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Outbreak

Measles virus, the causative agent of the disease measles (also called rubeola, MeV or MV) is classified by the ICTV into the family Paramyxoviridae and species Morbillivirus hominis. Measles is a highly contagious viral disease that primarily affects children but can impact individuals of all ages. The virus is known for its rapid spread through respiratory droplets and close contact, with outbreaks occurring primarily in areas with low vaccination coverage. Two does of the MMR vaccine has a 97% efficacy for protection against measles.

In early 2025, a measles outbreak began in Texas, with cases quickly spreading to multiple states. Cases continue to increase and an up-to-date list of states, age distribution and hospital status can be found on the CDC website. The outbreak has been driven by low vaccination rates, with varying percentages of cases occurring in individuals who were either unvaccinated or had an unknown vaccination status.

Measles Outbreak Map

Measles Map

Epidemiology and Transmission

Measles is one of the most contagious viral diseases, with a basic reproduction number (R0) ranging from 12 to 18. The virus spreads through respiratory droplets and can linger in the air for up to two hours after an infected person leaves an area. Unvaccinated individuals, particularly young children, are at the highest risk of severe complications, including pneumonia, encephalitis, and death.

The 2025 outbreak has predominantly affected children under five (34% of cases) and school-aged individuals (42%). Among hospitalized cases, young children remain the most vulnerable, with 27% of those under five requiring hospitalization.

Genetic Characteristics and Diagnostic Challenges

Measles virus is an RNA virus with limited genetic variability compared to other viruses. However, genomic surveillance remains essential to track transmission chains and identify potential new variants.

Diagnostic confirmation is primarily achieved through PCR-based testing or serological analysis.

Since 1990 these 19 genotypes have been detected; A, B2, B3, C1, C2, D2, D3, D4, D5, D6, D7, D8, D9, D10, D11, G2, G3, H1, H2. Vaccine strains are genotype A.

Regional and Global Implications

The resurgence of measles cases in 2025 underscores the ongoing challenge of vaccine hesitancy and declining immunization coverage. While the U.S. has maintained high overall vaccination rates, localized pockets of unvaccinated populations have facilitated the spread of the virus. The outbreak has also highlighted the need for enhanced public health measures, including catch-up vaccination campaigns, improved surveillance, and rapid response strategies.

Internationally, the measles outbreak has raised concerns about global vaccination gaps, with similar surges reported in parts of Europe and Africa. Public health agencies continue to emphasize the critical role of measles-mumps-rubella (MMR) vaccination in preventing future outbreaks.

Timeline

Year Event
Prior to 1963 Estimated 2.6 million deaths worldwide each year.
1963 Measles vaccine first introduced, significantly reducing global cases.
2000 Measles declared eliminated in the U.S., after no continuous transmission for over a year.
2014 Measles resurgence in the U.S., with 667 cases reported—the highest since elimination.
2019 Largest U.S. measles outbreak since 1992, with over 1,200 cases linked to unvaccinated communities.
2023 Measles cases rise globally due to pandemic-related disruptions in vaccination efforts.
2024 285 measles cases reported in the U.S. across 33 jurisdictions, with 16 separate outbreaks.
2025 A new outbreak of measles begins in Texas, spreading to at least 18 states by April.

Measles Taxonomy

  • Realm: Riboviria
  • Kingdom: Orthornavirae
  • Phylum: Negarnaviricota
  • Subphylum: Haploviricotina
  • Class: Monjiviricetes
  • Order: Mononegavirales
  • Family: Paramyxoviridae
  • SubFamily: Orthoparamyxovirinae
  • Genus: Morbillivirus
  • Species: Morbillivirus hominis
Taxonomy from ICTV

Measles Virus Genomic Information

Measles virus genome from ViralZone

The measles virus genome consists of a single-stranded, negative-sense RNA genome of approximately 16 kb. It encodes eight proteins, including hemagglutinin (H) and fusion (F) proteins that are critical for viral entry into host cells. Genetic sequencing is used to monitor viral evolution and potential shifts in transmission dynamics


News

Recent PubMed Articles

    This map provides a comprehensive summary of sequenced measles virus isolates in 2025. It includes publicly available genomic data at both state and country levels. Each marker on the map is interactive, allowing users to click and access the corresponding genomic data. The map currently has limited data and will continue to be updated as data is publicly available.

    Loading Map of Seq. Isolates...
    Country-level cases
    State-level cases

    Measles Outbreak Genomes in 2025

    Measles genomes in 2025

    Measles Outbreak Genomes

    All Measles genomes

    Measles outbreak FASTA, MSA and phylogenetic tree files from 2025 available in the BV-BRC workspace .

    These files contain the data used to generate the phylogenetic trees provided on the Phylogenetics tab on the Measles Outbreak page.

    Select genome sequences were downloaded from NCBI and BV-BRC.

    Sequences were then aligned using MAFFT. Multiple sequence alignment columns with more than 50% gaps were deleted. A minimal evolution phylogenetic tree was then inferred with the FastME program based on maximum likelihood pairwise distances calculated by TREE-PUZZLE using the GTR model. Custom scripts were used to add meta-data to the resulting tree.


    Resource Description
    BV-BRC Annotation Tool Annotation of genomic features using VIGOR4.
    BV-BRC Gene Tree Build your own gene/protein tree using our phylogenetic tree tool.
    BV-BRC Meta-CATS Look for statistically significant position changes using the Metadata-driven comparative analysis tool.
    BV-BRC MSA Tool Choose an alignment algorithm to align sequences.
    BV-BRC Subspecies Classification Assign the genotype/subtype of a virus, based on the genotype/subtype assignments maintained by ICTV.
    BV-BRC Viral Genome Tree Build your own genomic phylogenetic tree using our phylogenetic tree tool.

    Other Resources

    Resource Description
    WHO Measles virus nomenclature update
    CDC Nextstrain Measles
    ASM Journals Complete Genome Sequences of Six Measles Virus Strains
    Pathogens Portal Outbreak Sequences
    BRC Analytics Analyze your own data in the genomic context
     
    Last updated on 04/07/2025

    Below are some of useful command line tool reference and examples to search and download bulk data from BV-BRC. Complete command line interface (CLI) guide is available at Command Line Interface. CLI installation guide is available at Installing the BV-BRC Command Line Interface.

    Search Genome

    User can search genomes using p3-all-genomes command. Complete help and guide are at p3-all-genomes.

    Example of p3-all-genomes command.

    Following command is to download measles genomes collected in 2025. Please make sure you format the date correctly.

    $ p3-all-genomes --eq taxon_lineage_ids,11234 --eq collection_year,2025 --in genome_status,Complete,Partial
    genome.genome_id
    658048.5627
    658048.5626
    658048.5624
    658048.5625
    658048.5623
    170528.8105
    658048.5738

    Following commands will get the genome id of all measles genomes from 2024 from USA in FASTA format.

    $ p3-all-genomes \
      --eq=taxon_lineage_ids,11234 \
      --eq=isolation_country,USA \
      --eq=host_common_name,* \
      --eq=collection_year,2024 \
      | head -n 10 > measles_virus.txt
    
    #Example output
    $ more measles_virus.txt
    genome.genome_id
    170528.6574
    170528.6572
    170528.6571
    

    Download Annotation

    User can download annotation in two steps.

    1. Download the GenomeType
    2. Convert the GenomeType to desired format.
    GenomeType conversion format options
    genbank         Genbank format
    genbank_merged  Genbank format as single merged locus.
    feature_data    Tabular form of feature data
    protein_fasta   Protein translations in fasta format
    contig_fasta    Contig DNA in fasta format
    feature_dna     Feature DNA sequences in fasta format
    gff             GFF format
    embl            EMBL format
    
    More details of commands available at p3-gto and RASTtk, The Incremental Commands.

    1. Download the GenomeType

    First, download the GenomeType using the Genome ID.

    p3-gto [Genome ID]

    Example:

    p3-gto 170528.6574

    2. Convert GenomeType to Desired Format

    Once you have the GenomeType file, you can convert it to your desired format.

    rast-export-genome [Format] < [GenomeType File] > [Output File]
    • Replace [Format] with one of the conversion options (e.g. gff, genbank, protein_fasta, etc.).
    • Replace [GenomeType File] with the filename of the downloaded GenomeType file.
    • Replace [Output File] with the desired name for the converted file.

    Example:

    rast-export-genome gff < 170528.6574.gto > 170528.6574.gto.gff

    Download genome data in FASTA format

    $ p3-genome-fasta -h
    p3-genome-fasta.pl [-h] [long options...] genomeid
    --protein  feature protein fasta
    --feature  feature dna fasta
    --contig   contig dna fasta
    -h --help  display usage information
    

    Example of downloading genome using genome id:

    $ p3-genome-fasta --contig 170528.6574
    >170528.6574.con.0001
    gtcagttccacattggcatctgaactcggtatcactgccgaggatgcaaggcttgtttca
    gagattgcaatgcacaccaccgaggacaggaccagcagagcagttggacccagacaagct
    …
    

    Example of searching and downloading data using pipe command:

    p3-all-genomes  --eq taxon_lineage_ids,11234 --gt date_inserted,"2024-08-01T00:00:00.000Z" \
     | sed -n '2,$p' | xargs -n 1 p3-genome-fasta --contig

    Search genome list and then download data based on genome list:

    #Search the genome list
    $ p3-all-genomes  --eq taxon_lineage_ids,11234 --gt date_inserted,"2024-08-01T00:00:00.000Z" \
     > genome_list.txt
    
    #Download fasta file for genome list. You can remove the genomes for genome-list as needed
    $ for i in $(cat genome_list.txt); do
        if [ $i != "genome.genome_id" ]; then
           p3-genome-fasta --contig $i
        fi
     done >> genome.fasta
    
    #View the genome fasta file
    $ more genome.fasta
    >170528.7065.con.0001
    atggccacacttttaaggagcttagcattgttcaaaagaaacaaggacaaaccacccatt
    acatcaggatccggtggagccatcagaggaatcaaacacattattatagtaccaatccct
    ggagattcctcaattaccacccgatccaggctactggaccgattggtcaggttaattgga
    aacccagatgtgagcggacccaaactaacaggggcactaataggtatattatctttgttt
    ...