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

IF 1.9 4区医学 Q2 PATHOLOGY

American journal of clinical pathology Pub Date : 2025-09-09 DOI:10.1093/ajcp/aqaf064

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

{"title":"Establishment of the Veterans Affairs SeqFORCE (Sequencing for Research Clinical and Epidemiology) program for SARS-CoV-2 whole-genome sequencing.","authors":"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","doi":"10.1093/ajcp/aqaf064","DOIUrl":null,"url":null,"abstract":"Objective: 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: Clinical criteria were established for sending patient and employee samples from 145 VHA medical centers to 10 VHA clinical laboratories using 4 different WGS platforms. A linked pipeline among laboratories for SARS-CoV-2 clade and lineage interpretation, result transmission to electronic health records, and data storage was developed.Results: The SeqFORCE program went live on July 1, 2021. As of December 15, 2024, 51 307 samples have been analyzed by WGS for SARS-CoV-2. The median participant age was 60 years, 76.6% were male, and 13.5% were inpatients; 96.5% were Delta, Omicron, and Recombinant sublineages; and 78.5% represented SARS-CoV-2 postvaccination samples among patients and staff.Conclusions: Establishment of VA SeqFORCE enabled national population analysis for use in epidemiologic response and population health policy as well as expanded SARS-CoV-2 sequencing capacity to meet the demand for clinical and public health sequencing. The program consolidated operations using standardized procedures, test setup, analysis, reporting, and tracking. It also improved oversight and governance of VA contributions to global databases, mitigated system inefficiencies, and prepared VHA for future genomic challenges.","PeriodicalId":7506,"journal":{"name":"American journal of clinical pathology","volume":" ","pages":"302-309"},"PeriodicalIF":1.9000,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"American journal of clinical pathology","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1093/ajcp/aqaf064","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"PATHOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Objective: 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: Clinical criteria were established for sending patient and employee samples from 145 VHA medical centers to 10 VHA clinical laboratories using 4 different WGS platforms. A linked pipeline among laboratories for SARS-CoV-2 clade and lineage interpretation, result transmission to electronic health records, and data storage was developed.

Results: The SeqFORCE program went live on July 1, 2021. As of December 15, 2024, 51 307 samples have been analyzed by WGS for SARS-CoV-2. The median participant age was 60 years, 76.6% were male, and 13.5% were inpatients; 96.5% were Delta, Omicron, and Recombinant sublineages; and 78.5% represented SARS-CoV-2 postvaccination samples among patients and staff.

Conclusions: Establishment of VA SeqFORCE enabled national population analysis for use in epidemiologic response and population health policy as well as expanded SARS-CoV-2 sequencing capacity to meet the demand for clinical and public health sequencing. The program consolidated operations using standardized procedures, test setup, analysis, reporting, and tracking. It also improved oversight and governance of VA contributions to global databases, mitigated system inefficiencies, and prepared VHA for future genomic challenges.

查看原文本刊更多论文

建立退伍军人事务SeqFORCE（临床和流行病学研究测序）项目，进行SARS-CoV-2全基因组测序。

目的：建立美国退伍军人事务部（VA）退伍军人健康管理局（VHA）临床和流行病学研究测序（SeqFORCE）多实验室联盟，进行SARS-CoV-2全基因组测序（WGS）。方法：建立临床标准，将145个VHA医疗中心的患者和员工样本通过4种不同的WGS平台发送到10个VHA临床实验室。在实验室之间建立了一条连接管道，用于SARS-CoV-2进化支和谱系解释、结果传输到电子健康记录和数据存储。结果：SeqFORCE项目于2021年7月1日投入使用。截至2024年12月15日，WGS已对51 307份样本进行了SARS-CoV-2分析。参与者年龄中位数为60岁，76.6%为男性，13.5%为住院患者；96.5%为Delta、Omicron和Recombinant亚系；78.5%为患者和工作人员接种疫苗后的SARS-CoV-2样本。结论：VA SeqFORCE的建立使国家人口分析能够用于流行病学应对和人口卫生政策，并扩大了SARS-CoV-2测序能力，以满足临床和公共卫生测序需求。该程序使用标准化的程序、测试设置、分析、报告和跟踪来整合操作。它还改善了VHA对全球数据库贡献的监督和治理，减轻了系统效率低下的问题，并为未来的基因组挑战做好了准备。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

American journal of clinical pathology 医学-病理学

CiteScore

7.70

自引率

2.90%

发文量

367

审稿时长

3-6 weeks

期刊介绍： The American Journal of Clinical Pathology (AJCP) is the official journal of the American Society for Clinical Pathology and the Academy of Clinical Laboratory Physicians and Scientists. It is a leading international journal for publication of articles concerning novel anatomic pathology and laboratory medicine observations on human disease. AJCP emphasizes articles that focus on the application of evolving technologies for the diagnosis and characterization of diseases and conditions, as well as those that have a direct link toward improving patient care.