Ackerman, C. M., C. Myhrvold, S. G. Thakku, C. A. Freije, H. C. Metsky, D. K. Yang, S. H. Ye, C. K. Boehm, T. F. Kosoko-Thoroddsen, J. Kehe, T. G. Nguyen, A. Carter, A. Kulesa, J. R. Barnes, V. G. Dugan, D. T. Hung, P. C. Blainey, and P. C. Sabeti. 2020. Massively multiplexed nucleic acid detection with Cas13. Nature 582(7811):277–282.
Andersen, K. G., A. Rambaut, W. I. Lipkin, E. C. Holmes, and R. F. Garry. 2020. The proximal origin of SARS-CoV-2. Nature Medicine 26(4):450–452.
Anzalone, A. J., W. H. Beasley, K. Murray, W. B. Hillegass, M. Schissel, M. T. Vest, S. A. Chapman, R. Horswell, L. Miele, J. Z. Porterfield, H. T. Bunnell, B. S. Price, S. Patrick, C. J. Rosen, S. L. Santangelo, J. C. McClay, S. L. Hodder, and National COVID Cohort Collaborative Consortium. 2024. Associations between COVID-19 therapies and outcomes in rural and urban America: A multisite, temporal analysis from the Alpha to Omicron SARS-CoV-2 variants. Journal of Rural Health 41(1):e12857.
Barnes, K. G., J. I. Levy, J. Gauld, J. Rigby, O. Kanjerwa, C. B. Uzzell, C. Chilupsya, C. Anscombe, C. Tomkins-Tinch, O. Mbeti, E. Cairns, H. Thole, S. McSweeney, M. G. Chibwana, P. M. Ashton, K. C. Jere, J. S. Meschke, P. Diggle, J. Cornick, B. Chilima, K. Jambo, K. G. Andersen, G. Kawalazira, S. Paterson, T. S. Nyirenda, and N. Feasey. 2023. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems. Nature Communications 14(1):7883.
Bendix, A. 2021. You aren’t legally allowed to know which variant gave you COVID-19 in the US, even if it’s Delta. Business Insider, https://www.businessinsider.com/covid-patients-cant-know-which-variant-infected-them-delta-2021-8 (accessed October 11, 2024).
Benoit, P., N. Brazer, M. de Lorenzi-Tognon, E. Kelly, V. Servellita, M. Oseguera, J. Nguyen, J. Tang, C. Omura, J. Streithorst, M. Hillberg, D. Ingebrigtsen, K. Zorn, M. R. Wilson, T. Blicharz, A. P. Wong, B. O’Donovan, B. Murray, S. Miller, and C. Y. Chiu. 2024. Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections. Nature Medicine 30:3522–3533.
Berkman, B. E., A. C. Mastroianni, L. Jamal, C. Solis, H. A. Taylor, and S. C. Hull. 2021. The ethics of repurposing previously collected research biospecimens in an infectious disease pandemic. Ethics of Human Research 43(2):2–18.
Blane, B., K. E. Raven, N. M. Brown, E. M. Harrison, F. Coll, R. Thaxter, D. A. Enoch, T. Gouliouris, D. Leek, S. T. Girgis, A. Akram, M. Matuszewska, P. Rhodes, J. Parkhill, and S. J. Peacock. 2024. Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions. Microbial Genomics 10(4).
Bradwell, K. R., J. T. Wooldridge, B. Amor, T. D. Bennett, A. Anand, C. Bremer, Y. J. Yoo, Z. Qian, S. G. Johnson, E. R. Pfaff, A. T. Girvin, A. Manna, E. A. Niehaus, S. S. Hong, X. T. Zhang, R. L. Zhu, M. Bissell, N. Qureshi, J. Saltz, M. A. Haendel, C. G. Chute, H. P. Lehmann, R. A. Moffitt, and N3C Consortium. 2022. Harmonizing units and values of quantitative data elements in a very large nationally pooled electronic health record (EHR) dataset. Journal of the American Medical Informatics Association 29(7):1172–1182.
Brannock, M. D., R. F. Chew, A. J. Preiss, E. C. Hadley, S. Redfield, J. A. McMurry, P. J. Leese, A. T. Girvin, M. Crosskey, A. G. Zhou, R. A. Moffitt, M. J. Funk, E. R. Pfaff, M. A. Haendel, C. G. Chute, N3C, and R. Consortia. 2023. Long COVID risk and pre-COVID vaccination in an EHR-based cohort study from the RECOVER program. Nature Communications 14(1):2914.
Burrough, E. R., D. R. Magstadt, B. Petersen, S. J. Timmermans, P. C. Gauger, J. Zhang, C. Siepker, M. Mainenti, G. Li, A. C. Thompson, P. J. Gorden, P. J. Plummer, and R. Main. 2024. Highly pathogenic avian influenza A (H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Emerging Infectious Diseases 30(7):1335–1343.
CDC (U.S. Centers for Disease Control and Prevention). 2024a. What Is Genomic Sequencing? https://www.cdc.gov/advanced-molecular-detection/about/what-is-genomic-sequencing.html (accessed January 24, 2025).
CDC. 2024b. Listeria Infection (Listeriosis). https://www.cdc.gov/listeria/about/index.html (accessed November 7, 2024).
CDC. 2024c. HAI and Antimicrobial Use Prevalence Surveys. https://www.cdc.gov/healthcareassociated-infections/php/haic-eip/antibiotic-use.html (accessed December 5, 2024).
Chandrakumar, I., N. P. G. Gauthier, C. Nelson, M. B. Bonsall, K. Locher, M. Charles, C. MacDonald, M. Krajden, A. R. Manges, and S. D. Chorlton. 2022. Bugsplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies. Communications Biology 5(1):151.
Chen, Z., A. S. Azman, X. Chen, J. Zou, Y. Tian, R. Sun, X. Xu, Y. Wu, W. Lu, S. Ge, Z. Zhao, J. Yang, D. T. Leung, D. B. Domman, and H. Yu. 2022. Global landscape of SARS-CoV-2 genomic surveillance and data sharing. Nature Genetics 54(4):499–507.
Connor, R., M. Shakya, D. A. Yarmosh, W. Maier, R. Martin, R. Bradford, J. R. Brister, P. S. G. Chain, C. A. Copeland, J. di Iulio, B. Hu, P. Ebert, J. Gunti, Y. Jin, K. S. Katz, A. Kochergin, T. LaRosa, J. Li, P. E. Li, C. C. Lo, S. Rashid, E. S. Maiorova, C. Xiao, V. Zalunin, L. Purcell, and K. D. Pruitt. 2024. Recommendations for uniform variant calling of SARS-CoV-2 genome sequence across bioinformatic workflows. Viruses 16(3).
Gatton, M. L., J. Dunn, A. Chaudhry, S. Ciketic, J. Cunningham, and Q. Cheng. 2017. Implications of parasites lacking Plasmodium falciparum histidine-rich protein 2 on malaria morbidity and control when rapid diagnostic tests are used for diagnosis. Journal of Infectious Diseases 215(7):1156–1166.
Gire, S. K., A. Goba, K. G. Andersen, R. S. Sealfon, D. J. Park, L. Kanneh, S. Jalloh, M. Momoh, M. Fullah, G. Dudas, S. Wohl, L. M. Moses, N. L. Yozwiak, S. Winnicki, C. B. Matranga, C. M. Malboeuf, J. Qu, A. D. Gladden, S. F. Schaffner, X. Yang, P. P. Jiang, M. Nekoui, A. Colubri, M. R. Coomber, M. Fonnie, A. Moigboi, M. Gbakie, F. K. Kamara, V. Tucker, E. Konuwa, S. Saffa, J. Sellu, A. A. Jalloh, A. Kovoma, J. Koninga,
I. Mustapha, K. Kargbo, M. Foday, M. Yillah, F. Kanneh, W. Robert, J. L. Massally, S. B. Chapman, J. Bochicchio, C. Murphy, C. Nusbaum, S. Young, B. W. Birren, D. S. Grant, J. S. Scheiffelin, E. S. Lander, C. Happi, S. M. Gevao, A. Gnirke, A. Rambaut, R. F. Garry, S. H. Khan, and P. C. Sabeti. 2014. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345(6202):1369-1372.
Griffiths, E. J., R. E. Timme, C. I. Mendes, A. J. Page, N. F. Alikhan, D. Fornika, F. Maguire, J. Campos, D. Park, I. B. Olawoye, P. E. Oluniyi, D. Anderson, A. Christoffels, A. G. da Silva, R. Cameron, D. Dooley, L. S. Katz, A. Black, I. Karsch-Mizrachi, T. Barrett, A. Johnston, T. R. Connor, S. M. Nicholls, A. A. Witney, G. H. Tyson, S. H. Tausch, A. R. Raphenya, B. Alcock, D. M. Aanensen, E. Hodcroft, W. W. L. Hsiao, A. T. R. Vasconcelos, and D. R. MacCannell. 2022. Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. Gigascience 11.
Grubaugh, N. D., S. Saraf, K. Gangavarapu, A. Watts, A. L. Tan, R. J. Oidtman, J. T. Ladner, G. Oliveira, N. L. Matteson, M. U. G. Kraemer, C. B. F. Vogels, A. Hentoff, D. Bhatia, D. Stanek, B. Scott, V. Landis, I. Stryker, M. R. Cone, E. W. t. Kopp, A. C. Cannons, L. Heberlein-Larson, S. White, L. D. Gillis, M. J. Ricciardi, J. Kwal, P. K. Lichtenberger, D. M. Magnani, D. I. Watkins, G. Palacios, D. H. Hamer, N. GeoSentinel Surveillance, L. M. Gardner, T. A. Perkins, G. Baele, K. Khan, A. Morrison, S. Isern, S. F. Michael, and K. G. Andersen. 2019. Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic. Cell 178(5):1057–1071, e1011.
Gu, W., X. Deng, M. Lee, Y. D. Sucu, S. Arevalo, D. Stryke, S. Federman, A. Gopez, K. Reyes, K. Zorn, H. Sample, G. Yu, G. Ishpuniani, B. Briggs, E. D. Chow, A. Berger, M. R. Wilson, C. Wang, E. Hsu, S. Miller, J. L. DeRisi, and C. Y. Chiu. 2021. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nature Medicine 27(1):115–124.
Hadley, E., Y. J. Yoo, S. Patel, A. Zhou, B. Laraway, R. Wong, A. Preiss, R. Chew, H. Davis, M. D. Brannock, C. G. Chute, E. R. Pfaff, J. Loomba, M. Haendel, E. Hill, N3C, RECOVER Consortia, and R. Moffitt. 2024. Insights from an N3C RECOVER EHR-based cohort study characterizing SARS-CoV-2 reinfections and long COVID. Communications Medicine (London) 4(1):129.
Haendel, M. A., C. G. Chute, T. D. Bennett, D. A. Eichmann, J. Guinney, W. A. Kibbe, P. R. O. Payne, E. R. Pfaff, P. N. Robinson, J. H. Saltz, H. Spratt, C. Suver, J. Wilbanks, A. B. Wilcox, A. E. Williams, C. Wu, C. Blacketer, R. L. Bradford, J. J. Cimino, M. Clark, E. W. Colmenares, P. A. Francis, D. Gabriel, A. Graves, R. Hemadri, S. S. Hong, G. Hripscak, D. Jiao, J. G. Klann, K. Kostka, A. M. Lee, H. P. Lehmann, L. Lingrey, R. T. Miller, M. Morris, S. N. Murphy, K. Natarajan, M. B. Palchuk, U. Sheikh, H. Solbrig, S. Visweswaran, A. Walden, K. M. Walters, G. M. Weber, X. T. Zhang, R. L. Zhu, B. Amor, A. T. Girvin, A. Manna, N. Qureshi, M. G. Kurilla, S. G. Michael, L. M. Portilla, J. L. Rutter, C. P. Austin, K. R. Gersing, and N. C. Consortium. 2021. The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. Journal of the American Medical Informatics Association 28(3):427–443.
Holmes, E. C., S. A. Goldstein, A. L. Rasmussen, D. L. Robertson, A. Crits-Christoph, J. O. Wertheim, S. J. Anthony, W. S. Barclay, M. F. Boni, P. C. Doherty, J. Farrar, J. L. Geoghegan, X. Jiang, J. L. Leibowitz, S. J. D. Neil, T. Skern, S. R. Weiss, M. Worobey, K. G. Andersen, R. F. Garry, and A. Rambaut. 2021. The origins of SARS-CoV-2: A critical review. Cell 184(19):4848–4856.
Jackson, B. R., C. Tarr, E. Strain, K. A. Jackson, A. Conrad, H. Carleton, L. S. Katz, S. Stroika, L. H. Gould, R. K. Mody, B. J. Silk, J. Beal, Y. Chen, R. Timme, M. Doyle, A. Fields, M. Wise, G. Tillman, S. Defibaugh-Chavez, Z. Kucerova, A. Sabol, K. Roache, E. Trees, M. Simmons, J. Wasilenko, K. Kubota, H. Pouseele, W. Klimke, J. Besser, E. Brown, M. Al-
lard, and P. Gerner-Smidt. 2016. Implementation of nationwide real-time whole-genome sequencing to enhance listeriosis outbreak detection and investigation. Clinical Infectious Diseases 63(3):380–386.
Kalantar, K. L., T. Carvalho, C. F. A. de Bourcy, B. Dimitrov, G. Dingle, R. Egger, J. Han, O. B. Holmes, Y. F. Juan, R. King, A. Kislyuk, M. F. Lin, M. Mariano, T. Morse, L. V. Reynoso, D. R. Cruz, J. Sheu, J. Tang, J. Wang, M. A. Zhang, E. Zhong, V. Ahyong, S. Lay, S. Chea, J. A. Bohl, J. E. Manning, C. M. Tato, and J. L. DeRisi. 2020. IDseq—an open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. Gigascience 9(10).
Karthikeyan, S., J. I. Levy, P. De Hoff, G. Humphrey, A. Birmingham, K. Jepsen, S. Farmer, H. M. Tubb, T. Valles, C. E. Tribelhorn, R. Tsai, S. Aigner, S. Sathe, N. Moshiri, B. Henson, A. M. Mark, A. Hakim, N. A. Baer, T. Barber, P. Belda-Ferre, M. Chacon, W. Cheung, E. S. Cresini, E. R. Eisner, A. L. Lastrella, E. S. Lawrence, C. A. Marotz, T. T. Ngo, T. Ostrander, A. Plascencia, R. A. Salido, P. Seaver, E. W. Smoot, D. McDonald, R. M. Neuhard, A. L. Scioscia, A. M. Satterlund, E. H. Simmons, D. B. Abelman, D. Brenner, J. C. Bruner, A. Buckley, M. Ellison, J. Gattas, S. L. Gonias, M. Hale, F. Hawkins, L. Ikeda, H. Jhaveri, T. Johnson, V. Kellen, B. Kremer, G. Matthews, R. W. McLawhon, P. Ouillet, D. Park, A. Pradenas, S. Reed, L. Riggs, A. Sanders, B. Sollenberger, A. Song, B. White, T. Winbush, C. M. Aceves, C. Anderson, K. Gangavarapu, E. Hufbauer, E. Kurzban, J. Lee, N. L. Matteson, E. Parker, S. A. Perkins, K. S. Ramesh, R. Robles-Sikisaka, M. A. Schwab, E. Spencer, S. Wohl, L. Nicholson, I. H. McHardy, D. P. Dimmock, C. A. Hobbs, O. Bakhtar, A. Harding, A. Mendoza, A. Bolze, D. Becker, E. T. Cirulli, M. Isaksson, K. M. Schiabor Barrett, N. L. Washington, J. D. Malone, A. M. Schafer, N. Gurfield, S. Stous, R. Fielding-Miller, R. S. Garfein, T. Gaines, C. Anderson, N. K. Martin, R. Schooley, B. Austin, D. R. MacCannell, S. F. Kingsmore, W. Lee, S. Shah, E. McDonald, A. T. Yu, M. Zeller, K. M. Fisch, C. Longhurst, P. Maysent, D. Pride, P. K. Khosla, L. C. Laurent, G. W. Yeo, K. G. Andersen, and R. Knight. 2022. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature 609(7925):101–108.
Karthikeyan, S., A. Nguyen, D. McDonald, Y. Zong, N. Ronquillo, J. Ren, J. Zou, S. Farmer, G. Humphrey, D. Henderson, T. Javidi, K. Messer, C. Anderson, R. Schooley, N. K. Martin, and R. Knight. 2021. Rapid, large-scale wastewater surveillance and automated reporting system enable early detection of nearly 85% of COVID-19 cases on a university campus. mSystems 6(4):e0079321.
Katz, K. S., O. Shutov, R. Lapoint, M. Kimelman, J. R. Brister, and C. O’Sullivan. 2021. STAT: A fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions. Genome Biology 22(1):270.
Lagerborg, K. A., E. Normandin, M. R. Bauer, G. Adams, K. Figueroa, C. Loreth, A. Gladden-Young, B. M. Shaw, L. R. Pearlman, D. Berenzy, H. B. Dewey, S. Kales, S. T. Dobbins, E. S. Shenoy, D. Hooper, V. M. Pierce, K. C. Zachary, D. J. Park, B. L. MacInnis, R. Tewhey, J. E. Lemieux, P. C. Sabeti, S. K. Reilly, and K. J. Siddle. 2022. Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows. Nature Microbiology 7(1):108–119.
Lehnertz, N. B., X. Wang, J. Garfin, J. Taylor, J. Zipprich, B. VonBank, K. Martin, D. Eikmeier, C. Medus, B. Wiedinmyer, C. Bernu, M. Plumb, K. Pung, M. A. Honein, R. Carter, D. MacCannell, K. E. Smith, K. Como-Sabetti, K. Ehresmann, R. Danila, and R. Lynfield. 2021. Transmission dynamics of severe acute respiratory syndrome coronavirus 2 in high-density settings, Minnesota, USA, March-June 2020. Emerging Infectious Diseases 27(8):2052–2063.
Lemieux, J. E., K. J. Siddle, B. M. Shaw, C. Loreth, S. F. Schaffner, A. Gladden-Young, G. Adams, T. Fink, C. H. Tomkins-Tinch, L. A. Krasilnikova, K. C. DeRuff, M. Rudy, M. R. Bauer, K. A. Lagerborg, E. Normandin, S. B. Chapman, S. K. Reilly, M. N. Anahtar, A.
E. Lin, A. Carter, C. Myhrvold, M. E. Kemball, S. Chaluvadi, C. Cusick, K. Flowers, A. Neumann, F. Cerrato, M. Farhat, D. Slater, J. B. Harris, J. A. Branda, D. Hooper, J. M. Gaeta, T. P. Baggett, J. O’Connell, A. Gnirke, T. D. Lieberman, A. Philippakis, M. Burns, C. M. Brown, J. Luban, E. T. Ryan, S. E. Turbett, R. C. LaRocque, W. P. Hanage, G. R. Gallagher, L. C. Madoff, S. Smole, V. M. Pierce, E. Rosenberg, P. C. Sabeti, D. J. Park, and B. L. MacInnis. 2020. Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science 371(6529).
Levy, J. I., K. G. Andersen, R. Knight, and S. Karthikeyan. 2023. Wastewater surveillance for public health. Science 379(6627):26–27.
Li, Z., X. Guan, N. Mao, H. Luo, Y. Qin, N. He, Z. Zhu, J. Yu, Y. Li, J. Liu, Z. An, W. Gao, X. Wang, X. Sun, T. Song, X. Yang, M. Wu, X. Wu, W. Yao, Z. Peng, J. Sun, L. Wang, Q. Guo, N. Xiang, J. Liu, B. Zhang, X. Su, L. Rodewald, L. Li, W. Xu, H. Shen, Z. Feng, and G. F. Gao. 2021. Antibody seroprevalence in the epicenter Wuhan, Hubei, and six selected provinces after containment of the first epidemic wave of COVID-19 in China. The Lancet Regional Health - Western Pacific 8:100094.
Libuit, K. G., J. Guthrie, F. Ambrosio, C. Kapsak, Gultekin Unal, J. Holmes, S. Wright, J. Nguinkal, E. Doughty, J. Southgate, C. O’Cathail, H. Carleton, L. Kingwara, W. Khan, K. Baker, A. Diallo, T. Connor, S. Kanwar, P. Maturure, S. James, I. Cuesta, V. Dyster, A. Gaskin, C. Williams, E. Smith, A. Rokney, A. Petkau, S. Varona, E. Gnimpieba, S. Rey, G. Macori, and G. Mboowa. 2024. Ten best practices for public health bioinformatics pipelines. https://github.com/pha4ge/public-health-pipeline-best-practices/blob/main/docs/pipeline-best-practices.md (accessed October 4, 2024).
Lu, J., N. Rincon, D. E. Wood, F. P. Breitwieser, C. Pockrandt, B. Langmead, S. L. Salzberg, and M. Steinegger. 2022. Metagenome analysis using the Kraken software suite. Nature Protocols 17(12):2815–2839.
Lytras, S., W. Xia, J. Hughes, X. Jiang, and D. L. Robertson. 2021. The animal origin of SARS-CoV-2. Science 373(6558):968–970.
Markin, A., S. Wagle, S. Grover, A. L. Vincent Baker, O. Eulenstein, and T. K. Anderson. 2023. Parnas: Objectively selecting the most representative taxa on a phylogeny. Systemic Biology 72(5):1052–1063.
Matteson, N. L., G. W. Hassler, E. Kurzban, M. A. Schwab, S. A. Perkins, K. Gangavarapu, J. I. Levy, E. Parker, D. Pride, A. Hakim, P. De Hoff, W. Cheung, A. Castro-Martinez, A. Rivera, A. Veder, A. Rivera, C. Wauer, J. Holmes, J. Wilson, S. N. Ngo, A. Plascencia, E. S. Lawrence, E. W. Smoot, E. R. Eisner, R. Tsai, M. Chacon, N. A. Baer, P. Seaver, R. A. Salido, S. Aigner, T. T. Ngo, T. Barber, T. Ostrander, R. Fielding-Miller, E. H. Simmons, O. E. Zazueta, I. Serafin-Higuera, M. Sanchez-Alavez, J. L. Moreno-Camacho, A. Garcia-Gil, A. R. Murphy Schafer, E. McDonald, J. Corrigan, J. D. Malone, S. Stous, S. Shah, N. Moshiri, A. Weiss, C. Anderson, C. M. Aceves, E. G. Spencer, E. C. Hufbauer, J. J. Lee, A. J. King, K. S. Ramesh, K. N. Nguyen, K. Saucedo, R. Robles-Sikisaka, K. M. Fisch, S. L. Gonias, A. Birmingham, D. McDonald, S. Karthikeyan, N. K. Martin, R. T. Schooley, A. J. Negrete, H. J. Reyna, J. R. Chavez, M. L. Garcia, J. M. Cornejo-Bravo, D. Becker, M. Isaksson, N. L. Washington, W. Lee, R. S. Garfein, M. A. Luna-Ruiz Esparza, J. Alcantar-Fernandez, B. Henson, K. Jepsen, B. Olivares-Flores, G. Barrera-Badillo, I. Lopez-Martinez, J. E. Ramirez-Gonzalez, R. Flores-Leon, S. F. Kingsmore, A. Sanders, A. Pradenas, B. White, G. Matthews, M. Hale, R. W. McLawhon, S. L. Reed, T. Winbush, I. H. McHardy, R. A. Fielding, L. Nicholson, M. M. Quigley, A. Harding, A. Mendoza, O. Bakhtar, S. H. Browne, J. Olivas Flores, D. G. Rincon Rodriguez, M. Gonzalez Ibarra, L. C. Robles Ibarra, B. J. Arellano Vera, J. Gonzalez Garcia, A. Harvey-Vera, R. Knight, L. C. Laurent, G. W. Yeo, J. O. Wertheim, X. Ji, M. Worobey, M. A. Suchard, K. G. Andersen, A. Campos-Romero, S. Wohl, and M. Zeller. 2023. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell 186(26):5690–5704, e5620.
Metsky, H. C., N. L. Welch, P. P. Pillai, N. J. Haradhvala, L. Rumker, S. Mantena, Y. B. Zhang, D. K. Yang, C. M. Ackerman, J. Weller, P. C. Blainey, C. Myhrvold, M. Mitzenmacher, and P. C. Sabeti. 2022. Designing sensitive viral diagnostics with machine learning. Nature Biotechnology 40(7):1123–1131.
Mielke, L. 2024. Eyes are focused on an illness affecting milk output in dairy cows in the Texas Panhandle. Farmers’ Advance. https://www.farmersadvance.com/story/news/2024/03/25/illness-is-affecting-milk-output-in-dairy-cows-in-the-texas-panhandle/73092627007/ (accessed September 25, 2024).
Miller, S., S. N. Naccache, E. Samayoa, K. Messacar, S. Arevalo, S. Federman, D. Stryke, E. Pham, B. Fung, W. J. Bolosky, D. Ingebrigtsen, W. Lorizio, S. M. Paff, J. A. Leake, R. Pesano, R. DeBiasi, S. Dominguez, and C. Y. Chiu. 2019. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Research 29(5):831–842.
Mukhwana, A., S. Oluwaseyi, D.-F. Ndlovu, and J. Osaso. 2024. Slow, difficult and expensive: How the lab supplies market is crippling African science. Nature Index. https://www.nature.com/nature-index/news/slow-difficult-expensive-how-lab-supplies-market-crippling-african-science (accessed October 11, 2024).
Naccache, S. N., S. Federman, N. Veeraraghavan, M. Zaharia, D. Lee, E. Samayoa, J. Bouquet, A. L. Greninger, K. C. Luk, B. Enge, D. A. Wadford, S. L. Messenger, G. L. Genrich, K. Pellegrino, G. Grard, E. Leroy, B. S. Schneider, J. N. Fair, M. A. Martinez, P. Isa, J. A. Crump, J. L. DeRisi, T. Sittler, J. Hackett, Jr., S. Miller, and C. Y. Chiu. 2014. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Research 24(7):1180–1192.
National Human Genome Research Institute. 2023. DNA sequencing costs: Data. https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data (accessed September 10, 2024).
NCBI (National Center for Biotechnology Information). 2024. New Milestone! NCBI Pathogen Detection Reaches 2 Million Isolates. https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/03/milestone-ncbi-pathogen-detection-2m-isolates/ (accessed November 12, 2024).
Nguyen, T.-Q., C. Hutter, A. Markin, M. Thomas, K. Lantz, M. L. Killian, G. M. Janzen, S. Vijendran, S. Wagle, B. Inderski, D. R. Magstadt, G. Li, D. G. Diel, E. A. Frye, K. M. Dimitrov, A. K. Swinford, A. C. Thompson, K. R. Snevik, D. L. Suarez, E. Spackman, S. M. Lakin, S. C. Ahola, K. R. Johnson, A. L. Baker, S. Robbe-Austerman, M. K. Torchetti, and T. K. Anderson. 2024. Emergence and interstate spread of highly pathogenic avian influenza A (H5N1) in dairy cattle—preprint. https://doi.org/10.1101/2024.05.01.591751.
NLM (National Library of Medicine). 2024a. MicroBIGG-E Map. https://www.ncbi.nlm.nih.gov/pathogens/microbigge_map/ (accessed September 30, 2024).
NLM. 2024b. Pathogen Detection. https://www.ncbi.nlm.nih.gov/pathogens/ (accessed September 28, 2024).
O’Toole, A., R. A. Neher, N. Ndodo, V. Borges, B. Gannon, J. P. Gomes, N. Groves, D. J. King, D. Maloney, P. Lemey, K. Lewandowski, N. Loman, R. Myers, I. F. Omah, M. A. Suchard, M. Worobey, M. Chand, C. Ihekweazu, D. Ulaeto, I. Adetifa, and A. Rambaut. 2023. APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016. Science 382(6670):595–600.
Pekar, J. E., A. Magee, E. Parker, N. Moshiri, K. Izhikevich, J. L. Havens, K. Gangavarapu, L. M. Malpica Serrano, A. Crits-Christoph, N. L. Matteson, M. Zeller, J. I. Levy, J. C. Wang, S. Hughes, J. Lee, H. Park, M. S. Park, K. Ching Zi Yan, R. T. P. Lin, M. N. Mat Isa, Y. M. Noor, T. I. Vasylyeva, R. F. Garry, E. C. Holmes, A. Rambaut, M. A. Suchard, K. G. Andersen, M. Worobey, and J. O. Wertheim. 2022. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science 377(6609):960–966.
Pfaff, E. R., A. T. Girvin, T. D. Bennett, A. Bhatia, I. M. Brooks, R. R. Deer, J. P. Dekermanjian, S. E. Jolley, M. G. Kahn, K. Kostka, J. A. McMurry, R. Moffitt, A. Walden, C. G. Chute, M. A. Haendel, and N. C. Consortium. 2022a. Identifying who has long COVID in the USA: A machine learning approach using N3C data. The Lancet Digital Health 4(7):e532–e541.
Pfaff, E. R., A. T. Girvin, D. L. Gabriel, K. Kostka, M. Morris, M. B. Palchuk, H. P. Lehmann, B. Amor, M. Bissell, K. R. Bradwell, S. Gold, S. S. Hong, J. Loomba, A. Manna, J. A. McMurry, E. Niehaus, N. Qureshi, A. Walden, X. T. Zhang, R. L. Zhu, R. A. Moffitt, M. A. Haendel, C. G. Chute, N. C. Consortium, W. G. Adams, S. Al-Shukri, A. Anzalone, A. Baghal, T. D. Bennett, E. V. Bernstam, E. V. Bernstam, M. M. Bissell, B. Bush, T. R. Campion, V. Castro, J. Chang, D. D. Chaudhari, W. Chen, S. Chu, J. J. Cimino, K. A. Crandall, M. Crooks, S. J. D. Davies, J. DiPalazzo, D. Dorr, D. Eckrich, S. E. Eltinge, D. G. Fort, G. Golovko, S. Gupta, M. A. Haendel, J. G. Hajagos, D. A. Hanauer, B. M. Harnett, R. Horswell, N. Huang, S. G. Johnson, M. Kahn, K. Khanipov, C. Kieler, K. R. Luzuriaga, S. Maidlow, A. Martinez, J. Mathew, J. C. McClay, G. McMahan, B. Melancon, S. Meystre, L. Miele, H. Morizono, R. Pablo, L. Patel, J. Phuong, D. J. Popham, C. Pulgarin, C. Santos, I. N. Sarkar, N. Sazo, S. Setoguchi, S. Soby, S. Surampalli, C. Suver, U. M. R. Vangala, S. Visweswaran, J. V. Oehsen, K. M. Walters, L. Wiley, D. A. Williams, and A. Zai. 2022b. Synergies between centralized and federated approaches to data quality: A report from the National COVID Cohort Collaborative. Journal of the American Medical Informatics Association 29(4):609–618.
Preiss, A., A. Bhatia, L. V. Aragon, J. M. Baratta, M. Baskaran, F. Blancero, M. D. Brannock, R. F. Chew, I. Diaz, M. Fitzgerald, E. P. Kelly, A. G. Zhou, T. W. Carton, C. G. Chute, M. Haendel, R. Moffitt, E. Pfaff, N3C, and RECOVER. 2024. Effect of Paxlovid treatment during acute COVID-19 on long COVID onset: An EHR-based target trial emulation from the N3C and RECOVER Consortia. medRxiv.
Rounds, J. M., A. J. Taylor, D. Eikmeier, M. M. Nichols, V. Lappi, S. E. Wirth, D. J. Boxrud, K. E. Smith, and C. Medus. 2020. Prospective Salmonella Enteritidis surveillance and outbreak detection using whole genome sequencing, Minnesota, 2015–2017. Epidemio-logic Infections 148:e254.
Scallan, E., P. M. Griffin, F. J. Angulo, R. V. Tauxe, and R. M. Hoekstra. 2011. Foodborne illness acquired in the United States—unspecified agents. Emerging Infectious Diseases 17(1):16–22.
Servellita, V., A. Sotomayor Gonzalez, D. M. Lamson, A. Foresythe, H. J. Huh, A. L. Bazinet, N. H. Bergman, R. L. Bull, K. Y. Garcia, J. S. Goodrich, S. P. Lovett, K. Parker, D. Radune, A. Hatada, C. Y. Pan, K. Rizzo, J. B. Bertumen, C. Morales, P. E. Oluniyi, J. Nguyen, J. Tan, D. Stryke, R. Jaber, M. T. Leslie, Z. Lyons, H. D. Hedman, U. Parashar, M. Sullivan, K. Wroblewski, M. S. Oberste, J. E. Tate, J. M. Baker, D. Sugerman, C. Potts, X. Lu, P. Chhabra, Pediatric Hepatitis of Unknown Etiology Working Group, L. A. Ingram, H. Shiau, W. Britt, L. H. Gutierrez Sanchez, C. Ciric, C. A. Rostad, J. Vinje, H. L. Kirking, D. A. Wadford, R. T. Raborn, K. St George, and C. Y. Chiu. 2023. Adeno-associated virus type 2 in US children with acute severe hepatitis. Nature 617(7961):574–580.
Shafer, M. M., M. J. Bobholz, W. C. Vuyk, D. A. Gregory, A. Roguet, L. A. Haddock Soto, C. Rushford, K. H. Janssen, I. E. Emmen, H. J. Ries, H. E. Pilch, P. A. Mullen, R. B. Fahney, W. Wei, M. Lambert, J. Wenzel, P. Halfmann, Y. Kawaoka, N. A. Wilson, T. C. Friedrich, I. W. Pray, R. Westergaard, D. H. O’Connor, and M. C. Johnson. 2024. Tracing the origin of SARS-CoV-2 Omicron-like spike sequences detected in an urban sewershed: A targeted, longitudinal surveillance study of a cryptic wastewater lineage. Lancet Microbe 5(4):e335–e344.
Sheikhzadeh, C. H. S., L. Gonzalez-barranca, A. M. Adams, O. Ott, S. Karthikeyan, L. Marotz, and G. Humphrey. 2021. High-throughput wastewater SARS-CoV2 detection pipeline. dx.doi.org/10.17504/protocols.io.bshvnb66 (accessed September 24, 2024).
Smith, D. J., J. A. W. Gold, T. Chiller, N. D. Bustamante, M. J. Marinissen, G. G. Rodriquez, V. B. G. Cortes, C. D. Molina, S. Williams, A. A. Vazquez Deida, K. Byrd, P. G. Pappas, T. F. Patterson, N. P. Wiederhold, G. R. Thompson III, L. Ostrosky-Zeichner, and Fungal Meningitis Response Team. 2024. Update on outbreak of fungal meningitis among US residents who received epidural anesthesia at two clinics in Matamoros, Mexico. Clinical Infectious Diseases 78(6):1554–1558.
Smith, D. J., S. Williams, A. P. Litvintseva, N. D. Bustamante, L. Ostrosky-Zeichner, S. God-win, J. C. Pearson, J. Rivas, N. Evert, T. Dang, A. Guevara, L. Koenecke, T. M. Chiller, and J. A. W. Gold. 2023. Outbreak of fungal meningitis in US patients who received surgical procedures under epidural anesthesia in Matamoros, Mexico. Open Forum Infectious Diseases 10(Supplement_2).
Stevens, E. L., H. A. Carleton, J. Beal, G. E. Tillman, R. L. Lindsey, A. C. Lauer, A. Pightling, K. G. Jarvis, A. Ottesen, P. Ramachandran, L. Hintz, L. S. Katz, J. P. Folster, J. M. Whichard, E. Trees, R. E. Timme, D. P. Mc, B. Wolpert, M. Bazaco, S. Zhao, S. Lindley, B. B. Bruce, P. M. Griffin, E. Brown, M. Allard, S. Tallent, K. Irvin, M. Hoffmann, M. Wise, R. Tauxe, P. Gerner-Smidt, M. Simmons, B. Kissler, S. Defibaugh-Chavez, W. Klimke, R. Agarwala, J. Lindsay, K. Cook, S. R. Austerman, D. Goldman, S. McGarry, K. R. Hale, U. Dessai, S. M. Musser, and C. Braden. 2022. Use of whole genome sequencing by the federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States. Journal of Food Protection 85(5):755–772.
Tabak, L. 2022. Using AI to advance understanding of long COVID syndrome. https://directorsblog.nih.gov/tag/national-covid-cohort-collaborative/ (accessed September 30, 2024).
Timme, R. E., I. Karsch-Mizrachi, Z. Waheed, M. Arita, D. MacCannell, F. Maguire, R. Petit III, A. J. Page, C. I. Mendes, M. I. Nasar, P. Oluniyi, A. D. Tyler, A. R. Raphenya, J. L. Guthrie, I. Olawoye, G. Rinck, C. O’Cathail, J. Lees, G. Cochrane, C. Cummins, J. R. Brister, W. Klimke, M. Feldgarden, and E. Griffiths. 2023. Putting everything in its place: Using the INSDC compliant pathogen data object model to better structure genomic data submitted for public health applications. Microbial Genomics 9(12).
United Nations Conference of the Parties. 2022. Decision adopted by the Conference of the Parties to the Convention on Biological Diversity. https://www.cbd.int/decisions/cop?m=cop-15 (accessed October 8, 2024).
Washington, N. L., K. Gangavarapu, M. Zeller, A. Bolze, E. T. Cirulli, K. M. Schiabor Barrett, B. B. Larsen, C. Anderson, S. White, T. Cassens, S. Jacobs, G. Levan, J. Nguyen, J. M. Ramirez III, C. Rivera-Garcia, E. Sandoval, X. Wang, D. Wong, E. Spencer, R. Robles-Sikisaka, E. Kurzban, L. D. Hughes, X. Deng, C. Wang, V. Servellita, H. Valentine, P. De Hoff, P. Seaver, S. Sathe, K. Gietzen, B. Sickler, J. Antico, K. Hoon, J. Liu, A. Harding, O. Bakhtar, T. Basler, B. Austin, D. MacCannell, M. Isaksson, P. G. Febbo, D. Becker, M. Laurent, E. McDonald, G. W. Yeo, R. Knight, L. C. Laurent, E. de Feo, M. Worobey, C. Y. Chiu, M. A. Suchard, J. T. Lu, W. Lee, and K. G. Andersen. 2021. Emergence and rapid transmission of SARS-CoV-2 b.1.1.7 in the United States. Cell 184(10):2587–2594, e2587.
Welch, N. L., M. Zhu, C. Hua, J. Weller, M. E. Mirhashemi, T. G. Nguyen, S. Mantena, M. R. Bauer, B. M. Shaw, C. M. Ackerman, S. G. Thakku, M. W. Tse, J. Kehe, M. M. Uwera, J. S. Eversley, D. A. Bielwaski, G. McGrath, J. Braidt, J. Johnson, F. Cerrato, G. K. Moreno, L. A. Krasilnikova, B. A. Petros, G. L. Gionet, E. King, R. C. Huard, S. K. Jalbert, M. L. Cleary, N. A. Fitzgerald, S. B. Gabriel, G. R. Gallagher, S. C. Smole, L. C. Madoff, C. M. Brown, M. W. Keller, M. M. Wilson, M. K. Kirby, J. R. Barnes, D. J. Park, K. J. Siddle, C. T. Happi, D. T. Hung, M. Springer, B. L. MacInnis, J. E. Lemieux, E. Rosenberg, J.
A. Branda, P. C. Blainey, P. C. Sabeti, and C. Myhrvold. 2022. Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nature Medicine 28(5):1083–1094.
WHO (World Health Organization). 2011. Pandemic influenza preparedness framework for the sharing of influenza viruses and access to vaccines and other benefits. Geneva: World Health Organization.
WHO. 2017. WHO guidelines on ethical issues in public health surveillance. Geneva: World Health Organization.
WHO. 2020. GLASS whole-genome sequencing for surveillance of antimicrobial resistance. Geneva: World Health Organization.
WHO. 2022. Global genomic surveillance strategy for pathogens with pandemic and epidemic potential, 2022–2032. Geneva: World Health Organization.
WHO. 2023. International Pathogen Surveillance Network. https://www.who.int/initiatives/international-pathogen-surveillance-network (accessed October 26, 2024).
WHO Health Emergencies Programme. 2023. Defining collaborative surveillance: A core concept for strengthening the global architecture for health emergency preparedness, response, and resilience. Geneva: World Health Organization.
Wilson, M. R., H. A. Sample, K. C. Zorn, S. Arevalo, G. Yu, J. Neuhaus, S. Federman, D. Stryke, B. Briggs, C. Langelier, A. Berger, V. Douglas, S. A. Josephson, F. C. Chow, B. D. Fulton, J. L. DeRisi, J. M. Gelfand, S. N. Naccache, J. Bender, J. Dien Bard, J. Murkey, M. Carlson, P. M. Vespa, T. Vijayan, P. R. Allyn, S. Campeau, R. M. Humphries, J. D. Klausner, C. D. Ganzon, F. Memar, N. A. Ocampo, L. L. Zimmermann, S. H. Cohen, C. R. Polage, R. L. DeBiasi, B. Haller, R. Dallas, G. Maron, R. Hayden, K. Messacar, S. R. Dominguez, S. Miller, and C. Y. Chiu. 2019. Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis. New England Journal of Medicine 380(24):2327–2340.
Wohl, S., H. C. Metsky, S. F. Schaffner, A. Piantadosi, M. Burns, J. A. Lewnard, B. Chak, L. A. Krasilnikova, K. J. Siddle, C. B. Matranga, B. Bankamp, S. Hennigan, B. Sabina, E. H. Byrne, R. J. McNall, R. R. Shah, J. Qu, D. J. Park, S. Gharib, S. Fitzgerald, P. Barreira, S. Fleming, S. Lett, P. A. Rota, L. C. Madoff, N. L. Yozwiak, B. L. MacInnis, S. Smole, Y. H. Grad, and P. C. Sabeti. 2020. Combining genomics and epidemiology to track mumps virus transmission in the United States. PLoS Biology 18(2):e3000611.
Worobey, M. 2021. Dissecting the early COVID-19 cases in Wuhan. Science 374(6572):1202–1204.
Worobey, M., J. I. Levy, L. Malpica Serrano, A. Crits-Christoph, J. E. Pekar, S. A. Goldstein, A. L. Rasmussen, M. U. G. Kraemer, C. Newman, M. P. G. Koopmans, M. A. Suchard, J. O. Wertheim, P. Lemey, D. L. Robertson, R. F. Garry, E. C. Holmes, A. Rambaut, and K. G. Andersen. 2022. The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science 377(6609):951–959.
Yousif, M., S. Rachida, S. Taukobong, N. Ndlovu, C. Iwu-Jaja, W. Howard, S. Moonsamy, N. Mhlambi, S. Gwala, J. I. Levy, K. G. Andersen, C. Scheepers, A. von Gottberg, N. Wolter, J. N. Bhiman, D. G. Amoako, A. Ismail, M. Suchard, and K. McCarthy. 2023. SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses. Nature Communications 14(1):6325.
Yurkovetskiy, L., X. Wang, K. E. Pascal, C. Tomkins-Tinch, T. P. Nyalile, Y. Wang, A. Baum, W. E. Diehl, A. Dauphin, C. Carbone, K. Veinotte, S. B. Egri, S. F. Schaffner, J. E. Lemieux, J. B. Munro, A. Rafique, A. Barve, P. C. Sabeti, C. A. Kyratsous, N. V. Dudkina, K. Shen, and J. Luban. 2020. Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant. Cell 183(3):739–751, e738.
This page intentionally left blank.