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Volume 30, Supplement—October 2024
SUPPLEMENT ISSUE
Articles

Next-Generation Sequencing and Bioinformatics Consortium Approach to Genomic Surveillance

Lindsay C. Morton1Comments to Author , Nazia Rahman1, and Kimberly A. Bishop-Lilly1
Author affiliation: Cherokee Nation Strategic Programs, Tulsa, Oklahoma, USA (L.C. Morton, N. Rahman); Global Emerging Infections Surveillance Branch, Silver Spring, Maryland, USA (L.C. Morton, N. Rahman); Naval Medical Research Command Biological Defense Research Directorate, Fort Detrick, Maryland, USA (K.A. Bishop-Lilly)

Main Article

Figure

Tiered sequencing and bioinformatics capabilities for genomic surveillance within the US DoD. Modified from (15). DoD, Department of Defense; GEIS, Global Emerging Infections Surveillance.

Figure. Tiered sequencing and bioinformatics capabilities for genomic surveillance within the US DoD. Modified from (15). DoD, Department of Defense; GEIS, Global Emerging Infections Surveillance.

Main Article

References
  1. 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
  2. Rothberg  JM, Leamon  JH. The development and impact of 454 sequencing. Nat Biotechnol. 2008;26:111724. DOIPubMedGoogle Scholar
  3. 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):S292307.PubMedGoogle Scholar
  4. 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
  5. 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;38:20112. DOIPubMedGoogle Scholar
  6. 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;15:1618. DOIPubMedGoogle Scholar
  7. Bennett  AJ, Paskey  AC, Ebinger  A, Pfaff  F, Priemer  G, Höper  D, et al. Relatives of rubella virus in diverse mammals. Nature. 2020;586:4248. DOIPubMedGoogle Scholar
  8. 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;25:1621.PubMedGoogle Scholar
  9. 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
  10. 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;59:3907. DOIPubMedGoogle Scholar
  11. 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
  12. Illumina. Illumina sequencing platforms [cited 2024 Feb 25]. https://www.illumina.com/systems/sequencing-platforms.html
  13. Nanopore Technologies. Sequencing devices [cited 2024 Feb 25]. https://nanoporetech.com/products/sequence
  14. 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
  15. 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:e7606. DOIPubMedGoogle Scholar
  16. 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
  17. 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;29:118.PubMedGoogle Scholar
  18. 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
  19. 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
  20. 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:e28278. DOIPubMedGoogle Scholar
  21. 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
  22. 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;33:797807. DOIPubMedGoogle Scholar
  23. 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;45:74852. DOIPubMedGoogle Scholar
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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;71:27981. DOIPubMedGoogle Scholar
  29. 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
  30. 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
  31. 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
  32. Boddie  C, Watson  M, Sell  TK. Federal funding for health security in FY2017. Health Secur. 2016;14:284304. DOIPubMedGoogle Scholar

Main Article

1These authors contributed equally to this article.

Page created: October 30, 2024
Page updated: November 11, 2024
Page reviewed: November 11, 2024
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