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1. Household Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Alpha Variant-United States, 2021.

Author

Donnelly, Marisa, Chuey, Meagan, Soto, Raymond, Schwartz, Noah, Chu, Victoria, Konkle, Stacey, Sleweon, Sadia, Ruffin, Jasmine, Haberling, Dana, Guagliardo, Sarah, Stoddard, Robyn, Anderson, Raydel, Morgan, Clint, Rossetti, Rebecca, McCormick, David, Magleby, Reed, Sheldon, Sarah, Dietrich, Elizabeth, Uehara, Anna, Retchless, Adam, Tong, Suxiang, Folster, Jennifer, Drobeniuc, Jan, Petway, Marla, Austin, Brett, Stous, Sarah, McDonald, Eric, Jain, Seema, Hudziec, Meghan, Stringer, Ginger, Albanese, Bernadette, Totten, Sarah, Staples, J, Killerby, Marie, Hughes, Laura, Matanock, Almea, Beatty, Mark, Tate, Jacqueline, Kirking, Hannah, and Hsu, Christopher

Subjects
Alpha, COVID-19, SARS-CoV-2, household, transmission, COVID-19, Family Characteristics, Humans, SARS-CoV-2, United States
Abstract

BACKGROUND: In Spring 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.7 (Alpha) became the predominant variant in the United States. Research suggests that Alpha has increased transmissibility compared with non-Alpha lineages. We estimated household secondary infection risk (SIR), assessed characteristics associated with transmission, and compared symptoms of persons with Alpha and non-Alpha infections. METHODS: We followed households with SARS-CoV-2 infection for 2 weeks in San Diego County and metropolitan Denver, January to April 2021. We collected epidemiologic information and biospecimens for serology, reverse transcription-polymerase chain reaction (RT-PCR), and whole-genome sequencing. We stratified SIR and symptoms by lineage and identified characteristics associated with transmission using generalized estimating equations. RESULTS: We investigated 127 households with 322 household contacts; 72 households (56.7%) had member(s) with secondary infections. SIRs were not significantly higher for Alpha (61.0% [95% confidence interval, 52.4-69.0%]) than non-Alpha (55.6% [44.7-65.9%], P = .49). In households with Alpha, persons who identified as Asian or Hispanic/Latino had significantly higher SIRs than those who identified as White (P = .01 and .03, respectively). Close contact (eg, kissing, hugging) with primary cases was associated with increased transmission for all lineages. Persons with Alpha infection were more likely to report constitutional symptoms than persons with non-Alpha (86.9% vs 76.8%, P = .05). CONCLUSIONS: Household SIRs were similar for Alpha and non-Alpha. Comparable SIRs may be due to saturation of transmission risk in households due to extensive close contact, or true lack of difference in transmission rates. Avoiding close contact within households may reduce SARS-CoV-2 transmission for all lineages among household members.

Published
2022

2. Household Transmission and Symptomology of Severe Acute Respiratory Syndrome Coronavirus 2 Alpha Variant among Children-California and Colorado, 2021.

Author

Waltenburg, Michelle, Whaley, Melissa, Chancey, Rebecca, Donnelly, Marisa, Chuey, Meagan, Soto, Raymond, Schwartz, Noah, Chu, Victoria, Sleweon, Sadia, McCormick, David, Uehara, Anna, Retchless, Adam, Tong, Suxiang, Folster, Jennifer, Petway, Marla, Thornburg, Natalie, Drobeniuc, Jan, Austin, Brett, Hudziec, Meghan, Stringer, Ginger, Albanese, Bernadette, Totten, Sarah, Matzinger, Shannon, Staples, J, Killerby, Marie, Hughes, Laura, Matanock, Almea, Beatty, Mark, Tate, Jacqueline, Kirking, Hannah, and Hsu, Christopher

Subjects
COVID-19, alpha variant, children, household transmission, Adult, COVID-19, California, Child, Colorado, Humans, SARS-CoV-2
Abstract

OBJECTIVE: To assess the household secondary infection risk (SIR) of B.1.1.7 (Alpha) and non-Alpha lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among children. STUDY DESIGN: During January to April 2021, we prospectively followed households with a SARS-CoV-2 infection. We collected questionnaires, serial nasopharyngeal swabs for reverse transcription polymerase chain reaction testing and whole genome sequencing, and serial blood samples for serology testing. We calculated SIRs by primary case age (pediatric vs adult), household contact age, and viral lineage. We evaluated risk factors associated with transmission and described symptom profiles among children. RESULTS: Among 36 households with pediatric primary cases, 21 (58%) had secondary infections. Among 91 households with adult primary cases, 51 (56%) had secondary infections. SIRs among pediatric and adult primary cases were 45% and 54%, respectively (OR, 0.79; 95% CI, 0.41-1.54). SIRs among pediatric primary cases with Alpha and non-Alpha lineage were 55% and 46%, respectively (OR, 1.52; 95% CI, 0.51-4.53). SIRs among pediatric and adult household contacts were 55% and 49%, respectively (OR, 1.01; 95% CI, 0.68-1.50). Among pediatric contacts, no significant differences in the odds of acquiring infection by demographic or household characteristics were observed. CONCLUSIONS: Household transmission of SARS-CoV-2 from children and adult primary cases to household members was frequent. The risk of secondary infection was similar among child and adult household contacts. Among children, household transmission of SARS-CoV-2 and the risk of secondary infection was not influenced by lineage. Continued mitigation strategies (eg, masking, physical distancing, vaccination) are needed to protect at-risk groups regardless of virus lineage circulating in communities.

Published
2022

3. List of contributors

Author

Aizawa, Shin-Ichi, primary, Alberdi, Pilar, additional, Alexander, David C., additional, Alía, Alberto, additional, Allison, D.G., additional, Amyes, Sebastian G.B., additional, An, Haoran, additional, Andrade, María J., additional, Antelmann, Haike, additional, Arias, Cesar A., additional, Asensio, Miguel A., additional, Axell-House, Dierdre B., additional, Bae, Hee-Won, additional, Baena, Laura Muñoz, additional, Baig, Abdul Mannan, additional, Bailey, Spenser O., additional, Baize, Sylvain, additional, Baldi, Pablo C., additional, Barbosa, Angela Silva, additional, Barbuddhe, Sukhadeo B., additional, Bard, Emilie, additional, Barry, Eileen M., additional, Basarab, Gregory S., additional, Beloborodova, N.V, additional, Bermúdez, Elena, additional, Bidmos, Fadil A., additional, Bisgaard, Magne, additional, Blakely, Garry W., additional, Bloch, Evan, additional, Boesen, Thias Oberg, additional, Bose, Dipayan, additional, Botero, Javier Enrique, additional, Bouabe, Hicham, additional, Bouchard, Michael J., additional, Bozue, Joel A., additional, Bradbury, Richard S., additional, Brett Moreau, G., additional, Cabezas-Cruz, Alejandro, additional, Cai, Rong-Jun, additional, Calderón, Enrique J., additional, Cao, Boyang, additional, Carmena, David, additional, Carvalho, Eneas, additional, Caulfield, Amanda D., additional, Cen, Shan, additional, Chai, Jong-Yil, additional, Chamberland, Robin R., additional, Champredon, David, additional, Chan, Edward D., additional, Charbon, Godefroid, additional, Chato, Connor, additional, Chelomina, G.N., additional, Chen, Jingyu, additional, Chen, Min, additional, Chen, Shuyu, additional, Chen, Suilin, additional, Chen, Yanfei, additional, Chen, Zhaoyuan, additional, Cheng, Aimin, additional, Cheng, Keding, additional, Chiu, Charles Y., additional, Cho, You-Hee, additional, Christensen, Henrik, additional, Chrtdernevskaya, E.A., additional, Contreras, Adolfo, additional, Contreras, Marinela, additional, Córdoba, Juan J., additional, Córdoba, María G., additional, Costa, Rita, additional, Cote, Christopher K., additional, Cui, Xiangling, additional, Cui, Yujun, additional, Dacal, Elena, additional, Dammann, Allison N., additional, Das, Shubhagata, additional, Dashti, Alejandro, additional, de la Fuente, José, additional, de la Garza, Mireya, additional, Delgado, Josué, additional, Delgado-Cuesta, Juan, additional, Deng, Haiteng, additional, Deng, Li, additional, Dey, Debajit, additional, Dhama, Kuldeep, additional, Diego, Juan García-Bernalt, additional, Ding, Hao, additional, Doern, Christopher D., additional, Dorman, Charles J., additional, Du, Zongmin, additional, Dunbar, Sherry A., additional, Duthie, Malcolm, additional, Dybvig, Kevin F., additional, Eakin, Ann E., additional, Eallonardo, Samuel J., additional, Eberly, Allison R., additional, Echeverry, Adriana Jaramillo, additional, Egland, Paul G., additional, El Zowalaty, Mohamed E., additional, Endsley, Janice Jones, additional, Eom, Keeseon S., additional, Evans, Benjamin A., additional, Falkinham, Joseph O., additional, Feng, Siwei, additional, Feng, Yaoyu, additional, Feng, Zongdi, additional, Fernández-Soto, Pedro, additional, Ferreira, Roux-Cil, additional, Flores-Huerta, Nadia, additional, Foster, Timothy J., additional, Fox-Moon, Sandra M., additional, Fraga, Tatiana Rodrigues, additional, Fredricks, David N., additional, Freitag, Nancy E., additional, Frimodt-Møller, Jakob, additional, Fuller, Risa, additional, Ganesh, Balasubramanian, additional, Gao, Ning, additional, García-Carnero, Laura C., additional, Garzetti, Debora, additional, Geoghegan, Joan A., additional, Ghenim, Raed, additional, Giambartolomei, Guillermo H., additional, Gilbert, Nicole M., additional, Gillis, Thomas Phillip, additional, Gladstone, Camilla A., additional, Gómez-Gaviria, Manuela, additional, Gómez-Marín, Jorge E., additional, Gong, Tengfang, additional, González, Ramón A., additional, Gray-Owen, Scott D., additional, Gu, Bing, additional, Guzmán-Téllez, Paula, additional, Hajal, Caroline, additional, Han, Yanping, additional, Hao, Yi, additional, Harrington, Amanda T., additional, Harris, Jason B., additional, Harvill, Eric T., additional, Hasan, S. Saif, additional, He, Guang-Jun, additional, He, Yongqun, additional, Heffron, Jared D., additional, Hidalgo, Paloma, additional, Hindiyeh, Musa Y., additional, Hreha, Teri N., additional, Hu, Xiaoyu, additional, Huang, Guanghua, additional, Huang, Jiangqing, additional, Huang, Liang, additional, Huang, Shifeng, additional, Huang, Xingxu, additional, Huang, Xueting, additional, Huang, Yilun, additional, Huffman, Anthony, additional, Humphreys, Tricia L., additional, Hunstad, David A., additional, Inglis, Timothy J.J., additional, Isaac, Lourdes, additional, Jacobs, Samantha E., additional, Janowicz, Diane M., additional, Jeon, Hyeong-Kyu, additional, Ji, Quanjiang, additional, Jia, Qi, additional, Jia, Wei, additional, Jin, Shouguang, additional, Jneidi, Lama, additional, Jose, Shinsmon, additional, Jung, Bong-Kwang, additional, Kattan, Randa, additional, Kaushik, Rahul, additional, Khare, Reeti, additional, Kim, Eun Sook, additional, Kirn, Thomas J., additional, Koo, Hyun, additional, Köster, Pamela C., additional, Krause, Peter J., additional, Kumar, Sanjai, additional, Kupz, Andreas, additional, Lambert, P.A., additional, Lamont, Richard J., additional, Langford, Paul R., additional, Lebeaux, David, additional, Legname, Giuseppe, additional, Li, Bin, additional, Li, Chunhao, additional, Li, Fen, additional, Li, Jun, additional, Li, Lanjuan, additional, Li, Ruofan, additional, Li, Ruoyu, additional, Li, Ting, additional, Li, Yang-Yang, additional, Li, Yanhua, additional, Li, Zhuorong, additional, Liang, Xiaomeng, additional, Liao, Guojian, additional, Lin, Ping, additional, Ling, Yun, additional, Liu, Bo, additional, Liu, Dongyou, additional, Liu, Guohua, additional, Liu, Huidi, additional, Liu, Jiafeng, additional, Liu, Jintao, additional, Liu, Qi, additional, Liu, Shu-Lin, additional, Liu, Taiping, additional, Liu, Tongbao, additional, Liu, Wei, additional, Liu, Yan, additional, Liu, Yanni, additional, Liu, Yisong, additional, Liu, Yuan, additional, Løbner-Olesen, Anders, additional, Loeffelholz, Michael, additional, Lu, Hongzhou, additional, Luna, Brian, additional, Ma, Bingting, additional, Ma, Chengying, additional, Ma, Shuang, additional, Ma, TianLi, additional, Madan, Rajat, additional, Mahle, Rachael E., additional, Mahlen, Steven D., additional, Malik, Satya Veer Singh, additional, Malik, Yashpal Singh, additional, Malvy, Denis, additional, Mann, Barbara J., additional, Marasini, Daya, additional, Maris, Alexander S., additional, Marjomäki, Varpu, additional, Marjuki, Henju, additional, Martín, Alberto, additional, Martín, Irene, additional, Martínez-Castillo, Moisés, additional, Martínez-Pabón, María Cecilia, additional, Mathison, Blaine A., additional, Ma’ayeh, Showgy, additional, McDowell, Andrew, additional, McLaughlin, Stephanie E., additional, McSheffrey, Gordon G., additional, Medrano, Francisco J., additional, Meehan, Conor J., additional, Mehta, Dhwani, additional, Mejía-Oquendo, Manuela, additional, Melo-Cristino, José, additional, Mendoza-Barberá, Elena, additional, Meng, Xinan, additional, Merino, Susana, additional, Merritt, Adam J., additional, Miller, Steve, additional, Miller, William R., additional, Minamino, Tohru, additional, Mirzaei, Mohammadali Khan, additional, Mora-Montes, Héctor M., additional, Mortensen, Joel, additional, Mostafa, Heba H., additional, Muhsen, Khitam, additional, Mujahed, Ahlam, additional, Muro, Antonio, additional, Murphy, Olwen C., additional, Newton, Hayley J., additional, Nguyen, April H., additional, Nichols, Wright W., additional, Niu, Siqiang, additional, Núñez, Félix, additional, Obregon, Dasiel, additional, Okamoto, Akira, additional, Okutani, Akiko, additional, Olabode, Abayomi, additional, Omar, Muna, additional, Ong, Edison, additional, Ouyang, Zhiming, additional, Pacak, Christina A., additional, Pacheco-Yépez, Judith, additional, Palmer, John, additional, Pang, Xiaoli, additional, Paredes-Sabja, Daniel, additional, Peng, Zhong, additional, Peng, Zonggen, additional, Pérez-Nevado, Francisco, additional, Poon, Art, additional, Pospíšilová, Petra, additional, Potts, Caelin C., additional, Pu, Qinqin, additional, Pujic, Petar, additional, Qi, Rui, additional, Qian, Chenyun, additional, Qian, Liu, additional, Qin, Aiping, additional, Qu, Fen, additional, Rakin, Alexander, additional, Ramesh, Ashwin, additional, Ramirez, Mario, additional, Rao, Yu, additional, Ratner, Adam J., additional, Rawool, Deepak B., additional, Rehman, Asma, additional, Ren, Jie, additional, Ren, Ping, additional, Retchless, Adam C., additional, Robertson, Erle S., additional, Rodríguez, Alicia, additional, Rodriguez, Azucena, additional, Rodríguez-Medina, Carolina, additional, Rodriguez-Nava, Veronica, additional, Rohde, Manfred, additional, Romero-Rodríguez, Alba, additional, Rosales-Morgan, Gabriela, additional, Rosenkranz, Andrea L., additional, Ruiz-Moyano, Santiago, additional, Ruokolainen, Visa, additional, Sabateen, Ali, additional, Sahu, Radhakrishna, additional, Sails, Andrew, additional, Sang, Yu, additional, Santana, Clarissa H., additional, Santos, Jesus A., additional, Santos, Renato L., additional, Schmitz, Jonathan E., additional, Serrano-Luna, Jesús, additional, Shen, Jianzhong, additional, Shen, Zhangqi, additional, Shibayama, Mineko, additional, Shirtliff, Mark E., additional, Silva-Costa, Catarina, additional, Silva-Olivares, Angélica, additional, Singh, Niraj Kumar, additional, Šmajs, David, additional, Smith, Robert P., additional, Smith, Sophie, additional, Snyder, Lori A.S., additional, Song, Yinggai, additional, Soro, Aurea Simon, additional, Spearman, Paul, additional, Spellberg, Brad, additional, Sprague, Lisa D., additional, Stratton, Charles W., additional, Strenk, Susan M., additional, Strugnell, Richard A., additional, Sun, Keer, additional, Suo, Xun, additional, Suzuki-Hatano, Silveli, additional, Svärd, Staffan, additional, Talbot, Elizabeth A., additional, Tamez-Castrellón, Alma K., additional, Tan, Nie, additional, Tang, Cynthia Y., additional, Tang, Yi-Wei, additional, Tao, Jia, additional, Tao, Lili, additional, Terrero-Salcedo, David, additional, Tharmalingam, Jayaraman, additional, Thwe, Phyu M., additional, Tiamani, Kawtar, additional, Tomás, Juan M., additional, Topaz, Nadav, additional, Tsai, Ang-Chen, additional, Tsalik, Ephraim L., additional, Tuomanen, Elaine I., additional, Turenne, Christine Y., additional, Tyagi, Anuj, additional, Uprety, Priyanka, additional, Valour, Florent, additional, van Hensbergen, Vincent P., additional, Venkatesan, Arun, additional, Vergis, Jess, additional, Villar, Margarita, additional, Vollmer, Waldemar, additional, Waites, Ken B., additional, Wan, Xiu-Feng, additional, Wang, Guiqing, additional, Wang, Lijun, additional, Wang, Lin, additional, Wang, Linqi, additional, Wang, Xiangru, additional, Wang, Xin, additional, Wang, Xinjie, additional, Wang, Ya-Ting, additional, Wang, Yang, additional, Wang, Yating, additional, Weil, Ana A., additional, Welkos, Susan L., additional, Wengenack, Nancy L., additional, Westblade, Lars F., additional, Whitfield, Chris, additional, Wu, Hui, additional, Wu, Lijuan, additional, Wu, Min, additional, Wu, Yarong, additional, Wu, Zhaowei, additional, Xiang, Ye, additional, Xiao, Di, additional, Xiao, Li, additional, Xiao, Lihua, additional, Xu, Tao, additional, Xu, Wenyue, additional, Xu, Xinping, additional, Xue, Jinling, additional, Yadav, Jay Prakash, additional, Yan, Junxiang, additional, Yan, Yixin, additional, Yang, Changmei, additional, Yang, Ruifu, additional, Yang, Ying, additional, Yao, Kaihu, additional, Yao, Yu-Feng, additional, Yeakle, Kyle C., additional, Yu, Demin, additional, Yu, Hao, additional, Yu, Xue-Jie, additional, Yuan, Zhenghong, additional, Zai, Wenjing, additional, Zhang, Jianzhong, additional, Zhang, Jing-Ren, additional, Zhang, Lanyue, additional, Zhang, Lijie, additional, Zhang, Qiwei, additional, Zhang, Wenbao, additional, Zhang, Wenhong, additional, Zhang, Xinxin, additional, Zhao, Youbao, additional, Zhou, Chuanmin, additional, Zhu, Feng, additional, Zhu, Jingting, additional, and Zhu, Yongqun, additional

Published
2024
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4. Haemophilus influenzae

Author

Retchless, Adam C., primary, Topaz, Nadav, additional, Marjuki, Henju, additional, Marasini, Daya, additional, Potts, Caelin C., additional, and Wang, Xin, additional

Published
2024
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6. Household Transmission and Symptomology of Severe Acute Respiratory Syndrome Coronavirus 2 Alpha Variant among Children—California and Colorado, 2021

Author

Alford, Alexis, Baird, Samuel, Bankers, Laura, Bello, Jazmin, Bolcen, Shanna, Browning, Peter, Cook, Peter W., David, Ebenezer, Harcourt, Jennifer L., Hareland, Geir, Jr., Hetherington-Rauth, Molly C., Ir, Diana, Jain, Shilpi, Jia, Tao Lily, Johnson, Ralen, Kelleher, Anna, Kim, Gimin, Li, Yan, Lynch, Brian, Mallal, Daniel, Maniatis, Panagiotis, Marine, Rachel, Medrzycki, Magdalena, Metz, John M., Montmayeur, Anna Maria, Moss, Kimberly M., Justin Ng, Han Jia, Nyugen, Van, Ortiz, Kristina, Paden, Clinton R., Park, So Hee, Queen, Krista, Rossheim, Alexandria E.B., Semenova, Vera, Shepard, Samuel S., Tamin, Azaibi, Tao, Ying, Tejada-Strop, Alexandra, Wong, Phili, Zellner, Briana, Zhang, Jing, Waltenburg, Michelle A., Whaley, Melissa J., Chancey, Rebecca J., Donnelly, Marisa A.P., Chuey, Meagan R., Soto, Raymond, Schwartz, Noah G., Chu, Victoria T., Sleweon, Sadia, McCormick, David W., Uehara, Anna, Retchless, Adam C., Tong, Suxiang, Folster, Jennifer M., Petway, Marla, Thornburg, Natalie J., Drobeniuc, Jan, Austin, Brett, Hudziec, Meghan M., Stringer, Ginger, Albanese, Bernadette A., Totten, Sarah E., Matzinger, Shannon R., Staples, J. Erin, Killerby, Marie E., Hughes, Laura J., Matanock, Almea, Beatty, Mark, Tate, Jacqueline E., Kirking, Hannah L., and Hsu, Christopher H.

Published
2022
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7. Epidemiologic and Genomic Evidence for Zoonotic Transmission of SARS-CoV-2 among People and Animals on a Michigan Mink Farm, United States, 2020

Author

Ghai, Ria R., primary, Straily, Anne, additional, Wineland, Nora, additional, Calogero, Jennifer, additional, Stobierski, Mary Grace, additional, Signs, Kimberly, additional, Blievernicht, Melissa, additional, Torres-Mendoza, Yaritbel, additional, Waltenburg, Michelle A., additional, Condrey, Jillian A., additional, Blankenship, Heather M., additional, Riner, Diana, additional, Barr, Nancy, additional, Schalow, Michele, additional, Goodrich, Jarold, additional, Collins, Cheryl, additional, Ahmad, Ausaf, additional, Metz, John Michael, additional, Herzegh, Owen, additional, Straka, Kelly, additional, Arsnoe, Dustin M., additional, Duffiney, Anthony G., additional, Shriner, Susan A., additional, Kainulainen, Markus H., additional, Carpenter, Ann, additional, Whitehill, Florence, additional, Wendling, Natalie M., additional, Stoddard, Robyn A., additional, Retchless, Adam C., additional, Uehara, Anna, additional, Tao, Ying, additional, Li, Yan, additional, Zhang, Jing, additional, Tong, Suxiang, additional, and Barton Behravesh, Casey, additional

Published
2023
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9. One Health Investigation of SARS-CoV-2 in People and Animals on Multiple Mink Farms in Utah

Author

Cossaboom, Caitlin M., primary, Wendling, Natalie M., additional, Lewis, Nathaniel M., additional, Rettler, Hannah, additional, Harvey, Robert R., additional, Amman, Brian R., additional, Towner, Jonathan S., additional, Spengler, Jessica R., additional, Erickson, Robert, additional, Burnett, Cindy, additional, Young, Erin L., additional, Oakeson, Kelly, additional, Carpenter, Ann, additional, Kainulainen, Markus H., additional, Chatterjee, Payel, additional, Flint, Mike, additional, Uehara, Anna, additional, Li, Yan, additional, Zhang, Jing, additional, Kelleher, Anna, additional, Lynch, Brian, additional, Retchless, Adam C., additional, Tong, Suxiang, additional, Ahmad, Ausaf, additional, Bunkley, Paige, additional, Godino, Claire, additional, Herzegh, Owen, additional, Drobeniuc, Jan, additional, Rooney, Jane, additional, Taylor, Dean, additional, and Barton Behravesh, Casey, additional

Published
2022
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10. Benchmark datasets for SARS-CoV-2 surveillance bioinformatics

Author

Xiaoli, Lingzi, primary, Hagey, Jill V., additional, Park, Daniel J., additional, Gulvik, Christopher A., additional, Young, Erin L., additional, Alikhan, Nabil-Fareed, additional, Lawsin, Adrian, additional, Hassell, Norman, additional, Knipe, Kristen, additional, Oakeson, Kelly F., additional, Retchless, Adam C., additional, Shakya, Migun, additional, Lo, Chien-Chi, additional, Chain, Patrick, additional, Page, Andrew J., additional, Metcalf, Benjamin J., additional, Su, Michelle, additional, Rowell, Jessica, additional, Vidyaprakash, Eshaw, additional, Paden, Clinton R., additional, Huang, Andrew D., additional, Roellig, Dawn, additional, Patel, Ketan, additional, Winglee, Kathryn, additional, Weigand, Michael R., additional, and Katz, Lee S., additional

Published
2022
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11. Household Transmission and Symptomology of Severe Acute Respiratory Syndrome Coronavirus 2 Alpha Variant among Children—California and Colorado, 2021

Author

Waltenburg, Michelle A., primary, Whaley, Melissa J., additional, Chancey, Rebecca J., additional, Donnelly, Marisa A.P., additional, Chuey, Meagan R., additional, Soto, Raymond, additional, Schwartz, Noah G., additional, Chu, Victoria T., additional, Sleweon, Sadia, additional, McCormick, David W., additional, Uehara, Anna, additional, Retchless, Adam C., additional, Tong, Suxiang, additional, Folster, Jennifer M., additional, Petway, Marla, additional, Thornburg, Natalie J., additional, Drobeniuc, Jan, additional, Austin, Brett, additional, Hudziec, Meghan M., additional, Stringer, Ginger, additional, Albanese, Bernadette A., additional, Totten, Sarah E., additional, Matzinger, Shannon R., additional, Staples, J. Erin, additional, Killerby, Marie E., additional, Hughes, Laura J., additional, Matanock, Almea, additional, Beatty, Mark, additional, Tate, Jacqueline E., additional, Kirking, Hannah L., additional, Hsu, Christopher H., additional, Alford, Alexis, additional, Baird, Samuel, additional, Bankers, Laura, additional, Bello, Jazmin, additional, Bolcen, Shanna, additional, Browning, Peter, additional, Cook, Peter W., additional, David, Ebenezer, additional, Harcourt, Jennifer L., additional, Hareland, Geir, additional, Hetherington-Rauth, Molly C., additional, Ir, Diana, additional, Jain, Shilpi, additional, Jia, Tao Lily, additional, Johnson, Ralen, additional, Kelleher, Anna, additional, Kim, Gimin, additional, Li, Yan, additional, Lynch, Brian, additional, Mallal, Daniel, additional, Maniatis, Panagiotis, additional, Marine, Rachel, additional, Medrzycki, Magdalena, additional, Metz, John M., additional, Montmayeur, Anna Maria, additional, Moss, Kimberly M., additional, Justin Ng, Han Jia, additional, Nyugen, Van, additional, Ortiz, Kristina, additional, Paden, Clinton R., additional, Park, So Hee, additional, Queen, Krista, additional, Rossheim, Alexandria E.B., additional, Semenova, Vera, additional, Shepard, Samuel S., additional, Tamin, Azaibi, additional, Tao, Ying, additional, Tejada-Strop, Alexandra, additional, Wong, Phili, additional, Zellner, Briana, additional, and Zhang, Jing, additional

Published
2022
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13. Invasive Meningococcal Disease Among People Experiencing Homelessness—United States, 2016–2019

Author

Rudmann, Keegan C, primary, Brown, Nicole E, additional, Rubis, Amy B, additional, Burns, Meagan, additional, Ramsey, April, additional, De Las Nueces, Denise, additional, Martin, Tasha, additional, Barnes, Meghan, additional, Davizon, Emily Spence, additional, Retchless, Adam C, additional, Potts, Caelin, additional, Wang, Xin, additional, Hariri, Susan, additional, and McNamara, Lucy A, additional

Published
2022
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14. Transmission of SARS‐CoV‐2 Delta variant (B.1.617.2) from a fully vaccinated human to a canine in Georgia, July 2021

Author

Wendling, Natalie M., primary, Carpenter, Ann, additional, Liew, Amanda, additional, Ghai, Ria R., additional, Gallardo‐Romero, Nadia, additional, Stoddard, Robyn A., additional, Tao, Ying, additional, Zhang, Jing, additional, Retchless, Adam C., additional, Ahmad, Ausaf, additional, Bunkley, Paige, additional, Godino, Claire, additional, Mauldin, Matthew R., additional, Varela, Kate, additional, Ritter, Jana M., additional, Hennebelle, Janemarie, additional, Feldpausch, Amanda, additional, Gabel, Julie, additional, Kainulainen, Markus H., additional, Herzegh, Owen, additional, Tong, Suxiang, additional, Spengler, Jessica R., additional, and Barton Behravesh, Casey, additional

Published
2022
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16. Investigation of SARS-CoV-2 Transmission Associated With a Large Indoor Convention — New York City, November–December 2021

Author

Sami, Samira, primary, Horter, Libby, additional, Valencia, Diana, additional, Thomas, Isabel, additional, Pomeroy, Mary, additional, Walker, Brianna, additional, Smith-Jeffcoat, Sarah E., additional, Tate, Jacqueline E., additional, Kirking, Hannah L., additional, Kyaw, Nang Thu Thu, additional, Burns, Rebecca, additional, Blaney, Kathleen, additional, Dorabawila, Vajeera, additional, Hoen, Rebecca, additional, Zirnhelt, Zachary, additional, Schardin, Cody, additional, Uehara, Anna, additional, Retchless, Adam C., additional, Brown, Vance R., additional, Gebru, Yonathan, additional, Powell, Charles, additional, Bart, Stephen M., additional, Vostok, Johanna, additional, Lund, Hannah, additional, Kaess, Jessica, additional, Gumke, Megan, additional, Propper, Randy, additional, Thomas, Deepam, additional, Ojo, Mojisola, additional, Green, Alison, additional, Wieck, Morgan, additional, Wilson, Erica, additional, Hollingshead, Ryan J., additional, Nunez, Sheila V., additional, Saady, Dawn M., additional, Porse, Charsey Cole, additional, Gardner, Kyle, additional, Drociuk, Daniel, additional, Scott, Julia, additional, Perez, Taidy, additional, Collins, Jim, additional, Shaffner, Julie, additional, Pray, Ian, additional, Rust, Laura T., additional, Brady, Shane, additional, Kerins, Janna L., additional, Teran, Richard A., additional, Hughes, Victoria, additional, Sepcic, Victoria, additional, Low, Eleanor W., additional, Kemble, Sarah K., additional, Berkley, Alexandra, additional, Cleavinger, Kate, additional, Safi, Haytham, additional, Webb, Lindsey Martin, additional, Hutton, Scott, additional, Dewart, Courtney, additional, Dickerson, Kristen, additional, Hawkins, Eric, additional, Zafar, Javeria, additional, Krueger, Anna, additional, Bushman, Dena, additional, Ethridge, Bailee, additional, Hansen, Katrina, additional, Tant, Jake, additional, Reed, Christy, additional, Boutwell, Carla, additional, Hanson, Jennifer, additional, Gillespie, Meagan, additional, Donahue, Matthew, additional, Lane, Pilar, additional, Serrano, Ruby, additional, Hernandez, Lorena, additional, Dethloff, Michelle A., additional, Lynfield, Ruth, additional, Como-Sabetti, Kathryn, additional, Lutterloh, Emily, additional, Ackelsberg, Joel, additional, and Ricaldi, Jessica N., additional

Published
2022
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17. Genomic Insights on Variation Underlying Capsule Expression in Meningococcal Carriage Isolates From University Students, United States, 2015–2016

Author

Whaley, Melissa J., primary, Vuong, Jeni T., additional, Topaz, Nadav, additional, Chang, How-Yi, additional, Thomas, Jennifer Dolan, additional, Jenkins, Laurel T., additional, Hu, Fang, additional, Schmink, Susanna, additional, Steward-Clark, Evelene, additional, Mathis, Marsenia, additional, Rodriguez-Rivera, Lorraine D., additional, Retchless, Adam C., additional, Joseph, Sandeep J., additional, Chen, Alexander, additional, Acosta, Anna M., additional, McNamara, Lucy, additional, Soeters, Heidi M., additional, Mbaeyi, Sarah, additional, Marjuki, Henju, additional, and Wang, Xin, additional

Published
2022
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20. Benchmark datasets for SARS-CoV-2 surveillance bioinformatics.

Author

Lingzi Xiaoli, Hagey, Jill V., Park, Daniel J., Gulvik, Christopher A., Young, Erin L., Alikhan, Nabil-Fareed, Lawsin, Adrian, Hassell, Norman, Knipe, Kristen, Oakeson, Kelly F., Retchless, Adam C., Shakya, Migun, Chien-Chi Lo, Chain, Patrick, Page, Andrew J., Metcalf, Benjamin J., Su, Michelle, Rowell, Jessica, Vidyaprakash, Eshaw, and Paden, Clinton R.

Subjects
SARS-CoV-2, COVID-19, BIOINFORMATICS software, NUCLEOTIDE sequencing, WHOLE genome sequencing
Abstract

Background. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. Methods. We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study. Results. The benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. There are six datasets: three were derived from recent publications; two were derived from data mining public databases to answer common questions not covered by published datasets; one unique dataset representing common sequence failures was obtained by rigorously scrutinizing data that did not pass quality checks. The dataset summary table, data mining script and quality control (QC) values for all sequence data are publicly available on GitHub: https://github.com/CDCgov/datasets-sars-cov-2. Discussion. The datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. Together, improvements in these areas support accurate and timely outbreak investigation and surveillance, providing actionable data for pandemic management. Furthermore, these publicly available and standardized benchmark data will facilitate the development and adjudication of new pipelines. [ABSTRACT FROM AUTHOR]

Published
2022
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21. Infection With the US Neisseria meningitidis Urethritis Clade Does Not Lower Future Risk of Urethral Gonorrhea.

Author

Turner, Abigail Norris, Carter, Alexandria M, Tzeng, Yih-Ling, Stephens, David S, Brown, Morgan A, Snyder, Brandon M, Retchless, Adam C, Wang, Xin, and Bazan, Jose A

Subjects
GONORRHEA, CONFIDENCE intervals, IMMUNIZATION, RETROSPECTIVE studies, URETHRITIS, RISK assessment, COMPARATIVE studies, URETHRA diseases, IMMUNITY, NEISSERIA infections, SENSITIVITY & specificity (Statistics), ODDS ratio, LONGITUDINAL method, DISEASE risk factors
Abstract

Background Cross-protective immunity between Neisseria meningitidis (Nm) and Neisseria gonorrhoeae (Ng) may inform gonococcal vaccine development. Meningococcal serogroup B (MenB) outer membrane vesicle (OMV) vaccines confer modest protection against gonorrhea. However, whether urethral Nm infection protects against gonorrhea is unknown. We examined gonorrhea risk among men with US Nm urethritis clade (US_NmUC) infections. Methods We conducted a retrospective cohort study of men with urethral US_NmUC (n = 128) between January 2015 and April 2018. Using diagnosis date as the baseline visit, we examined Ng status at return visits to compute urethral Ng risk. We compared these data to 3 referent populations: men with urethral Ng (n = 253), urethral chlamydia (Ct) (n = 251), and no urethral Ng or Ct (n = 255). We conducted sensitivity analyses to assess varied approaches to censoring, missing data, and anatomical site of infection. We also compared sequences of protein antigens in the OMV-based MenB-4C vaccine, US_NmUC, and Ng. Results Participants were primarily Black (65%) and heterosexual (82%). Over follow-up, 91 men acquired urethral Ng. Men with urethral US_NmUC had similar Ng risk to men with prior urethral Ng (adjusted hazard ratio [aHR]: 1.27; 95% CI:.65–2.48). Men with urethral US_NmUC had nonsignificantly increased Ng risk compared with men with urethral Ct (aHR: 1.51; 95% CI:.79–2.88), and significantly increased Ng risk compared with men without urethral Ng or Ct (aHR: 3.55; 95% CI: 1.27–9.91). Most of the protein antigens analyzed shared high sequence similarity. Conclusions Urethral US_NmUC infection did not protect against gonorrhea despite substantial sequence similarities in shared protein antigens. [ABSTRACT FROM AUTHOR]

Published
2022
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22. Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants - United States, June 2021-January 2022.

Author

Lambrou AS, Shirk P, Steele MK, Paul P, Paden CR, Cadwell B, Reese HE, Aoki Y, Hassell N, Zheng XY, Talarico S, Chen JC, Oberste MS, Batra D, McMullan LK, Halpin AL, Galloway SE, MacCannell DR, Kondor R, Barnes J, MacNeil A, Silk BJ, Dugan VG, Scobie HM, Wentworth DE, Caravas J, Kovacs NA, Gerhart JG, Jia Ng H, Beck A, Chau R, Cintron R, Cook PW, Gulvik CA, Howard D, Jang Y, Knipe K, Lacek KA, Moser KA, Paskey AC, Rambo-Martin BL, Nagilla RR, Retchless AC, Schmerer MW, Seby S, Shepard SS, Stanton RA, Stark TJ, Uehara A, Unoarumhi Y, Bentz ML, Burgin A, Burroughs M, Davis ML, Keller MW, Keong LM, Le SS, Lee JS, Madden Jr JC, Nobles S, Owuor DC, Padilla J, Sheth M, and Wilson MM

Subjects
Centers for Disease Control and Prevention, U.S., Genomics, Humans, Prevalence, Public Health Surveillance methods, United States epidemiology, COVID-19 epidemiology, COVID-19 virology, SARS-CoV-2 genetics
Abstract

Genomic surveillance is a critical tool for tracking emerging variants of SARS-CoV-2 (the virus that causes COVID-19), which can exhibit characteristics that potentially affect public health and clinical interventions, including increased transmissibility, illness severity, and capacity for immune escape. During June 2021-January 2022, CDC expanded genomic surveillance data sources to incorporate sequence data from public repositories to produce weighted estimates of variant proportions at the jurisdiction level and refined analytic methods to enhance the timeliness and accuracy of national and regional variant proportion estimates. These changes also allowed for more comprehensive variant proportion estimation at the jurisdictional level (i.e., U.S. state, district, territory, and freely associated state). The data in this report are a summary of findings of recent proportions of circulating variants that are updated weekly on CDC's COVID Data Tracker website to enable timely public health action. † The SARS-CoV-2 Delta (B.1.617.2 and AY sublineages) variant rose from 1% to >50% of viral lineages circulating nationally during 8 weeks, from May 1-June 26, 2021. Delta-associated infections remained predominant until being rapidly overtaken by infections associated with the Omicron (B.1.1.529 and BA sublineages) variant in December 2021, when Omicron increased from 1% to >50% of circulating viral lineages during a 2-week period. As of the week ending January 22, 2022, Omicron was estimated to account for 99.2% (95% CI = 99.0%-99.5%) of SARS-CoV-2 infections nationwide, and Delta for 0.7% (95% CI = 0.5%-1.0%). The dynamic landscape of SARS-CoV-2 variants in 2021, including Delta- and Omicron-driven resurgences of SARS-CoV-2 transmission across the United States, underscores the importance of robust genomic surveillance efforts to inform public health planning and practice., Competing Interests: All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

Published
2022
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