Volume 30, Supplement—October 2024
SUPPLEMENT ISSUE
Articles
Next-Generation Sequencing and Bioinformatics Consortium Approach to Genomic Surveillance
Figure
References
- The White House. Addressing the threat of emerging infectious diseases [cited 2024 Mar 21]. https://clintonwhitehouse4.archives.gov/WH/EOP/OSTP/Security/html/whfactsht.html
- Rothberg JM, Leamon JH. The development and impact of 454 sequencing. Nat Biotechnol. 2008;26:1117–24. DOIPubMedGoogle Scholar
- Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, et al. Next generation sequencing and bioinformatics methodologies for infectious disease research and public health: approaches, applications, and considerations for development of laboratory capacity. J Infect Dis. 2020;221(Suppl 3):S292–307.PubMedGoogle Scholar
- Frey KG, Herrera-Galeano JE, Redden CL, Luu TV, Servetas SL, Mateczun AJ, et al. Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood. BMC Genomics. 2014;15:96. DOIPubMedGoogle Scholar
- Diao Z, Han D, Zhang R, Li J. Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections. J Adv Res. 2021;38:201–12. DOIPubMedGoogle Scholar
- Simmonds P, Adams MJ, Benkő M, Breitbart M, Brister JR, Carstens EB, et al. Consensus statement: Virus taxonomy in the age of metagenomics. Nat Rev Microbiol. 2017;15:161–8. DOIPubMedGoogle Scholar
- Bennett AJ, Paskey AC, Ebinger A, Pfaff F, Priemer G, Höper D, et al. Relatives of rubella virus in diverse mammals. Nature. 2020;586:424–8. DOIPubMedGoogle Scholar
- Fries AC, Gruner W, Hanson J. Sampling considerations for detecting genetic diversity of influenza viruses in the DoD Global Respiratory Pathogen Surveillance Program. MSMR. 2018;25:16–21.PubMedGoogle Scholar
- Lesho E, Clifford R, Onmus-Leone F, Appalla L, Snesrud E, Kwak Y, et al. The challenges of implementing next generation sequencing across a large healthcare system, and the molecular epidemiology and antibiotic susceptibilities of carbapenemase-producing bacteria in the healthcare system of the U.S. Department of Defense. PLoS One. 2016;11:
e0155770 . DOIPubMedGoogle Scholar - Lesho EP, Waterman PE, Chukwuma U, McAuliffe K, Neumann C, Julius MD, et al. The antimicrobial resistance monitoring and research (ARMoR) program: the US Department of Defense response to escalating antimicrobial resistance. Clin Infect Dis. 2014;59:390–7. DOIPubMedGoogle Scholar
- US Department of Defense. Fiscal year (FY) 2019 budget estimates [cited 2024 Jan 12]. https://comptroller.defense.gov/Portals/45/Documents/defbudget/fy2019/budget_justification/pdfs/02_Procurement/01_CBDP_FY19_PB-Procurement_Exhibits.pdf
- US Department of Defense. DOD INSTRUCTION 6000.11 PATIENT MOVEMENT (PM). 2018 [cited 2024 Feb 27]. https://www.esd.whs.mil/Portals/54/Documents/DD/issuances/dodi/600011p.pdf?ver=2018-06-29-125141-720
- Illumina. Illumina sequencing platforms [cited 2024 Feb 25]. https://www.illumina.com/systems/sequencing-platforms.html
- Nanopore Technologies. Sequencing devices [cited 2024 Feb 25]. https://nanoporetech.com/products/sequence
- Maljkovic Berry I, Rutvisuttinunt W, Voegtly LJ, Prieto K, Pollett S, Cer RZ, et al. A Department of Defense Laboratory Consortium approach to next generation sequencing and bioinformatics training for infectious disease surveillance in Kenya. Front Genet. 2020;11:
577563 . DOIPubMedGoogle Scholar - Velasco JM, Navarro FC, Diones PC, Villa V, Valderama MT, Tabinas H, et al. SARS-CoV-2 among military and civilian patients, metro Manila, Philippines. Mil Med. 2021;186:e760–6. DOIPubMedGoogle Scholar
- US Department of Defense. SARS-CoV-2 whole genome sequencing action plan for the Department of Defense Military Health System [cited 2024 Feb 27]. https://carepoint.health.mil/sites/AFHSB/geis/programmatics/ngsbc/SC2WGS/Documents/(CATMS1)%20TAB%20B%20-%20SARS-CoV-2%20WGS%20Expansion%20Action%20Plan%20-%20UPR002841-21.pdf
- Morton L, Forshey B, Bishop-Lilly K, Cer R, Fries A, Bogue A, et al. Establishment of SARS-CoV-2 genomic surveillance within the Military Health System during 1 March-31 December 2020. MSMR. 2022;29:11–8.PubMedGoogle Scholar
- Waitumbi JN, Omuseni E, Nyataya J, Masakhwe C, Sigei F, Lemtudo A, et al. COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya. Afr J Lab Med. 2022;11:1737. DOIPubMedGoogle Scholar
- Kimita G, Nyataya J, Omuseni E, Sigei F, Lemtudo A, Muthanje E, et al. Temporal lineage replacements and dominance of imported variants of concern during the COVID-19 pandemic in Kenya. Commun Med (Lond). 2022;2:103. DOIPubMedGoogle Scholar
- Larson D, Brodniak SL, Voegtly LJ, Cer RZ, Glang LA, Malagon FJ, et al. A case of early reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Clin Infect Dis. 2021;73:e2827–8. DOIPubMedGoogle Scholar
- Thommana A, Shakya M, Gandhi J, Fung CK, Chain PSG, Maljkovic Berry I, et al. Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns. Viruses. 2022;14:2128. DOIPubMedGoogle Scholar
- Lizewski RA, Sealfon RSG, Park SW, Smith GR, Porter CK, Gonzalez-Reiche AS, et al. SARS-CoV-2 outbreak dynamics in an isolated US military recruit training center with rigorous prevention measures. Epidemiology. 2022;33:797–807. DOIPubMedGoogle Scholar
- Hakre S, Maljkovic-Berry I, Hang J, Conte MA, Pollio AR, Fung CK, et al. Transmission of SARS-CoV-2 among recruits in a US Army training environment: a brief report. J Public Health (Oxf). 2023;45:748–52. DOIPubMedGoogle Scholar
- Cer RZ, Voegtly LJ, Adhikari BN, Pike BL, Lueder MR, Glang LA, et al. Genomic and virologic characterization of samples from a shipboard outbreak of COVID-19 reveals distinct variants within limited temporospatial parameters. Front Microbiol. 2022;13:
960932 . DOIPubMedGoogle Scholar - Maljkovic Berry I, Hang J, Fung C, Yang Y, Chibucos M, Pollio A, et al. Genomic surveillance of SARS-CoV-2 in US military compounds in Afghanistan reveals multiple introductions and outbreaks of Alpha and Delta variants. BMC Genomics. 2022;23:513. DOIPubMedGoogle Scholar
- Hakre S, Lam EY, Maljkovic-Berry I, Hang J, Pow Sang LA, Bianchi EJ, et al. Investigation of an outbreak of COVID-19 among U.S. military personnel and beneficiaries stationed in the Republic of Korea, June-July 2021. PLOS Glob Public Health. 2022;2:
e0000236 . DOIPubMedGoogle Scholar - Arnold CE, Voegtly LJ, Stefanov EK, Lueder MR, Luquette AE, Miller RH, et al. SARS-CoV-2 infections in vaccinated and unvaccinated populations in Camp Lemonnier, Djibouti, from April 2020 to January 2022. Viruses. 2022;14:1918. DOIPubMedGoogle Scholar
- Servies TE, Larsen EC, Lindsay RC, Jones JS, Cer RZ, Voegtly LJ, et al. Notes from the field: outbreak of COVID-19 among a highly vaccinated population aboard a U.S. Navy ship after a port visit—Reykjavik, Iceland, July 2021. MMWR Morb Mortal Wkly Rep. 2022;71:279–81. DOIPubMedGoogle Scholar
- Smith DR, Singh C, Green J, Lueder MR, Arnold CE, Voegtly LJ, et al. Genomic and virological characterization of SARS-CoV-2 variants in a subset of unvaccinated and vaccinated U.S. military personnel. Front Med (Lausanne). 2022;8:
836658 . DOIPubMedGoogle Scholar - US Department of Defense. 2023 Biodefense posture review [cited 2024 Feb 27]. https://media.defense.gov/2023/Aug/17/2003282337/-1/-1/1/2023_BIODEFENSE_POSTURE_REVIEW.PDF
- Morton L, Creppage K, Rahman N, Early J, Hartman L, Hydrick A, et al. Challenges and opportunities in pathogen agnostic sequencing for public health surveillance: lessons learned from the global emerging infections surveillance program. Health Secur. 2023.PubMedGoogle Scholar
- Boddie C, Watson M, Sell TK. Federal funding for health security in FY2017. Health Secur. 2016;14:284–304. DOIPubMedGoogle Scholar
1These authors contributed equally to this article.
Page created: October 30, 2024
Page updated: November 11, 2024
Page reviewed: November 11, 2024
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.