Genotyping of recent measles virus strains from Russia and Vietnam by nucleotide-specific multiplex PCR

Global genetic diversity of measles virus (Paramyxoviridae: Morbillivirus: Morbillivirus hominis): historical aspects and current state

Monitoring the circulation of the measles virus and studying its genetic diversity is an important component of the measles elimination program. A methodological approach to molecular genetic studies and their interpretation in the measles surveillance was developed in the early 2000s. During its development, clear areas of circulation of each genotype of the virus were identified, therefore, the determination of viruses' genotypes was proposed to monitor circulation and identify transmission pathways. However, in the future, due to a significant decrease in the number of active genotypes, an approach based on sub-genotyping was proposed: determining not only the genotype of the virus, but also its genetic lineage/genetic variant. The Global Measles and Rubella Laboratory Network (GMRLN) systematically monitors the circulation of the measles virus at the sub-genotypic level, depositing the results in a specialized database MeaNS2. It is this database that is the most complete and reliable source of information about the genetic characteristic of measles viruses. This review presents both historical information and the latest data on the global genetic diversity of the measles virus.

Diagnostic challenges and pockets of susceptibility identified during a measles outbreak, Luxembourg, 2019

Luxembourg was among the first countries in the World Health Organization (WHO) European Region documenting interruption of endemic measles transmission, but an increased incidence was registered in spring 2019. The outbreak started with an unvaccinated student who had been to a winter sports resort in a neighbouring country, where a measles outbreak was ongoing. Subsequently, 12 secondary and two tertiary cases were confirmed among students from the same school, relatives and healthcare workers, as well as six probably unrelated cases. Only 11 cases initially fulfilled the WHO definition for suspected measles cases. Fourteen of 20 cases with information on country of birth and the majority of unvaccinated cases (10/12) were born outside of Luxembourg. Measles IgM antibody results were available for 16 of the confirmed cases, and five of the eight IgM negative cases had been vaccinated at least once. All 21 cases were PCR positive, but for three previously vaccinated cases with multiple specimen types, at least one of these samples was negative. The outbreak highlighted diagnostic challenges from clinical and laboratory perspectives in a measles elimination setting and showed that people born abroad and commuters may represent important pockets of susceptible people in Luxembourg.

Epidemiological and molecular characteristics of a measles outbreak in northern Vietnam, 2013-2014

BACKGROUND

A nationwide measles outbreak occurred in Vietnam between 2013 and 2014.

OBJECTIVES

To provide an overview on the 2013-2014 measles outbreak in northern Vietnam using epidemiological and molecular analysis of the measles virus (MeV).

STUDY DESIGN

Epidemiological information was collected from all suspected cases of measles/rubella. Serum and/or throat swabs were collected for laboratory confirmation of measles. MeV genomes were detected and sequenced for phylogenetic analysis.

RESULTS

A total of 9577 confirmed measles cases were reported in northern Vietnam with an incidence rate of 116.4/1,000,000 population. Of these, approximately 76.3% had unvaccinated or unknown vaccination history and 55.7% were under five years old. The outbreak started in a minority population from the mountainous area bordering Lao PDR and China and exploded in high-density population areas. Molecular analysis of MeV revealed co-circulation of genotypes H1 and D8, with H1 as the predominant strain, and divided into two clusters: cluster 1, sharing high similarity with those detected in China and Lao PDR, and cluster 2, circulating locally with unidentified origin. The minor D8 strains belonged to the D8-Frankfurt cluster.

CONCLUSION

The outbreak originated in and spread from a population with limited access to vaccines. Molecular analysis revealed co-circulation of MeVs with three different origins during the outbreak. This is the first report to provide an overview of the 2013-2014 measles outbreak in northern Vietnam, demonstrating the need for vaccination strategies against measles that are tailored to local conditions with enhanced molecular surveillance to achieve measles elimination.

Trends in childhood measles vaccination highlight socioeconomic inequalities in Vietnam

OBJECTIVES

To describe trends in measles vaccine coverage rates and their association with socioeconomic characteristics among children from age 12 to 23 months in Vietnam from the year 2000 to 2014.

METHODS

Data were drawn from the Vietnam Multiple Indicator Cluster Surveys in years 2000, 2006, 2011, and 2014. Concentration indices were used to determine the magnitude of socioeconomic inequalities in measles vaccine coverage. Associations between measles vaccine coverage and relevant social factors were assessed using logistic regression.

RESULTS

Socioeconomic inequalities in measles vaccine coverage rates decreased during 2000-2014. Children belonging to ethnic minority groups, having mothers with lower education, and belonging to the poorest group were less likely to receive measles vaccine; although, their vaccine coverage rates did increase with time. Measles vaccine coverage declined among children of mothers with more education and belonging to the wealthiest socioeconomic group.

CONCLUSIONS

Understanding the social factors influencing adherence to recommend childhood vaccination protocols is essential. Attempts to regain and retain herd immunity must be guided by an understanding of these social factors if they are to succeed.

Identification of congenital rubella syndrome in Sudan

Background

Epidemiological data about congenital rubella syndrome (CRS) are scarce and rubella vaccine is not yet included in the childhood immunization schedule in Sudan. This study aimed to identify and describe CRS cases among Sudanese infants with congenital eye or heart defects.

Methods

Between February and September 2010, paired oral fluid and dried blood spot samples were collected from 98 infants aged up to 12 months. These infants were enrolled during their visits to five hospitals in Khartoum, Sudan. Clinical samples were screened for rubella IgM and for ≥ 6 months old infants also for IgG antibodies by ELISA. The oral fluid of IgM and/or IgG positive patients was tested for rubella RNA by reverse transcriptase PCR.

Results

Our findings revealed that two children (2.0%) were IgM positive and another five children (5.1%) were positive for IgG antibodies. None of the five infants of which enough oral fluid was available for RNA investigation was PCR positive.

Conclusions

This study documented the presence of CRS in Sudan and highlighted the importance of rubella vaccine introduction for preventing future CRS cases in the country.

Improving molecular tools for global surveillance of measles virus

BACKGROUND

The genetic characterization of wild-type measles viruses plays an important role in the description of viral transmission pathways and the verification of measles elimination. The 450 nucleotides that encode the carboxyl-terminus of the nucleoprotein (N-450) are routinely sequenced for genotype analysis.

OBJECTIVES

The objectives of this study were to develop improved primers and controls for RT-PCR reactions used for genotyping of measles samples and to develop a method to provide a convenient, safe, and inexpensive means to distribute measles RNA for RT-PCR assays and practice panels.

STUDY DESIGN

A newly designed, genetically defined synthetic RNA and RNA isolated from cells infected with currently circulating genotypes were used to compare the sensitivity of primer pairs in RT-PCR and nested PCR. FTA® cards loaded with lysates of measles infected cells were tested for their ability to preserve viral RNA and destroy virus infectivity.

RESULTS

A new primer pair, MeV216/MeV214, was able to amplify N-450 from viruses representing 10 currently circulating genotypes and a genotype A vaccine strain and demonstrated 100-fold increased sensitivity compared to the previously used primer set. A nested PCR assay further increased the sensitivity of detection from patient samples. A synthetic positive control RNA was developed that produced PCR products that are distinguishable by size from PCR products amplified from clinical samples. FTA® cards completely inactivated measles virus and stabilized RNA for at least six months.

CONCLUSIONS

These improved molecular tools will advance molecular characterization of circulating measles viruses globally and provide enhanced quality control measures.

Revealing new measles virus transmission routes by use of sequence analysis of phosphoprotein and hemagglutinin genes

With improved measles virus (MV) control, the genetic variability of the MV-nucleoprotein hypervariable region (NP-HVR) decreases. Thus, it becomes increasingly difficult to determine the origin of a virus using only this part of the genome. During outbreaks in Europe and Africa, we found MV strains with identical NP-HVR sequences. However, these strains showed considerable diversity within a larger sequencing window based on concatenated MV phosphoprotein and hemagglutinin genes (P/H pseudogenes). In Belarus, Germany, Russia, and the Democratic Republic of Congo, the P/H pseudogenes provided insights into chains of transmission, whereas identical NP-HVR provided none. In Russia, for instance, the P/H pseudogene identified temporal clusters rather than geographical clusters, demonstrating the circulation and importation of independent variants rather than large local outbreaks lasting for several years, as suggested by NP-HVR. Thus, by extending the sequencing window for molecular epidemiology, a more refined picture of MV circulation was obtained with more clearly defined links between outbreaks and transmission chains. Our results also suggested that in contrast to the P gene, the H gene acquired fixed substitutions that continued to be found in subsequent outbreaks, possibly with consequences for its antigenicity. Thus, a longer sequencing window has true benefits both for the epidemiological surveillance of measles and for the better monitoring of viral evolution.

Interplay of measles virus with early induced cytokines reveals different wild type phenotypes

Differential effects of measles virus (MV) on the innate immune response may influence virus spread and severity of disease. Using a representative panel of 22 MV strains including 14 different genotypes, we found that wild-type (wt) differ considerably in their sensitivity to type I interferon (IFN). The wt virus production was 2-47-fold lower in IFN-alpha treated Vero/hSLAM cells, whereas vaccine virus production was reduced only 2-3-fold. Sequence analysis of the MV-P/C/V gene, revealed no obvious amino acid mutations that correlated with the different phenotypes. Strains also widely differed in their ability to induce type I IFN, tumor necrosis factor (TNF) alpha and other cytokines in human A549/hSLAM cells. Some wt strains that were highly sensitive to type I IFN induced only low levels of these and other cytokines. In vitro wt strains that produced the 5' copy-back defective interfering RNAs (5'cb-diRNA) characterized by Shingai et al. (2007), induced high levels of cytokines that otherwise were only reached by vaccine strains. These 5'cb-diRNAs emerged only in virus cultures during multiple passaging and were not detectable in clinical samples of measles patients. These subgenomic RNAs are an important confounding parameter in passaged wt viruses which must be carefully assessed in all in vitro studies. The present data show that MV wt strains differ in their sensitivity and their ability to temper with the innate immune response, which may result in differences in virulence.

Molecular epidemiology of measles virus

Genetic characterization of wild-type measles viruses provides a means to study the transmission pathways of the virus and is an essential component of laboratory-based surveillance. Laboratory-based surveillance for measles and rubella, including genetic characterization of wild-type viruses, is performed throughout the world by the WHO Measles and Rubella Laboratory Network, which serves 166 countries in all WHO regions. In particular, the genetic data can help confirm the sources of virus or suggest a source for unknown-source cases as well as to establish links, or lack thereof, between various cases and outbreaks. Virologic surveillance has helped to document the interruption of transmission of endemic measles in some regions. Thus, molecular characterization of measles viruses has provided a valuable tool for measuring the effectiveness of measles control programs, and virologic surveillance needs to be expanded in all areas of the world and conducted during all phases of measles control.

A multiplex TaqMan PCR assay for the detection of measles and rubella virus

Measles and rubella virus cause fever/rash diseases that are difficult to differentiate clinically. Both viruses can be detected in the same clinical specimens and are propagated on the same cell cultures. A single-tube multiplex TaqMan assay is described for the simultaneous and rapid detection of the full spectrum of known genetic variants. The performance of the assay is similar to a conventional nested PCR and generates cDNA with random primers which can be used directly for virus genotyping.

Measles cases in highly vaccinated population of Novosibirsk, Russia, 2000-2005

While the proportion of measles cases in vaccinees is expected to increase as vaccine coverage increases, such cases must be carefully investigated. The present study was conducted to examine possible contributions to vaccine failures (VFs) and to genetically characterize measles virus (MV) strains circulating in Novosibirsk, Russia during 2000-2005. Totally, 27 adult measles patients admitted to a regional hospital were prospectively enrolled in our study. Genetic characterization of the MV strains revealed circulation of genotypes A, D4 and D6 between 2000 and 2003 years; a genotype D6 MV was associated with the 2005 measles outbreak. Based on IgG avidity testing, half of the vaccinated patients demonstrated evidence of secondary vaccine failure (SVF). Patients, representing both levels of vaccine failure in our study were characterized by the lack of protective titers of neutralizing antibodies against circulating MVs, despite high IgG levels in many cases and high IgG avidity in SVF cases.