48 results on '"Barnes, Kayla G."'
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2. Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever
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Kotliar, Dylan, Raju, Siddharth, Tabrizi, Shervin, Odia, Ikponmwosa, Goba, Augustine, Momoh, Mambu, Sandi, John Demby, Nair, Parvathy, Phelan, Eric, Tariyal, Ridhi, Eromon, Philomena E., Mehta, Samar, Robles-Sikisaka, Refugio, Siddle, Katherine J., Stremlau, Matt, Jalloh, Simbirie, Gire, Stephen K., Winnicki, Sarah, Chak, Bridget, Schaffner, Stephen F., Pauthner, Matthias, Karlsson, Elinor K., Chapin, Sarah R., Kennedy, Sharon G., Branco, Luis M., Kanneh, Lansana, Vitti, Joseph J., Broodie, Nisha, Gladden-Young, Adrianne, Omoniwa, Omowunmi, Jiang, Pan-Pan, Yozwiak, Nathan, Heuklom, Shannon, Moses, Lina M., Akpede, George O., Asogun, Danny A., Rubins, Kathleen, Kales, Susan, Happi, Anise N., Iruolagbe, Christopher O., Dic-Ijiewere, Mercy, Iraoyah, Kelly, Osazuwa, Omoregie O., Okonkwo, Alexander K., Kunz, Stefan, McCormick, Joseph B., Khan, S. Humarr, Honko, Anna N., Lander, Eric S., Oldstone, Michael B. A., Hensley, Lisa, Folarin, Onikepe A., Okogbenin, Sylvanus A., Günther, Stephan, Ollila, Hanna M., Tewhey, Ryan, Okokhere, Peter O., Schieffelin, John S., Andersen, Kristian G., Reilly, Steven K., Grant, Donald S., Garry, Robert F., Barnes, Kayla G., Happi, Christian T., and Sabeti, Pardis C.
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- 2024
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3. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems
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Barnes, Kayla G., Levy, Joshua I., Gauld, Jillian, Rigby, Jonathan, Kanjerwa, Oscar, Uzzell, Christopher B., Chilupsya, Chisomo, Anscombe, Catherine, Tomkins-Tinch, Christopher, Mbeti, Omar, Cairns, Edward, Thole, Herbert, McSweeney, Shannon, Chibwana, Marah G., Ashton, Philip M., Jere, Khuzwayo C., Meschke, John Scott, Diggle, Peter, Cornick, Jennifer, Chilima, Benjamin, Jambo, Kondwani, Andersen, Kristian G., Kawalazira, Gift, Paterson, Steve, Nyirenda, Tonney S., and Feasey, Nicholas
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- 2023
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4. Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques
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Santus, Luisa, Sopena-Rios, Maria, García-Pérez, Raquel, Lin, Aaron E., Adams, Gordon C., Barnes, Kayla G., Siddle, Katherine J., Wohl, Shirlee, Reverter, Ferran, Rinn, John L., Bennett, Richard S., Hensley, Lisa E., Sabeti, Pardis C., and Melé, Marta
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- 2023
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5. A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study
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Anscombe, Catherine, Lissauer, Samantha, Thole, Herbert, Rylance, Jamie, Dula, Dingase, Menyere, Mavis, Kutambe, Belson, van der Veer, Charlotte, Phiri, Tamara, Banda, Ndaziona P., Mndolo, Kwazizira S., Mponda, Kelvin, Phiri, Chimota, Mallewa, Jane, Nyirenda, Mulinda, Katha, Grace, Mwandumba, Henry, Gordon, Stephen B., Jambo, Kondwani C., Cornick, Jennifer, Feasey, Nicholas, Barnes, Kayla G., Morton, Ben, and Ashton, Philip M.
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- 2023
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6. Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics
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Kotliar, Dylan, Lin, Aaron E., Logue, James, Hughes, Travis K., Khoury, Nadine M., Raju, Siddharth S., Wadsworth, Marc H., II, Chen, Han, Kurtz, Jonathan R., Dighero-Kemp, Bonnie, Bjornson, Zach B., Mukherjee, Nilanjan, Sellers, Brian A., Tran, Nancy, Bauer, Matthew R., Adams, Gordon C., Adams, Ricky, Rinn, John L., Melé, Marta, Schaffner, Stephen F., Nolan, Garry P., Barnes, Kayla G., Hensley, Lisa E., McIlwain, David R., Shalek, Alex K., Sabeti, Pardis C., and Bennett, Richard S.
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- 2020
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7. Spatially resolved single-cell atlas of the lung in fatal Covid19 in an African population reveals a distinct cellular signature and an interferon gamma dominated response
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Nyirenda, James, primary, Hardy, Olympia, additional, Da Silva Filho, João, additional, Herder, Vanessa, additional, Attipa, Charalampos, additional, Ndovi, Charles, additional, Siwombo, Memory, additional, Namalima, Takondwa, additional, Suwedi, Leticia, additional, Nyasulu, Watipenge, additional, Ngulube, Thokozile, additional, Nyirenda, Deborah, additional, Mvaya, Leonard, additional, Phiri, Joseph, additional, Chasweka, Dennis, additional, Eneya, Chisomo, additional, Makwinja, Chikondi, additional, Phiri, Chisomo, additional, Ziwoya, Frank, additional, Tembo, Abel, additional, Makwangwala, Kingsley, additional, Khoswe, Stanley, additional, Banda, Peter, additional, Morton, Ben, additional, Hilton, Orla, additional, Lawrence, Sarah, additional, dos Reis, Monique Freire, additional, Melo, Gisely Cardoso, additional, de Lacerda, Marcus Vinicius Guimaraes, additional, Costa, Fabio Trindade Maranhão, additional, Monteiro, Wuelton Marcelo, additional, de Lima Ferreira, Luiz Carlos, additional, Johnson, Carla, additional, McGuinness, Dagmara, additional, Jambo, Kondwani, additional, Haley, Michael, additional, Kumwenda, Benjamin, additional, Palmarini, Massimo, additional, Barnes, Kayla G., additional, Denno, Donna M., additional, Voskuijl, Wieger, additional, Kamiza, Steve, additional, Couper, Kevin, additional, Marti, Matthias, additional, Otto, Thomas, additional, and Moxon, Christopher A., additional
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- 2023
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8. Field-deployable viral diagnostics using CRISPR-Cas13
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Myhrvold, Cameron, Freije, Catherine A., Gootenberg, Jonathan S., Abudayyeh, Omar O., Metsky, Hayden C., Durbin, Ann F., Kellner, Max J., Tan, Amanda L., Paul, Lauren M., Parham, Leda A., Garcia, Kimberly F., Barnes, Kayla G., Chak, Bridget, Mondini, Adriano, Nogueira, Mauricio L., Isern, Sharon, Michael, Scott F., Lorenzana, Ivette, Yozwiak, Nathan L., MacInnis, Bronwyn L., Bosch, Irene, Gehrke, Lee, Zhang, Feng, and Sabeti, Pardis C.
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- 2018
9. Retrospective Cohort Study of Lassa Fever in Pregnancy, Southern Nigeria
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Okogbenin, Sylvanus, Okoeguale, Joseph, Akpede, George, Colubri, Andres, Barnes, Kayla G., Mehta, Samar, Eifediyi, Reuben, Okogbo, Felix, Eigbefoh, Joseph, Momoh, Mojeed, Rafiu, Mojeed, Adomeh, Donatus, Odia, Ikponmwosa, Aire, Chris, Atafo, Rebecca, Okonofua, Martha, Pahlman, Meike, Becker-Ziaja, Beate, Asogun, Danny, Okokhere, Peter, Happi, Christian, Gunther, Stephan, Sabeti, Pardis C., and Ogbaini-Emovon, Ephraim
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Infant mortality ,Obstetrics ,Lassa fever ,Medical research ,Pregnancy ,Pregnant women ,Death ,Urination disorders ,Hospital patients ,Ribavirin ,Teachers ,Fetal death ,Convulsions ,Health - Abstract
Lassa fever (LF), a viral hemorrhagic fever endemic to West Africa (1-3), was first reported in 1969 from northern Nigeria (4,5). Since that time, LF has been documented in several [...]
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- 2019
10. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design
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Metsky, Hayden C., Siddle, Katherine J., Gladden-Young, Adrianne, Qu, James, Yang, David K., Brehio, Patrick, Goldfarb, Andrew, Piantadosi, Anne, Wohl, Shirlee, Carter, Amber, Lin, Aaron E., Barnes, Kayla G., Tully, Damien C., Corleis, Bjӧrn, Hennigan, Scott, Barbosa-Lima, Giselle, Vieira, Yasmine R., Paul, Lauren M., Tan, Amanda L., Garcia, Kimberly F., Parham, Leda A., Odia, Ikponmwosa, Eromon, Philomena, Folarin, Onikepe A., Goba, Augustine, Simon-Lorière, Etienne, Hensley, Lisa, Balmaseda, Angel, Harris, Eva, Kwon, Douglas S., Allen, Todd M., Runstadler, Jonathan A., Smole, Sandra, Bozza, Fernando A., Souza, Thiago M. L., Isern, Sharon, Michael, Scott F., Lorenzana, Ivette, Gehrke, Lee, Bosch, Irene, Ebel, Gregory, Grant, Donald S., Happi, Christian T., Park, Daniel J., Gnirke, Andreas, Sabeti, Pardis C., and Matranga, Christian B.
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- 2019
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11. Evidence of Ebola Virus Replication and High Concentration in Semen of a Patient During Recovery
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Barnes, Kayla G., Kindrachuk, Jason, Lin, Aaron E., Wohl, Shirlee, Qu, James, Tostenson, Samantha D., Dorman, William R., Busby, Michele, Siddle, Katherine J., Luo, Cynthia Y., Matranga, Christian B., Davey, Richard T., Sabeti, Pardis C., and Chertow, Daniel S.
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- 2017
12. Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time
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Barnes, Kayla G., Lachenauer, Anna E., Nitido, Adam, Siddiqui, Sameed, Gross, Robin, Beitzel, Brett, Siddle, Katherine J., Freije, Catherine A., Dighero-Kemp, Bonnie, Mehta, Samar B., Carter, Amber, Uwanibe, Jessica, Ajogbasile, Fehintola, Olumade, Testimony, Odia, Ikponmwosa, Sandi, John Demby, Momoh, Mambu, Metsky, Hayden C., Boehm, Chloe K., Lin, Aaron E., Kemball, Molly, Park, Daniel J., Branco, Luis, Boisen, Matt, Sullivan, Brian, Amare, Mihret F., Tiamiyu, Abdulwasiu B., Parker, Zahra F., Iroezindu, Michael, Grant, Donald S., Modjarrad, Kayvon, Myhrvold, Cameron, Garry, Robert F., Palacios, Gustavo, Hensley, Lisa E., Schaffner, Stephen F., Happi, Christian T., Colubri, Andres, and Sabeti, Pardis C.
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- 2020
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13. Field evaluation of a Pan-Lassa rapid diagnostic test during the 2018 Nigerian Lassa fever outbreak
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Boisen, Matthew L., Uyigue, Eghosa, Aiyepada, John, Siddle, Katherine J., Oestereich, Lisa, Nelson, Diana K. S., Bush, Duane J., Rowland, Megan M., Heinrich, Megan L., Eromon, Philomena, Kayode, Adeyemi T., Odia, Ikponmwosa, Adomeh, Donatus I., Muoebonam, Ekene B., Akhilomen, Patience, Okonofua, Grace, Osiemi, Blessing, Omoregie, Omigie, Airende, Michael, Agbukor, Jacqueline, Ehikhametalor, Solomon, Aire, Chris Okafi, Duraffour, Sophie, Pahlmann, Meike, Böhm, Wiebke, Barnes, Kayla G., Mehta, Samar, Momoh, Mambu, Sandi, John Demby, Goba, Augustine, Folarin, Onikepe A., Ogbaini-Emovan, Ephraim, Asogun, Danny A., Tobin, Ekaete A., Akpede, George O., Okogbenin, Sylvanus A., Okokhere, Peter O., Grant, Donald S., Schieffelin, John S., Sabeti, Pardis C., Günther, Stephan, Happi, Christian T., Branco, Luis M., and Garry, Robert F.
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- 2020
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14. Acute rotavirus infection is associated with the induction of circulating memory CD4+ T cell subsets
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Malamba-Banda, Chikondi, primary, Mhango, Chimwemwe, additional, Benedicto-Matambo, Prisca, additional, Mandolo, Jonathan J., additional, Chinyama, End, additional, Kumwenda, Orpha, additional, Barnes, Kayla G., additional, Cunliffe, Nigel A., additional, Iturriza-Gomara, Miren, additional, Jambo, Kondwani C., additional, and Jere, Khuzwayo C., additional
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- 2023
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15. Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi.
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Mhango, Chimwemwe, primary, Banda, Akuzike, additional, Chinyama, End, additional, Mandolo, Jonathan J, additional, Kumwenda, Orpha, additional, Malamba-Banda, Chikondi, additional, Barnes, Kayla G, additional, Kumwenda, Benjamin, additional, Jambo, Kondwani, additional, Donato, Celeste M, additional, Esona, Mathew D, additional, Mwangi, Peter N, additional, Steele, A Duncan, additional, Iturriza-Gomara, Miren, additional, Cunliffe, Nigel A, additional, Ndze, Valentine N, additional, Kamng’ona, Arox W, additional, Dennis, Francis E, additional, Nyaga, Martin M, additional, Chaguza, Chrispin, additional, and Jere, Khuzwayo C, additional
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- 2023
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16. Restriction to gene flow is associated with changes in the molecular basis of pyrethroid resistance in the malaria vector Anopheles funestus
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Barnes, Kayla G., Irving, Helen, Chiumia, Martin, Mzilahowa, Themba, Coleman, Michael, Hemingway, Janet, and Wondji, Charles S.
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- 2017
17. Different clinical features in Malawian outpatients presenting with COVID-19 prior to and during Omicron variant dominance: A prospective observational study
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Epi Infectieziekten Team 1, Chibwana, Marah G., Thole, Herbert W., Anscombe, Cat, Ashton, Philip M., Green, Edward, Barnes, Kayla G., Cornick, Jen, Turner, Ann, Witte, Desiree, Nthala, Sharon, Thom, Chikondi, Kanyandula, Felistas, Ainani, Anna, Mtike, Natasha, Tambala, Hope, N'goma, Veronica, Mwafulirwa, Dorah, Asima, Erick, Morton, Ben, Gmeiner, Markus, Gundah, Zaziwe, Kawalazira, Gift, French, Neil, Feasey, Nicholas, Heyderman, Robert S., Swarthout, Todd D., Jambo, Kondwani C., Epi Infectieziekten Team 1, Chibwana, Marah G., Thole, Herbert W., Anscombe, Cat, Ashton, Philip M., Green, Edward, Barnes, Kayla G., Cornick, Jen, Turner, Ann, Witte, Desiree, Nthala, Sharon, Thom, Chikondi, Kanyandula, Felistas, Ainani, Anna, Mtike, Natasha, Tambala, Hope, N'goma, Veronica, Mwafulirwa, Dorah, Asima, Erick, Morton, Ben, Gmeiner, Markus, Gundah, Zaziwe, Kawalazira, Gift, French, Neil, Feasey, Nicholas, Heyderman, Robert S., Swarthout, Todd D., and Jambo, Kondwani C.
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- 2023
18. Different clinical features in Malawian outpatients presenting with COVID-19 prior to and during Omicron variant dominance: A prospective observational study
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Chibwana, Marah G., primary, Thole, Herbert W., additional, Anscombe, Cat, additional, Ashton, Philip M., additional, Green, Edward, additional, Barnes, Kayla G., additional, Cornick, Jen, additional, Turner, Ann, additional, Witte, Desiree, additional, Nthala, Sharon, additional, Thom, Chikondi, additional, Kanyandula, Felistas, additional, Ainani, Anna, additional, Mtike, Natasha, additional, Tambala, Hope, additional, N’goma, Veronica, additional, Mwafulirwa, Dorah, additional, Asima, Erick, additional, Morton, Ben, additional, Gmeiner, Markus, additional, Gundah, Zaziwe, additional, Kawalazira, Gift, additional, French, Neil, additional, Feasey, Nicholas, additional, Heyderman, Robert S., additional, Swarthout, Todd D., additional, and Jambo, Kondwani C., additional
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- 2023
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19. Additional file 2 of A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study
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Anscombe, Catherine, Lissauer, Samantha, Thole, Herbert, Rylance, Jamie, Dula, Dingase, Menyere, Mavis, Kutambe, Belson, van der Veer, Charlotte, Phiri, Tamara, Banda, Ndaziona P., Mndolo, Kwazizira S., Mponda, Kelvin, Phiri, Chimota, Mallewa, Jane, Nyirenda, Mulinda, Katha, Grace, Mwandumba, Henry, Gordon, Stephen B., Jambo, Kondwani C., Cornick, Jennifer, Feasey, Nicholas, Barnes, Kayla G., Morton, Ben, and Ashton, Philip M.
- Abstract
Additional file 2. Supplementary figures.
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- 2023
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20. Circulating cytokine-producing VP6-specific CD4+ T cells are rarely detectable in Rotarix -vaccinated Malawian children with severe rotavirus diarrhoea
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Banda, Chikondi Malamba-, primary, Mhango, Chimwemwe, additional, Benedicto-Matambo, Prisca, additional, Mandolo, Jonathan J., additional, Chinyama, End, additional, Kumwenda, Orpha, additional, Barnes, Kayla G., additional, Cunliffe, Nigel A., additional, Iturriza-Gomara, Miren, additional, Jambo, Kondwani C., additional, and Jere, Khuzwayo C., additional
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- 2022
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21. Comparative whole genome analysis reveals re-emergence of typical human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi
- Author
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Mhango, Chimwemwe, primary, Banda, Akuzike, additional, Chinyama, End, additional, Mandolo, Jonathan J., additional, Kumwenda, Orpha, additional, Malamba-Banda, Chikondi, additional, Barnes, Kayla G., additional, Kumwenda, Benjamin, additional, Jambo, Kondwani, additional, Donato, Celeste M., additional, Esona, Mathew D., additional, Mwangi, Peter N., additional, Steele, A. Duncan, additional, Iturriza-Gomara, Miren, additional, Cunliffe, Nigel A., additional, Ndze, Valentine N., additional, Kamng’ona, Arox W., additional, Dennis, Francis E., additional, Nyaga, Martin M., additional, Chaguza, Chrispin, additional, and Jere, Khuzwayo C., additional
- Published
- 2022
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22. Acute rotavirus infection is associated with the induction of circulating memory CD4+ T cell subsets.
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Malamba-Banda, Chikondi, Mhango, Chimwemwe, Benedicto-Matambo, Prisca, Mandolo, Jonathan J., Chinyama, End, Kumwenda, Orpha, Barnes, Kayla G., Cunliffe, Nigel A., Iturriza-Gomara, Miren, Jambo, Kondwani C., and Jere, Khuzwayo C.
- Subjects
ROTAVIRUS diseases ,T cells ,IMMUNOLOGIC memory ,T helper cells ,SYMPTOMS ,CHILD development - Abstract
Strong CD4
+ T cell-mediated immune protection following rotavirus infection has been observed in animal models, but its relevance in humans remains unclear. Here, we characterized acute and convalescent CD4+ T cell responses in children who were hospitalized with rotavirus-positive and rotavirus-negative diarrhoea in Blantyre, Malawi. Children presenting with laboratory-confirmed rotavirus infection had higher proportions of effector and central memory T helper 2 cells during acute infection i.e., at disease presentation compared to convalescence, 28 days post-infection defined by a follow-up 28 days after acute infection. However, circulating cytokine-producing (IFN-γ and/or TNF-α) rotavirus-specific VP6-specific CD4+ T cells were rarely detectable in children with rotavirus infection at both acute and convalescent stages. Moreover, following whole blood mitogenic stimulation, the responding CD4+ T cells were predominantly non-cytokine producers of IFN-γ and/or TNF-α. Our findings demonstrate limited induction of anti-viral IFN-γ and/or TNF-α-producing CD4+ T cells in rotavirus-vaccinated Malawian children following the development of laboratory-confirmed rotavirus infection. [ABSTRACT FROM AUTHOR]- Published
- 2023
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23. Differential symptoms among COVID-19 outpatients before and during periods of SARS-CoV-2 Omicron variant dominance in Blantyre, Malawi: a prospective observational study
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Chibwana, Marah G., primary, Thole, Herbert W., additional, Anscombe, Cat, additional, Ashton, Philip M., additional, Green, Edward, additional, Barnes, Kayla G., additional, Cornick, Jen, additional, Turner, Ann, additional, Witte, Desiree, additional, Nthala, Sharon, additional, Thom, Chikondi, additional, Kanyandula, Felistas, additional, Ainani, Anna, additional, Mtike, Natasha, additional, Tambala, Hope, additional, N’goma, Veronica, additional, Mwafulirwa, Dorah, additional, Asima, Erick, additional, Morton, Ben, additional, Gmeiner, Markus, additional, Gundah, Zaziwe, additional, Kawalazira, Gift, additional, French, Neil, additional, Feasey, Nicholas, additional, Heyderman, Robert S., additional, Swarthout, Todd D, additional, and Jambo, Kondwani C., additional
- Published
- 2022
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24. Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics
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Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Kotliar, Dylan, Lin, Aaron E, Logue, James, Hughes, Travis K, Khoury, Nadine M, Raju, Siddharth S, Wadsworth, Marc H, Chen, Han, Kurtz, Jonathan R, Dighero-Kemp, Bonnie, Bjornson, Zach B, Mukherjee, Nilanjan, Sellers, Brian A, Tran, Nancy, Bauer, Matthew R, Adams, Gordon C, Adams, Ricky, Rinn, John L, Melé, Marta, Schaffner, Stephen F, Nolan, Garry P, Barnes, Kayla G, Hensley, Lisa E, McIlwain, David R, Shalek, Alex K, Sabeti, Pardis C, Bennett, Richard S, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research at MIT, Ragon Institute of MGH, MIT and Harvard, Kotliar, Dylan, Lin, Aaron E, Logue, James, Hughes, Travis K, Khoury, Nadine M, Raju, Siddharth S, Wadsworth, Marc H, Chen, Han, Kurtz, Jonathan R, Dighero-Kemp, Bonnie, Bjornson, Zach B, Mukherjee, Nilanjan, Sellers, Brian A, Tran, Nancy, Bauer, Matthew R, Adams, Gordon C, Adams, Ricky, Rinn, John L, Melé, Marta, Schaffner, Stephen F, Nolan, Garry P, Barnes, Kayla G, Hensley, Lisa E, McIlwain, David R, Shalek, Alex K, Sabeti, Pardis C, and Bennett, Richard S
- Abstract
© 2020 The Author(s) Single-cell profiling of circulating immune cells during Ebola virus (EBOV) infection in non-human primates resolves molecular correlates of viral tropism, characterizes replication dynamics within infected cells, and distinguishes expression changes that are mediated by viral infection from those due to cytokine signaling.
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- 2022
25. In vivo single-cell profiling of lncRNAs during Ebola virus infection
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Santus, Luisa, primary, García-Pérez, Raquel, additional, Sopena-Rios, Maria, additional, Lin, Aaron E, additional, Adams, Gordon C, additional, Barnes, Kayla G, additional, Siddle, Katherine J, additional, Wohl, Shirlee, additional, Reverter, Ferran, additional, Rinn, John L, additional, Bennett, Richard S, additional, Hensley, Lisa E, additional, Sabeti, Pardis C, additional, and Melé, Marta, additional
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- 2022
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26. Distinct clinical and immunological profiles of patients with evidence of SARS-CoV-2 infection in sub-Saharan Africa
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Morton, Ben, Barnes, Kayla G., Anscombe, Catherine, Jere, Khuzwayo, Matambo, Prisca, Mandolo, Jonathan, Kamng’ona, Raphael, Brown, Comfort, Nyirenda, James, Phiri, Tamara, Banda, Ndaziona P., Van Der Veer, Charlotte, Mndolo, Kwazizira S., Mponda, Kelvin, Rylance, Jamie, Phiri, Chimota, Mallewa, Jane, Nyirenda, Mulinda, Katha, Grace, Kambiya, Paul, Jafali, James, Mwandumba, Henry C., Gordon, Stephen B., Cornick, Jennifer, Jambo, Kondwani C., Phulusa, Jacob, Mkandawire, Mercy, Kaimba, Sylvester, Thole, Herbert, Nthala, Sharon, Nsomba, Edna, Keyala, Lucy, Mandala, Peter, Chinoko, Beatrice, Gmeiner, Markus, Kaudzu, Vella, Lissauer, Samantha, Freyne, Bridget, MacPherson, Peter, Swarthout, Todd D., Iroh Tam, Pui-Ying, Sichone, Simon, Ahmadu, Ajisa, Kanjewa, Oscar, Nyasulu, Vita, Chinyama, End, Zuza, Allan, Denis, Brigitte, Storey, Evance, Bondera, Nedson, Matchado, Danford, Chande, Adams, Chingota, Arthur, Ntwea, Chimenya, Mkandawire, Langford, Mhango, Chimwemwe, Lakudzala, Agness, Chaponda, Mphatso, Mwenechanya, Percy, Mvaya, Leonard, Tembo, Dumizulu, Henrion, Marc Y. R., Chirombo, James, Masesa, Clemens, and Gondwe, Joel
- Subjects
wa_105 ,qw_568 ,mental disorders ,wc_505 ,qw_160 ,wa_395 - Abstract
Although the COVID-19 pandemic has left no country untouched there has been limited research to understand clinical and immunological responses in African populations. Here we characterise patients hospitalised with suspected (PCR-negative/IgG-positive) or confirmed (PCR-positive) COVID-19, and healthy community controls (PCR-negative/IgG-negative). PCR-positive COVID-19 participants were more likely to receive dexamethasone and a beta-lactam antibiotic, and survive to hospital discharge than PCR-negative/IgG-positive and PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants exhibited a nasal and systemic cytokine signature analogous to PCR-positive COVID-19 participants, predominated by chemokines and neutrophils and distinct from PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants had increased propensity for Staphylococcus aureus and Streptococcus pneumoniae colonisation. PCR-negative/IgG-positive individuals with high COVID-19 clinical suspicion had inflammatory profiles analogous to PCR-confirmed disease and potentially represent a target population for COVID-19 treatment strategies.
- Published
- 2021
27. Zika virus evolution and spread in the Americas
- Author
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Metsky, Hayden C., Matranga, Christian B., Wohl, Shirlee, Schaffner, Stephen F., Freije, Catherine A., Winnicki, Sarah M., West, Kendra, Qu, James, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Tomkins-Tinch, Christopher H., Ye, Simon H., Park, Daniel J., Luo, Cynthia Y., Barnes, Kayla G., Shah, Rickey R., Chak, Bridget, Barbosa-Lima, Giselle, Delatorre, Edson, Vieira, Yasmine R., Paul, Lauren M., Tan, Amanda L., Barcellona, Carolyn M., Porcelli, Mario C., Vasquez, Chalmers, Cannons, Andrew C., Cone, Marshall R., Hogan, Kelly N., Kopp, Edgar W., Anzinger, Joshua J., Garcia, Kimberly F., Parham, Leda A., Ramrez, Rosa M. Glvez, Montoya, Maria C. Miranda, Rojas, Diana P., Brown, Catherine M., Hennigan, Scott, Sabina, Brandon, Scotland, Sarah, Gangavarapu, Karthik, Grubaugh, Nathan D., Oliveira, Glenn, Robles-Sikisaka, Refugio, Rambaut, Andrew, Gehrke, Lee, Smole, Sandra, Halloran, M. Elizabeth, Villar, Luis, Mattar, Salim, Lorenzana, Ivette, Cerbino-Neto, Jose, Valim, Clarissa, Degrave, Wim, Bozza, Patricia T., Gnirke, Andreas, Andersen, Kristian G., Isern, Sharon, Michael, Scott F., Bozza, Fernando A., Souza, Thiago M. L., Bosch, Irene, Yozwiak, Nathan L., MacInnis, Bronwyn L., and Sabeti, Pardis C.
- Subjects
America -- Health aspects ,Zika virus -- Natural history ,Zika virus infection -- Distribution ,Company distribution practices ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Hayden C. Metsky [1, 2]; Christian B. Matranga [1]; Shirlee Wohl [1, 3]; Stephen F. Schaffner [1, 3, 4]; Catherine A. Freije [1, 3]; Sarah M. Winnicki [1]; Kendra [...]
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- 2017
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28. Genomic epidemiology reveals multiple introductions of Zika virus into the United States
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Grubaugh, Nathan D., Ladner, Jason T., Kraemer, Moritz U. G., Dudas, Gytis, Tan, Amanda L., Gangavarapu, Karthik, Wiley, Michael R., White, Stephen, Thz, Julien, Magnani, Diogo M., Prieto, Karla, Reyes, Daniel, Bingham, Andrea M., Paul, Lauren M., Robles-Sikisaka, Refugio, Oliveira, Glenn, Pronty, Darryl, Barcellona, Carolyn M., Metsky, Hayden C., Baniecki, Mary Lynn, Barnes, Kayla G., Chak, Bridget, Freije, Catherine A., Gladden-Young, Adrianne, Gnirke, Andreas, Luo, Cynthia, MacInnis, Bronwyn, Matranga, Christian B., Park, Daniel J., Qu, James, Schaffner, Stephen F., Tomkins-Tinch, Christopher, West, Kendra L., Winnicki, Sarah M., Wohl, Shirlee, Yozwiak, Nathan L., Quick, Joshua, Fauver, Joseph R., Khan, Kamran, Brent, Shannon E., Reiner, Robert C., Jr, Lichtenberger, Paola N., Ricciardi, Michael J., Bailey, Varian K., Watkins, David I., Cone, Marshall R., Kopp, Edgar W., IV, Hogan, Kelly N., Cannons, Andrew C., Jean, Reynald, Monaghan, Andrew J., Garry, Robert F., Loman, Nicholas J., Faria, Nuno R., Porcelli, Mario C., Vasquez, Chalmers, Nagle, Elyse R., Cummings, Derek A. T., Stanek, Danielle, Rambaut, Andrew, Sanchez-Lockhart, Mariano, Sabeti, Pardis C., Gillis, Leah D., Michael, Scott F., Bedford, Trevor, Pybus, Oliver G., Isern, Sharon, Palacios, Gustavo, and Andersen, Kristian G.
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Zika virus -- Health aspects -- Genetic aspects ,Gene expression -- Health aspects ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Nathan D. Grubaugh [1]; Jason T. Ladner [2]; Moritz U. G. Kraemer [3, 4, 5]; Gytis Dudas [6]; Amanda L. Tan [7]; Karthik Gangavarapu [1]; Michael R. Wiley [2, [...]
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- 2017
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29. Rotavirus Genotypes in Hospitalized Children With Acute Gastroenteritis Before and After Rotavirus Vaccine Introduction in Blantyre, Malawi, 1997-2019.
- Author
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Mhango, Chimwemwe, Mandolo, Jonathan J, Chinyama, End, Wachepa, Richard, Kanjerwa, Oscar, Malamba-Banda, Chikondi, Matambo, Prisca B, Barnes, Kayla G, Chaguza, Chrispin, Shawa, Isaac T, Nyaga, Martin M, Hungerford, Daniel, Parashar, Umesh D, Pitzer, Virginia E, Kamng'ona, Arox W, Iturriza-Gomara, Miren, Cunliffe, Nigel A, and Jere, Khuzwayo C
- Abstract
Background: Rotavirus vaccine (Rotarix [RV1]) has reduced diarrhea-associated hospitalizations and deaths in Malawi. We examined the trends in circulating rotavirus genotypes in Malawi over a 22-year period to assess the impact of RV1 introduction on strain distribution.Methods: Data on rotavirus-positive stool specimens among children aged <5 years hospitalized with diarrhea in Blantyre, Malawi before (July 1997-October 2012, n = 1765) and after (November 2012-October 2019, n = 934) RV1 introduction were analyzed. Rotavirus G and P genotypes were assigned using reverse-transcription polymerase chain reaction.Results: A rich rotavirus strain diversity circulated throughout the 22-year period; Shannon (H') and Simpson diversity (D') indices did not differ between the pre- and postvaccine periods (H' P < .149; D' P < .287). Overall, G1 (n = 268/924 [28.7%]), G2 (n = 308/924 [33.0%]), G3 (n = 72/924 [7.7%]), and G12 (n = 109/924 [11.8%]) were the most prevalent genotypes identified following RV1 introduction. The prevalence of G1P[8] and G2P[4] genotypes declined each successive year following RV1 introduction, and were not detected after 2018. Genotype G3 reemerged and became the predominant genotype from 2017 onward. No evidence of genotype selection was observed 7 years post-RV1 introduction.Conclusions: Rotavirus strain diversity and genotype variation in Malawi are likely driven by natural mechanisms rather than vaccine pressure. [ABSTRACT FROM AUTHOR]- Published
- 2022
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30. Rotavirus Genotypes in Hospitalized Children With Acute Gastroenteritis Before and After Rotavirus Vaccine Introduction in Blantyre, Malawi, 1997–2019
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Mhango, Chimwemwe, primary, Mandolo, Jonathan J, additional, Chinyama, End, additional, Wachepa, Richard, additional, Kanjerwa, Oscar, additional, Malamba-Banda, Chikondi, additional, Matambo, Prisca B, additional, Barnes, Kayla G, additional, Chaguza, Chrispin, additional, Shawa, Isaac T, additional, Nyaga, Martin M, additional, Hungerford, Daniel, additional, Parashar, Umesh D, additional, Pitzer, Virginia E, additional, Kamng’ona, Arox W, additional, Iturriza-Gomara, Miren, additional, Cunliffe, Nigel A, additional, and Jere, Khuzwayo C, additional
- Published
- 2020
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31. Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics
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Kotliar, Dylan, primary, Lin, Aaron E., additional, Logue, James, additional, Hughes, Travis K., additional, Khoury, Nadine M., additional, Raju, Siddharth S., additional, Wadsworth, Marc H., additional, Chen, Han, additional, Kurtz, Jonathan R., additional, Dighero-Kemp, Bonnie, additional, Bjornson, Zach B., additional, Mukherjee, Nilanjan, additional, Sellers, Brian A., additional, Tran, Nancy, additional, Bauer, Matthew R., additional, Adams, Gordon C., additional, Adams, Ricky, additional, Rinn, John L., additional, Melé, Marta, additional, Nolan, Garry P., additional, Barnes, Kayla G., additional, Hensley, Lisa E., additional, McIlwain, David R., additional, Shalek, Alex K., additional, Sabeti, Pardis C., additional, and Bennett, Richard S., additional
- Published
- 2020
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32. Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time
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Barnes, Kayla G., primary, Lachenauer, Anna E., additional, Nitido, Adam, additional, Siddiqui, Sameed, additional, Gross, Robin, additional, Beitzel, Brett, additional, Siddle, Katherine J., additional, Freije, Catherine A., additional, Dighero-Kemp, Bonnie, additional, Mehta, Samar, additional, Carter, Amber, additional, Uwanibe, Jessica, additional, Ajogbasile, Fehintola, additional, Olumade, Testimony J., additional, Odia, Ikponmwosa, additional, Sandi, John Demby, additional, Momoh, Mambu, additional, Metsky, Hayden C., additional, Boehm, Chloe K., additional, Lin, Aaron E., additional, Kemball, Molly, additional, Park, Daniel J., additional, Grant, Donald S., additional, Happi, Christian T., additional, Branco, Luis, additional, Boisen, Matt, additional, Sullivan, Brian M., additional, Amare, Mihret, additional, Tiamiyu, Abdulwasiu, additional, Parker, Zahra, additional, Iroezindu, Michael, additional, Modjarrad, Kayvon, additional, Myhrvold, Cameron, additional, Garry, Robert F., additional, Palacios, Gustavo, additional, Hensley, Lisa E., additional, Schaffner, Stephen F., additional, Colubri, Andres, additional, and Sabeti, Pardis C., additional
- Published
- 2020
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33. Field-deployable viral diagnostics using CRISPR-Cas13
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McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology. Department of Biological Engineering, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Myhrvold, Cameron, Freije, Catherine A., Gootenberg, Jonathan S, Abudayyeh, Omar O., Metsky, Hayden C., Durbin, Ann F, Kellner, Max J., Tan, Amanda L., Paul, Lauren M., Parham, Leda A., Garcia, Kimberly F., Barnes, Kayla G., Chak, Bridget, Mondini, Adriano, Nogueira, Mauricio L., Isern, Sharon, Michael, Scott F., Lorenzana, Ivette, Yozwiak, Nathan L., MacInnis, Bronwyn L., Bosch, Irene, Gehrke, Lee, Zhang, Feng, Sabeti, Pardis C., McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology. Department of Biological Engineering, Harvard University--MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Myhrvold, Cameron, Freije, Catherine A., Gootenberg, Jonathan S, Abudayyeh, Omar O., Metsky, Hayden C., Durbin, Ann F, Kellner, Max J., Tan, Amanda L., Paul, Lauren M., Parham, Leda A., Garcia, Kimberly F., Barnes, Kayla G., Chak, Bridget, Mondini, Adriano, Nogueira, Mauricio L., Isern, Sharon, Michael, Scott F., Lorenzana, Ivette, Yozwiak, Nathan L., MacInnis, Bronwyn L., Bosch, Irene, Gehrke, Lee, Zhang, Feng, and Sabeti, Pardis C.
- Abstract
Mitigating global infectious disease requires diagnostic tools that are sensitive, specific, and rapidly field deployable. In this study, we demonstrate that the Cas13-based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) platform can detect Zika virus (ZIKV) and dengue virus (DENV) in patient samples at concentrations as low as 1 copy per microliter. We developed HUDSON (heating unextracted diagnostic samples to obliterate nucleases), a protocol that pairs with SHERLOCK for viral detection directly from bodily fluids, enabling instrument-free DENV detection directly from patient samples in <2 hours. We further demonstrate that SHERLOCK can distinguish the four DENV serotypes, as well as region-specific strains of ZIKV from the 2015–2016 pandemic. Finally, we report the rapid (<1 week) design and testing of instrument-free assays to detect clinically relevant viral single-nucleotide polymorphisms., NIH (Grants AI-100190, 1R01-HG009761, 1R01-MH110049, and 1DP1-HL141201)
- Published
- 2020
34. Implementation of the Ebola Virus Persistence in Ocular Tissues and Fluids (EVICT) study: Lessons learned for vision health systems strengthening in Sierra Leone.
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Shantha, Jessica G., Crozier, Ian, Kraft, Colleen S., Grant, Donald G., Goba, Augustine, Hayek, Brent R., Hartley, Caleb, Barnes, Kayla G., Uyeki, Timothy M., Schieffelin, John, Garry, Robert F., Bausch, Daniel G., Farmer, Paul E., Mattia, John G., Vandy, Matthew J., and Yeh, Steven
- Subjects
EBOLA virus ,EBOLA virus disease ,VISUAL acuity ,VISION disorders ,INFECTION prevention ,CATARACT surgery ,EYE care ,HIV prevention - Abstract
Background: Following the West African Ebola virus disease (EVD) outbreak of 2013–2016 and more recent EVD outbreaks in the Democratic Republic of Congo, thousands of EVD survivors are at-risk for sequelae including uveitis, which can lead to unremitting inflammation and vision loss from cataract. Because of the known risk of Ebola virus persistence in ocular fluid and the need to provide vision-restorative, safe cataract surgery, the Ebola Virus Persistence in Ocular Tissues and Fluids (EVICT) Study was implemented in Sierra Leone. During implementation of this multi-national study, challenges included regulatory approvals, mobilization, community engagement, infection prevention and control, and collaboration between multiple disciplines. In this report, we address the multifacted approach to address these challenges and the impact of implementation science research to address an urgent clinical subspecialty need in an outbreak setting. Methodology/Principal findings: Given the patient care need to develop a protocol to evaluate ocular fluid for Ebola virus RNA persistence prior to cataract surgery, as well as protocols to provide reassurance to ophthalmologists caring for EVD survivors with cataracts, the EVICT study was designed and implemented through the work of the Ministry of Health, Sierra Leone National Eye Programme, and international partnerships. The EVICT study showed that all 50 patients who underwent ocular fluid sampling at 19 and 34 months, respectively, tested negative for Ebola virus RNA. Thirty-four patients underwent successful cataract surgery with visual acuity improvement. Here we describe the methodology for study implementation, challenges encountered, and key issues that impacted EVD vision care in the immediate aftermath of the EVD outbreak. Key aspects of the EVICT study included defining the pertinent questions and clinical need, partnership alignment with key stakeholders, community engagement with EVD survivor associations, in-country and international regulatory approvals, study site design for infection prevention and control, and thorough plans for EVD survivor follow-up care and monitoring. Challenges encountered included patient mobilization owing to transportation routes and distance of patients in rural districts. Strong in-country partnerships and multiple international organizations overcame these challenges so that lessons learned could be applied for future EVD outbreaks in West and Central Africa including EVD outbreaks that are ongoing in Guinea and Democratic Republic of Congo. Conclusions/Significance: The EVICT Study showed that cataract surgery with a protocol-driven approach was safe and vision-restorative for EVD survivors, which provided guidance for EVD ophthalmic surgical care. Ophthalmologic care remains a key aspect of the public health response for EVD outbreaks but requires a meticulous, yet partnered approach with international and local in-country partners. Future efforts may build on this framework for clinical care and to improve our understanding of ophthalmic sequelae, develop treatment paradigms for EVD survivors, and strengthen vision health systems in resource-limited settings. [ABSTRACT FROM AUTHOR]
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- 2021
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35. Genome sequencing reveals Zika virus diversity and spread in the Americas
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Metsky, Hayden C, Matranga, Christian B, Wohl, Shirlee, Schaffner, Stephen F., Freije, Catherine A, Winnicki, Sarah, West, Kendra, Qu, J, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Christopher, Tomkins-Tinch, Ye, S.H, Park, Daniel J, Luo, Cynthia, Barnes, Kayla G, Shah, R.R., Chak, Bridget, Barbosa-Lima, G., Delatorre, E., Vieira, Y.R., Paul, Lauren M, Tan, Amanda L, Barcellona, Carolyn M, Porcelli, Mario C, Vasquez, Chalmers, Cannons, Andrew C, Cone, Marshall R, Hogan, Kelly N, Kopp IV, Edgar W, Anzinger, J.J., Garcia, K.F., Parhap, L.A., Gelvez Ramirez, R.M., Montoya, Miranda, Rojas, D.P., Brown, C.M., Hennigan, S., Sabina, B., Scotland, S., Gangavarapu, K., Grubaugh, N.D., Oliveira, G., Robles-Sikisaka, R., Rambaut, Andrew, Gehrke, L., Smole, S., Halloran, M.E., Villar Centeno, L.A., Mattar, S., Lorenzana, I., Cerbino-Neto, J., Valim, C., Degrave, W., Bozza, P.T., Souza, T.M.L., Bosch, I., Yozwiak, N.L., MacInnis, B.L., and Sabeti, P.C.
- Abstract
Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part due to a lack of genomic data. We applied multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analyzed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental US. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of viral surveillance. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those potentially relevant to the effectiveness of diagnostic tests.
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- 2017
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36. Genomic Footprints of Selective Sweeps from Metabolic Resistance to Pyrethroids in African Malaria Vectors Are Driven by Scale up of Insecticide-Based Vector Control
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Barnes, Kayla G., Weedall, Gareth D., Ndula, Miranda, Irving, Helen, Mzihalowa, Themba, Hemingway, Janet, and Wondji, Charles S.
- Subjects
Malawi ,Insecticides ,Heredity ,Epidemiology ,Disease Vectors ,Mosquitoes ,Geographical Locations ,Insecticide Resistance ,Cytochrome P-450 Enzyme System ,Pyrethrins ,Medicine and Health Sciences ,qu_460 ,Mozambique ,Phylogeny ,Agriculture ,Genomics ,Insects ,Genetic Mapping ,Insect Proteins ,Agrochemicals ,Research Article ,RM ,Arthropoda ,lcsh:QH426-470 ,Quantitative Trait Loci ,wc_765 ,Host-Parasite Interactions ,Sequence Homology, Nucleic Acid ,qx_600 ,Anopheles ,parasitic diseases ,Genetics ,Animals ,Humans ,Selection, Genetic ,Evolutionary Biology ,Population Biology ,Base Sequence ,Models, Genetic ,Organisms ,wa_240 ,Biology and Life Sciences ,Genetic Variation ,R1 ,Invertebrates ,wc_750 ,Insect Vectors ,Malaria ,lcsh:Genetics ,qx_650 ,Haplotypes ,Genetic Loci ,People and Places ,Africa ,Population Genetics ,Microsatellite Repeats - Abstract
Insecticide resistance in mosquito populations threatens recent successes in malaria prevention. Elucidating patterns of genetic structure in malaria vectors to predict the speed and direction of the spread of resistance is essential to get ahead of the ‘resistance curve’ and to avert a public health catastrophe. Here, applying a combination of microsatellite analysis, whole genome sequencing and targeted sequencing of a resistance locus, we elucidated the continent-wide population structure of a major African malaria vector, Anopheles funestus. We identified a major selective sweep in a genomic region controlling cytochrome P450-based metabolic resistance conferring high resistance to pyrethroids. This selective sweep occurred since 2002, likely as a direct consequence of scaled up vector control as revealed by whole genome and fine-scale sequencing of pre- and post-intervention populations. Fine-scaled analysis of the pyrethroid resistance locus revealed that a resistance-associated allele of the cytochrome P450 monooxygenase CYP6P9a has swept through southern Africa to near fixation, in contrast to high polymorphism levels before interventions, conferring high levels of pyrethroid resistance linked to control failure. Population structure analysis revealed a barrier to gene flow between southern Africa and other areas, which may prevent or slow the spread of the southern mechanism of pyrethroid resistance to other regions. By identifying a genetic signature of pyrethroid-based interventions, we have demonstrated the intense selective pressure that control interventions exert on mosquito populations. If this level of selection and spread of resistance continues unabated, our ability to control malaria with current interventions will be compromised., Author Summary Malaria control currently relies heavily on insecticide-based vector control interventions. Unfortunately, resistance to insecticides threatens the continued effectiveness of these measures. Metabolic resistance, caused by increased detoxification of insecticides, presents the greatest threat to vector control, yet it remains unclear how these mechanisms are linked to underlying genetic changes driven by the massive selection pressure from these interventions, such as the widespread use of Long Lasting Insecticide Nets (LLINs) across Africa. Therefore, understanding the direction and speed at which this operationally important form of resistance spreads through mosquito populations is essential if we are to get ahead of the ‘resistance curve’ and avert a public health catastrophe. Here, using microsatellite markers, whole genome sequencing and fine-scale sequencing at a major resistance locus, we elucidated the Africa-wide population structure of Anopheles funestus, a major African malaria vector, and detected a strong selective sweep occurring in a genomic region controlling cytochrome P450-based metabolic pyrethroid resistance in this species. Furthermore, we demonstrated that this selective sweep is driven by the scale-up of insecticide-based malaria control in Africa, highlighting the risk that if this level of selection and spread of resistance continues unabated, our ability to control malaria with current interventions will be compromised.
- Published
- 2017
37. Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018
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Siddle, Katherine J., primary, Eromon, Philomena, additional, Barnes, Kayla G., additional, Mehta, Samar, additional, Oguzie, Judith U., additional, Odia, Ikponmwosa, additional, Schaffner, Stephen F., additional, Winnicki, Sarah M., additional, Shah, Rickey R., additional, Qu, James, additional, Wohl, Shirlee, additional, Brehio, Patrick, additional, Iruolagbe, Christopher, additional, Aiyepada, John, additional, Uyigue, Eghosa, additional, Akhilomen, Patience, additional, Okonofua, Grace, additional, Ye, Simon, additional, Kayode, Tolulope, additional, Ajogbasile, Fehintola, additional, Uwanibe, Jessica, additional, Gaye, Amy, additional, Momoh, Mambu, additional, Chak, Bridget, additional, Kotliar, Dylan, additional, Carter, Amber, additional, Gladden-Young, Adrianne, additional, Freije, Catherine A., additional, Omoregie, Omigie, additional, Osiemi, Blessing, additional, Muoebonam, Ekene B., additional, Airende, Michael, additional, Enigbe, Rachael, additional, Ebo, Benevolence, additional, Nosamiefan, Iguosadolo, additional, Oluniyi, Paul, additional, Nekoui, Mahan, additional, Ogbaini-Emovon, Ephraim, additional, Garry, Robert F., additional, Andersen, Kristian G., additional, Park, Daniel J., additional, Yozwiak, Nathan L., additional, Akpede, George, additional, Ihekweazu, Chikwe, additional, Tomori, Oyewale, additional, Okogbenin, Sylvanus, additional, Folarin, Onikepe A., additional, Okokhere, Peter O., additional, MacInnis, Bronwyn L., additional, Sabeti, Pardis C., additional, and Happi, Christian T., additional
- Published
- 2018
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38. Field validation of recombinant antigen immunoassays for diagnosis of Lassa fever
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Boisen, Matthew L., primary, Hartnett, Jessica N., additional, Shaffer, Jeffrey G., additional, Goba, Augustine, additional, Momoh, Mambu, additional, Sandi, John Demby, additional, Fullah, Mohamed, additional, Nelson, Diana K. S., additional, Bush, Duane J., additional, Rowland, Megan M., additional, Heinrich, Megan L., additional, Koval, Anatoliy P., additional, Cross, Robert W., additional, Barnes, Kayla G., additional, Lachenauer, Anna E., additional, Lin, Aaron E., additional, Nekoui, Mahan, additional, Kotliar, Dylan, additional, Winnicki, Sarah M., additional, Siddle, Katherine J., additional, Gbakie, Michael, additional, Fonnie, Mbalu, additional, Koroma, Veronica J., additional, Kanneh, Lansana, additional, Kulakosky, Peter C., additional, Hastie, Kathryn M., additional, Wilson, Russell B., additional, Andersen, Kristian G., additional, Folarin, Onikepe O., additional, Happi, Christian T., additional, Sabeti, Pardis C., additional, Geisbert, Thomas W., additional, Saphire, Erica Ollmann, additional, Khan, S. Humarr, additional, Grant, Donald S., additional, Schieffelin, John S., additional, Branco, Luis M., additional, and Garry, Robert F., additional
- Published
- 2018
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39. Ebola Virus Persistence in Ocular Tissues and Fluids (EVICT) Study: Reverse Transcription-Polymerase Chain Reaction and Cataract Surgery Outcomes of Ebola Survivors in Sierra Leone
- Author
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Shantha, Jessica G., primary, Mattia, John G., additional, Goba, Augustine, additional, Barnes, Kayla G., additional, Ebrahim, Faiqa K., additional, Kraft, Colleen S., additional, Hayek, Brent R., additional, Hartnett, Jessica N., additional, Shaffer, Jeffrey G., additional, Schieffelin, John S., additional, Sandi, John D., additional, Momoh, Mambu, additional, Jalloh, Simbirie, additional, Grant, Donald S., additional, Dierberg, Kerry, additional, Chang, Joyce, additional, Mishra, Sharmistha, additional, Chan, Adrienne K., additional, Fowler, Rob, additional, O'Dempsey, Tim, additional, Kaluma, Erick, additional, Hendricks, Taylor, additional, Reiners, Roger, additional, Reiners, Melanie, additional, Gess, Lowell A., additional, ONeill, Kwame, additional, Kamara, Sarian, additional, Wurie, Alie, additional, Mansaray, Mohamed, additional, Acharya, Nisha R., additional, Liu, William J., additional, Bavari, Sina, additional, Palacios, Gustavo, additional, Teshome, Moges, additional, Crozier, Ian, additional, Farmer, Paul E., additional, Uyeki, Timothy M., additional, Bausch, Daniel G., additional, Garry, Robert F., additional, Vandy, Matthew J., additional, and Yeh, Steven, additional
- Published
- 2018
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40. Restriction to gene flow is associated with changes in the molecular basis of pyrethroid resistance in the malaria vector Anopheles funestus
- Author
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Barnes, Kayla G, Irving, Helen, Chiumia, Martin, Mzilahowa, Themba, Coleman, Michael, Hemingway, Janet, and Wondji, Charles
- Subjects
qx_650 ,parasitic diseases ,qx_600 ,qu_475 ,qx_515 ,wc_750 - Abstract
Resistance to pyrethroids, the sole insecticide class recommended for treating bed nets, threatens the control of major malaria vectors, including Anopheles funestus Effective management of resistance requires an understanding of the dynamics and mechanisms driving resistance. Here, using genome-wide transcription and genetic diversity analyses, we show that a shift in the molecular basis of pyrethroid resistance in southern African populations of this species is associated with a restricted gene flow. Across the most highly endemic and densely populated regions in Malawi, An. funestus is resistant to pyrethroids, carbamates, and organochlorides. Genome-wide microarray-based transcription analysis identified overexpression of cytochrome P450 genes as the main mechanism driving this resistance. The most up-regulated genes include cytochrome P450s (CYP) CYP6P9a, CYP6P9b and CYP6M7. However, a significant shift in the overexpression profile of these genes was detected across a south/north transect, with CYP6P9a and CYP6P9b more highly overexpressed in the southern resistance front and CYP6M7 predominant in the northern front. A genome-wide genetic structure analysis of southern African populations of An. funestus from Zambia, Malawi, and Mozambique revealed a restriction of gene flow between populations, in line with the geographical variation observed in the transcriptomic analysis. Genetic polymorphism analysis of the three key resistance genes, CYP6P9a, CYP6P9b, and CYP6M7, support barriers to gene flow that are shaping the underlying molecular basis of pyrethroid resistance across southern Africa. This barrier to gene flow is likely to impact the design and implementation of resistance management strategies in the region.
- Published
- 2016
41. Multiple introductions of Zika virus into the United States revealed through genomic epidemiology
- Author
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Grubaugh, Nathan D, primary, Ladner, Jason T, additional, Kraemer, Moritz UG, additional, Dudas, Gytis, additional, Tan, Amanda L, additional, Gangavarapu, Karthik, additional, Wiley, Michael R, additional, White, Stephen, additional, Thézé, Julien, additional, Magnani, Diogo M, additional, Prieto, Karla, additional, Reyes, Daniel, additional, Bingham, Andrea, additional, Paul, Lauren M, additional, Robles-Sikisaka, Refugio, additional, Oliveira, Glenn, additional, Pronty, Darryl, additional, Metsky, Hayden C, additional, Baniecki, Mary Lynn, additional, Barnes, Kayla G, additional, Chak, Bridget, additional, Freije, Catherine A, additional, Gladden-Young, Adrianne, additional, Gnirke, Andreas, additional, Luo, Cynthia, additional, MacInnis, Bronwyn, additional, Matranga, Christian B, additional, Park, Daniel J, additional, Qu, James, additional, Schaffner, Stephen F, additional, Tomkins-Tinch, Christopher, additional, West, Kendra L, additional, Winnicki, Sarah M, additional, Wohl, Shirlee, additional, Yozwiak, Nathan L, additional, Quick, Joshua, additional, Fauver, Joseph R, additional, Khan, Kamran, additional, Brent, Shannon E, additional, Reiner, Robert C, additional, Lichtenberger, Paola N, additional, Ricciardi, Michael, additional, Bailey, Varian K, additional, Watkins, David I, additional, Cone, Marshall R, additional, Kopp, Edgar W, additional, Hogan, Kelly N, additional, Cannons, Andrew C, additional, Jean, Reynald, additional, Garry, Robert F, additional, Loman, Nicholas J, additional, Faria, Nuno R, additional, Porcelli, Mario C, additional, Vasquez, Chalmers, additional, Nagle, Elyse R, additional, Cummings, Derek AT, additional, Stanek, Danielle, additional, Rambaut, Andrew, additional, Sanchez-Lockhart, Mariano, additional, Sabeti, Pardis C, additional, Gillis, Leah D, additional, Michael, Scott F, additional, Bedford, Trevor, additional, Pybus, Oliver G, additional, Isern, Sharon, additional, Palacios, Gustavo, additional, and Andersen, Kristian G, additional
- Published
- 2017
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42. Restriction to gene flow is associated with changes in the molecular basis of pyrethroid resistance in the malaria vector Anopheles funestus
- Author
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Barnes, Kayla G., primary, Irving, Helen, additional, Chiumia, Martin, additional, Mzilahowa, Themba, additional, Coleman, Michael, additional, Hemingway, Janet, additional, and Wondji, Charles S., additional
- Published
- 2016
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43. Rise of multiple insecticide resistance in Anopheles funestus in Malawi: a major concern for malaria vector control
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Riveron, Jacob M., primary, Chiumia, Martin, additional, Menze, Benjamin D., additional, Barnes, Kayla G., additional, Irving, Helen, additional, Ibrahim, Sulaiman S., additional, Weedall, Gareth D., additional, Mzilahowa, Themba, additional, and Wondji, Charles S., additional
- Published
- 2015
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44. Restriction to gene flow is associated with changes in the molecular basis of pyrethroid resistance in the malaria vector Anopheles funestus.
- Author
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Irving, Helen, Coleman, Michael, Hemingway, Janet, Barnes, Kayla G., Wondji, Charles S., Chiumia, Martin, and Mzilahowa, Themba
- Subjects
MALARIA ,PYRETHROIDS ,GENE flow ,CARBAMATES ,GENETIC polymorphisms - Abstract
Resistance to pyrethroids, the sole insecticide class recommended for treating bed nets, threatens the control of major malaria vectors, including Anopheles funestus. Effective management of resistance requires an understanding of the dynamics and mechanisms driving resistance. Here, using genome-wide transcription and genetic diversity analyses, we show that a shift in the molecular basis of pyrethroid resistance in southern African populations of this species is associated with a restricted gene flow. Across the most highly endemic and densely populated regions in Malawi, An. funestus is resistant to pyrethroids, carbamates, and organochlorides. Genome-wide microarraybased transcription analysis identified overexpression of cytochrome P450 genes as the main mechanism driving this resistance. The most up-regulated genes include cytochrome P450s (CYP) CYP6P9a, CYP6P9b and CYP6M7. However, a significant shift in the overexpression profile of these genes was detected across a south/north transect, with CYP6P9a and CYP6P9b more highly overexpressed in the southern resistance front and CYP6M7 predominant in the northern front. A genome- wide genetic structure analysis of southern African populations of An. funestus from Zambia, Malawi, and Mozambique revealed a restriction of gene flow between populations, in line with the geographical variation observed in the transcriptomic analysis. Genetic polymorphism analysis of the three key resistance genes, CYP6P9a, CYP6P9b, and CYP6M7, support barriers to gene flow that are shaping the underlying molecular basis of pyrethroid resistance across southern Africa. This barrier to gene flow is likely to impact the design and implementation of resistance management strategies in the region. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
45. Field validation of recombinant antigen immunoassays for diagnosis of Lassa fever
- Author
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Boisen, Matthew L., Hartnett, Jessica N., Shaffer, Jeffrey G., Goba, Augustine, Momoh, Mambu, Sandi, John Demby, Fullah, Mohamed, Nelson, Diana K. S., Bush, Duane J., Rowland, Megan M., Heinrich, Megan L., Koval, Anatoliy P., Cross, Robert W., Barnes, Kayla G., Lachenauer, Anna E., Lin, Aaron E., Nekoui, Mahan, Kotliar, Dylan, Winnicki, Sarah M., Siddle, Katherine J., Gbakie, Michael, Fonnie, Mbalu, Koroma, Veronica J., Kanneh, Lansana, Kulakosky, Peter C., Hastie, Kathryn M., Wilson, Russell B., Andersen, Kristian G., Folarin, Onikepe O., Happi, Christian T., Sabeti, Pardis C., Geisbert, Thomas W., Saphire, Erica Ollmann, Khan, S. Humarr, Grant, Donald S., Schieffelin, John S., Branco, Luis M., and Garry, Robert F.
- Abstract
Lassa fever, a hemorrhagic fever caused by Lassa virus (LASV), is endemic in West Africa. It is difficult to distinguish febrile illnesses that are common in West Africa from Lassa fever based solely on a patient’s clinical presentation. The field performance of recombinant antigen-based Lassa fever immunoassays was compared to that of quantitative polymerase chain assays (qPCRs) using samples from subjects meeting the case definition of Lassa fever presenting to Kenema Government Hospital in Sierra Leone. The recombinant Lassa virus (ReLASV) enzyme-linked immunosorbant assay (ELISA) for detection of viral antigen in blood performed with 95% sensitivity and 97% specificity using a diagnostic standard that combined results of the immunoassays and qPCR. The ReLASV rapid diagnostic test (RDT), a lateral flow immunoassay based on paired monoclonal antibodies to the Josiah strain of LASV (lineage IV), performed with 90% sensitivity and 100% specificity. ReLASV immunoassays performed better than the most robust qPCR currently available, which had 82% sensitivity and 95% specificity. The performance characteristics of recombinant antigen-based Lassa virus immunoassays indicate that they can aid in the diagnosis of LASV Infection and inform the clinical management of Lassa fever patients.
- Published
- 2018
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46. Acute rotavirus infection is associated with the induction of circulating memory CD4 + T cell subsets.
- Author
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Malamba-Banda C, Mhango C, Benedicto-Matambo P, Mandolo JJ, Chinyama E, Kumwenda O, Barnes KG, Cunliffe NA, Iturriza-Gomara M, Jambo KC, and Jere KC
- Subjects
- Child, Animals, Humans, Tumor Necrosis Factor-alpha, T-Lymphocyte Subsets, Cytokines, CD4-Positive T-Lymphocytes, Rotavirus Infections prevention & control, Rotavirus
- Abstract
Strong CD4
+ T cell-mediated immune protection following rotavirus infection has been observed in animal models, but its relevance in humans remains unclear. Here, we characterized acute and convalescent CD4+ T cell responses in children who were hospitalized with rotavirus-positive and rotavirus-negative diarrhoea in Blantyre, Malawi. Children presenting with laboratory-confirmed rotavirus infection had higher proportions of effector and central memory T helper 2 cells during acute infection i.e., at disease presentation compared to convalescence, 28 days post-infection defined by a follow-up 28 days after acute infection. However, circulating cytokine-producing (IFN-γ and/or TNF-α) rotavirus-specific VP6-specific CD4+ T cells were rarely detectable in children with rotavirus infection at both acute and convalescent stages. Moreover, following whole blood mitogenic stimulation, the responding CD4+ T cells were predominantly non-cytokine producers of IFN-γ and/or TNF-α. Our findings demonstrate limited induction of anti-viral IFN-γ and/or TNF-α-producing CD4+ T cells in rotavirus-vaccinated Malawian children following the development of laboratory-confirmed rotavirus infection., (© 2023. The Author(s).)- Published
- 2023
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47. A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study.
- Author
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Anscombe C, Lissauer S, Thole H, Rylance J, Dula D, Menyere M, Kutambe B, van der Veer C, Phiri T, Banda NP, Mndolo KS, Mponda K, Phiri C, Mallewa J, Nyirenda M, Katha G, Mwandumba H, Gordon SB, Jambo KC, Cornick J, Feasey N, Barnes KG, Morton B, and Ashton PM
- Abstract
Background: Compared to the abundance of clinical and genomic information available on patients hospitalised with COVID-19 disease from high-income countries, there is a paucity of data from low-income countries. Our aim was to explore the relationship between viral lineage and patient outcome., Methods: We enrolled a prospective observational cohort of adult patients hospitalised with PCR-confirmed COVID-19 disease between July 2020 and March 2022 from Blantyre, Malawi, covering four waves of SARS-CoV-2 infections. Clinical and diagnostic data were collected using an adapted ISARIC clinical characterization protocol for COVID-19. SARS-CoV-2 isolates were sequenced using the MinIONâ"¢ in Blantyre., Results: We enrolled 314 patients, good quality sequencing data was available for 55 patients. The sequencing data showed that 8 of 11 participants recruited in wave one had B.1 infections, 6/6 in wave two had Beta, 25/26 in wave three had Delta and 11/12 in wave four had Omicron. Patients infected during the Delta and Omicron waves reported fewer underlying chronic conditions and a shorter time to presentation. Significantly fewer patients required oxygen (22.7% [17/75] vs. 58.6% [140/239], p<0.001) and steroids (38.7% [29/75] vs. 70.3% [167/239], p<0.001) in the Omicron wave compared with the other waves. Multivariable logistic-regression demonstrated a trend toward increased mortality in the Delta wave (OR 4.99 [95% CI 1.0-25.0 p=0.05) compared to the first wave of infection., Conclusions: Our data show that each wave of patients hospitalised with SARS-CoV-2 was infected with a distinct viral variant. The clinical data suggests that patients with severe COVID-19 disease were more likely to die during the Delta wave., Summary: We used genome sequencing to identify the variants of SARS-CoV-2 causing disease in Malawi, and found that each of the four waves was caused by a distinct variant. Clinical investigation suggested that the Delta wave had the highest mortality.
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- 2022
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48. Distinct clinical and immunological profiles of patients with evidence of SARS-CoV-2 infection in sub-Saharan Africa.
- Author
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Morton B, Barnes KG, Anscombe C, Jere K, Matambo P, Mandolo J, Kamng'ona R, Brown C, Nyirenda J, Phiri T, Banda NP, Van Der Veer C, Mndolo KS, Mponda K, Rylance J, Phiri C, Mallewa J, Nyirenda M, Katha G, Kambiya P, Jafali J, Mwandumba HC, Gordon SB, Cornick J, and Jambo KC
- Subjects
- Adult, Africa South of the Sahara epidemiology, Anti-Bacterial Agents administration & dosage, Antibodies blood, COVID-19 blood, COVID-19 epidemiology, Coinfection immunology, Cytokines blood, Dexamethasone administration & dosage, Female, Humans, Immunoglobulin G blood, Immunoglobulin M blood, Male, Middle Aged, Pandemics, SARS-CoV-2 isolation & purification, COVID-19 Drug Treatment, COVID-19 immunology
- Abstract
Although the COVID-19 pandemic has left no country untouched there has been limited research to understand clinical and immunological responses in African populations. Here we characterise patients hospitalised with suspected (PCR-negative/IgG-positive) or confirmed (PCR-positive) COVID-19, and healthy community controls (PCR-negative/IgG-negative). PCR-positive COVID-19 participants were more likely to receive dexamethasone and a beta-lactam antibiotic, and survive to hospital discharge than PCR-negative/IgG-positive and PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants exhibited a nasal and systemic cytokine signature analogous to PCR-positive COVID-19 participants, predominated by chemokines and neutrophils and distinct from PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants had increased propensity for Staphylococcus aureus and Streptococcus pneumoniae colonisation. PCR-negative/IgG-positive individuals with high COVID-19 clinical suspicion had inflammatory profiles analogous to PCR-confirmed disease and potentially represent a target population for COVID-19 treatment strategies.
- Published
- 2021
- Full Text
- View/download PDF
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