Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study

Authors: Cheemarla, Nagarjuna R, Hanron, Amelia, Fauver, Joseph R, Bishai, Jason, Watkins, Timothy A, Brito, Anderson F, Zhao, Dejian, Alpert, Tara, Vogels, Chantal B F, Ko, Albert I, Schulz, Wade L, Landry, Marie L, Grubaugh, Nathan D, van Dijk, David, Foxman, Ellen F ^*

Source: In The Lancet Microbe January 2023 4(1):e38-e46

A new lineage nomenclature to aid genomic surveillance of dengue virus.

Authors: Hill, Verity¹, verity.hill@yale.edu, Cleemput, Sara², Pereira, James Siqueira³, Gifford, Robert J.^4,5, Fonseca, Vagner^5,6, Tegally, Houriiyah⁷, Brito, Anderson F.⁸, Ribeiro, Gabriela³, de Souza, Vinicius Carius³, Brcko, Isabela Carvalho³, Ribeiro, Igor Santana³, De Lima, Iago Trezena Tavares³, Slavov, Svetoslav Nanev³, Sampaio, Sandra Coccuzzo³, Elias, Maria Carolina³, Tran, Vi Thuy⁹, Kien, Duong Thi Hue⁹, Huynh, Tuyen⁹, Yacoub, Sophie⁹, Dieng, Idrissa¹⁰

Source: PLoS Biology; 9/16/2024, Vol. 22 Issue 9, p1-27, 27p

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

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

Source: In Cell 13 May 2021 184(10):2595-2604

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

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

Source: In Cell 28 May 2020 181(5):990-996

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

Authors: 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., Grubaugh, Nathan D.

Source: Nature microbiology. 5(10):1299-1305

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100174419988.0x000001&indx=1&recIds=ETOCvdc_100174419988.0x000001

Multiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020¹.

Authors: Bart, Stephen M.^1,2, sbart@cdc.gov, Flaherty, Eileen², Alpert, Tara³, Carlson, Sherry⁴, Fasulo, Lisa⁴, Earnest, Rebecca³, White, Elizabeth B.³, Dickens, Noel³, Brito, Anderson F.³, Grubaugh, Nathan D.³, Hadler, James L.³, Sosa, Lynn E.²

Source: Emerging Infectious Diseases; Oct2021, Vol. 27 Issue 10, p2669-2672, 4p

Intrahost speciations and host switches played an important role in the evolution of herpesviruses

Authors: Brito, Anderson F, Baele, Guy, Nahata, Kanika D, Grubaugh, Nathan D, Pinney, John W

Source: Virus evolution. 7(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100134585029.0x000001&indx=1&recIds=ETOCvdc_100134585029.0x000001

Multiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020¹.

Authors: Bart, Stephen M., Flaherty, Eileen, Alpert, Tara, Carlson, Sherry, Fasulo, Lisa, Earnest, Rebecca, White, Elizabeth B., Dickens, Noel, Brito, Anderson F., Grubaugh, Nathan D., Hadler, James L., Sosa, Lynn E.

Source: Emerging Infectious Diseases. Oct2021, Vol. 27 Issue 10, p2669-2672. 4p.

Subjects: COVID-19, SARS-CoV-2, PHYSICAL fitness centers, RESPIRATORY infections

Geographic Terms: CONNECTICUT

Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain.

Authors: Hadfield, James¹ (AUTHOR), Brito, Anderson F.² (AUTHOR), Swetnam, Daniele M.³ (AUTHOR), Vogels, Chantal B. F.² (AUTHOR), Tokarz, Ryan E.⁴ (AUTHOR), Andersen, Kristian G.^5,6 (AUTHOR), Smith, Ryan C.⁴ (AUTHOR), Bedford, Trevor¹ (AUTHOR), Grubaugh, Nathan D.² (AUTHOR) nathan.grubaugh@yale.edu

Source: PLoS Pathogens. 10/31/2019, Vol. 15 Issue 10, p1-18. 18p.

Subject Terms: *WEST Nile virus, *VIRUS diseases, *VIRAL genomes, *VIRAL encephalitis, *BIOLOGICAL evolution

Multiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020¹.

Authors: Bart, Stephen M.^1,2, sbart@cdc.gov, Flaherty, Eileen², Alpert, Tara³, Carlson, Sherry⁴, Fasulo, Lisa⁴, Earnest, Rebecca³, White, Elizabeth B.³, Dickens, Noel³, Brito, Anderson F.³, Grubaugh, Nathan D.³, Hadler, James L.³, Sosa, Lynn E.²

Source: Emerging Infectious Diseases; Oct2021, Vol. 27 Issue 10, p2669-2672, 4p

Risk factors for long coronavirus disease 2019 (long COVID) among healthcare personnel, Brazil, 2020–2022

Authors: Marra, Alexandre R., Sampaio, Vanderson Souza, Ozahata, Mina Cintho, Lopes, Rafael, Brito, Anderson F., Bragatte, Marcelo, Kalil, Jorge, Miraglia, João Luiz, Malheiro, Daniel Tavares, Guozhang, Yang, Teich, Vanessa Damazio, Victor, Elivane da Silva, Pinho, João Renato Rebello, Cypriano, Adriana, Vieira, Laura Wanderly, Polonio, Miria, de Oliveira, Solange Miranda, Ricardo, Victória Catharina Volpe, Maezato, Aline Miho, Callado, Gustavo Yano, Schettino, Guilherme de Paula Pinto, de Oliveira, Ketti Gleyzer, Santana, Rúbia Anita Ferraz, Malta, Fernanda de Mello, Amgarten, Deyvid, Boechat, Ana Laura, Kobayashi, Takaaki, Perencevich, Eli, Edmond, Michael B., Rizzo, Luiz Vicente

Source: Infection Control & Hospital Epidemiology; December 2023, Vol. 44 Issue: 12 p1972-1978, 7p

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

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

Source: Proceedings of the National Academy of Sciences of the United States of America; 4/18/2023, Vol. 120 Issue 16, Following p1-9, 19p

Subject Terms: IXODES scapularis, WHITE-tailed deer, VIRAL transmission, CLUSTER sampling

Geographic Terms: UNITED States

Thinking out of the box: revisiting health surveillance based on medical records.

Authors: Sampaio, Vanderson S., Lopes, Rafael, Cintho Ozahata, Mina, Nakaya, Helder I., Sousa, Erick, Araújo, José D., Bragatte, Marcelo A. S., Brito, Anderson F., Zettoni Grespan, Regina Maura, Damato Capuani, Maria Ligia, Humberto Domingues, Helves, Guedes Pellini, Alessandra Cristina, de Oliveira Garcia Mateos, Sheila, Reis Pessoa Conde, Mônica Tilli, Eudes Leal, Fabio, Sabino, Ester, Simão, Mariangela, Kalil, Jorge

Source: Antimicrobial Stewardship & Healthcare Epidemiology; 2023, Vol. 3 Issue 1, p1-5, 5p

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

Authors: Kalinich, Chaney C.¹, chaney.kalinich@yale.edu, Jensen, Cole G.¹, Neugebauer, Peter¹, Petrone, Mary E.¹, Peña-Hernández, Mario², Ott, Isabel M.¹, Wyllie, Anne L.¹, Alpert, Tara¹, Vogels, Chantal B. F.¹, Fauver, Joseph R.¹, Grubaugh, Nathan D.¹, chaney.kalinich@yale.edu, Brito, Anderson F.¹, chaney.kalinich@yale.edu

Source: PLoS Biology; 8/21/2020, Vol. 18 Issue 8, p1-5, 5p, 1 Diagram

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

Authors: 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

Source: Communications Biology; 5/11/2022, Vol. 5 Issue 1, p1-10, 10p

Subject Terms: SARS-CoV-2, INFECTIOUS disease transmission, COVID-19 pandemic, COVID-19, PHYLOGEOGRAPHY

Geographic Terms: CONNECTICUT

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

Authors: Klein, Jonathan¹ (AUTHOR), Brito, Anderson F² (AUTHOR), Trubin, Paul³ (AUTHOR), Lu, Peiwen¹ (AUTHOR), Wong, Patrick¹ (AUTHOR), Alpert, Tara² (AUTHOR), Peña-Hernández, Mario A⁴ (AUTHOR), Haynes, Winston⁵ (AUTHOR), Kamath, Kathy⁵ (AUTHOR), Liu, Feimei¹ (AUTHOR), Vogels, Chantal B F² (AUTHOR), Fauver, Joseph R² (AUTHOR), Lucas, Carolina¹ (AUTHOR), Oh, Jieun¹ (AUTHOR), Mao, Tianyang¹ (AUTHOR), Silva, Julio¹ (AUTHOR), Wyllie, Anne L² (AUTHOR), Muenker, M Catherine² (AUTHOR), Casanovas-Massana, Arnau² (AUTHOR), Moore, Adam J² (AUTHOR)

Source: Journal of Infectious Diseases. Feb2022, Vol. 225 Issue 3, p374-384. 11p.

Subject Terms: *CORONAVIRUS diseases, *HUMORAL immunity, *TRANSPLANTATION of organs, tissues, etc., *COVID-19, *REINFECTION, *WHOLE genome sequencing, *INFECTION

Multiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020¹.

Authors: Bart, Stephen M., Flaherty, Eileen, Alpert, Tara, Carlson, Sherry, Fasulo, Lisa, Earnest, Rebecca, White, Elizabeth B., Dickens, Noel, Brito, Anderson F., Grubaugh, Nathan D., Hadler, James L., Sosa, Lynn E.

Source: Emerging Infectious Diseases; Oct2021, Vol. 27 Issue 10, p2669-2672, 4p

Subject Terms: COVID-19, SARS-CoV-2, PHYSICAL fitness centers, RESPIRATORY infections

Geographic Terms: CONNECTICUT

COVID-19 one year into the pandemic: from genetics and genomics to therapy, vaccination, and policy.

Authors: Novelli, Giuseppe, Biancolella, Michela, Mehrian-Shai, Ruty, Colona, Vito Luigi, Brito, Anderson F., Grubaugh, Nathan D., Vasiliou, Vasilis, Luzzatto, Lucio, Reichardt, Juergen K. V.

Source: Human Genomics; 5/10/2021, Vol. 15 Issue 1, p1-13, 13p

The evolution of protein domain repertoires: Shedding light on the origins of the Herpesviridae family.

Authors: Brito, Anderson F, Pinney, John W

Source: Virus Evolution; Jan2020, Vol. 6 Issue 1, p1-12, 12p

Subject Terms: PROTEINS, HERPESVIRUSES, GENOMES, HIDDEN Markov models, PARSIMONIOUS models, PHYLOGENY

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