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CPHST Beltsville Laboratory

CPHST Beltsville Lab, Beltsville, MD

Location: BARC-East, Bldg. 580, Powder Mill Rd., Beltsville, MD
Phone: (301) 313-9200
Fax: (301) 313-9232
Contact:Mark Nakhla

The CPHST Beltsville Laboratory mission is to develop, adapt, validate, and implement advanced biochemical and molecular methods for the detection of high consequence plant pathogens, including the APHIS Select Agents and plant pathogens in foreign germplasm. The CPHST Beltsville Laboratory is committed to quality in biochemical and molecular diagnostics and is the only Federal Plant Pathology ISO/IEC 17025:2005 accredited laboratory that conducts operational diagnostics for plant pathogens of regulatory concern. The laboratory routinely tests for Citrus Huanglongbing (HLB) aka Citrus Greening, Phytophthora ramorum, Plum Pox virus and Citrus Canker (Xanthomonas axonopodis pv. citri); molecular confirmation/identification of other plant pathogens of concern is also conducted.
Laboratory programs use cutting-edge technologies from the fields of plant pathology, molecular biology, human and animal clinical diagnostics, and bio-detection to develop, adapt, and improve methods for accurate and rapid diagnosis of plant pathogens. The laboratory uses these methods to diagnose and differentiate high consequence and select agent plant pathogens that require federal confirmation. The Beltsville Laboratory strives to achieve timely transfer of diagnostic tools that are field deployable for PPQ emergency response and eradication programs, as well as the Cooperative Agricultural Pest Survey (CAPS) program. Tools are deployed to stakeholders through clear-written standard operating procedures and hands-on laboratory training for end users within and outside of PPQ.

The laboratory is also a key component of the PPQ National Plant Protection Laboratory Accreditation Program (NPPLAP). Beltsville Laboratory is responsible for proficiency test panel development, validation, and delivery to laboratories who perform diagnostics on behalf of PPQ using CPHST-validated methods. The laboratory is also provider of validated diagnostic controls to the National Plant Diagnostic Network (NPDN). Beltsville staff routinely conducts outreach to the plant pathology diagnostic community by providing technical support to scientists within the NPDN, PPQ port and regional identifiers, and state departments of agriculture in the detection of regulatory plant pathogens by providing protocols, hands-on laboratory training, and troubleshooting for PPQ validated diagnostics. Beltsville scientists also contribute their expertise by serving as members of scientific groups and committees.

Recent Accomplishments

Diagnostic Tools

  • A new DNA-based (qPCR) assay targeting the ribonucleotide reductase (RNR) gene of HLB was developed, validated, and incorporated as part of our federal confirmatory diagnostics.
  • A new DNA method for the genotyping of HLB via sequence-based analysis has been developed and implemented, allowing us to infer possible origins for introductions.
  • Completed Work Instruction and verification testing of a new qPCR assay for the detection of Phytophthora ramorum.
  • Developed and optimized reaction conditions for three conventional PCR primer sets for differentiation of citrus canker pathotypes A, Aw and A* with each assay being specific for one pathotype.
  • Optimized two multiplex RT-PCR assays for simultaneous detection of five cytoplasmic and three nuclear viruses associated with the Citrus Leprosis (CiLV) Virus complex.


  • Provided hands-on diagnostic methods training for 74 diagnosticians from the NPDN, State Departments of Agriculture, and Universities. Seven workshops with 11 instructors provided training on: Bioinformatics of Plant Pathogens and Molecular diagnostics for Phytophthora ramorum, Phytophthora kernoviae, Plum pox virus, HLB, and Phytoplasma. 


  • Provided PPQ Operational Diagnostics for a total of 654 suspect samples.
  • Successfully obtained ISO/IEC 17025 re-accreditation from ANAB valid until 2019.
  • Implemented the Laboratory Information Management System (LIMS) for documenting, tracking and reporting of confirmatory diagnostic testing.
  • Confirmed Phytophthora parvispora, as a new record for the USA and a new host [as the pathogen was associated with Choisya ternata (Mexican orange)].
  • Confirmed Colletotricum queenslandicum which represents a new record for Texas and the first known report of this pathogen on citrus.
  • Confirmed the 1st report of Tuberose mild mosaic virus in Florida.
  • Confirmed the 1st report of Taro bacilliform China virus in Hawaii.
  • Completed the determination of strain identity of three recent Texas citrus canker isolates using High Throughput Sequencing (HTS).   

High Throughput Sequencing Technologies

  • Completed the setup and implementation of HTS capabilities for the laboratory.
  • Completed a 950,456 bp genome sequence for 'Candidatus Phytoplasma pini' isolate from MD.
  • Completed Whole Genome Sequencing (WGS) and draft genome assemblies of isolates from two exotic species of Monilinia [M. laxa and M. fructigena] and two domestic species M. fructicola and M. laxa. The sequences have been deposited into the NCBI DDBJ/ENA/GenBank.
  • Completed WGS draft of Peronosclerospora sacchari (Taiwan), P. australiensis (Australia), and P. sorghi (USA).
  • Completed WGS and draft genome assembly of three US isolates and one historic strain of Xanthomonas vasicola. 
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