Genetic diversity of wild-type measles viruses: implications for global measles elimination programs

Detection of Measles Virus Genotype A in a Non-Endemic Wastewater Setting: Insights from Measles Wastewater and Environmental Monitoring in Canada's Capital Region

The recent global resurgence of measles in 2023-2024, despite vaccine preventability, underscores a critical public health issue, largely due to reduced vaccination coverage during the SARS-CoV-2 pandemic. In response, Ottawa Public Health intensified vaccination efforts in 2023 and 2024. Additionally, a research initiative began in April 2024 to monitor Ottawa wastewater for measles virus (MeV) using established wastewater and environmental surveillance (WES) protocols. Unexpected positive MeV detections through RT-qPCR in Ottawa wastewater-despite no active regional cases-prompted genotypic and retrospective analyses of archived RNA samples dating back to 2020. The genotypic analysis identified positive detection to belong to genotype A, the progenitor strain of the viral vaccines, marking the first report of MeV vaccine RNA in a large catchment area. Linear regression analysis revealed detections aligned with intensified vaccination efforts by Ottawa Public Health. These findings emphasize the importance of integrating genotypic analysis into WES practices to mitigate possible confounding factors, such as vaccine shedding into wastewater. Additionally, this research highlights potential public health applications using MeV WES as a complementary tool. Implementing the findings of this study for MeV WES, and for other re-emerging viruses, could improve public health response and resource allocation.

Surveillance and agnostic capture sequencing of samples from individuals with rash-associated illness in Mali indicates regional transmission of measles virus from West and Central Africa

Measles is vaccine-preventable extremely contagious disease caused by the measles virus. High vaccination coverage is needed to prevent outbreaks of disease. Although molecular surveillance of measles is critical to characterize outbreaks and track viral evolution, few whole-genome sequences of measles virus from West Africa are available despite continual outbreaks in the region. Using VirCapSeq-VERT, an enhanced and comprehensive metagenomic sequencing technique that allows for simultaneous identification of all vertebrate viruses, 23 wild-type near-complete genomes of measles virus from across Mali were obtained from samples collected between January 2012 to October 2022. Other febrile rash illnesses were also identified by VirCapSeq-VERT, demonstrating the advantage of using broad detection agnostic methods when the clinical diagnosis is unclear. Whereas one measles virus sequence was consistent with measles vaccine-associated rash illness (VARI), the remaining 38 were classified within the B3.1 genotype. Broad surveillance throughout Mali reveals regional measles virus transmission across West and Central Africa into Mali, while local clinical testing in Bamako shows stable sequence conservation within genotype B3.1 evolving from Nigerian sequences. The genomic information generated in this study is critical in addressing the lack of whole genome sequences available in West Africa and these findings show the importance of phylogenetically tracking measles outbreaks given recent increases in measles cases globally.

The Health and Economic Benefits of United States Investments in Measles and Rubella Control and Elimination

Background: Prior to measles vaccine introduction in 1963, measles virus caused hundreds of thousands of annual reported cases, which led to substantial US morbidity, mortality, and costs. Similarly, congenital rubella syndrome (CRS) led to highly visible and tragic lifelong disability for thousands of Americans, before rubella vaccine introduction in 1969. The US certified national virus transmission elimination of indigenous measles in 2000 and rubella in 2004. Methods: Applying an existing integrated transmission and economic model, this analysis characterizes the net benefits of US investments in measles (1963-2030) and rubella (1969-2030) immunization assuming continued high routine immunization coverage. Due to importation risks, the US maintains two doses of both vaccines in its routine immunization schedule. Results: This analysis estimates total US costs of 8.1 billion (economics reported in 2023 US dollars) for measles immunization for 1963-2023 and 14.1 billion for rubella immunization for 1969-2023. The analysis estimates an additional approximately 1.2 billion for measles immunization and 1.5 billion for rubella immunization expected for 2024-2030. Historical and future US investments prevented an estimated approximately 237 million measles infections, 228,000 measles deaths, 193 million rubella infections, and 166,000 CRS cases. These investments imply net benefits (from avoided treatment costs minus immunization costs) of approximately 310 billion for measles and 430 billion for rubella and CRS, even without incorporating avoided productivity losses and intangible costs. Conclusions: US investments in measles and rubella immunization continue to provide enormous savings of human and financial costs and to prevent substantial mortality and morbidity.

M-F noncoding region sequences of H1 genotype measles virus provide higher resolution for virus transmission tracing

As countries and regions move toward measles elimination, extended sequence window including noncoding region located between the matrix and fusion protein genes (M - F NCR) was considered to be used in molecular surveillance. The molecular resolution of M - F NCR was evaluated with 192 genotype H1 strains circulating during 2011-2018 in China. Phylogenetic analyses of the N450 and M - F NCR targets indicated that both two targets could confirm epi-linked outbreak, while M - F NCR target could further improve resolution of the molecular characterization: (1) it could differentiate the strains with identical N450 circulated in one county within one month of disease onset; (2) different transmission chains could be distinguished for strains with identical N450; (3) better spatial-temporal consistency with topology could be provided among sporadic cases with inconsistent N450. Accordingly, M - F NCR could be used to complement the information from N450 to address the specific questions in tracking the virus transmission chains.

Genetic Analysis of the Measles Virus From the Outbreaks in South Korea, 2019

Three genotypes (B3, D8, and H1) of the measles virus (MeV) have recently caused global outbreaks. In Korea, four measles outbreaks were reported during 2018–2019 and most patients were infants and health care workers in their 20s and 30s. To investigate the genetic characteristics and molecular epidemiology of the outbreaks, we analyzed the sequence of MeVs by targeting the N-450, MF-NCR, and/or H gene regions. Considering their phylogenetic relationships, besides the N-450 and MF-NCR sequences that are commonly used for genotyping MeVs, the MF-NCR-H sequence was related to the dynamics for identifying the transmission of MeVs. Phylogenetic clustering patterns reconstructed from the MF-NCR-H sequence set revealed that genotype D8 caused three of the four outbreaks, while B3 seemed to have induced the fourth outbreak. These results suggest that the MF-NCR-H sequence is useful for rapid confirmation of measles outbreaks and to identify the epidemiological routes of MeVs.

Measles, mumps, rubella prevention: how can we do better?

INTRODUCTION

Measles, mumps, and rubella incidence decreased drastically following vaccination programs' implementation. However, measles and mumps' resurgence was recently reported, outbreaks still occur, and challenges remain to control these diseases.

AREAS COVERED

This qualitative narrative review provides an objective appraisal of the literature regarding current challenges in controlling measles, mumps, rubella infections, and interventions to address them.

EXPERT OPINION

While vaccines against measles, mumps, and rubella (including trivalent vaccines) are widely used and effective, challenges to control these diseases are mainly related to insufficient immunization coverage and changing vaccination needs owing to new global environment (e.g. traveling, migration, population density). By understanding disease transmission peculiarities by setting, initiatives are needed to optimize vaccination policies and increase vaccination coverage, which was further negatively impacted by COVID-19 pandemic. Also, awareness of the potential severity of infections and the role of vaccines should increase. Reminder systems, vaccination of disadvantaged, high-risk and difficult-to-reach populations, accessibility of vaccination, healthcare infrastructure, and vaccination services management should improve. Outbreak preparedness should be strengthened, including implementation of high-quality surveillance systems to monitor epidemiology. While the main focus should be on these public health initiatives to increase vaccination coverage, slightly more benefits could come from evolution of current vaccines.

Environmental Risk Assessment of Recombinant Viral Vector Vaccines against SARS-Cov-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. Over the past months, considerable efforts have been put into developing effective and safe drugs and vaccines against SARS-CoV-2. Various platforms are being used for the development of COVID-19 vaccine candidates: recombinant viral vectors, protein-based vaccines, nucleic acid-based vaccines, and inactivated/attenuated virus. Recombinant viral vector vaccine candidates represent a significant part of those vaccine candidates in clinical development, with two already authorised for use in the European Union and one currently under rolling review by the European Medicines Agency (EMA). Since recombinant viral vector vaccine candidates are considered as genetically modified organisms (GMOs), their regulatory oversight includes besides an assessment of their quality, safety and efficacy, also an environmental risk assessment (ERA). The present article highlights the main characteristics of recombinant viral vector vaccine (candidates) against SARS-CoV-2 in the pipeline and discusses their features from an environmental risk point of view.

Measles is Back - Considerations for laboratory diagnosis

Measles is a highly contagious viral illness that continues to cause significant mortality among young children worldwide despite the availability of a safe and effective vaccine. During the first half of 2019, over 182 countries reported more than 300,000 measles cases; greater than double the number from the same period in 2018. Timely recognition and laboratory confirmation of infected individuals as well as appropriate infection prevention measures are crucial to avert further transmission. This review highlights the importance of early recognition of the signs and symptoms of measles and provides details on the laboratory methods commonly employed to confirm cases, investigate outbreaks and characterize the virus. It's critical that clinicians, laboratorians and public health administrations work together to rapidly identify, confirm and contain the spread of measles globally.

Differential Features of Fusion Activation within the Paramyxoviridae

Paramyxovirus (PMV) entry requires the coordinated action of two envelope glycoproteins, the receptor binding protein (RBP) and fusion protein (F). The sequence of events that occurs during the PMV entry process is tightly regulated. This regulation ensures entry will only initiate when the virion is in the vicinity of a target cell membrane. Here, we review recent structural and mechanistic studies to delineate the entry features that are shared and distinct amongst the Paramyxoviridae. In general, we observe overarching distinctions between the protein-using RBPs and the sialic acid- (SA-) using RBPs, including how their stalk domains differentially trigger F. Moreover, through sequence comparisons, we identify greater structural and functional conservation amongst the PMV fusion proteins, as compared to the RBPs. When examining the relative contributions to sequence conservation of the globular head versus stalk domains of the RBP, we observe that, for the protein-using PMVs, the stalk domains exhibit higher conservation and find the opposite trend is true for SA-using PMVs. A better understanding of conserved and distinct features that govern the entry of protein-using versus SA-using PMVs will inform the rational design of broader spectrum therapeutics that impede this process.

Complete Genome Sequences of Measles Virus Genotype D8 Isolates from South Korea in 2016

The complete genome sequences of three wild-type measles viruses (genotype D8) isolated from patients in South Korea were determined. These are the first reported complete genome sequences of measles viruses obtained from South Korea, and the availability of these sequences will improve our understanding of measles virus transmission and genetic diversity.

The complete genome sequences of three wild-type measles viruses (genotype D8) isolated from patients in South Korea were determined. These are the first reported complete genome sequences of measles viruses obtained from South Korea, and the availability of these sequences will improve our understanding of measles virus transmission and genetic diversity.

Molecular characterization of measles viruses in China: Circulation dynamics of the endemic H1 genotype from 2011 to 2017

Due to the Expanded Program on Immunization (EPI) and supplementary immunization activities (SIAs) in China, the incidence of measles in China has decreased extensively. The incidence reached its lowest levels in contemporary history in 2012 and 2017, with incidence rates of 4.6 and 4.3 per million population, respectively. However, more than 147,000 measles cases were reported from 2013 to 2016. Furthermore, the proportions of cases in infants < 8 months and adults have been increasing since 2013, representing a considerable challenge for measles elimination in China. A total of 14,868 measles viruses were isolated from confirmed measles cases from 2011 to 2017, of which 14,631 were identified as the predominant endemic genotype, H1; 87 were identified as genotype A viruses that were vaccine associated strains; and 150 were identified as non-H1 genotype viruses. The non-H1 genotype viruses included 62 D8 viruses, 70 D9 viruses, 3 D11 viruses, 14 B3 viruses, and 1 G3 virus, which were identified as imported or import-related viruses that caused sporadic cases or small outbreaks. Most of the transmission chains detected during the period 2011–2012 were interrupted and were followed by many new transmission chains of unknown origin that spread, causing a large measles resurgence in China during 2013–2016. After 4 years of measles resurgence and continuous implementation of the routine immunization program and SIAs, the population immunity reached a sufficiently high level to interrupt most of the transmission chains; only a few strains survived, which continued to be sporadically detected in China in 2017. In the present study, the results from the combined epidemiological and molecular virological data demonstrated the great progress towards measles elimination in China by the further analysis of circulation dynamics for the endemic H1 genotype measles virus from 2011 to 2017. And this study accumulated critical baseline data on circulating wild-type measles viruses in China and provides comprehensive information to the world. These comprehensive baseline data provide evidence to support measles elimination in the future, not only in China but also in other countries worldwide. In addition, the information will be very useful to other countries for tracing their sources of measles cases and for identifying transmission links, which can help prevent potential measles outbreaks.

Molecular epidemiology study of measles viruses in Kunming area of China

The present study assessed the variation of measles viruses (MV) and its association with clinical manifestations in patients with MV. A total of 38 pediatric patients with MV at the acute infection stage were selected and 2 ml venous blood was collected from each of them. Serum immunoglobulin M antibodies were determined by ELISA. Urine specimens were collected from 30 of the 38 patients and associated genetic structures were detected by reverse-transcription polymerase chain reaction mapping. At the same time, clinical epidemiological manifestations were collected to perform an epidemiological analysis. The MV-positive rate within the cohort determined in serum was 100%. Seven MV strains were isolated from urine specimens of 30 patients and the positive rate was 23.33%. Four MV strains were randomly selected from the 7 strains and the results revealed that they were all of the H_1a genotype. In addition, there was no significant correlation between clinical manifestation of pediatric patients with measles and the genotype of the MV. In conclusion, the preponderant genotype of MV in Kunming was H_1a and there was obvious nucleotide or amino acid mutation. The clinical manifestation of MV infection in pediatric patients was not associated with the MV genotype.

Global Transmission Dynamics of Measles in the Measles Elimination Era

Although there have been many epidemiological reports of the inter-country transmission of measles, systematic analysis of the global transmission dynamics of the measles virus (MV) is limited. In this study, we applied phylogeographic analysis to characterize the global transmission dynamics of the MV using large-scale genetic sequence data (obtained for 7456 sequences) from 115 countries between 1954 and 2015. These analyses reveal the spatial and temporal characteristics of global transmission of the virus, especially in Australia, China, India, Japan, the UK, and the USA in the period since 1990. The transmission is frequently observed, not only within the same region but also among distant and frequently visited areas. Frequencies of export from measles-endemic countries, such as China, India, and Japan are high but decreasing, while the frequencies from countries where measles is no longer endemic, such as Australia, the UK, and the USA, are low but slightly increasing. The world is heading toward measles eradication, but the disease is still transmitted regionally and globally. Our analysis reveals that countries wherein measles is endemic and those having eliminated the disease (apart from occasional outbreaks) both remain a source of global transmission in this measles elimination era. It is therefore crucial to maintain vigilance in efforts to monitor and eradicate measles globally.

Constraints on the Genetic and Antigenic Variability of Measles Virus

Antigenic drift and genetic variation are significantly constrained in measles virus (MeV). Genetic stability of MeV is exceptionally high, both in the lab and in the field, and few regions of the genome allow for rapid genetic change. The regions of the genome that are more tolerant of mutations (i.e., the untranslated regions and certain domains within the N, C, V, P, and M proteins) indicate genetic plasticity or structural flexibility in the encoded proteins. Our analysis reveals that strong constraints in the envelope proteins (F and H) allow for a single serotype despite known antigenic differences among its 24 genotypes. This review describes some of the many variables that limit the evolutionary rate of MeV. The high genomic stability of MeV appears to be a shared property of the Paramyxovirinae, suggesting a common mechanism that biologically restricts the rate of mutation.

Biosafety considerations for attenuated measles virus vectors used in virotherapy and vaccination

Attenuated measles virus (MV) is one of the most effective and safe vaccines available, making it attractive candidate vector to prevent infectious diseases. Attenuated MV have acquired the ability to use the complement regulator CD46 as a major receptor to mediate virus entry and intercellular fusion. Therefore, attenuated MV strains preferentially infect and destroy a wide variety of cancer cells making them also attractive oncolytic vectors. The use of recombinant MV vector has to comply with various regulatory requirements, particularly relating to the assessment of potential risks for human health and the environment. The present article highlights the main characteristics of MV and recombinant MV vectors used for vaccination and virotherapy and discusses these features from a biosafety point of view.

Phylodynamic analysis of the canine distemper virus hemagglutinin gene

Background

Canine distemper (CD) is one of the most contagious and lethal viral diseases in dogs. Despite the widespread use of vaccines, the prevalence of the CD virus (CDV) has increased at an alarming rate in recent years. In this phylodynamic study, we investigated the spatiotemporal modes of dispersal, viral demographic trends, and effectiveness of vaccines for CDV. A total of 188 full-length CDV hemagglutinin (H) gene sequences dataset were subjected to recombination analysis, including seven from modified live vaccine (MLV) strains and 12 from Taiwan specimens. After excluding the MLV strains and potential recombinant strains, alignments of 176 of 188 previous CDV strains were further used to analyze phylodynamic characteristics, and evidence of selection, and co-evolution.

Results

The CDV genotype consisted of MLV-associated genotypes such as America-1 and Rockborn-like strains, which were characterized by long terminal branches and no distinct geographical patterns among lineages. In contrast, wild-type isolates clustered into lineages with a spatiotemporal structure and short terminal branches. Co-circulation and extensive diversification were simultaneously observed. The sequence variation signature was shaped by both geographic diversity and host tropism. Codon 506 was identified as a multi-epistatic interacting in the H protein.

Conclusions

The topological signature revealed in this study suggests different epidemic scenarios. For example, a ladder-like backbone is a hallmark of directional selection, and cladogenesis at long terminal branches indicates the emergence of a surviving lineage. The stable effective viral population of CDV indicate the effectiveness of vaccines currently used to control the virus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-015-0491-9) contains supplementary material, which is available to authorized users.

Mutational Analysis of Measles Virus Suggests Constraints on Antigenic Variation of the Glycoproteins

Measles virus undergoes error-prone replication like other RNA viruses, but over time, it has remained antigenically monotypic. The constraints on the virus that prevent the emergence of antigenic variants are unclear. As a first step in understanding this question, we subjected the measles virus genome to unbiased insertional mutagenesis, and viruses that could tolerate insertions were rescued. Only insertions in the nucleoprotein, phosphoprotein, matrix protein, as well as intergenic regions were easily recoverable. Insertions in the glycoproteins of measles virus were severely under-represented in our screen. Host immunity depends on developing neutralizing antibodies to the hemagglutinin and fusion glycoproteins; our analysis suggests that these proteins occupy very little evolutionary space and therefore have difficulty changing in the face of selective pressures. We propose that the inelasticity of these proteins prevents the sequence variation required to escape antibody neutralization in the host, allowing for long-lived immunity after infection with the virus.

Molecular epidemiology of measles virus infection in Shanghai in 2000-2012: the first appearance of genotype D8

Purpose

The purpose of this study was to identify measles virus in Shanghai in 2012 and study the genotype trend of measles virus epidemic strains during 2000–2012.

Methods

Nose and throat swab specimens were collected from 34 suspected measles cases in Shanghai. Measles virus was isolated using Vero-SLAM cells (African green monkey kidney cells/lymphoid signal activating factor-transfected African green monkey kidney cells). The 450 bp of C terminus of the N gene and the entire hemagglutinin gene sequence was amplified using RT-PCR. Phylogenetic analysis was performed by comparing the seven measles strains in Shanghai with the reference strains for H1a, H1b and D8 genotypes, as well as the Chinese measles virus vaccine strain.

Results

Seven measles viruses strains were isolated from the 34 throat swap specimens. Six strains were genotype H1a, which is the predominant strain in China and one strain was genotype D8, which is the first imported strain since 2000. All these seven strains maintained most of the glycosylation sites except subtype H1a, which lost one glycosylation site.

Conclusion

Since 2000, measles virus strains in Shanghai are consistent with measles virus from other provinces in China with H1a being the predominant genotype. This study is also the first report of genotype D8 strain in Shanghai. All strains maintained their glycosylation sites except H1a that lost one glycosylation site. These strains could still be neutralized by the Chinese measles vaccine. We suggest that Shanghai Center for Disease Control laboratories should strengthen their approaches to monitor measles cases to prevent further spread of imported strains.

Oncolytic measles virus strains as novel anticancer agents

INTRODUCTION

Replication-competent oncolytic measles virus (MV) strains preferentially infect and destroy a wide variety of cancer tissues. Clinical translation of engineered attenuated MV vaccine derivatives is demonstrating the therapeutic potential and negligible pathogenicity of these strains in humans.

AREAS COVERED

The present review summarizes the mechanisms of MV tumor selectivity and cytopathic activity as well as the current data on the oncolytic efficacy and preclinical testing of MV strains. Investigational strategies to reprogram MV selectivity, escape antiviral immunity and modulate the immune system to enhance viral delivery and tumor oncolysis are also discussed.

EXPERT OPINION

Clinical viral kinetic data derived from noninvasive monitoring of reporter transgene expression will guide future protocols to enhance oncolytic MV efficacy. Anti-measles immunity is a major challenge of measles-based therapeutics and various strategies are being investigated to modulate immunity. These include the combination of MV therapy with immunosuppressive drugs, such as cyclophosphamide, the use of cell carriers and the introduction of immunomodulatory transgenes and wild-type virulence genes. Available MV retargeting technologies can address safety considerations that may arise as more potent oncolytic MV vectors are being developed.

Single endemic genotype of measles virus continuously circulating in China for at least 16 years

The incidence of measles in China from 1991 to 2008 was reviewed, and the nucleotide sequences from 1507 measles viruses (MeV) isolated during 1993 to 2008 were phylogenetically analyzed. The results showed that measles epidemics peaked approximately every 3 to 5 years with the range of measles cases detected between 56,850 and 140,048 per year. The Chinese MeV strains represented three genotypes; 1501 H1, 1 H2 and 5 A. Genotype H1 was the predominant genotype throughout China continuously circulating for at least 16 years. Genotype H1 sequences could be divided into two distinct clusters, H1a and H1b. A 4.2% average nucleotide divergence was found between the H1a and H1b clusters, and the nucleotide sequence and predicted amino acid homologies of H1a viruses were 92.3%-100% and 84.7%-100%, H1b were 97.1%-100% and 95.3%-100%, respectively. Viruses from both clusters were distributed throughout China with no apparent geographic restriction and multiple co-circulating lineages were present in many provinces. Cluster H1a and H1b viruses were co-circulating during 1993 to 2005, while no H1b viruses were detected after 2005 and the transmission of that cluster has presumably been interrupted. Analysis of the nucleotide and predicted amino acid changes in the N proteins of H1a and H1b viruses showed no evidence of selective pressure. This study investigated the genotype and cluster distribution of MeV in China over a 16-year period to establish a genetic baseline before MeV elimination in Western Pacific Region (WPR). Continuous and extensive MeV surveillance and the ability to quickly identify imported cases of measles will become more critical as measles elimination goals are achieved in China in the near future. This is the first report that a single endemic genotype of measles virus has been found to be continuously circulating in one country for at least 16 years.

Molecular epidemiology of measles virus in Iran 2009-2010: first detection of measles genotype H1

Measles virus (MV) genotyping is an important component of measles surveillance in the context of monitoring immunization program effectiveness and documenting MV elimination. The molecular epidemiology and genetic variability of circulating MV strains in Iran during the 2009-2010 were studied in consecutive MV isolates from throat swab and urine. Sequence information obtained from 41 cases based on the 456 nucleotides of the most variable region of the C-terminal part of the N-protein revealed that these sequences belonged to two different genotypes. This is the first description of the genetic characterization of sporadic MV genotype H1 cases in northern Iran. Cases were probably linked to MV importation from distant parts of Asia. The genotype H1 has not been detected in the Eastern Mediterranean Region. In addition, both sequence analysis and epidemiologic data indicated that the more recently detected genotype D4 viruses in Iran were related very closely to viruses that were detected in Pakistan, suggesting that these viruses may have been imported from Pakistan. J. Med. Virol. 83:2200-2207, 2011. © 2011 Wiley Periodicals, Inc.

Risk analysis for measles reintroduction after global certification of eradication

BACKGROUND

Measles virus will continue to exist after certification of global eradication as virus stocks and infectious materials held in laboratories, in persistently and chronically infected individuals, and possibly in undetected foci of transmission. A literature search was undertaken to identify and evaluate the main risks for reintroduction of measles transmission in the absence of universal measles immunization.

METHODS

A qualitative risk assessment was conducted following a series of literature searches using the PubMed database.

RESULTS

If the criteria for global certification of eradication are stringent and require rigorous validation, then the risk of undetected measles transmission after certification is very low. Risk of unintentional reintroduction from any source, including persistent infections and laboratory materials is low to very low but depends on the extent of measles vaccine use. If immunization levels decrease, measles will become a credible agent for bioterrorism through intentional release.

CONCLUSIONS

Posteradication risks are low and should not deter any attempt at measles eradication. More information on measles transmission dynamics and the role of atypical infections is required to determine requirements for global certification of eradication. Posteradication risks would be minimized through development and implementation of an international risk management strategy, including requirements for a posteradication vaccine stockpile.

Application of DNA array technology for diagnostic microbiology

Microarrays or DNA chips have been hailed as the ultimate experimental tool for research, drug discovery and diagnostics. They have the potential to perform a multitude of molecular tests simultaneously and to produce a wealth of information from a single clinical sample. Applications include genotyping, expression analysis and sequencing (1-4). The aim of this review is to provide a brief summary of current microarray technology and highlight the many ways in which it is being developed for use in clinical microbiology laboratories.

Molecular Epidemiology of Measles Virus before and after the 2003 Mass Vaccination Campaign for Measles/Rubella in Iran

BACKGROUND

Molecular epidemiology of measles virus (MV) is important, not only to measure the success of measles vaccination programs but also to monitor the circulation and elimination of the virus worldwide. In this study, we compared MV obtained from patients before the 2003 mass vaccination MR campaign and viruses detected after 2003 until 2008 in Iran.

METHODS

The nucleoprotein (N) gene of 29 MV strains circulating in Iran between 2002 and 2008 were amplified by RT-PCR and subjected to sequence and phylogenetic analysis.

RESULTS

Molecular characterization of MV studied here revealed that although the outbreaks in Iran were associated with MV genotype D4, the isolated viruses clearly belonged to several different lineages. Maximum and minimum homology within the 29 Iranian strains in our study was100% and 94.9% within the carboxyl terminus of the N gene, respectively. Using ClustalX program, the alignment of Iranian MV sequences showed nine lineages.

CONCLUSION

This study provides the usefulness of MV sequence analysis for the demonstration of local interruption of indigenous strain transmission as well as providing a valuable means for monitoring the elimination processes of MV control.

Genome sequence conservation of Hendra virus isolates during spillover to horses, Australia

Bat-to-horse transmission of Hendra virus has occurred at least 14 times. Although clinical signs in horses have differed, genome sequencing has demonstrated little variation among the isolates. Our sequencing of 5 isolates from recent Hendra virus outbreaks in horses found no correlation between sequences and time or geographic location of outbreaks.

Genetic characterization of clade B measles viruses isolated in Tunisia and Libya 2002-2009 and a proposed new subtype within the B3 genotype

Genetic characterization was conducted on 18 wild-type measles viruses, detected in Tunisia and Libya from 2002 to 2009. Sequence analysis of the 456 nucleotides in the carboxy terminus of the nucleoprotein (N) gene and the entire hemagglutinin (H) gene indicated that all isolates were in genotype B3. All of the viruses from 2002 to 2007 and some of the isolates from 2009 belonged to subtype B3.1. In contrast, 7 of the viruses isolated during 2008 and 2009 were quite divergent from all B3 isolates. The nucleotide sequences of the N gene of these 7 isolates differed from the sequences of the Ibadan and New York reference strain by an average of 3.1 and 4.4%, respectively. The H gene sequences differed by 1.1 and 2.6% with the same reference strains. This is the first report describing the genetic characteristics of measles viruses from clade B isolated in North Africa; the results suggest that these viruses represent a new subtype of genotype B3.

New measles virus genotype associated with outbreak, China

To determine the origin of the virus associated with a measles outbreak in Menglian County, Yunnan Province, People's Republic of China, in 2009, we conducted genetic analyses. Phylogenetic analyses based on nucleoprotein (N) and hemagglutinin (H) gene sequences showed that these Menglian viruses were not closely related to sequences of any World Health Organization (WHO) reference strains representing the 23 currently recognized genotypes. The minimum nucleotide divergence between the Menglian viruses and the most closely related reference strain, genotype D7, was 3.3% for the N gene and 3.0% for the H gene. A search of the databases of GenBank, WHO, and the Health Protection Agency Measles Nucleotide Surveillance showed that the Menglian viruses, together with the 2 older non-Menglian viruses, could be members of a new proposed measles genotype, d11. The new genotype designation will allow for better description of measles transmission patterns, especially in the Southeast Asian and Western Pacific regions.

Genetic characterization of wild-type measles viruses isolated in China, 2006-2007

Molecular characterization of wild-type measles viruses in China during 1995-2004 demonstrated that genotype H1 was endemic and widely distributed throughout the country. H1-associated cases and outbreaks caused a resurgence of measles beginning in 2005. A total of 210,094 measles cases and 101 deaths were reported by National Notifiable Diseases Reporting System (NNDRS) and Chinese Measles Laboratory Network (LabNet) from 2006 to 2007, and the incidences of measles were 6.8/100,000 population and 7.2/100,000 population in 2006 and 2007, respectively. Five hundred and sixty-five wild-type measles viruses were isolated from 24 of 31 provinces in mainland China during 2006 and 2007, and all of the wild type virus isolates belonged to cluster 1 of genotype H1. These results indicated that H1-cluster 1 viruses were the predominant viruses circulating in China from 2006 to 2007. This study contributes to previous efforts to generate critical baseline data about circulating wild-type measles viruses in China that will allow molecular epidemiologic studies to help measure the progress made toward China's goal of measles elimination by 2012.

Measles resurgence associated with continued circulation of genotype H1 viruses in China, 2005

Measles morbidity and mortality decreased significantly after measles vaccine was introduced into China in 1965. From 1995 to 2004, average annual measles incidence decreased to 5.6 cases per 100,000 population following the establishment of a national two-dose regimen. Molecular characterization of wild-type measles viruses demonstrated that genotype H1 was endemic and widely distributed throughout the country in China during 1995-2004. A total of 124,865 cases and 55 deaths were reported from the National Notifiable Diseases Reporting System (NNDRS) in 2005, which represented a 69.05% increase compared with 2004. Over 16,000 serum samples obtained from 914 measles outbreaks and the measles IgM positive rate was 81%. 213 wild-type measles viruses were isolated from 18 of 31 provinces in China during 2005, and all of the isolates belonged to genotype H1. The ranges of the nucleotide sequence and predicted amino acid sequence homologies of the 213 genotype H1 strains were 93.4%-100% and 90.0%-100%, respectively. H1-associated cases and outbreaks caused the measles resurgence in China in 2005. H1 genotype has the most inner variation within genotype, it could be divided into 2 clusters, and cluster 1 viruses were predominant in China throughout 2005.

The evolutionary and epidemiological dynamics of the paramyxoviridae

Paramyxoviruses are responsible for considerable disease burden in human and wildlife populations: measles and mumps continue to affect the health of children worldwide, while canine distemper virus causes serious morbidity and mortality in a wide range of mammalian species. Although these viruses have been studied extensively at both the epidemiological and the phylogenetic scales, little has been done to integrate these two types of data. Using a Bayesian coalescent approach, we infer the evolutionary and epidemiological dynamics of measles, mumps and canine distemper viruses. Our analysis yielded data on viral substitution rates, the time to common ancestry, and elements of their demographic history. Estimates of rates of evolutionary change were similar to those observed in other RNA viruses, ranging from 6.585 to 11.350 x 10(-4 )nucleotide substitutions per site, per year. Strikingly, the mean Time to the Most Recent Common Ancestor (TMRCA) was both similar and very recent among the viruses studied, ranging from only 58 to 91 years (1908 to 1943). Worldwide, the paramyxoviruses studied here have maintained a relatively constant level of genetic diversity. However, detailed heterchronous samples illustrate more complex dynamics in some epidemic populations, and the relatively low levels of genetic diversity (population size) in all three viruses is likely to reflect the population bottlenecks that follow recurrent outbreaks.

Genetic characterization of measles virus strains isolated during an epidemic cluster in Puglia, Italy 2006-2007

The genetic characterization of wild-type measles strains isolated during an epidemic cluster of measles occurred in Puglia (South Italy), between November 2006 and January 2007, was performed. Measles virus (MV) detection was carried out by a nested RT-PCR on 8 of 18 total cases. The viruses were analyzed using the standard genotyping protocols. The N gene sequences of the strains from outbreak were identical to each other, and sequence analysis revealed that the viruses belonged to genotype B3, subgroup B3.1, never identified before in Italy. An importation of measles B3.1 strains from Africa was hypothesized. Molecular surveillance will help to monitor the progress in measles elimination.

Molecular epidemiology of measles viruses in China, 1995-2003

This report describes the genetic characterization of 297 wild-type measles viruses that were isolated in 24 provinces of China between 1995 and 2003. Phylogenetic analysis of the N gene sequences showed that all of the isolates belonged to genotype H1 except 3 isolates, which were genotype A. The nucleotide sequence and predicted amino acid homologies of the 294-genotype H1 strains were 94.7%-100% and 93.3%-100%, respectively. The genotype H1 isolates were divided into 2 clusters, which differed by approximately 2.9% at the nucleotide level. Viruses from both clusters were distributed throughout China with no apparent geographic restriction and multiple co-circulating lineages were present in many provinces. Even though other measles genotypes have been detected in countries that border China, this report shows that genotype H1 is widely distributed throughout the country and that China has a single, endemic genotype. This important baseline data will help to monitor the progress of measles control in China.

Genotyping of measles virus in clinical specimens on the basis of oligonucleotide microarray hybridization patterns

An oligonucleotide microarray hybridization method for identification of most known measles virus (MV) genotypes was developed. Like the conventional genotyping method, the microarray relied on detecting sequence differences in the 450-nucleotide region coding for the COOH-terminal 150 amino acids of the nucleoprotein (N). This region was amplified using PCR primers binding to all known MV genotypes. The microarray included 71 pairs of oligonucleotide probes (oligoprobes) immobilized on glass slides. Each pair consisted of a genotype-specific oligoprobe, which matched the sequence of only one target genotype, and a control oligoprobe, which contained mismatches at the nucleotide positions unique to this genotype. A pattern recognition algorithm based on cluster analysis of the ratios of hybridization signals from specific and control oligoprobes was used to identify the specific MV genotype. Following the initial validation, the method was used for rapid genotyping of two panels of coded samples. The results of this study showed good sensitivity (90.7%), specificity (100%), and genotype agreement (91.8%) for the new method compared to the results of genotyping conducted using phylogenetic analysis of viral sequences of the C terminus of the N gene. In addition, the microarray demonstrated the ability to identify potential new genotypes of MV based on the similarity of their hybridization patterns with those of known MV genotypes.

The genomic termini of wild-type and vaccine strains of measles virus

The genomic termini from 18 strains of measles virus (MV) including wild-type MVs from the pre-vaccine period, recent wild-type isolates and various vaccine strains were sequenced. The first 25 nucleotides of the 3' terminus and last 52 nucleotides of the 5' terminus were conserved in all of the viruses examined. Nucleotides 26 and 42 of the 3' leader were A and G, respectively, in all genotype A viruses except Edmonston wild-type (Ed-WT). All non-genotype A viruses and Ed-WT had U in both positions. No consistent substitution pattern was found in the 5' trailer region of the genome. The nucleotide substitutions at positions 26 and 42 in the 3' leader region were introduced into a MV-CAT mini-genome to test for their effect on the production of reporter protein in both a vaccinia T7-driven, plasmid-based replication assay as well as in a helper virus system. Regardless of the source of the polymerase proteins or the natural leader sequence of the helper viruses, the mini-genome 26A42G produced more CAT protein than 26U42U. The nucleotide substitution at 26 had the greatest effect on CAT production. These results indicated that naturally occurring nucleotide variations in the 3' leader region can affect the levels of reporter protein synthesis, and presumably affected the level of replication of the virus.

Review of the temporal and geographical distribution of measles virus genotypes in the prevaccine and postvaccine eras

Molecular epidemiological investigation of measles outbreaks can document the interruption of endemic measles transmission and is useful for establishing and clarifying epidemiological links between cases in geographically distinct clusters. To determine the distribution of measles virus genotypes in the prevaccine and postvaccine eras, a literature search of biomedical databases, measles surveillance websites and other electronic sources was conducted for English language reports of measles outbreaks or genetic characterization of measles virus isolates. Genotype assignments based on classification systems other than the currently accepted WHO nomenclature were reassigned using the current criteria. This review gives a comprehensive overview of the distribution of MV genotypes in the prevaccine and postvaccine eras and describes the geographically diverse distribution of some measles virus genotypes and the localized distributions of other genotypes.

Identification of measles virus genotypes from recent outbreaks in countries from the Eastern Mediterranean Region

BACKGROUND

Molecular characterization of measles viruses (MV) helps to identify transmission pathways of the virus and to document persistence or interruption of endemic virus circulation. In the Eastern Mediterranean Region, measles genotypes from only few countries have been documented.

OBJECTIVES

This study reports the genetic characteristics of virus strains from recent measles outbreaks in Tunisia, Libya, Syria and Iran in 2002-2003.

STUDY DESIGN

Virus sequences in the nucleoprotein gene were obtained by PCR amplification of virus isolates or serum samples. The sequences were compared to the reference ones for genotype identification and to other published sequences within the same genotype.

RESULTS AND CONCLUSIONS

The Tunisian and Libyan epidemic strains belonged to genotype B3, they were closely related to each other and to isolates from Western Africa. The Syrian and Iranian viruses belonged to genotype D4, and differed from each other and from the other published sequences within this genotype. Our results provide valuable baseline and new tools for improved virological measles surveillance in the future, at country, regional and global levels.

Applicability of oral fluid collected onto filter paper for detection and genetic characterization of measles virus strains

Expansion of measles molecular surveillance to developing countries where measles is endemic will help facilitate measles control. Limited infrastructure in these areas is a barrier to referral of specimens suitable for measles virus (MV) genotyping. In this study, we demonstrate that oral fluid dried onto filter paper can be used for the detection and characterization of MV strains. Using this approach, an MV-positive sample by reverse transcriptase PCR could be obtained from 67% of serologically confirmed acute measles cases. Mimicking certain environmental conditions and duration of transportation established that MV RNA remained detectable and suitable for nucleic acid sequencing in oral fluid spots for at least 1 week. In the context of a measles outbreak in a remote region of the world where infrastructure is poor, oral fluid samples dried onto filter paper and sent to a specialized laboratory for testing will aid in the identification and characterization of the causative MV strain.

Genetic characterization of measles viruses isolated in Turkey during 2000 and 2001

BACKGROUND

Molecular epidemiologic studies have made significant contributions to measles surveillance activities by helping to identify source and transmission pathways of the virus. This report describes the genetic characterization of wild-type measles viruses isolated in Turkey in 2000 and 2001.

RESULTS

Wild-type measles viruses were isolated from 24 cases from five provinces in Turkey during 2001. The viruses were analyzed using the standard genotyping protocols. All isolates were classified as genotype D6, the same genotype that was identified in Turkey in previous outbreaks during 1998.

CONCLUSION

Turkey has begun implementation of a national program to eliminate measles by 2010. Therefore, this baseline genotype data will provide a means to monitor the success of the elimination program.

Epitope analysis for influenza vaccine design

Until now, design of the annual influenza vaccine has relied on phylogenetic or whole-sequence comparisons of the viral coat proteins hemagglutinin and neuraminidase, with vaccine effectiveness assumed to correlate monotonically to the vaccine-influenza sequence difference. We use a theory from statistical mechanics to quantify the non-monotonic immune response that results from antigenic drift in the epitopes of the hemagglutinin and neuraminidase proteins. The results explain the ineffectiveness of the 2003-2004 influenza vaccine in the United States and provide an accurate measure by which to optimize the effectiveness of future annual influenza vaccines.

Measles virus genotyping by nucleotide-specific multiplex PCR

A simple genotyping method based on multiplex PCR has been developed to discriminate between all active measles virus (MV) clades and genotypes (A, B3.1, B3.2, C2, D2-D9, G2-G3, and H1-H2). The sequencing reaction was replaced by six multiplex PCRs: one to identify the clade and five to identify the respective genotype. Primers were sensitive to clade- and genotype-specific nucleotides and generated fragments of type-specific sizes that were analyzed by conventional agarose gel electrophoresis. On the basis of all published MV sequences, positive and negative predictive values of 99.2% and 98.6% were calculated. Variability in the primer binding sites, which could potentially reduce sensitivity, was very limited among published sequences. As new genotypes are described, additional specific primers can be included in the multiplex PCR with relative ease. Although sequencing remains the "gold standard," the present method should facilitate MV genotyping especially in developing countries and will therefore contribute to enhanced MV control and elimination strategies as recommended by the World Health Organization.

Incremental effectiveness of 2 doses of measles-containing vaccine compared with 1 dose among high school students during an outbreak

A measles outbreak occurred among a highly vaccinated population in Alaska during 1998, providing an opportunity to determine the incremental efficacy of >or=2 doses of measles-containing vaccine (MCV) compared with 1 dose. Of 33 confirmed case patients identified, 31 had been vaccinated with 1 dose of MCV, 1 had received 2 doses, and vaccination status was unknown in 1 case. Seventy percent of cases were school-associated; 58% of cases occurred in 2 high schools. Of 3679 students attending the 2 schools, 50.4% and 45.5% had received >or=2 doses of MCV before measles introduction at the schools. The relative risk of developing measles among persons vaccinated with >or=2 doses of MCV compared with 1 dose was 0.06 (95% confidence interval, 0.01-0.44; P<.001), yielding an estimated incremental vaccine efficacy of 94.1% (95% confidence interval, 55.9%-99.2%; P<.001). Rapid implementation of a mandatory second-dose MCV requirement probably limited the extent of this outbreak.

Genotyping of Measles Virus in Canada: 1979-2002

Genotyping is an important component of measles surveillance. In this study, we report the genotypes of 30 measles viruses from cases in Canada; 6 of these were collected between 1979 and 1996 and 24 were collected from 1997 through 2002. Many measles virus genotypes were found (C1, C2, D3, D4, D5, D6, D7, D8, E, and H1). These data indicate that the predominant measles virus genotypes detected from 1979 to 1997 in Canada are no longer commonly found. Since the implementation of a routine second dose of measles vaccine and catch-up campaigns in 1996-1997, the wide variety of measles virus genotypes found supports epidemiological data showing that importation of measles is the source of current measles cases in Canada.

Genetic Analysis of Measles Viruses Isolated in the United States between 1989 and 2001: Absence of an Endemic Genotype since 1994

This report describes measles virus surveillance in the United States for 1989-2001. During the resurgence of measles in the United States between 1989 and 1992, only viruses of genotype D3 were isolated. In contrast, virological surveillance conducted after the resurgence period showed that at least 12 different genotypes were associated with the greatly reduced number of measles cases. Eight different genotypes were identified for 27 chains of transmission in which the source of infection was unknown. The diversity of measles virus genotypes observed in the United States between 1994 and 2001 reflected multiple imported sources of virus and indicated that no genotype of measles is endemic in the United States. Therefore, the data obtained from virological surveillance are consistent with the conclusions made by disease surveillance and epidemiological investigations that measles is no longer an endemic disease in the United States.