---
title: "Whole-Genome Sequencing Reveals Expanding D8 Measles Lineage in 2025 Texas Outbreak"
id: "cdc-emerging-infectious-diseases-journal-3-whole-genome-sequencing-of-measles-virus-from-2025-outbreak-texas-usa"
canonical_url: "https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-3-whole-genome-sequencing-of-measles-virus-from-2025-outbreak-texas-usa"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "CDC Emerging Infectious Diseases Journal"
source_url: "https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article"
published_at: "2026-09-21T04:00:00.000Z"
evidence_level: "Agency Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Whole-Genome Sequencing Reveals Expanding D8 Measles Lineage in 2025 Texas Outbreak
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-3-whole-genome-sequencing-of-measles-virus-from-2025-outbreak-texas-usa
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** CDC Emerging Infectious Diseases Journal
- **Source URL:** [Original Journal Publication](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article)
- **Published At:** 2026-09-21T04:00:00.000Z
- **Evidence Rating:** Agency Feed
## Executive GIST (TL;DR)
- The 2025 Texas measles outbreak centered in Gaines County produced 762 confirmed cases, predominantly in children, adolescents, and persons unvaccinated or with unknown vaccination status; the outbreak occurred amid increased measles activity across North America. - Investigators applied tiled amplicon **whole-genome sequencing** (WGS) to 491 RT-PCR–positive samples; 368 genomes from 359 persons met coverage thresholds for phylogenetic analysis. - Routine genotyping using the **N-450** region provided limited resolution; WGS identified a closely related expanding **D8 genotype** lineage among Texas genomes. - Of genomes with N-450 DSIds (240), 220 (92%) were DSId 9171, a D8 lineage. Pairwise SNP distances among Texas genomes ranged 0–15 (median 3), indicating tight genetic relatedness. - A **Fusion gene H419R (F:H419R)** substitution was fixed in all Texas genomes; screening of public D8 genomes showed an increase in F:H419R frequency from 2% in 2023 to 65.4% in 2025. - Texas genomes clustered with contemporaneous genomes from Utah and the Netherlands in a Nextstrain time-scaled analysis; investigators subsampled public genomes to reduce sampling bias. - Molecular-clock analysis showed weak temporal signal when excluding a temporally distant D8 reference genome, so tMRCA from Texas genomes alone was not used to infer introduction timing. - An exploratory genome-wide association analysis found no variants significantly associated with vaccination status, but that analysis was underpowered. - Selection analysis identified two polymerase-gene codons interpreted as subclade markers rather than evidence of immune escape or functional adaptation. - The report emphasizes that WGS can strengthen measles surveillance and outbreak investigations; functional, clinical, vaccine-effectiveness, or transmission consequences of F:H419R were not evaluated in this study.
## Clinical Analysis & Structured Key Points
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[EID Journal](https://wwwnc.cdc.gov/eid/) 2. [Volume 32](https://wwwnc.cdc.gov/eid/early-release) 3. [Early Release](https://wwwnc.cdc.gov/eid/early-release#issue-1346) 4. [Main Article](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article) * [Facebook](https://www.facebook.com/sharer/sharer.php?u=%2Feid%2Farticle%2F32%2F10%2F26-0494_article "Share to Facebook") * [Twitter](http://twitter.com/share?url=%2Feid%2Farticle%2F32%2F10%2F26-0494_article&text= "Share to Twitter") * [LinkedIn](https://www.linkedin.com/shareArticle?url=%2Feid%2Farticle%2F32%2F10%2F26-0494_article&title= "Share to LinkedIn") * [Syndicate](https://tools.cdc.gov/medialibrary/index.aspx#/sharecontent//eid/article/32/10/26-0494_article "Embed this Page") [ Emerging Infectious Disease journal ISSN: 1080-6059 ](https://wwwnc.cdc.gov/eid/) _Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released._ #### Volume 32, Number 10—October 2026 ##### _Dispatch_ ### Whole-Genome Sequencing of Measles Virus from 2025 Outbreak, Texas, USA On This Page [The Study](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article) * * * [Conclusion](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article) * * * [Suggested Citation](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article) Figures [Figure 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f1) * * * [Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f2) * * * [Figure 3](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f3) * * * [Figure 4](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f4) Downloads [Appendix ](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-app1.pdf) * * * [RIS [TXT - 2 KB] ](https://wwwnc.cdc.gov/eid/article/32/10/26-0494.ris) Article Metrics [Metric Details](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article) Piyada Juntawong[![Comments to Author](https://wwwnc.cdc.gov/eid/content/images/icon/email.gif)](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article#comment) , Bonnie Oh, Richard Bovio, Jie Lu, Sydney Stanley, Robert F. Potter, Yan Sun, Casey Schroeder, Olivia A. Smith, Elise Huebner, Stephen L. White, Saroj Rai, Varun Shetty, and Grace Kubin Author affiliation: Texas Department of State Health Services, Austin, Texas, USA (P. Juntawong, B. Oh, R. Bovio, J. Lu, Y. Sun, C. Schroeder, O.A. Smith, E. Huebner, S.L. White, S. Rai, V. Shetty, G. Kubin); Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (S. Stanley, R.F. Potter); Perelman School of Medicine at the University of Pennsylvania, Philadelphia (S. Stanley, R.F. Potter) [Suggested citation for this article](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article#suggestedcitation) ### Abstract We sequenced measles-positive samples from the 2025 outbreak in Texas, USA, and identified the expansion of a closely related genotype D8 lineage within broader strain diversity from North America. F:H419R was used as a lineage-associated genomic surveillance marker. Our findings demonstrate that whole-genome sequencing can strengthen measles surveillance and enhance outbreak investigations. Measles virus importations continue to cause outbreaks in undervaccinated communities in the United States despite elimination since 2000 ([_1_](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article#r1 "1")). In early 2025, the Texas Department of State Health Services reported the state’s largest measles outbreak after elimination, centered in Gaines County and neighboring West Texas communities ([_2_](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article#r2 "2")). Epidemiologic reports indicated 762 confirmed measles cases; more than half occurred in Gaines County, and most cases were among children, adolescents, and persons who were unvaccinated or had unknown vaccination status ([_3_](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article#r3 "3")). The outbreak occurred during expanded measles activity in North America, raising questions about local expansion, interstate relatedness, and the utility of whole-genome sequencing (WGS) to resolve transmission patterns beyond routine genotyping. Routine measles molecular surveillance commonly relies on the 450-nucleotide region of the nucleoprotein gene (N-450), which supports genotype and distinct sequence identifier (DSId) assignment. However, N-450 provides limited resolution of transmission chains during large outbreaks involving closely related viruses ([_4_](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article#r4 "4")). We used WGS to characterize the measles outbreak in Texas and assessed genomic diversity and genomic relatedness to other measles virus genomes from North America. ### The Study We performed tiled amplicon-based sequencing on 491 reverse transcription PCR–positive measles samples ([Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-app1.pdf)). After quality assessment, 368 measles virus genomes from 359 persons met the predefined coverage threshold for phylogenetic analysis; 9 persons each had 2 samples sequenced ([Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-app1.pdf) Table 1). Among the 359 persons with sequenced samples and epidemiologic metadata, 204 (56.8%) were unvaccinated, 139 (38.7%) had unknown vaccination status, 7 (2.0%) had received 1 measles vaccine dose, and 9 (2.5%) had received 2 measles vaccine doses ([Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-app1.pdf) Table 2). We determined vaccination status by using patient records. Patients without confirmed vaccination status were classified as unknown. We performed an exploratory genome-wide association study to evaluate if measles variants were associated with vaccination status, but we did not detect any variants significantly associated with vaccination status; however, our analysis was underpowered. Figure 1 ![Genomic diversity of measles virus genomes from study of whole-genome sequencing of measles virus from 2025 outbreak, Texas, USA. A\) Maximum-likelihood phylogenetic tree of 368 Texas measles genomes \(January–August 2025\). Color strip annotations denote epidemiologic week of specimen collection and county. Red branches indicate clusters with an ultrafast bootstrap value >90. Red asterisk indicates reference D8 strain \(GenBank accession no. KJ018971.2\). B\) Distribution of pairwise SNP distances among Texas measles genomes. SNP, single-nucleotide polymorphism.](https://wwwnc.cdc.gov/eid/images/26-0494-F1-tn.jpg) [Figure 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f1 "Figure 1"). Genomic diversity of measles virus genomes from study of whole-genome sequencing of measles virus from 2025 outbreak, Texas, USA. A) Maximum-likelihood phylogenetic tree of 368 Texas measles genomes (January–August 2025).... We performed a maximum-likelihood phylogenic analysis by using the 368 sequenced measles virus genomes. N-450 DSIds were available for 240 measles virus genomes, of which 220 (92%) were DSId 9171, a specific measles virus lineage belonging to the D8 genotype. We assigned epidemiologic weeks to measles virus genomes by using Morbidity and Mortality Weekly Report numbering ([_5_](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article#r5 "5")). Maximum-likelihood phylogenetic analysis revealed that measles virus genomes from Texas formed a closely related genotype D8 lineage ([Figure 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f1), panel A). Pairwise single-nucleotide polymorphism (SNP) distances ranged from 0–15 SNPs (median 3 SNPs), supporting close genetic relatedness among outbreak genomes ([Figure 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f1), panel B). To estimate the time to most recent common ancestor (tMRCA) for the measles virus genomes associated with the outbreak in Texas, we performed a molecular clock analysis. We did not use tMRCA estimates from the Texas measles virus genomes alone to infer introduction timing because our molecular clock analysis revealed weak temporal signal after we excluded the temporally distant D8 reference genome ([Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-app1.pdf) Figure 1). Early measles virus genomes from epidemiologic weeks 5–8 were concentrated in Gaines County, Texas, the outbreak epicenter. We later observed closely related genomes in nearby and more distant Texas counties (Appendix Figure 2). Those results support early localized amplification followed by wider spread, although multiple closely related introductions cannot be ruled out ([_6_](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article#r6 "6")). Figure 2 ![Genomic surveillance context of F:H419R among publicly available measles virus genomes from study of whole-genome sequencing of measles virus from 2025 outbreak, Texas, USA. A\) Nextstrain time-scaled global phylogeny of measles viruses showing genotype B3 and D8 measles virus genomes with the F:H419R substitution highlighted \(https://nextstrain.org/measles/genome@2025-09-24?gt=F.419R&treeZoom=selected\). B\) Global genotype D8 context of representative measles genomes associated with the outbreak in Texas and representative publicly available F:H419R-positive D8 genomes. F:H419R, Fusion gene H419R substitution.](https://wwwnc.cdc.gov/eid/images/26-0494-F2-tn.jpg) [Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f2 "Figure 2"). Genomic surveillance context of F:H419R among publicly available measles virus genomes from study of whole-genome sequencing of measles virus from 2025 outbreak, Texas, USA. A) Nextstrain time-scaled global phylogeny of... To provide genomic surveillance context, we conducted a targeted evaluation of the Fusion gene H419R substitution (F:H419R), fixed in all measles viral genomes from Texas, rather than a comprehensive genome-wide screen for recurrent, homoplasic substitution, or substitutions of functional effect. To place F:H419R in broader context, we screened publicly available genotype D8 whole genomes with adequate Fusion gene coverage >12,500 bp of total genome coverage with an unambiguous call for the fusion gene codon encoding residue 419). We detected F:H419R among recent publicly available D8 measles virus genomes ([Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f2), panel A; [Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-app1.pdf) Table 3). The proportion of D8 genomes with the F:H419R substitution increased from 2% (1/49) in 2023 to 8.5% (10/118) in 2024 and 65.4% (34/52) in 2025 ([Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-app1.pdf) Figure 3). Although residue 419 has prior residue-level annotation ([_7_](https://wwwnc.cdc.gov/eid/article/32/10/26-0494_article#r7 "7")), this study did not evaluate functional, immunologic, vaccine-effectiveness, transmission, or clinical consequences. Selection analysis identified 2 polymerase-gene codons, which we interpreted as subclade markers rather than evidence of immune escape or functional adaptation ([Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-app1.pdf) Figure 4). We placed the measles genomes from Texas in the global context by using the Nextstrain measles workflow ( [External Link](https://github.com/nextstrain/measles)). To reduce geographic and temporal sampling imbalance, we subsampled genomes to <30 per country–year group. Consequently, the phylogeny includes only a representative subset of 2025 measles genomes from the United States ([Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f2), panel B). Measles virus genomes from Texas clustered with contemporaneous genomes from Utah, USA, and the Netherlands ([Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f2), panel B). Figure 3 ![Maximum-likelihood phylogeny of the focal expanding North American genotype D8 measles virus lineage from study of whole-genome sequencing of measles virus from 2025 outbreak, Texas, USA. Phylogeny shows 1,760 genomes from Texas, Utah, Arizona, South Carolina, and other jurisdictions in North America included in the focal expanding North American genotype D8 lineage. We excluded 11 contextual genomes outside the focal lineage from this display. Tips are colored by jurisdiction; Canada genomes and US genomes outside Texas, Arizona, Utah, and South Carolina are grouped as other North American genomes. Tips identified by TreeTime \(https://github.com/neherlab/treetime\) as molecular-clock outliers are shown with black open circles. Branch lengths represent substitutions per site. The tree was rooted for visualization only; root placement should not be interpreted as evidence of ancestry, source, or transmission direction.](https://wwwnc.cdc.gov/eid/images/26-0494-F3-tn.jpg) [Figure 3](https://wwwnc.cdc.gov/eid/article/32/10/26-0494-f3 "Figure 3"). Maximum-likelihood phylogeny of the focal expanding North American genotype D8 measles virus lineage from study of whole-genome sequencing of measles virus from 2025 outbreak, Texas, USA. Phylogeny shows 1,760 genomes... We analyzed a comparative dataset including genomes from Texas, Arizona, Utah, South Carolina, and other jurisdictions in N
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