Attention A T users. To access the menus on this page please perform the following steps. 1. Please switch auto forms mode to off. 2. Hit enter to expand a main menu option (Health, Benefits, etc). 3. To enter and activate the submenu links, hit the down arrow. You will now be able to tab or arrow up or down through the submenu options to access/activate the submenu links.

Patient Care Services

Menu
Menu
Quick Links
Veterans Crisis Line Badge
My healthevet badge
 

VHA Public Health National Program Office (PHNPO)

Establishment of the Veterans Affairs SeqFORCE (Sequencing for Research Clinical and Epidemiology) program for SARS-CoV-2 whole-genome sequencing


Staff from VA’s Public Health Reference Laboratory and National Program Office, along with colleagues from across VHA recently published an article on June 30, 2025 in the American Journal of Clinical Pathology. This paper highlights the work of a multi-laboratory consortium for whole genome sequencing known as SeqFORCE (Sequencing for Research, Clinical and Epidemiology). The project was started to meet the clinical and public health demand for genomic sequencing data, including variant detection and geographic tracking, during the height of the COVID-19 pandemic.

The program developed a consolidated and standardized operation for VA sites to submit and receive genomic data, contributed important data to global sequencing databases, and helped prepare VA for future genomic challenges.  As the article states, “the VA SeqFORCE program demonstrated the feasibility and effectiveness of a coordinated, multi-laboratory approach to SARS-CoV-2 genomic surveillance. This initiative not only enhanced the VA’s capacity to respond to the current pandemic but also laid the groundwork for future genomic surveillance and epidemiologic research. The integration of sequencing data into patient records offers a model for other health care systems aiming to improve their response to infectious diseases.

Congratulations to the team on this publication and thanks to all VA clinical laboratories for their important contributions and support of this effort.

ARTICLE:   
Establishment of the Veterans Affairs SeqFORCE (Sequencing for Research Clinical and Epidemiology) program for SARS-CoV-2 whole-genome sequencing*   - PDF

Cite

Mark Holodniy, Ying Pei, Gary Stack, Christopher Wade, Yashpal Agrawal, Nicholas Barasch, Fady Baddoura, Carmen Kletecka, Patrick Adegboyega, Christina Trevino, Joel Mewton, Vafa Bayat, Anosh Mostaghimi, James S Klutts, Jessica Wang-Rodriguez, Establishment of the Veterans Affairs SeqFORCE (Sequencing for Research Clinical and Epidemiology) program for SARS-CoV-2 whole-genome sequencing, American Journal of Clinical Pathology, 2025;, aqaf064, https://doi.org/10.1093/ajcp/aqaf064

KEY POINTS

  • We addressed the epidemiology of SARS-CoV-2 variants within the VHA and the challenges and logistics involved in whole-genome sequencing during the COVID-19 pandemic.
  • Despite challenges, SeqFORCE has successfully set up a consortium for sequencing SARS-CoV-2 and integrating results into patient EHRs, preparing the VA for future pandemic threats.
  • The VA successfully established a system that exported SARS-CoV-2 sequencing results directly into individual EHRs, making the VA data timely and aligned with larger, nationwide efforts.

Article Contents

Abstract* 

INTRODUCTION*

We sought to establish the US Department of Veterans Affairs (VA) Veterans Health Administration (VHA) Sequencing for Research Clinical and Epidemiology (SeqFORCE) multilaboratory consortium for SARS-CoV-2 whole-genome sequencing (WGS).

METHODS*

Organizational structure

Governance for VA SeqFORCE was jointly managed by the VA Public Health National Program Office (PHNPO) and Pathology and Laboratory Medicine Service (P&LMS). The PHNPO and P&LMS established command and control structures and secured funding for a national network of VHA clinical laboratories to conduct sequencing for clinical operations. An operations manual was created detailing funding mechanisms; organizational structure; and harmonization of operations, including information technology (IT) infrastructure, data management, and sample and sequence file storage for future analysis and research.

VA medical centers (VAMCs) were selected as referral laboratories based on WGS experience, interest, capacity, and geographical diversity. Each VAMC director signed a memorandum of agreement requiring laboratories to provide equipment, reagents, trained and staff and to establish a laboratory exchange data interface for ordering and reporting results. Laboratories had to participate in the VHA Clinical Laboratory Improvement Amendments (CLIA) program, use standardized testing and reporting conventions, and notify PHNPO and P&LMS of changes affecting participation.

Approval from the VAMC director, PHNPO, and P&LMS was required before engaging in non-VA testing, ensuring that VHA patient testing remained a priority. Laboratories were required to have excess capacity for VA Fourth Mission testing, with a recharge mechanism for chargebacks. The VA has the authority to provide health care to civilians under a humanitarian basis if necessary during disasters or emergencies.15,16 Each laboratory was assigned to serve 1 primary and 1 secondary Veterans Integrated Services Network (VISN).

The PHNPO tracked and distributed funding, oversaw operations, and assisted P&LMS with data analysis, epidemiologic tracking, and trending. Meanwhile, P&LMS provided regulatory oversight, ensured effective communication with VHA leadership, established quality metrics, monitored productivity and timeliness, and standardized testing and reporting protocols across the network.

Sequencing platforms

Each SeqFORCE laboratory was allowed to choose the nucleic acid extraction procedure or platform and the WGS platform they would use for the effort. Some laboratories already had a WGS platform in place for other ongoing clinical work. The WGS platforms among the SeqFORCE laboratories included the Clear Dx platform using the Clear Dx WGS SARS-CoV-2 assay (Clear Labs), the MiSeq or NextSeq 550 platform using the COVIDSeq Assay (Illumina), and the Ion GeneStudio S5 system or Genexus System using the Ion AmpliSeq SARS-CoV-2 Insight Research Assay (Thermo Fisher Scientific).

As this sequencing assay was considered a laboratory-developed test (LDT), each site first performed an analytical validation study based on the specific manufacturer’s instructions for use and individual vendor data analysis tools to generate FASTA files and using the Pangolin or Nextclade platforms to determine SARS-CoV-2 clade and lineage. All LDT analytical validations were reviewed and approved by the CLIA director at each site.

Training, verification, and proficiency testing sample panels

Initially, all SeqFORCE laboratories received a verification panel consisting of 12 blinded clinical respiratory samples prepared by the VA Public Health Reference Laboratory (PHRL), which included 10 SARS-CoV-2 samples positive by polymerase chain reaction (PCR) representing different lineages and 2 negative samples and 2 blinded proficiency test panels that included 5 SARS-CoV-2–positive controls (Twist BioScience) representing different lineages. During the second through fourth years, each laboratory received an additional proficiency testing panel annually for testing (see Table S1 for all variants tested). These panels generally reflected emerging SARS-CoV-2 variants circulating at the time. The PHRL reviewed each laboratory’s verification and proficiency testing panel results. Laboratories were required to provide the correct clade and variant name as well as the FASTA file for each panel member. If there was a discordant result, the PHRL would analyze the FASTA file, if required, to resolve any discrepancies. The expectation was that all verification and proficiency testing panel results were required to be correct for laboratories to be approved for clinical testing. This training and verification process ensured high standards for clinical genomic sequencing. The use of blinded panels validated the accuracy and reliability of the sequencing results, establishing a robust framework for ongoing proficiency and quality assurance.

Data analysis, reporting, and storage

To electronically integrate all laboratories, we established an enclave in a VA Office of Information and Technology (OIT) data center to store data files for each laboratory and house the software that would enable simultaneous and harmonized processing, analysis, and reporting of sequencing results. This storage solution was made operational based on SeqFORCE group boundaries and was implemented on a network storage array conformant with VA’s security policies.

PraediGene (Bitscopic) is a laboratory workflow tool linked to the Veterans Health Information System Technology Architecture (VistA) and the electronic health record (EHR) system. It incorporates processes to detect orders for SARS-CoV-2 sequencing from any VAMC, scan barcoded samples received in a SeqFORCE laboratory, and convert FASTQ files to FASTA files in an agnostic manner. The tool then analyzes the FASTA file sequences using application programming interface calls to the Nextclade and Pangolin tools to generate clade and lineage information, respectively17,18 and generate a VistA-formatted report linked to middleware (Data Innovations) that translates the results into a format readable by the VistA/Computerized Patient Record System (CPRS). These results are then transferred via the VA laboratory exchange data interface into the EHR. To ensure accuracy and reliability, we established minimum acceptable criteria for reporting clade and lineage, requiring that samples have a minimum depth of 100 reads and greater than 90% genome coverage. In addition, samples were required to have a real-time PCR result with a cycle threshold (Ct) less than 30 using any VA-approved real-time PCR platform and be shipped frozen to the designated SeqFORCE referral laboratory. PraediGene also includes a financial module that monitors workload, turnaround time, and produces invoicing information for a central fund.

The test set up was standardized in the EHR (VistA/CPRS) as an orderable test for clinicians and laboratory accessioning. All the laboratories were required to follow the standardized test build. SeqFORCE laboratories validated the laboratory information management interfaces to the VAMCs sending samples to them and the PraediGene interface for transmission of clade and variant calling using Pangolin and Nextclade, after which the CLIA director for each SeqFORCE laboratory signed off on the LDT. Proficiency panel testing was then conducted shortly after in fall 2021 and annually thereafter using a blinded 5-member panel.

Collaboration with VA COVID-19 research efforts

During SeqFORCE working group meetings, it was established that remnant clinical samples and sequence data files would be made available to VHA investigators for downstream research projects. In support of this initiative, VA Office of Research and Development established a SARS-CoV-2 biorepository program called VA Science and Health Initiative to Combat Infectious and Emerging Life-Threatening Diseases (SHIELD). This program aims to collect, store, and provide access to clinical samples and sequence data for ongoing and future research endeavors19 as well as sweep clinical laboratory remnant samples before discarding and appropriately transferring them to a VA biorepository for future research needs. In addition, a long-term data repository for FASTQ/FASTA SARS-CoV-2 files was established to provide VHA researchers with access to sequence files and clinical metadata for further analyses. This process helps preserve valuable data and make them available for ongoing and future research efforts.

RESULTS*

Instructions provided to all clinicians and clinical laboratories are displayed in Figure 1, including clinical indications for testing, sample and shipping requirements, assigned SeqFORCE laboratory, and expected results. The overall workflow for sample and data management is presented in Figure 2. Indications for VA SARS-CoV-2 sequencing included outbreaks and clusters, reinfection, vaccine failure, COVID-19–associated death, recent international travel, and ongoing SARS-CoV-2 variant surveillance. Clinical testing for SARS-CoV-2 sequencing was voluntary and at the discretion of clinical staff at VAMCs. Because funding for the effort was centralized and not billed to individual VAMCs, there was no disincentive for ordering testing. The VA Office of Public Health also performed surveillance across the VA enterprise for the listed indications; notified VAMCs to send samples to SeqFORCE laboratories; and generated biweekly reports for VA leadership describing trends in clades, lineages, and basic demographics.

All SeqFORCE laboratories correctly identified all SARS-CoV-2 variants in the blinded clinical samples verification panel and proficiency testing panel before conducting clinical testing. Additional proficiency testing panels were provided to laboratories annually from 2022 to 2024 (see Table S1 for a list of all SARS-CoV-2 variants that were analyzed). All participating laboratories correctly identified all SARS-CoV-2 variants in these proficiency testing panels, as well. Initially, each referral laboratory used its own vendor genomic pipeline to convert FASTQ to FASTA files and analyze sample results for clade and lineage. Report results were harmonized across SeqFORCE sites, including clade and lineage, and sent back electronically to the EHR at the referral site. Samples were received from patients and employees. Additional phylogenetic analyses were performed by the SeqFORCE laboratory when requested by sites if outbreak-associated or cluster-associated samples were received, and findings were then reported back to facilities. Result reporting to local or state public health departments was performed by the referring VAMC as locally required. Sequence data and limited metadata were also uploaded to GISAID. In some cases, residual samples were sent to a VA biorepository for storage and downstream use by researchers. The current total of unique aliquoted SARS-CoV-2–containing samples stored in the VA SHIELD biorepository exceeds 50 000.

Current data management is depicted in Figure 3. Upon receiving a sample and generating FASTQ files, a SeqFORCE laboratory transferred these files to a VA OIT data center and stored them in the designated SeqFORCE laboratory folder. PraediGene then converted the FASTQ files to FASTA format and generated clade and variant calls using Nextclade and Pangolin, respectively. An autogenerated VistA-formatted report enabled the SeqFORCE laboratory to electronically and automatically transmit the sequence result to the referring site. Using PHRL as an example, this workflow reduced hands-on time for result creation by more than 90% and virtually eliminated user error

As of January 5, 2025, 11.97 million SARS-CoV-2 real-time PCR or antigen tests were conducted within the VA system, identifying 813 232 unique positive cases among veterans and employees. Between July 1, 2021, and December 15, 2024, 675 508 patients and staff tested positive. Of these positive results, SeqFORCE laboratories received 51 307 (7.6%) samples from 145 different VAMCs, successfully determining clade and lineage for 49 828 (97.1%) of these samples. Conversely, 1479 samples either failed to amplify or had inadequate sequence coverage, preventing clade and lineage determination.

Certain samples, reported as SARS-CoV-2 positive, were tested using the BioFire Respiratory Panel 2.1 (BioFire Diagnostics), which does not provide Ct values. Two laboratories continued to accept BioFire-tested samples. One laboratory performed an additional SARS-CoV-2 real-time PCR test on these samples and excluded any with Ct values greater than 30 from sequencing. The other laboratory conducted sequencing without the benefit of Ct values. Overall, VA data aligned with the US Centers for Disease Control and Prevention (CDC) reporting during periods when the Delta, Omicron, and Recombinant variants were predominant,20,21 as shown in Figure 4 and Figure 5.

Basic descriptive demographics of the patients whose samples yielded a SARS-CoV-2 variant result are presented in Table 1; 76.6% of these patients were male, with a median age of 60 years. Of the samples, 73.4% were from veteran patients, 25.2% were from employees (both veterans and nonveterans), 13.5% were from inpatients, and 2.0% of individuals died within 30 days of collection. In all, 78.5% had received at least 1 dose of the SARS-CoV-2 vaccine at least 14 days before sequencing; 96.5% of the identified variants were Delta, Omicron, or Recombinant (primarily the XBB sublineages), reflecting the general time frame of sample collection.

The pandemic posed challenges to timely WGS. Due to ongoing surges and voluntary sample submissions, submission rates varied among sites and VISNs. The average number of samples submitted by each VISN over the period was 758 per 10 000 COVID-19–positive patients or staff, with a range of 136 to 1649. This variability led to substantial backlogs in some SeqFORCE laboratories, particularly during the initial Omicron wave, lengthening turnaround times. Vendor supply chain issues and delays in receiving reagents, flow cells, and consumable materials exacerbated the problem. In addition, platform malfunctions at certain SeqFORCE labs further delayed operations, necessitating the rerouting of samples to already-strained laboratories. The average number of samples sequenced weekly varied considerably between laboratories, ranging from 40 to 250 per week. Turnaround time also varied widely, averaging from 5 to 30 days, and was influenced by surges in submissions.

DISCUSSION*

The pandemic necessitated an unparalleled global effort to track SARS-CoV-2 variants. More than 16 million variant sequences have been deposited in GISAID by more than 125 countries, providing invaluable data for epidemiologic and evolutionary studies.4 The VA successfully established a SARS-CoV-2 sequencing consortium, capable of WGS and harmonized data interpretation and storage. Results were electronically transmitted to the patient’s EHR at 145 VAMCs. SeqFORCE labs also contributed to research on variant-associated outbreaks, viral rebound following treatment with nirmatrelvir-ritonavir, and Delta/Omicron differentiation assays.6,22,23

Other SARS-CoV-2 WGS consortia were developed to meet public health tracking needs, including the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance (SPHERES) by the CDC. SPHERES incorporated federal, state, academic, and commercial laboratories.24 The COVID-19 Genomics UK Consortium, Indian SARS-CoV-2 Genomics Consortium, and Africa Pathogen Genomics Initiative are other notable examples.25-27 These consortia have been successful in uploading data to central repositories or GISAID. The VA system uniquely inputs SARS-CoV-2 sequence results directly into individual patient records in an automated fashion, aligning closely with the US variants tracked in SPHERES data.

There are several limitations to our study. Clinical samples were sent to SeqFORCE laboratories on a voluntary basis, dependent on whether clinicians at the VAMCs chose to send samples for sequencing. This could have limited our ability to detect other novel variants or unique clinical events. Although ongoing public health surveillance was conducted to determine SARS-CoV-2 evolution, provide VA leadership interval summary reports, or assist sites with possible outbreak analysis, no formal auditing was conducted to determine whether all samples sent for sequencing met inclusion criteria. Our sequencing efforts represented approximately 5% of all samples with real-time PCR results, recognizing that a statistically significant number of the total would not meet Ct threshold criteria for sequencing. We could not control all sample shipping and transportation variables, such as dry ice availability and weather-related delays, which could affect results. Supply chain issues and instrument malfunctions limited capacity at some SeqFORCE labs, necessitating load balancing or resulting in backlogs due to high sample volumes and reagent shortages. Given the extended turnround time for sequencing results resulting from these issues, results could not be used for clinical decision-making. Additional verification of all clade and lineage calls for clinical samples was not performed after initial verification and ongoing proficiency panel acceptance. Five VAMCs were transitioning to Oracle Cerner EHR, which required manual processes for orders and reporting because they were no longer linked to the VA VistA/CPRS system. An IT solution was eventually implemented to automate these processes between Cerner VHA EHR sites and SeqFORCE laboratories.

Although the Public Health Emergency was declared over in May 2023 and public health reporting on the ongoing pandemic has slowed or discontinued, new SARS-CoV-2 infections continue, along with continued SARS-CoV-2 variant evolution. Thus, there remains a need to continue monitoring COVID-19 cases for the emergence of new variants, which could affect new vaccines or antivirals or alter clinical outcomes. The VA SeqFORCE consortium ceased to function in December 2024. However, VA PHRL will continue to sequence and monitor SARS-CoV-2 variants for diagnostic and disease surveillance purposes. The successful establishment of the VA SeqFORCE WGS consortium has positioned the VA to be prepared and ready to provide genomic sequencing for future emerging or reemerging pathogens for clinical care and as part of the US National Biodefense Strategy and World Health Organization genomic surveillance plan for pathogens of pandemic or epidemic potential.28,29

In addition, SeqFORCE’s infrastructure can be adapted for future pathogens, ensuring rapid response capabilities for new public health threats. By using the existing network and standardized procedures, the VA can quickly pivot to address new challenges, contributing to national and international genomic surveillance efforts.

In summary, the VA SeqFORCE program demonstrated the feasibility and effectiveness of a coordinated, multilaboratory approach to SARS-CoV-2 genomic surveillance. This initiative not only enhanced the VA’s capacity to respond to the current pandemic but also laid the groundwork for future genomic surveillance and epidemiologic research. The integration of sequencing data into patient records offers a model for other health care systems aiming to improve their response to infectious diseases.

Acknowledgments

We thank colleagues at Bitscopic for development and management of the PraediGene platform as well as Dr Eugene Geis for assistance with data acquisition. The opinions expressed are those of the authors and do not necessarily reflect those of the VA or US government.

Conflicts of interest

None of the VA authors have a conflict of interest associated with this work. J. Mewton and V. Bayat are employees of Bitscopic

Funding

This work is supported by VA internal operational funding.

This work is written by (a) US Government employee(s) and is in the public domain in the US.

 

*By clicking on these links, you will leave the Department of Veterans Affairs Web site.