The Circulation of Measles Virus Variants with Mutations Affecting Molecular Diagnostics in Italy and Switzerland


In a recent groundbreaking study by Pérez-Rodríguez et al., the emergence of measles virus (MeV) variants displaying mutations that potentially impact the efficacy of molecular diagnostics has been documented, raising concerns within the global health community. The study, published in a renowned scientific journal, delineates the identification of three synonymous T-to-C substitutions within the 450 nucleotide-long C-terminal region of the nucleoprotein (N) gene. This region is crucial as it serves as the target for the real-time reverse-transcription (RT)-PCR assays widely utilized in surveillance laboratories for the detection of MeV. The mutations were located within the annealing site of the reverse primer recommended by the United States Centers for Disease Control and Prevention (CDC), thereby slightly reducing the sensitivity of the test.

This revelation has significant implications for measles surveillance networks worldwide, including the MoRoNet, a Subnational Reference Laboratory network focused on measles and rubella surveillance. In the Metropolitan City of Milan and surrounding areas in Lombardy, Northern Italy, a region with approximately 4 million residents, the MoRoNet has confirmed five cases of measles since January 2024. These cases were identified as genotype D8, the same genotype as the variants discussed by Pérez-Rodríguez and colleagues, and were found to be sporadic with no clear epidemiological links among them. Notably, three of these cases had a recent travel history to Uzbekistan, Thailand, and Southern Italy, with two of the cases infected with MeV strains characterized by the mutations described in the study.

The detection and confirmation of these cases were achieved through the analysis of virus-specific IgM in serum samples using an enzyme-linked immunosorbent assay, and of MeV-RNA in both urine and oropharyngeal swab samples by real-time RT-PCR. Subsequent genotyping of the MeV strains, following the World Health Organization (WHO) guidelines, involved sequencing the N-450 region. The sequences were then annotated and deposited in the WHO Measles Virus Nucleotide Surveillance (MeaNS2) database and GenBank, showcasing a distinct sequence identifier from those detected by Pérez-Rodríguez et al.

A comparative analysis using the Basic Local Alignment Search Tool (BLAST) revealed a 99.7% identity with strains previously identified in Moscow, Russia, in 2023, indicating a wider circulation of these variants. The discovery that none of the other 614 strains (comprising 453 D8 and 161 B3 genotypes) detected between 2017 and 2023 by the Lombardy laboratory possessed these mutations underscores the novelty and potential challenge posed by the emergence of these specific variants.

The findings from Lombardy, Italy, corroborate the observations made by Pérez-Rodríguez et al. in Switzerland, highlighting a cross-border circulation of these MeV variants. This scenario emphasizes the critical need for the global health community to adapt and update diagnostic assays promptly to ensure the effective detection of all circulating MeV strains, thereby safeguarding public health measures against measles outbreaks.

The swift communication by Pérez-Rodríguez and colleagues has been instrumental in raising awareness about the circulation of a MeV variant that poses challenges to the current diagnostic methodologies. This article not only confirms the findings reported by the Swiss researchers but also sheds light on the broader implications of these variants’ spread. As measles remains a significant public health challenge, the adaptability and responsiveness of surveillance and diagnostic networks are paramount in controlling its spread and mitigating its impact on communities worldwide.

Advances and Challenges in Measles Virus Diagnostic Techniques

The diagnosis of measles, a highly contagious and potentially fatal disease, has evolved significantly over the years, leveraging advancements in molecular diagnostics to improve detection accuracy and outbreak management. The core of measles diagnostic relies on the detection of viral RNA through real-time reverse-transcription PCR (RT-rPCR) and the identification of virus-specific IgM. However, the genetic variability of the measles virus poses a significant challenge to the sensitivity of RT-rPCR assays, due to potential mismatches between the primers or probe and the viral template.

Genetic Variability and Surveillance

The genetic analysis of measles viruses is a cornerstone in understanding the epidemiology and spread of the disease. Laboratories around the world, including the Centers for Disease Control and Prevention (CDC), employ RT-rPCR assays targeting the nucleoprotein (N) gene of the virus. This approach is supported by the World Health Organization (WHO) for routine genotyping, which involves comparing diagnostic PCR oligonucleotide sequences against viral sequences obtained through genotyping. Such efforts are crucial for identifying genetic mutations that could impact assay sensitivity.

Molecular Surveillance in Switzerland

In Switzerland, molecular surveillance conducted through 2023 revealed the predominance of genotype D8 in measles cases. This surveillance is pivotal for identifying mutations in the primer annealing sites, which could reduce the efficacy of RT-rPCR assays. One such instance involved mismatches between the assay’s reverse primer and the viral RNA of a particular measles strain (DSId 8248), highlighting the necessity for continuous monitoring and updating of diagnostic tools to accommodate viral evolution.

Impact on Diagnostic Sensitivity

The detection of mismatches in primer annealing sites necessitates a thorough evaluation of the RT-rPCR assay’s sensitivity. Serial dilutions of positive samples demonstrated a partial loss of sensitivity in detecting samples with specific mutations. This underscores the need for alternative or updated diagnostic assays that can accommodate genetic variability within the measles virus.

Global and Regional Efforts

The CDC and the WHO Global Measles and Rubella Laboratory Network (GMRLN) are at the forefront of these efforts, providing guidance and resources for the genetic characterization of measles viruses. The establishment of measles strain banks and the use of Vero/hSLAM cells for virus isolation are examples of initiatives aimed at enhancing laboratory capacity for measles surveillance and research.

Challenges and Outlook

Despite the availability of effective vaccines, measles remains endemic in many regions, causing significant morbidity and mortality. The COVID-19 pandemic has further complicated measles control efforts by disrupting vaccination campaigns and surveillance activities. The identification of genetic mutations that affect diagnostic assay sensitivity highlights the ongoing challenges in measles control and emphasizes the importance of global cooperation, continuous surveillance, and innovation in diagnostic technologies.

In conclusion, while significant progress has been made in the detection and surveillance of measles, genetic variability of the virus continues to challenge diagnostic accuracy. Ongoing research, surveillance, and the adaptation of diagnostic assays are essential to maintain and improve the sensitivity and specificity of measles diagnostics, ensuring effective disease control and prevention strategies.

reference link :

  • Centers for Disease Control and Prevention (CDC) (
  • ResearchGate (


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