. Vogels [sup.2] [...]

Published
2020
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19. Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets

Author

Vogels, Chantal B. F., Brito, Anderson F., Wyllie, Anne L., Fauver, Joseph R., Ott, Isabel M., Kalinich, Chaney C., Petrone, Mary E., Casanovas-Massana, Arnau, Catherine Muenker, M., Moore, Adam J., Klein, Jonathan, Lu, Peiwen, Lu-Culligan, Alice, Jiang, Xiaodong, Kim, Daniel J., Kudo, Eriko, Mao, Tianyang, Moriyama, Miyu, Oh, Ji Eun, Park, Annsea, Silva, Julio, Song, Eric, Takahashi, Takehiro, Taura, Manabu, Tokuyama, Maria, Venkataraman, Arvind, Weizman, Orr-El, Wong, Patrick, Yang, Yexin, Cheemarla, Nagarjuna R., White, Elizabeth B., Lapidus, Sarah, Earnest, Rebecca, Geng, Bertie, Vijayakumar, Pavithra, Odio, Camila, Fournier, John, Bermejo, Santos, Farhadian, Shelli, Dela Cruz, Charles S., Iwasaki, Akiko, Ko, Albert I., Landry, Marie L., Foxman, Ellen F., and Grubaugh, Nathan D.

Published
2020
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20. Longitudinal analyses reveal immunological misfiring in severe COVID-19

Author

Lucas, Carolina, Wong, Patrick, Klein, Jon, Castro, Tiago B. R., Silva, Julio, Sundaram, Maria, Ellingson, Mallory K., Mao, Tianyang, Oh, Ji Eun, Israelow, Benjamin, Takahashi, Takehiro, Tokuyama, Maria, Lu, Peiwen, Venkataraman, Arvind, Park, Annsea, Mohanty, Subhasis, Wang, Haowei, Wyllie, Anne L., Vogels, Chantal B. F., Earnest, Rebecca, Lapidus, Sarah, Ott, Isabel M., Moore, Adam J., Muenker, M. Catherine, Fournier, John B., Campbell, Melissa, Odio, Camila D., Casanovas-Massana, Arnau, Herbst, Roy, Shaw, Albert C., Medzhitov, Ruslan, Schulz, Wade L., Grubaugh, Nathan D., Dela Cruz, Charles, Farhadian, Shelli, Ko, Albert I., Omer, Saad B., and Iwasaki, Akiko

Published
2020
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23. Reply to: A finding of sex similarities rather than differences in COVID-19 outcomes

Author

Takahashi, Takehiro, Ellingson, Mallory K., Wong, Patrick, Israelow, Benjamin, Lucas, Carolina, Klein, Jon, Silva, Julio, Mao, Tianyang, Oh, Ji Eun, Tokuyama, Maria, Lu, Peiwen, Venkataraman, Arvind, Park, Annsea, Liu, Feimei, Meir, Amit, Sun, Jonathan, Wang, Eric Y., Casanovas-Massana, Arnau, Wyllie, Anne L., Vogels, Chantal B. F., Earnest, Rebecca, Lapidus, Sarah, Ott, Isabel M., Moore, Adam J., Shaw, Albert, Fournier, John B., Odio, Camila D., Farhadian, Shelli, Dela Cruz, Charles, Grubaugh, Nathan D., Schulz, Wade L., Ring, Aaron M., Ko, Albert I., Omer, Saad B., and Iwasaki, Akiko

Published
2021
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24. Acute encephalopathy with elevated CSF inflammatory markers as the initial presentation of COVID-19

Author

Farhadian, Shelli, Glick, Laura R., Vogels, Chantal B. F., Thomas, Jared, Chiarella, Jennifer, Casanovas-Massana, Arnau, Zhou, Jing, Odio, Camila, Vijayakumar, Pavithra, Geng, Bertie, Fournier, John, Bermejo, Santos, Fauver, Joseph R., Alpert, Tara, Wyllie, Anne L., Turcotte, Cynthia, Steinle, Matthew, Paczkowski, Patrick, Dela Cruz, Charles, Wilen, Craig, Ko, Albert I., MacKay, Sean, Grubaugh, Nathan D., Spudich, Serena, and Barakat, Lydia Aoun

Published
2020
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25. Introduction and Spread of Dengue Virus 3, Florida, USA, May 2022-April 2023.

Author

Jones, Forrest K., Morrison, Andrea M., Santiago, Gilberto A., Rysava, Kristyna, Zimler, Rebecca A., Heberlein, Lea A., Kopp, Edgar, Saunders, Katharine E., Baudin, Samantha, Rico, Edhelene, Mejía-Echeverri, Álvaro, Taylor-Salmon, Emma, Hill, Verity, Breban, Mallery I., Vogels, Chantal B. F., Grubaugh, Nathan D., Paul, Lauren M., Michael, Scott F., Johansson, Michael A., and Adams, Laura E.

Subjects
DENGUE viruses, VIRAL transmission, DENGUE hemorrhagic fever, DENGUE, GENOTYPES
Abstract

During May 2022-April 2023, dengue virus serotype 3 was identified among 601 travel-associated and 61 locally acquired dengue cases in Florida, USA. All 203 sequenced genomes belonged to the same genotype III lineage and revealed potential transmission chains in which most locally acquired cases occurred shortly after introduction, with little sustained transmission. [ABSTRACT FROM AUTHOR]

Published
2024
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26. Development of an amplicon-based sequencing approach in response to the global emergence of mpox

Author

Chen, Nicholas F. G., primary, Chaguza, Chrispin, additional, Gagne, Luc, additional, Doucette, Matthew, additional, Smole, Sandra, additional, Buzby, Erika, additional, Hall, Joshua, additional, Ash, Stephanie, additional, Harrington, Rachel, additional, Cofsky, Seana, additional, Clancy, Selina, additional, Kapsak, Curtis J., additional, Sevinsky, Joel, additional, Libuit, Kevin, additional, Park, Daniel J., additional, Hemarajata, Peera, additional, Garrigues, Jacob M., additional, Green, Nicole M., additional, Sierra-Patev, Sean, additional, Carpenter-Azevedo, Kristin, additional, Huard, Richard C., additional, Pearson, Claire, additional, Incekara, Kutluhan, additional, Nishimura, Christina, additional, Huang, Jian Ping, additional, Gagnon, Emily, additional, Reever, Ethan, additional, Razeq, Jafar, additional, Muyombwe, Anthony, additional, Borges, Vítor, additional, Ferreira, Rita, additional, Sobral, Daniel, additional, Duarte, Silvia, additional, Santos, Daniela, additional, Vieira, Luís, additional, Gomes, João Paulo, additional, Aquino, Carly, additional, Savino, Isabella M., additional, Felton, Karinda, additional, Bajwa, Moneeb, additional, Hayward, Nyjil, additional, Miller, Holly, additional, Naumann, Allison, additional, Allman, Ria, additional, Greer, Neel, additional, Fall, Amary, additional, Mostafa, Heba H., additional, McHugh, Martin P., additional, Maloney, Daniel M., additional, Dewar, Rebecca, additional, Kenicer, Juliet, additional, Parker, Abby, additional, Mathers, Katharine, additional, Wild, Jonathan, additional, Cotton, Seb, additional, Templeton, Kate E., additional, Churchwell, George, additional, Lee, Philip A., additional, Pedrosa, Maria, additional, McGruder, Brenna, additional, Schmedes, Sarah, additional, Plumb, Matthew R., additional, Wang, Xiong, additional, Barcellos, Regina Bones, additional, Godinho, Fernanda M. S., additional, Salvato, Richard Steiner, additional, Ceniseros, Aimee, additional, Breban, Mallery I., additional, Grubaugh, Nathan D., additional, Gallagher, Glen R., additional, and Vogels, Chantal B. F., additional

Published
2023
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27. Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States

Author

Vogels, Chantal B. F., primary, Brackney, Doug E., additional, Dupuis, Alan P., additional, Robich, Rebecca M., additional, Fauver, Joseph R., additional, Brito, Anderson F., additional, Williams, Scott C., additional, Anderson, John F., additional, Lubelczyk, Charles B., additional, Lange, Rachel E., additional, Prusinski, Melissa A., additional, Kramer, Laura D., additional, Gangloff-Kaufmann, Jody L., additional, Goodman, Laura B., additional, Baele, Guy, additional, Smith, Robert P., additional, Armstrong, Philip M., additional, Ciota, Alexander T., additional, Dellicour, Simon, additional, and Grubaugh, Nathan D., additional

Published
2023
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28. Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages

Author

Oliveira, Glenn, Vogels, Chantal B. F., Zolfaghari, Ashley, Saraf, Sharada, Klitting, Raphaelle, Weger-Lucarelli, James, Leon, Karla P., Ontiveros, Carlos O., Agarwal, Rimjhim, Tsetsarkin, Konstantin A., Harris, Eva, Ebel, Gregory D., Wohl, Shirlee, Grubaugh, Nathan D., Andersen, Kristian G., Oliveira, Glenn, Vogels, Chantal B. F., Zolfaghari, Ashley, Saraf, Sharada, Klitting, Raphaelle, Weger-Lucarelli, James, Leon, Karla P., Ontiveros, Carlos O., Agarwal, Rimjhim, Tsetsarkin, Konstantin A., Harris, Eva, Ebel, Gregory D., Wohl, Shirlee, Grubaugh, Nathan D., and Andersen, Kristian G.

Abstract

Zika virus was introduced to the Western Hemisphere, spread rapidly, and led to the 2015-2016 Zika epidemic and a rise in congenital microcephaly. It remains unclear whether Zika virus evolved to become more transmissible directly before or during the epidemic. To investigate whether Zika evolved to become more transmissible, we engineered a library of recombinant viruses that represent twelve major Zika virus lineages that circulated throughout the Americas. We measured the replicative fitness of each of these lineages by infecting live mosquitoes and human cells that are relevant for disease or transmission. We found that two of the lineages, one that dominated Central America and another that existed mostly in the Caribbean, appear to replicate more efficiently in human cells. While the fitness changes do not appear to have significant effects on the 2015-2016 Zika epidemic, our analysis suggests Zika virus evolved at least twice during this outbreak. Monitoring the phenotypic evolution during the course of an outbreak can help control spread and mitigate disease. We believe this framework can be applied to study phenotypic evolution during future epidemics caused by emerging RNA viruses. RNA viruses have short generation times and high mutation rates, allowing them to undergo rapid molecular evolution during epidemics. However, the extent of RNA virus phenotypic evolution within epidemics and the resulting effects on fitness and virulence remain mostly unknown. Here, we screened the 2015-2016 Zika epidemic in the Americas for lineage-specific fitness differences. We engineered a library of recombinant viruses representing twelve major Zika virus lineages and used them to measure replicative fitness within disease-relevant human primary cells and live mosquitoes. We found that two of these lineages conferred significant in vitro replicative fitness changes among human primary cells, but we did not find fitness changes in Aedes aegypti mosquitoes. Additionally, we

Published
2023

30. Nonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants

Author

Petrone, Mary E, primary, Lucas, Carolina, additional, Menasche, Bridget, additional, Breban, Mallery I, additional, Yildirim, Inci, additional, Campbell, Melissa, additional, Omer, Saad B, additional, Holmes, Edward C, additional, Ko, Albert I, additional, Grubaugh, Nathan D, additional, Iwasaki, Akiko, additional, Wilen, Craig B, additional, Vogels, Chantal B F, additional, and Fauver, Joseph R, additional

Published
2023
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31. Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages

Author

Oliveira, Glenn, primary, Vogels, Chantal B. F., additional, Zolfaghari, Ashley, additional, Saraf, Sharada, additional, Klitting, Raphaelle, additional, Weger-Lucarelli, James, additional, P. Leon, Karla, additional, Ontiveros, Carlos O., additional, Agarwal, Rimjhim, additional, Tsetsarkin, Konstantin A., additional, Harris, Eva, additional, Ebel, Gregory D., additional, Wohl, Shirlee, additional, Grubaugh, Nathan D., additional, and Andersen, Kristian G., additional

Published
2023
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32. Identification of Human Monkeypox Virus Genome Deletions That Impact Diagnostic Assays

Author

Garrigues, Jacob M., primary, Hemarajata, Peera, additional, Lucero, Briar, additional, Alarcón, Jemma, additional, Ransohoff, Heidi, additional, Marutani, Amy N., additional, Kim, Moon, additional, Marlowe, Elizabeth M., additional, Realegeno, Susan E., additional, Kagan, Ron M., additional, Montero, Clemente I., additional, Chen, Nicholas F. G., additional, Grubaugh, Nathan D., additional, Vogels, Chantal B. F., additional, and Green, Nicole M., additional

Published
2022
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34. Sex differences in immune responses that underlie COVID-19 disease outcomes

Author

Takahashi, Takehiro, Ellingson, Mallory K., Wong, Patrick, Israelow, Benjamin, Lucas, Carolina, Klein, Jon, Silva, Julio, Mao, Tianyang, Oh, Ji Eun, Tokuyama, Maria, Lu, Peiwen, Venkataraman, Arvind, Park, Annsea, Liu, Feimei, Meir, Amit, Sun, Jonathan, Wang, Eric Y., Casanovas-Massana, Arnau, Wyllie, Anne L., Vogels, Chantal B. F., Earnest, Rebecca, Lapidus, Sarah, Ott, Isabel M., Moore, Adam J., Anastasio, Kelly, Askenase, Michael H., Batsu, Maria, Beatty, Hannah, Bermejo, Santos, Bickerton, Sean, Brower, Kristina, Bucklin, Molly L., Cahill, Staci, Campbell, Melissa, Cao, Yiyun, Courchaine, Edward, Datta, Rupak, DeIuliis, Giuseppe, Geng, Bertie, Glick, Laura, Handoko, Ryan, Kalinich, Chaney, Khoury-Hanold, William, Kim, Daniel, Knaggs, Lynda, Kuang, Maxine, Kudo, Eriko, Lim, Joseph, Linehan, Melissa, Lu-Culligan, Alice, Malik, Amyn A., Martin, Anjelica, Matos, Irene, McDonald, David, Minasyan, Maksym, Mohanty, Subhasis, Muenker, M. Catherine, Naushad, Nida, Nelson, Allison, Nouws, Jessica, Nunez-Smith, Marcella, Obaid, Abeer, Ott, Isabel, Park, Hong-Jai, Peng, Xiaohua, Petrone, Mary, Prophet, Sarah, Rahming, Harold, Rice, Tyler, Rose, Kadi-Ann, Sewanan, Lorenzo, Sharma, Lokesh, Shepard, Denise, Silva, Erin, Simonov, Michael, Smolgovsky, Mikhail, Song, Eric, Sonnert, Nicole, Strong, Yvette, Todeasa, Codruta, Valdez, Jordan, Velazquez, Sofia, Vijayakumar, Pavithra, Wang, Haowei, Watkins, Annie, White, Elizabeth B., Yang, Yexin, Shaw, Albert, Fournier, John B., Odio, Camila D., Farhadian, Shelli, Dela Cruz, Charles, Grubaugh, Nathan D., Schulz, Wade L., Ring, Aaron M., Ko, Albert I., Omer, Saad B., and Iwasaki, Akiko

Subjects
0301 basic medicine, Multidisciplinary, Innate immune system, biology, business.industry, T cell, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, medicine.anatomical_structure, Immune system, Immunity, 030220 oncology & carcinogenesis, Immunology, biology.protein, Medicine, Antibody, business, Viral load, Sex characteristics, Cohort study
Abstract

There is increasing evidence that coronavirus disease 2019 (COVID-19) produces more severe symptoms and higher mortality among men than among women1-5. However, whether immune responses against severe acute respiratory syndrome coronavirus (SARS-CoV-2) differ between sexes, and whether such differences correlate with the sex difference in the disease course of COVID-19, is currently unknown. Here we examined sex differences in viral loads, SARS-CoV-2-specific antibody titres, plasma cytokines and blood-cell phenotyping in patients with moderate COVID-19 who had not received immunomodulatory medications. Male patients had higher plasma levels of innate immune cytokines such as IL-8 and IL-18 along with more robust induction of non-classical monocytes. By contrast, female patients had more robust T cell activation than male patients during SARS-CoV-2 infection. Notably, we found that a poor T cell response negatively correlated with patients' age and was associated with worse disease outcome in male patients, but not in female patients. By contrast, higher levels of innate immune cytokines were associated with worse disease progression in female patients, but not in male patients. These findings provide a possible explanation for the observed sex biases in COVID-19, and provide an important basis for the development of a sex-based approach to the treatment and care of male and female patients with COVID-19.

Published
2020
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35. Additional file 1 of Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques

Author

Baaijens, Jasmijn A., Zulli, Alessandro, Ott, Isabel M., Nika, Ioanna, van der Lugt, Mart J., Petrone, Mary E., Alpert, Tara, Fauver, Joseph R., Kalinich, Chaney C., Vogels, Chantal B. F., Breban, Mallery I., Duvallet, Claire, McElroy, Kyle A., Ghaeli, Newsha, Imakaev, Maxim, Mckenzie-Bennett, Malaika F., Robison, Keith, Plocik, Alex, Schilling, Rebecca, Pierson, Martha, Littlefield, Rebecca, Spencer, Michelle L., Simen, Birgitte B., Hanage, William P., Grubaugh, Nathan D., Peccia, Jordan, and Baym, Michael

Abstract

Additional file 1. Includes all supplementary information, supplementary figures and supplementary tables.

Published
2022
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36. Additional file 2 of Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques

Author

Baaijens, Jasmijn A., Zulli, Alessandro, Ott, Isabel M., Nika, Ioanna, van der Lugt, Mart J., Petrone, Mary E., Alpert, Tara, Fauver, Joseph R., Kalinich, Chaney C., Vogels, Chantal B. F., Breban, Mallery I., Duvallet, Claire, McElroy, Kyle A., Ghaeli, Newsha, Imakaev, Maxim, Mckenzie-Bennett, Malaika F., Robison, Keith, Plocik, Alex, Schilling, Rebecca, Pierson, Martha, Littlefield, Rebecca, Spencer, Michelle L., Simen, Birgitte B., Hanage, William P., Grubaugh, Nathan D., Peccia, Jordan, and Baym, Michael

Abstract

Additional file 2. Review history.

Published
2022
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37. Sequencing SARS-CoV-2 genomes from saliva

Author

Alpert, Tara, primary, Vogels, Chantal B F, additional, Breban, Mallery I, additional, Petrone, Mary E, additional, Wyllie, Anne L, additional, Grubaugh, Nathan D, additional, and Fauver, Joseph R, additional

Published
2022
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38. 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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39. Authors' Response to Peer Reviews of “COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis”

Author

Lee, Megan, primary, Sallah, Ya Haddy, additional, Petrone, Mary, additional, Ringer, Matthew, additional, Cosentino, Danielle, additional, Vogels, Chantal B F, additional, Fauver, Joseph R, additional, Alpert, Tara D, additional, Grubaugh, Nathan D, additional, and Gupta, Shaili, additional

Published
2021
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40. Authors' Response to Peer Reviews of “COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis” (Preprint)

Author

Lee, Megan, primary, Sallah, Ya Haddy, additional, Petrone, Mary, additional, Ringer, Matthew, additional, Cosentino, Danielle, additional, Vogels, Chantal B F, additional, Fauver, Joseph R, additional, Alpert, Tara D, additional, Grubaugh, Nathan D, additional, and Gupta, Shaili, additional

Published
2021
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41. Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies

Author

Kissler, Stephen M., primary, Fauver, Joseph R., additional, Mack, Christina, additional, Olesen, Scott W., additional, Tai, Caroline, additional, Shiue, Kristin Y., additional, Kalinich, Chaney C., additional, Jednak, Sarah, additional, Ott, Isabel M., additional, Vogels, Chantal B. F., additional, Wohlgemuth, Jay, additional, Weisberger, James, additional, DiFiori, John, additional, Anderson, Deverick J., additional, Mancell, Jimmie, additional, Ho, David D., additional, Grubaugh, Nathan D., additional, and Grad, Yonatan H., additional

Published
2021
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43. Diverse Functional Autoantibodies that Underlie Immune Perturbations in COVID-19

Author

Mao, Tianyang, primary, Wang, Eric Y., additional, Klein, Jon, additional, Dai, Yile, additional, Huck, John D., additional, Liu, Feimei, additional, Zheng, Neil S., additional, Zhou, Ting, additional, Goldman-Israelow, Benjamin, additional, Wong, Patrick, additional, Lucas, Carolina, additional, Silva, Julio, additional, Oh, Ji Eun, additional, Song, Eric, additional, Perotti, Emily S., additional, Fischer, Suzanne, additional, Campbell, Melissa, additional, Fournier, John B., additional, Wyllie, Anne L., additional, Vogels, Chantal B. F., additional, Ott, Isabel M., additional, Kalinich, Chaney C., additional, Petrone, Mary E., additional, Watkins, Anne E., additional, Cruz, Charles Dela, additional, Farhadian, Shelli F., additional, Schulz, Wade L., additional, Grubaugh, Nathan D., additional, Ko, Albert I., additional, Iwasaki, Akiko, additional, and Ring, Aaron M., additional

Published
2021
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44. Real-time public health communication of local SARS-CoV-2 genomic epidemiology

Author

Kalinich, Chaney C., primary, Jensen, Cole G., additional, Neugebauer, Peter, additional, Petrone, Mary E., additional, Peña-Hernández, Mario, additional, Ott, Isabel M., additional, Wyllie, Anne L., additional, Alpert, Tara, additional, Vogels, Chantal B. F., additional, Fauver, Joseph R., additional, Grubaugh, Nathan D., additional, and Brito, Anderson F., additional

Published
2020
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46. The invasive Asian bush mosquito Aedes japonicus found in the Netherlands can experimentally transmit Zika virus and Usutu virus

Author

Abbo, Sandra R., primary, Visser, Tessa M., additional, Wang, Haidong, additional, Göertz, Giel P., additional, Fros, Jelke J., additional, Abma-Henkens, Marleen H. C., additional, Geertsema, Corinne, additional, Vogels, Chantal B. F., additional, Koopmans, Marion P. G., additional, Reusken, Chantal B. E. M., additional, Hall-Mendelin, Sonja, additional, Hall, Roy A., additional, van Oers, Monique M., additional, Koenraadt, Constantianus J. M., additional, and Pijlman, Gorben P., additional

Published
2020
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47. Powassan Virus Lineage I in Field-Collected Dermacentor variabilis Ticks, New York, USA.

Author

Hart, Charles, Hassett, Erin, Vogels, Chantal B. F., Shapley, Daniel, Grubaugh, Nathan D., and Thangamani, Saravanan

Subjects
DERMACENTOR, TICKS, IXODES, FLAVIVIRUSES, SPECIES
Abstract

Powassan virus is a tickborne flavivirus that can cause lethal or debilitating neurologic illness. It is canonically transmitted by Ixodes spp. ticks but might spill over to sympatric Dermacentor species. We detected Powassan virus lineage I from a pool of field-collected D. variabilis ticks in New York, USA. [ABSTRACT FROM AUTHOR]

Published
2023
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48. Longitudinal Immune Profiling of a Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection in a Solid Organ Transplant Recipient.

Author

Klein, Jonathan, Brito, Anderson F, Trubin, Paul, Lu, Peiwen, Wong, Patrick, Alpert, Tara, Peña-Hernández, Mario A, Haynes, Winston, Kamath, Kathy, Liu, Feimei, Vogels, Chantal B F, Fauver, Joseph R, Lucas, Carolina, Oh, Jieun, Mao, Tianyang, Silva, Julio, Wyllie, Anne L, Muenker, M Catherine, Casanovas-Massana, Arnau, and Moore, Adam J

Subjects
CORONAVIRUS diseases, HUMORAL immunity, TRANSPLANTATION of organs, tissues, etc., COVID-19, REINFECTION, WHOLE genome sequencing, INFECTION
Abstract

Background: The underlying immunologic deficiencies enabling severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection are currently unknown. We describe deep longitudinal immune profiling of a transplant recipient hospitalized twice for coronavirus disease 2019 (COVID-19).Methods: A 66-year-old male renal transplant recipient was hospitalized with COVID-19 March 2020 then readmitted to the hospital with COVID-19 233 days after initial diagnosis. Virologic and immunologic investigations were performed on samples from the primary and secondary infections.Results: Whole viral genome sequencing and phylogenetic analysis revealed that viruses causing both infections were caused by distinct genetic lineages without evidence of immune escape mutations. Longitudinal comparison of cellular and humoral responses during primary SARS-CoV-2 infection revealed that this patient responded to the primary infection with low neutralization titer anti-SARS-CoV-2 antibodies that were likely present at the time of reinfection.Conclusions: The development of neutralizing antibodies and humoral memory responses in this patient failed to confer protection against reinfection, suggesting that they were below a neutralizing titer threshold or that additional factors may be required for efficient prevention of SARS-CoV-2 reinfection. Development of poorly neutralizing antibodies may have been due to profound and relatively specific reduction in naive CD4 T-cell pools. Seropositivity alone may not be a perfect correlate of protection in immunocompromised patients. [ABSTRACT FROM AUTHOR]

Published
2022
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49. Effect of overwintering on survival and vector competence of the West Nile virus vector Culex pipiens

Author

Koenraadt, Constantianus J M, Möhlmann, Tim W R, Verhulst, Niels O; https://orcid.org/0000-0002-1106-9711, Spitzen, Jeroen, Vogels, Chantal B F, Koenraadt, Constantianus J M, Möhlmann, Tim W R, Verhulst, Niels O; https://orcid.org/0000-0002-1106-9711, Spitzen, Jeroen, and Vogels, Chantal B F

Abstract

BACKGROUND:West Nile virus (WNV) is a mosquito-borne virus that is mainly transmitted among birds by Culex pipiens mosquitoes. The species Cx. pipiens consists of two biotypes named pipiens and molestus, which together can form h ybrids. One of the major distinctions between the biotypes is their overwintering behaviour. Adults of biotype pipiens diapause during winter, whereas biotype molestus remains actively blood-feeding. Diapausing may affect survival and vector competence of biotype pipiens. The aims of this study were therefore to identify the biotype composition of diapausing Cx. pipiens mosquitoes, to quantify survival throughout the autumn and winter months, and to determine effects of overwintering on vector competence of emerging Cx. pipiens mosquitoes for WNV. METHODS: Diapausing mosquitoes were collected at two typical overwintering locations in the Netherlands. A selection of Cx. pipiens mosquitoes was identified to biotype using real-time PCR. Survival of diapausing Cx. pipiens mosquitoes during autumn and winter was monitored by placing cages with either field-collected or laboratory-reared females in houses and sheds. Vector competence of field-collected (diapausing) and laboratory-reared (non-diapausing) Cx. pipiens mosquitoes was determined to gain insight in the effect of overwintering on WNV transmission. RESULTS: The majority (92%) of diapausing Cx. pipiens females were identified as biotype pipiens. More than 70% of diapausing Cx. pipiens mosquitoes was able to survive for more than four months in sheds, whereas diapausing in houses resulted in 100% mortality in that same period. In contrast, non-diapausing Cx. pipiens biotype pipiens mosquitoes reared in the laboratory died within a week in both houses and sheds. Vector competence of Cx. pipiens mosquitoes that had diapaused during the autumn and winter months was comparable to non-diapausing laboratory-reared mosquitoes. CONCLUSIONS: This study confirms that the majority of Cx. pipiens mosq

Published
2019

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